CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_004838	Yersinia pestis KIM10+ plasmid pMT-1, complete sequence	0 crisprs	NA	0	0	2	0
NC_004088	Yersinia pestis KIM10+, complete sequence	6 crisprs	DEDDh,csa3,cas3,cas1,cas3f,cas8f,cas5f,cas7f,cas6f,DinG	1	12	12	2

Results visualization

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CRISPR-Cas detection and classification

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

0 : 76603

Salmonella_phage(75.0%)

transposase,terminase,tail

The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002214164.1\|716_1781_-	replication protein RepA	J9Q7H0	Salmonella_phage	2.4e-188	98.6
WP_002214160.1\|2525_3170_+	hypothetical protein	J9Q739	Salmonella_phage	1.8e-122	98.1
WP_002213298.1\|3529_4552_-	ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_002213300.1\|4967_6053_+	metallophosphoesterase	J9Q7S9	Salmonella_phage	7.7e-206	98.6
WP_002214148.1\|6282_8199_+	AAA family ATPase	J9Q741	Salmonella_phage	0.0e+00	98.6
WP_011114035.1\|8188_8935_+	hypothetical protein	J9Q6J5	Salmonella_phage	1.2e-133	96.0
WP_002214145.1\|8947_9517_+	hypothetical protein	J9Q7Z7	Salmonella_phage	5.8e-104	100.0
WP_002213759.1\|9725_10184_+\|transposase	IS200/IS605-like element IS1541A family transposase	D9CGB6	Hyperthermophilic_Archaeal_Virus_2	5.0e-13	35.3
WP_002211802.1\|10383_10665_+	hypothetical protein	J9Q753	Salmonella_phage	6.1e-46	93.5
WP_002211801.1\|10870_11353_+	hypothetical protein	J9Q805	Salmonella_phage	5.1e-85	94.4
WP_002214137.1\|11991_12219_-	hypothetical protein	NA	NA	NA	NA
WP_002211799.1\|12303_12954_-	hypothetical protein	J9Q754	Salmonella_phage	4.1e-114	99.5
WP_002214134.1\|13277_13805_-	transcriptional regulator	J9Q6L0	Salmonella_phage	6.4e-81	98.0
WP_002211796.1\|13809_14232_-	hypothetical protein	J9Q806	Salmonella_phage	4.1e-62	85.0
WP_002214131.1\|14291_14570_-	hypothetical protein	J9Q7T9	Salmonella_phage	4.4e-41	97.8
WP_002211794.1\|14572_16132_-	DEAD/DEAH box helicase	J9Q7I4	Salmonella_phage	1.1e-293	99.0
WP_002228791.1\|16196_16895_+	ParB N-terminal domain-containing protein	J9Q756	Salmonella_phage	9.6e-125	98.7
WP_002211792.1\|16894_17563_+	ParB N-terminal domain-containing protein	J9Q6L1	Salmonella_phage	9.5e-114	98.2
WP_002211791.1\|17559_18198_+	ATP-binding cassette domain-containing protein	J9Q807	Salmonella_phage	4.7e-110	98.1
WP_002211790.1\|18190_18445_+	hypothetical protein	J9Q7U0	Salmonella_phage	2.0e-40	97.6
WP_002211789.1\|18450_19341_+	hypothetical protein	J9Q7I6	Salmonella_phage	6.2e-169	99.7
WP_000176291.1\|19350_19617_+	hypothetical protein	J9Q757	Salmonella_phage	1.3e-42	100.0
WP_002211788.1\|19812_20454_+	hypothetical protein	J9Q6D4	Salmonella_phage	1.2e-108	98.1
WP_002211787.1\|20456_21713_+\|terminase	terminase	J9Q7Y2	Salmonella_phage	1.8e-251	100.0
WP_002211786.1\|21746_23321_+	hypothetical protein	J9Q7R1	Salmonella_phage	2.4e-301	99.2
WP_002211784.1\|24270_25146_+	hypothetical protein	J9Q710	Salmonella_phage	8.5e-163	99.7
WP_002211783.1\|25220_25883_+	Ig domain-containing protein	J9Q6D6	Salmonella_phage	8.5e-107	97.2
WP_002211782.1\|25926_26361_+	hypothetical protein	J9Q7Y3	Salmonella_phage	3.1e-73	99.3
WP_002211781.1\|26360_27194_+	hypothetical protein	J9Q7R2	Salmonella_phage	2.9e-152	99.6
WP_001027662.1\|27291_27636_+	hypothetical protein	J9Q7F6	Salmonella_phage	1.9e-57	100.0
WP_002211780.1\|27626_28100_+	hypothetical protein	J9Q711	Salmonella_phage	8.9e-82	99.4
WP_002211779.1\|28101_28485_+	hypothetical protein	J9Q6D8	Salmonella_phage	1.1e-66	98.4
WP_002211778.1\|28559_29306_+	Ig domain-containing protein	J9Q7Y4	Salmonella_phage	5.2e-129	98.8
WP_000163862.1\|29365_29683_+	hypothetical protein	J9Q7R3	Salmonella_phage	6.0e-50	98.1
WP_000952684.1\|29808_30033_+	hypothetical protein	J9Q7F7	Salmonella_phage	4.2e-34	100.0
WP_002211776.1\|30040_34618_+	tape measure protein	J9Q712	Salmonella_phage	0.0e+00	90.5
WP_000440566.1\|34659_34995_+\|tail	phage tail protein	J9Q6E1	Salmonella_phage	5.7e-59	97.3
WP_002211775.1\|35084_35783_+\|tail	phage minor tail protein L	J9Q7Y5	Salmonella_phage	7.1e-136	99.1
WP_002211774.1\|35775_36573_+	C40 family peptidase	J9Q7R4	Salmonella_phage	1.4e-156	96.2
WP_002211773.1\|36560_37148_+\|tail	tail assembly protein	J9Q7F8	Salmonella_phage	5.1e-103	92.8
WP_002214118.1\|37169_41801_+	DUF1983 domain-containing protein	J9Q713	Salmonella_phage	0.0e+00	88.6
WP_002211771.1\|41857_42436_+	DUF4376 domain-containing protein	Q9LA61	Enterobacterial_phage	3.4e-27	38.8
WP_002211770.1\|42516_45405_+\|tail	phage tail protein	J9Q6E3	Salmonella_phage	4.5e-11	33.1
WP_002211769.1\|45706_46315_+\|tail	tail fiber assembly protein	K7PMH7	Enterobacteria_phage	4.8e-64	62.2
WP_001297096.1\|46448_47228_-	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_000255944.1\|47227_48250_-\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_002228771.1\|48651_49128_-	hypothetical protein	J9Q7R9	Salmonella_phage	5.1e-77	95.6
WP_002224265.1\|49209_50004_-	hypothetical protein	J9Q7Z0	Salmonella_phage	3.7e-141	96.6
WP_002224263.1\|50256_50979_+	DUF4145 domain-containing protein	NA	NA	NA	NA
WP_002209743.1\|51012_52221_+\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211760.1\|52689_53712_+\|transposase	IS110-like element IS1618 family transposase	NA	NA	NA	NA
WP_002211758.1\|55787_57551_-	phospholipase D	NA	NA	NA	NA
WP_002211757.1\|57628_58117_-	phospholipase D family protein	NA	NA	NA	NA
WP_002211756.1\|58855_59131_+	hypothetical protein	NA	NA	NA	NA
WP_002215065.1\|59153_60095_-\|transposase	Rpn family recombination-promoting nuclease/putative transposase	Q2A0A7	Sodalis_phage	1.0e-68	54.8
WP_002211754.1\|60160_60781_-	recombinase family protein	A0A1V0E035	Clostridioides_phage	6.5e-08	31.1
WP_002215068.1\|60980_61307_-	type II toxin-antitoxin system RelE/ParE family toxin	NA	NA	NA	NA
WP_002211753.1\|61306_61534_-	type II toxin-antitoxin system Phd/YefM family antitoxin	NA	NA	NA	NA
WP_002211752.1\|61835_63041_+	AAA family ATPase	Q1MVJ3	Enterobacteria_phage	1.7e-206	90.5
WP_002215070.1\|63037_64009_+	ParB/RepB/Spo0J family partition protein	Q1MVJ4	Enterobacteria_phage	1.5e-112	67.3
WP_002228775.1\|64387_65785_+	AAA family ATPase	NA	NA	NA	NA
WP_002211750.1\|65946_66147_-	hypothetical protein	NA	NA	NA	NA
WP_002211749.1\|66647_67325_+	DNA methylase	A0A2I7RE86	Vibrio_phage	1.6e-28	36.9
WP_002211748.1\|67324_67546_+	hypothetical protein	NA	NA	NA	NA
WP_002215082.1\|67556_67976_+	DUF1380 domain-containing protein	NA	NA	NA	NA
WP_002211747.1\|68029_68809_+	hypothetical protein	NA	NA	NA	NA
WP_002211746.1\|69207_69714_+	antirestriction protein ArdA	A0A1I9S7Y0	Rhodococcus_phage	1.1e-08	29.5
WP_002211745.1\|70426_70657_+	DUF905 domain-containing protein	NA	NA	NA	NA
WP_002211744.1\|70729_72739_+	ParB/RepB/Spo0J family partition protein	G8DH78	Emiliania_huxleyi_virus	7.7e-26	30.3
WP_000255944.1\|72862_73885_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|73884_74664_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002233024.1\|74739_75777_+	DNA ligase	J9Q7G5	Salmonella_phage	1.8e-207	99.4
WP_002224361.1\|75936_76152_+	hypothetical protein	J9Q6I3	Salmonella_phage	7.7e-33	98.6
WP_002225462.1\|76148_76301_+	hypothetical protein	J9Q7Z1	Salmonella_phage	2.0e-19	96.0
WP_002224363.1\|76297_76603_+	hypothetical protein	J9Q7S1	Salmonella_phage	3.2e-48	97.0

DBSCAN-SWA_2

83005 : 100925

Salmonella_phage(94.12%)

integrase

attL 76146:76163|attR 89205:89222

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
76146:76163	attL	NA	NA	NA	NA
WP_002353208.1\|83005_84109_+\|integrase	site-specific integrase	A0A1P8DTG6	Proteus_phage	5.2e-24	30.9
WP_002228802.1\|84103_84490_-	hypothetical protein	NA	NA	NA	NA
WP_002228800.1\|84752_84965_+	hypothetical protein	NA	NA	NA	NA
WP_002211766.1\|85074_87441_+	porphyrin biosynthesis protein	J9Q7G6	Salmonella_phage	0.0e+00	94.4
WP_002211767.1\|87538_88774_+	AAA family ATPase	J9Q733	Salmonella_phage	3.0e-238	99.3
WP_002221186.1\|88954_92479_+	DNA polymerase III subunit alpha	J9Q7Z2	Salmonella_phage	0.0e+00	99.2
89205:89222	attR	NA	NA	NA	NA
WP_002425587.1\|92493_92919_+	hypothetical protein	J9Q7S4	Salmonella_phage	7.5e-72	100.0
WP_002213141.1\|92948_93512_-	DNA-binding protein	J9Q7G7	Salmonella_phage	2.2e-63	64.6
WP_002215095.1\|93584_93836_-	hypothetical protein	NA	NA	NA	NA
WP_011114024.1\|94056_94488_+	hypothetical protein	J9Q6I8	Salmonella_phage	2.2e-71	97.9
WP_002213132.1\|94607_95636_+	hypothetical protein	J9Q7Z3	Salmonella_phage	1.3e-165	98.5
WP_002225551.1\|95696_96641_+	exonuclease	J9Q7S6	Salmonella_phage	1.3e-180	99.0
WP_000920226.1\|96640_96907_+	hypothetical protein	J9Q7G8	Salmonella_phage	1.6e-40	100.0
WP_002213439.1\|98076_98277_+	hypothetical protein	J9Q6J0	Salmonella_phage	1.1e-25	97.0
WP_002222866.1\|98280_99111_+	hypothetical protein	J9Q7Z4	Salmonella_phage	9.3e-127	98.6
WP_002222868.1\|99264_99636_+	DUF2591 domain-containing protein	J9Q7S7	Salmonella_phage	4.0e-61	87.8
WP_002222869.1\|99619_100030_+	hypothetical protein	J9Q7G9	Salmonella_phage	4.1e-75	97.8
WP_002228797.1\|100097_100373_+	hypothetical protein	J9Q738	Salmonella_phage	1.7e-45	95.6
WP_002228796.1\|100413_100593_+	hypothetical protein	J9Q6J1	Salmonella_phage	5.8e-18	86.4
WP_002227818.1\|100589_100925_+	hypothetical protein	J9Q7Z5	Salmonella_phage	5.2e-52	91.0

Anti-CRISPR protein detection

Acr ID	Acr position	Acr size	Homology with known anti	Neighbor HTH/AcRanker	Neighbor Aca	In prophage	Protospacer in prophage

2. NC_004088

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Crispr_ID: NC_004088_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_1

328327-328439

Orphan

Consensus_repeat	Method
CTTCACTCGGCTGCTCAAATGTGCTTT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_004088_1

>merge|NC_004088|1|328327-328439|CRISPRCasFinder
CTTCACTCGGCTGCTCAAATGTGCTTTGGACGTCAACAACCCATTCAAAATCAAAAACGTATTAAAAGCCTAAGGATGATGGTCTGGCTTCACTCGCTGCTCAAATGTGCTTT

>NC_004088|1|1|328327-328439|CRISPRCasFinder
CTTCACTCGGCTGCTCAAATGTGCTTT	GGACGTCAACAACCCATTCAAAATCAAAAACGTATTAAAAGCCTAAGGATGATGGTCTG
GCTTCACTCGCTGCTCAAATGTGCTTT

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002208943.1\|312871_314203_-\|HslU--HslV-peptidase-ATPase-subunit	unknown	unknown	gnl\|CDD\|235364
NC_004088.1\|WP_002209481.1\|344141_344945_+\|energy-transducer-TonB	unknown	unknown	gnl\|CDD\|223880
NC_004088.1\|WP_002216737.1\|319630_319846_+\|50S-ribosomal-protein-L31	unknown	unknown	gnl\|CDD\|234576
NC_004088.1\|WP_002208942.1\|314273_314798_-\|ATP-dependent-protease-subunit-HslV	unknown	unknown	gnl\|CDD\|235477
NC_004088.1\|WP_002208934.1\|323031_325467_+\|bifunctional-aspartate-kinase/homoserine-dehydrogenase-II	unknown	unknown	gnl\|CDD\|236530
NC_004088.1\|WP_002216730.1\|315808_316837_-\|DNA-binding-transcriptional-regulator-CytR	unknown	unknown	gnl\|CDD\|182923
NC_004088.1\|WP_002208941.1\|314897_315743_-\|cell-division-protein-FtsN	unknown	unknown	gnl\|CDD\|237191
NC_004088.1\|WP_002223919.1\|331868_333032_-\|acetylornithine-deacetylase	unknown	unknown	gnl\|CDD\|235346
NC_004088.1\|WP_002209489.1\|333282_334287_+\|N-acetyl-gamma-glutamyl-phosphate-reductase	unknown	unknown	gnl\|CDD\|234761
NC_004088.1\|WP_002208935.1\|321174_321492_-\|met-regulon-transcriptional-regulator-MetJ	unknown	unknown	gnl\|CDD\|179982
NC_004088.1\|WP_002208938.1\|317189_319388_-\|primosomal-protein-N'	unknown	unknown	gnl\|CDD\|235514
NC_004088.1\|WP_002209484.1\|340081_340699_+\|heme-acquisition-protein-HasA	unknown	unknown	gnl\|CDD\|368907
NC_004088.1\|WP_002208936.1\|320370_320826_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|227027
NC_004088.1\|WP_002215335.1\|334452_335229_+\|acetylglutamate-kinase	unknown	unknown	gnl\|CDD\|239782
NC_004088.1\|WP_002231870.1\|340864_342673_+\|type-I-secretion-system-permease/ATPase	unknown	unknown	gnl\|CDD\|226969
NC_004088.1\|WP_002209482.1\|342748_344077_+\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|130902
NC_004088.1\|WP_002208933.1\|325699_326584_+\|methylenetetrahydrofolate-reductase	unknown	unknown	gnl\|CDD\|181852
NC_004088.1\|WP_002209491.1\|328858_331495_-\|phosphoenolpyruvate-carboxylase	unknown	unknown	gnl\|CDD\|234570
NC_004088.1\|WP_002209485.1\|337367_339860_+\|TonB-dependent-hemoglobin/transferrin/lactoferrin-family-receptor	unknown	unknown	gnl\|CDD\|273807
NC_004088.1\|WP_002209487.1\|335395_336769_+\|argininosuccinate-lyase	unknown	unknown	gnl\|CDD\|179883

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002208943.1\|312871_314203_-\|HslU--HslV-peptidase-ATPase-subunit	gnl\|CDD\|235364	PRK05201, hslU, ATP-dependent protease ATPase subunit HslU.	0
NC_004088.1\|WP_002209481.1\|344141_344945_+\|energy-transducer-TonB	gnl\|CDD\|223880	COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane].	1.51188e-39
NC_004088.1\|WP_002216737.1\|319630_319846_+\|50S-ribosomal-protein-L31	gnl\|CDD\|234576	PRK00019, rpmE, 50S ribosomal protein L31; Reviewed.	4.16591e-39
NC_004088.1\|WP_002208942.1\|314273_314798_-\|ATP-dependent-protease-subunit-HslV	gnl\|CDD\|235477	PRK05456, PRK05456, ATP-dependent protease subunit HslV.	1.88144e-131
NC_004088.1\|WP_002208934.1\|323031_325467_+\|bifunctional-aspartate-kinase/homoserine-dehydrogenase-II	gnl\|CDD\|236530	PRK09466, metL, bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional.	0
NC_004088.1\|WP_002216730.1\|315808_316837_-\|DNA-binding-transcriptional-regulator-CytR	gnl\|CDD\|182923	PRK11041, PRK11041, DNA-binding transcriptional regulator CytR; Provisional.	0
NC_004088.1\|WP_002208941.1\|314897_315743_-\|cell-division-protein-FtsN	gnl\|CDD\|237191	PRK12757, PRK12757, cell division protein FtsN; Provisional.	2.3223e-148
NC_004088.1\|WP_002223919.1\|331868_333032_-\|acetylornithine-deacetylase	gnl\|CDD\|235346	PRK05111, PRK05111, acetylornithine deacetylase; Provisional.	0
NC_004088.1\|WP_002209489.1\|333282_334287_+\|N-acetyl-gamma-glutamyl-phosphate-reductase	gnl\|CDD\|234761	PRK00436, argC, N-acetyl-gamma-glutamyl-phosphate reductase; Validated.	0
NC_004088.1\|WP_002208935.1\|321174_321492_-\|met-regulon-transcriptional-regulator-MetJ	gnl\|CDD\|179982	PRK05264, PRK05264, met regulon transcriptional regulator MetJ.	5.3482e-81
NC_004088.1\|WP_002208938.1\|317189_319388_-\|primosomal-protein-N'	gnl\|CDD\|235514	PRK05580, PRK05580, primosome assembly protein PriA; Validated.	0
NC_004088.1\|WP_002209484.1\|340081_340699_+\|heme-acquisition-protein-HasA	gnl\|CDD\|368907	pfam06438, HasA, Heme-binding protein A (HasA). Free iron is limited in vertebrate hosts, thus an alternative to siderophores has been developed by pathogenic bacteria to access host iron bound in protein complexes. HasA is a secreted hemophore that has the ability to obtain iron from hemoglobin. Once bound to HasA, the heme is shuttled to the receptor HasR, which releases the heme into the bacterium.	9.51098e-102
NC_004088.1\|WP_002208936.1\|320370_320826_-\|hypothetical-protein	gnl\|CDD\|227027	COG4682, COG4682, Predicted membrane protein [Function unknown].	3.96467e-66
NC_004088.1\|WP_002215335.1\|334452_335229_+\|acetylglutamate-kinase	gnl\|CDD\|239782	cd04249, AAK_NAGK-NC, AAK_NAGK-NC: N-Acetyl-L-glutamate kinase - noncyclic (NAGK-NC) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of microbial arginine biosynthesis using the acetylated, noncyclic route of ornithine biosynthesis. There are two variants of this pathway. In one, typified by the pathway in Escherichia coli, glutamate is acetylated by acetyl-CoA and acetylornithine is deacylated hydrolytically. In this pathway, feedback inhibition by arginine occurs at the initial acetylation of glutamate and not at the phosphorylation of NAG by NAGK. Homodimeric NAGK-NC are members of the Amino Acid Kinase Superfamily (AAK).	2.52737e-136
NC_004088.1\|WP_002231870.1\|340864_342673_+\|type-I-secretion-system-permease/ATPase	gnl\|CDD\|226969	COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only].	0
NC_004088.1\|WP_002209482.1\|342748_344077_+\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	gnl\|CDD\|130902	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking].	3.16318e-105
NC_004088.1\|WP_002208933.1\|325699_326584_+\|methylenetetrahydrofolate-reductase	gnl\|CDD\|181852	PRK09432, metF, methylenetetrahydrofolate reductase.	0
NC_004088.1\|WP_002209491.1\|328858_331495_-\|phosphoenolpyruvate-carboxylase	gnl\|CDD\|234570	PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.	0
NC_004088.1\|WP_002209485.1\|337367_339860_+\|TonB-dependent-hemoglobin/transferrin/lactoferrin-family-receptor	gnl\|CDD\|273807	TIGR01785, Heme/hemopexin_utilization_protein_C, TonB-dependent heme/hemoglobin receptor family protein. This model represents the TonB-dependent outer membrane heme/hemoglobin receptor/transporter found in bacteria which live in contact with animals (which contain hemoglobin or other heme-bearing globins) or legumes (which contain leghemoglobin). Some species having hits to this model such as Nostoc, Caulobacter and Chlorobium do not have an obvious source of hemoglobin-like proteins in their biological niche and so the possibility exists that they act on some other substance. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins].	8.20794e-132
NC_004088.1\|WP_002209487.1\|335395_336769_+\|argininosuccinate-lyase	gnl\|CDD\|179883	PRK04833, PRK04833, argininosuccinate lyase; Provisional.	0

>NC_004088.1|WP_002208933.1|325699_326584_+|methylenetetrahydrofolate-reductase
MSFFHANQREALNQSLSELQGQINVSFEFFPPRTSEMEDTLWSSIDRLSTLKPKFVSVTYGANSGERDRTHSIIKGIKERTGLEAAPHLTCIDASPTQLRDIAIDYWNSGIRHIVALRGDLPPNSGKPEMYACDLVGLLKDVGDFDISVAAYPEIHPEAKSAQADLINLKRKIDAGANRAITQFFFDVESYLRFRDRCVATGIDVEIVPGILPVSNFKQLQRFATMTNVRVPNWMTSIFDGLDNDPETRKMVGASVAMDMVKILSREGVKDFHFYTLNRAELSYAICHTLGVRP
>NC_004088.1|WP_002208934.1|323031_325467_+|bifunctional-aspartate-kinase/homoserine-dehydrogenase-II
MNATAVAAAATGRQLHKFGGSSLADVKCYLRVANIMANYSHPGDLMVVSAAGSTTNQLISWLKLSQNDRLSAHQVQQSLRRYQHDLINGLLPPEMAEPLISEFIHDLERLAGLLDNKIDDVIYAEVVGHGEIWSARLMSALLNKLDMDAVWLDARRFLRAERAAQPQIDESRSYPLLQQLMAQHPHQRLVVTGFISRNEAGETVLLGRNGSDYSATQVGALAGAERVTIWSDVAGVYSADPRKVKDACLLPLLRLDEASELARLAAPVLHTRTLQPVSGSDIDLQLRCSYQPEQGSTRIERVLASGLGAKIVTSHDDVCLIELQIASHHDFSLAQKEIDLLLKRAQIKPLATGIHPDRNLLQLCYTSEVVNSALRVLEDAALPGKLSLREGLALVALVGAGVSKNPLHSHRFYQQLKDQPVEFVWQAEDGISMVAVLRLGPTEHLIQGLHQSLFRAEKRIGLMLFGKGNIGARWLELFAREQKSLSARSGFEFVLAGVVDSRRSLLSYDGLDASRTLAFYNDEAKEQDEESLFLWMRAHPFDDLVVLDVTASPSLAEQYLDFASYGFHVISANKLAGASSSNNYRQIRDAFAKTGRHWLYNATVGAGLPVNHTVRDLRDSGDSILAISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRVDLSGQDVMRKLVILAREAGYDIEPNQVRVESLVPAGAESGSVDQFFENGEALNQQMIQRLEAAKEMGLVLRYVARFDANGKARVGVEAVRTDHPLASLLPCDNVFAIESRWYRDNPLVIRGPGAGRDVTAGAIQSDLNRLSQLL
>NC_004088.1|WP_002208935.1|321174_321492_-|met-regulon-transcriptional-regulator-MetJ
MAEWNGEYVSPYAEHGKKSKQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPNDEDLRKERSDEIPEAAKILMRELGVDPDTWEY
>NC_004088.1|WP_002208936.1|320370_320826_-|hypothetical-protein
MNPNYAKPSAAFTAASWSALLGGFVIFLIGLWNADMQLNERGYYFAVLILGLFSAVSLQKTVRDKLEGLAITSIYYGLCWVAFIVAVLLLCIGLWNATLALSEKGFYGVTFFMTLFGAIAVQKNTRDSAMSSDTESASLFKKVRDQLKAED
>NC_004088.1|WP_002216737.1|319630_319846_+|50S-ribosomal-protein-L31
MKQGIHPKYEQVTASCSCGNVIKINSTVGHDLNLDVCGECHPFYTGKQRDVASGGRVDRFNKRFSVPGAKK
>NC_004088.1|WP_002208938.1|317189_319388_-|primosomal-protein-N'
MSVVQVALPVPLARTFDYRLDSAMACPVVGARVSVPFGKRKAIGIVVGLSDTSTFPLEQLKTIDAILDNHSLFPPSLWRILCWATEYYHYPIGEVLFHALPILLRQGRPAQSAPLWQWFVTEQGRATPPESLKRAPKQQQALAALLQKPVYRHQVNEMALTESALQALRSKGLIDLRAQEATTTDWRHSFSVLGERLRLNTEQATAVGAIRSEDNQFAAWLLAGVTGSGKTEVYLSVLENILAQGRQALILVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSVWLRARSGEAAIVIGTRSALFTPFSRLGVIIIDEEHDSSYKQQEGWRYHARDLAVFRAREEGIPIVMGTATPALETLHNVQMGKYRQLTLTKRAGSAKPAAQHLLDLKGLPLKVGLSQPLLKQMKTHLQAGNQVILFLNRRGYAPALLCHECGWIAECQRCDHYYTLHQNHRQLRCHHCDSQRPVPQQCPKCGSTHLVSVGVGTEQLENELAPLFPETPITRIDRDTTSRKGSLEQYLADVHQGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVSGRAGRAGKQGEVILQTHHPEHPLLQILLQQGYDAFAKQALEERKSVFLPPYTSHIIVRSEDHDNQQSALFLQQLRNLLEASPLKDEALWIMGPVPALQAKRGGRFRWQLLLQHPSRQLLQRLIKTSQPLISTLPQARKVKWTIDVDPIDS
>NC_004088.1|WP_002216730.1|315808_316837_-|DNA-binding-transcriptional-regulator-CytR
MENKKEFTMTTMKDVAEMAGVSTATVSRALMNPEKVSTVTRQKVEQAVLAVGYSPHALSRNIKRNESRTILVIVPDISDPFFADVIQGIEHAAAQQGYLILIGDCAQQTQQERTFVNLIITKQIDGMLLLGSNLPFDASKEEQRNLPPMVMANEFAPELELPTVHIDNLTAAYEAVNYLHELGHKRIACIAGPESLPLSHYRLQGYIQALRRNGITVDNDYIIRGDFSYEAGAQSFAALMELPHPPTAIFSHNDVMAVGAIWQAKQLGLRIPQDVSLVGFDDLKLSQFCDPPLTTVAQPRYQIGQQAMLLLLEQLQGHSVQSGSRLLDTELIIRESTAAPKH
>NC_004088.1|WP_002208941.1|314897_315743_-|cell-division-protein-FtsN
MAQRDYVSRGRSGARRKSTSRKKRSAPIVSKTVMALAVALLVVFVGGLYFITHNKPGELPLLPNHDPRTGNGLPPKPEERWRYIKELENRQIGVPMPTEPSAGGEVNAKTELTNEQRQLLEQMQADMRQQPTQLSEVPYNQGMQQVPRSAVTIKPPATSVQPQPVTPPRQTTIPVQPQAPAPVRTPPAAPVTQAVTPPKVEKEKEKTQRWMVQCGSFKAVDQAESIRAQLAFAGIESRITSGGGWNRVVLGPYNSKAAADKALQRLQGAGQSGCIPLSVGG
>NC_004088.1|WP_002208942.1|314273_314798_-|ATP-dependent-protease-subunit-HslV
MTTIVSVRRDGHVVIGGDGQVTLGNTVMKGNAKKVRRLYNNKVIAGFAGGTADAFTLFELFERKLEMHQGHLTKAAVELAKDWRTDRMLRKLEALLAVADETASLIITGNGDVVQPEDDLIAIGSGGPYAQSAARALLENTELGARDIVEKSLSIAGDICIYTNRFQTIEELTY
>NC_004088.1|WP_002208943.1|312871_314203_-|HslU--HslV-peptidase-ATPase-subunit
MSEMTPREIVSELDSHIIGQDKAKRAVAIALRNRWRRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKMVRHQSIEKMRYRAEELAEERILDVLIPPAKNNWGVPDESQEPSATRQTFRKKLREGQLDDKEIEIDLAAAPMGVEIMAPPGMEEMTNQLQSMFQNIAGQKQKPRKIKIKEALKLLIEEEAAKLVNPEELKQQAIDAVEQHGIVFIDEIDKICKRGQTSGPDVSREGVQRDLLPLVEGCTVSTKHGMVKTDHILFIASGAFQVSSPSDLIPELQGRLPIRVELQALTTDDFERILTEPSASLTEQYKALMATEGVTIEFTREGIRKIAEAAWQVNERTENIGARRLHTVLERLMEDISYDASESSGQSITIDAEYVGKHLDELVADEDLSRFIL
>NC_004088.1|WP_002209491.1|328858_331495_-|phosphoenolpyruvate-carboxylase
MNEQYSAMRSNVSMLGTLLGDTIKEALGEHILDRVETIRKLSKSSRAGNEASRQELLTTLQNLSNDELLPVARAFSQFLNLTNTAEQYHSISPHGEAASNPEALAQLFTRLKDKKLSDQDMRSAVDDLSIELVLTAHPTEITRRTLIHKLVEVNTCLSQLDHNDLADYERNKIMRRLRQLVAQSWHTDEIRKLRPSPVDEAKWGFAVVENSLWEGVPAFLREFNEQLENSLDYRLPVEAVPIRFTSWMGGDRDGNPNVTAEITRHVLLLSRWKATDLFLRDIQVLVSELSMSECTPELRELAGGEEVLEPYRQLMKNVRTQLTNTQAYLEARLKGERVLPPHDLLVSNDQLWEPLYACYQSLKACGMEIIANGQLLDTLRRVRCFGVPLVRIDVRQESTRHTDAIAELTRYLGLGDYESWSESDKQAFLVRELNSKRPLVPLKWEPSAETQEVLETCRVIAEAPQGSIAAYVISMAKVPSDVLAVHLLLKEAGCPFTLPVAPLFETLDDLNNADDVMTQLLGIDWYRGLIQGKQMVMIGYSDSAKDAGVMAASWAQYRAQDALIKTCEKAGITLTLFHGRGGSIGRGGAPAHAALLSQPPGSLKGGLRVTEQGEMIRFKFGLPEVTISSLALYAGAILEANLLPPPEPKKEWIEVMDLLSDASCDMYRSYVRENPEFVRYFRAATPELELGKLPLGSRPAKRRPDGGVESLRAIPWIFAWTQNRLMLPAWLGAGAGLQRAIDAGKQDVLATMCRDWPFFSTRIGMLEMVFAKADLWLAEYYDQRLVDKSLWPLGQQLRDQLAADIKVVLAIANDDHLMADLPWIAESIALRNVYTDPLNVLQAELLHRSRQQEHPDACVEQALMVTIAGVAAGMRNTG
>NC_004088.1|WP_002223919.1|331868_333032_-|acetylornithine-deacetylase
MKLPPFIELYRALIATPSISAADSALDQSNEALINLLAGWFADLGFRVEIQPVPDTRHKFNLLASIGENENGEGHGGLLLAGHTDTVPYDEGRWTRDPFTLTEHDHKLYGLGTADMKGFFAFILDAVRDIDASKLTKPLYILATADEETTMAGARYFAANTQLRPDFAIIGEPTSLQPVRAHKGHISNAIRITGQSGHSSDPARGVNAIDLMHESITQLMALRTTLQERYHNPAFTIPYPTMNFGHINGGDAANRICACCELHMDIRPLPGLTLSDLNELMTEALEPVSQRWPGRLSIDELHPPIPGYECPTDHHMVGVIEKLLGERTAVVNYCTEAPFIQQVCPTLVLGPGSINQAHQPDEFIDMAFIEPTRELIGQLVDHFCQQK
>NC_004088.1|WP_002209489.1|333282_334287_+|N-acetyl-gamma-glutamyl-phosphate-reductase
MLNTLIVGASGYAGAELTAYLNRHPHMNITGLAVSAQSADAGKLLSDLHPQLKGILDLPLQPLVDVAQAAKGIDVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVRDAAFYSQYYGFEHQHPDWLDKAVYGLAEWQSEDIKQAQLIAVPGCYPTASQLALKPLVDGQLLNDAQWPVINAVSGVSGAGRKASMGNSFCEVSLQPYGLFTHRHQPEIVTHLGTPVIFTPHLGNFARGILATITCRLKAGVTAQNIADAYHHAYQNKPLVRLYQQGVPALKAVVGLPFCDIGFSVQGEHLIIVATEDNLLKGAAAQAVQCMNIRFGFPETQSLL
>NC_004088.1|WP_002215335.1|334452_335229_+|acetylglutamate-kinase
MMNPLVIKLGGVLLDSEEALERLFTALVTYREKHERPLVIMHGGGCLVDELMKRLALPVVKKNGLRVTPADQIDIITGALAGTANKTLLAWAVKHQINAVGLCLADGNTVTVTLLDAELGHVGKAQPGSAALVQTLLAAGYMPIISSIGITVEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAQKAEQLIAQGIITDGMVVKVNAALDAARSLGRPVDIASWRHSEQLPALFNGVPIGTRISV
>NC_004088.1|WP_002209487.1|335395_336769_+|argininosuccinate-lyase
MALWGGRFSQAADQRFKQFNDSLRFDYRLAEQDIIGSVAWSKALVTVGVLNADEQQQLEQALSVLLEEVQANPHAILASDAEDIHSWVETKLIDKVGDLGKKLHTGRSRNDQVATDLKLWCKFQITELQTAVQQLQQALVMTAEANQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLSRDESRLQDTLKRLDVSPLGCGALAGTAYAIDREQLAGWLGFASATRNSLDSVSDRDHVLELLSDASIGMVHLSRFAEDLIFFNSGEAAFVDLSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGALTGMTMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCKEAAEQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKALEALALSDLQQFSSVIGDDVYPILALQSCLDKRVAKGGVSPQQVASAIAEAKARLF
>NC_004088.1|WP_002209485.1|337367_339860_+|TonB-dependent-hemoglobin/transferrin/lactoferrin-family-receptor
MDNIIRDKKTIISVNKITTCILFALVTQGYSGQLAANTAETPTNNNDMALDKLNVEGKGNAHDSDWIYDEPRSVSEITREQLDNRPARHAADILEQTPGVYSSVSQQDPGLSINIRGIQDYGRVNMNIDGMRQNFMKSGHGQRNGSMYIDPEILSNVVIERGIFNGIGGAGAIGGIATFNTINASDFLAPEKELGGHIRAMTGDNGTRFIGSGALALGNPNGDILLAVSERNLKDYWPGNKGVLAGLRLYSPTRNVGDDLKNTKTLFTGYKMRSQLAKVGWNFEAGQRLEFSYLQTQIASPNASMLSEVLALSPSGKEITKIGWRNTSFTNVENRNIALDYRLNPEHISWLDATAKIYYVDTNDETDNANSLFKEYFWTQTRLKTRGLQLQNTNTFTPSDAHQIRLKYGLEWFSDKSEGYSTRKLIERTTPPGKRAITSTFAQLNYEYDDWLRLEGGLRYDQFRLKGNTWLHTRSFLQPYTFENPCDRRIHEQSEKPGSRCSSRRPATMRWDVDRCEQQLSPTLAMGVKPGLEWLEFFGSYGKSWRPPAMTEVLATGTAHGYSWVLPNPFVAAERARTWEAGFNIQQSNLFIEDDHFAAKVAYFDTRIANYINLELGKAKPKFGGDSFTDVAYVNNLLKTRFRGLEYQLSYDAGTFYTNINYTRMIGVNNVCSPYAWLGGLQSVKYKYVGKVEQIYAVENEVANNYVTCMNANVLFGSSAYLPGDRGSLTLGSRIFDRRLDFGTVIRYNKGYQDRSAQDENGNPLTAYVADWPKYIVYDLYASYKVTNNLILRSSIENITNRAYLVNYGDTLSFAPSRGRTIQGGFEYKF
>NC_004088.1|WP_002209484.1|340081_340699_+|heme-acquisition-protein-HasA
MSTTIQYNSNYADYSISSYLREWANNFGDIDQAPAETKDRGSFSGSSTLFSGTQYAIGSSHSNPEGMIAEGDLKYSFMPQHTFHGQIDTLQFGKDLATNAGGPSAGKHLEKIDITFNELDLSGEFDSGKSMTENHQGDMHKSVRGLMKGNPDPMLEVMKAKGINVDTAFKDLSIASQYPDSGYMSDAPMVDTVGVVDCHDMLLAA
>NC_004088.1|WP_002231870.1|340864_342673_+|type-I-secretion-system-permease/ATPase
MESCKTPGASSVPPTILSVLAGNKKILWGIGLFTAVINLLMLAPAIYMLQVYDRVLASANTMTLLMLTVLVLGVFVFIGLLEWVRSAVVIRLGTQIDMQLNQPVFNAAFAANLKGHNTPAAQALNDLTVLRQFATGNALFAFFDAPWFPLYLLVIFLLHPWLGMLAAAGAGILVVLAWLNQWICKKPLHDASIITSHATQQANANLRNADVIEAMGMLKALRERWLMQHANFLYQQNLASDKSSRVTAVAKSSRQALQSMMLGLGALLVIYNEITAGVMIAGSILIGRVLGPIDQLIAVWKQWSHARLAYQRLSQLLAQHPSSPTGMVLPAPQGKLNVTQLMACKPGTHIPVLHSINFELQPGDVLGILGPSGSGKSTLAKLLVASQPTFSGTVRLDSADLSRWDKTQLGEFIGYLPQNIQLFRGTVAENIARFGAIDTAKVVAAAQLADVHDLILHLPQGYDTPLGDDGEGLSGGQRQRIALARAMYGIPRLIVLDEPDASLDKEGEQALLASIIQLKQQGCTIVMITHKPELLSGSDYLLFLKNGQMDLFDRTQAVLQNIQGKDKPAVQPEAKILNSRSGWSNGVSYGIGPARTTSSPKP
>NC_004088.1|WP_002209482.1|342748_344077_+|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit
MLPESVCYSVANANRQPPLQINSGRYLNIGGGLVVIGFIGFLLWAGLAPLDKGVAVTGLLVVAENRKVIQPLQGGRIQQLHVTEGDEIVSGQLLVTLDDTAIRNQRDNLQHQYLSALAQEARLTAEQNDLDVITFPQALLEHATQPAVERNIILQQQLLHHRRQAHLSEIARLSTQLTRHQARLDGLQAMRSNHQRQSNLFQQQLDSVQLLAKDGHIAKNKLLEMESQSTSLQARVEQSTSDIAEAHKLIDETEQHVLQRREQYQSENSEQLAKAQQNTQELVQRLNIAEYELSHTRIFAPVSGSVIALAQHTVGGVVSSGQALMEIVPSGQPLFVEAQLPVELIDKVAVGLPVDLNFSAFNQSNTPRLQGSVWRIGADRIQPPPTSPPYYPLTVAIDLDPTELAIRPGMAVDVFIRTGERSLLSYLFKPFTDRLHLALAEE
>NC_004088.1|WP_002209481.1|344141_344945_+|energy-transducer-TonB
MNRLQQSSDKLIFWLVGALLACGIHIYALWWLSTASIPAIPTSYPAAIMMELSAEPEFMQNLPQNSVVGITQNIIEPAVEQRVNQPDDIVDLPTLPEQPEGQREITRKEPIKVKRPAENRATSRKPVNKETQESDSKQSSPAAAASAMLSGTSQQVAAAVNSDSSHRQQAQVSWKSRLQGHLMGFKRYPSSARKQQQQGTAMIRFVVDKNGYVSSVQLSHSSGTSALDREALAIIKRAQPLPKPPAELLSQGQITLSLPVDFNLKRK

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Crispr_ID: NC_004088_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_2

1291480-1291750

Orphan

I-F

Consensus_repeat	Method
GTTCACTGCCGCACAGGCAGCTTAGAAA	PILER-CR
GTTCACTGCCGCACAGGCAGCTTAGAAA	CRISPRCasFinder
GTTCACTGCCGCACAGGCAGCTTAGAAA	CRT

4 spacers

The CRISPR arrays of NC_004088_2

>merge|NC_004088|2|1291480-1291750|PILER-CR,CRISPRCasFinder,CRT
GTTCACTGCCGCACAGGCAGCTTAGAAACCTGATACAATCATCCTATTTGTCCTATCCAGAAGTTCACTGCCGCACAGGCAGCTTAGAAAGACAAGAACCGAATCTTTCGCCGTGCCGTAAAGTTCACTGCCGCACAGGCAGCTTAGAAACCGAAATCATCAGATGTAATTAAGATTTTTGCTGTTCACTGCCGCACAGGCAGCTTAGAAAAGACTGATGCAAGATGGCGGTATGCGTACAGAGTTCACTGCCGCACAGGCAGCTTATAGA

>NC_004088|2|1|1291480-1291690|PILER-CR
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCTGATACAATCATCCTATTTGTCCTATCCAGAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	GACAAGAACCGAATCTTTCGCCGTGCCGTAAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCGAAATCATCAGATGTAATTAAGATTTTTGCT
GTTCACTGCCGCACAGGCAGCTTAGAAA

>NC_004088|2|2|1291480-1291750|CRISPRCasFinder
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCTGATACAATCATCCTATTTGTCCTATCCAGAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	GACAAGAACCGAATCTTTCGCCGTGCCGTAAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCGAAATCATCAGATGTAATTAAGATTTTTGCT
GTTCACTGCCGCACAGGCAGCTTAGAAA	AGACTGATGCAAGATGGCGGTATGCGTACAGA
GTTCACTGCCGCACAGGCAGCTTATAGA

>NC_004088|2|1|1291480-1291750|CRT
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCTGATACAATCATCCTATTTGTCCTATCCAGAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	GACAAGAACCGAATCTTTCGCCGTGCCGTAAA
GTTCACTGCCGCACAGGCAGCTTAGAAA	CCGAAATCATCAGATGTAATTAAGATTTTTGCT
GTTCACTGCCGCACAGGCAGCTTAGAAA	AGACTGATGCAAGATGGCGGTATGCGTACAGA
GTTCACTGCCGCACAGGCAGCTTATAGA

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002210306.1\|1305625_1306441_+\|5-deoxy-glucuronate-isomerase	unknown	unknown	gnl\|CDD\|226241
NC_004088.1\|WP_002210302.1\|1300355_1301384_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224093
NC_004088.1\|WP_002210303.1\|1301407_1302541_+\|Gfo/Idh/MocA-family-oxidoreductase	unknown	unknown	gnl\|CDD\|223745
NC_004088.1\|WP_002209748.1\|1278039_1278441_-\|DUF1240-domain-containing-protein	unknown	unknown	gnl\|CDD\|336520
NC_004088.1\|WP_002359655.1\|1294506_1296432_+\|3D-(3,5/4)-trihydroxycyclohexane-1,2-dione-acylhydrolase-(decyclizing)	unknown	unknown	gnl\|CDD\|226471
NC_004088.1\|WP_002210297.1\|1292945_1294472_+\|CoA-acylating-methylmalonate-semialdehyde-dehydrogenase	unknown	unknown	gnl\|CDD\|143404
NC_004088.1\|WP_002209745.1\|1280596_1280842_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|372675
NC_004088.1\|WP_002214721.1\|1304557_1305616_+\|myo-inosose-2-dehydratase	unknown	unknown	gnl\|CDD\|275172
NC_004088.1\|WP_002213775.1\|1283612_1284071_+\|IS200/IS605-like-element-IS1541B-family-transposase	unknown	unknown	gnl\|CDD\|224854
NC_004088.1\|WP_002223320.1\|1297818_1298748_+\|substrate-binding-domain-containing-protein	unknown	unknown	gnl\|CDD\|380623
NC_004088.1\|WP_138921619.1\|1281054_1283367_-\|penicillin-binding-protein-1C	unknown	unknown	gnl\|CDD\|273954
NC_004088.1\|WP_002223323.1\|1298796_1300344_+\|sugar-ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224053
NC_004088.1\|WP_002210296.1\|1291753_1292608_-\|MurR/RpiR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224651
NC_004088.1\|WP_002227852.1\|1277180_1277432_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002209751.1\|1276902_1277142_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002209749.1\|1277455_1278028_+\|Hcp-family-type-VI-secretion-system-effector	unknown	unknown	gnl\|CDD\|213799
NC_004088.1\|WP_002210294.1\|1284185_1290164_-\|alpha-2-macroglobulin-family-protein	unknown	unknown	gnl\|CDD\|225248
NC_004088.1\|WP_002209746.1\|1278673_1279075_-\|DUF1240-domain-containing-protein	unknown	unknown	gnl\|CDD\|336520
NC_004088.1\|WP_002210304.1\|1302572_1304543_+\|5-dehydro-2-deoxygluconokinase	unknown	unknown	gnl\|CDD\|378281
NC_004088.1\|WP_002223316.1\|1290570_1291119_-\|DUF1440-domain-containing-protein	unknown	unknown	gnl\|CDD\|226008

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002210306.1\|1305625_1306441_+\|5-deoxy-glucuronate-isomerase	gnl\|CDD\|226241	COG3718, IolB, Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism].	3.14642e-169
NC_004088.1\|WP_002210302.1\|1300355_1301384_+\|ABC-transporter-permease	gnl\|CDD\|224093	COG1172, AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism].	8.15893e-97
NC_004088.1\|WP_002210303.1\|1301407_1302541_+\|Gfo/Idh/MocA-family-oxidoreductase	gnl\|CDD\|223745	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only].	2.07432e-69
NC_004088.1\|WP_002209748.1\|1278039_1278441_-\|DUF1240-domain-containing-protein	gnl\|CDD\|336520	pfam06836, DUF1240, Protein of unknown function (DUF1240). This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Yersinia pestis. The function of this family is unknown.	7.32611e-43
NC_004088.1\|WP_002359655.1\|1294506_1296432_+\|3D-(3,5/4)-trihydroxycyclohexane-1,2-dione-acylhydrolase-(decyclizing)	gnl\|CDD\|226471	COG3962, COG3962, Acetolactate synthase [Amino acid transport and metabolism].	0
NC_004088.1\|WP_002210297.1\|1292945_1294472_+\|CoA-acylating-methylmalonate-semialdehyde-dehydrogenase	gnl\|CDD\|143404	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2. Methylmalonate semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27) [acylating] from Bacillus subtilis is involved in valine metabolism and catalyses the NAD+- and CoA-dependent oxidation of methylmalonate semialdehyde into propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and Arabidopsis MMSDH ALDH6B2 are also present in this CD.	0
NC_004088.1\|WP_002209745.1\|1280596_1280842_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|372675	pfam13693, HTH_35, Winged helix-turn-helix DNA-binding.	5.27401e-36
NC_004088.1\|WP_002214721.1\|1304557_1305616_+\|myo-inosose-2-dehydratase	gnl\|CDD\|275172	TIGR04379, myo-inositol_catabolism_protein, myo-inosose-2 dehydratase. Members of this family include the enzyme myo-inosose-2 dehydratase, product of the gene iolE, as found in inositol utilization cassettes in many species. [Energy metabolism, Sugars].	4.28689e-165
NC_004088.1\|WP_002213775.1\|1283612_1284071_+\|IS200/IS605-like-element-IS1541B-family-transposase	gnl\|CDD\|224854	COG1943, COG1943, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	2.50747e-46
NC_004088.1\|WP_002223320.1\|1297818_1298748_+\|substrate-binding-domain-containing-protein	gnl\|CDD\|380623	cd19968, PBP1_ABC_IbpA-like, periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins. The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.	3.60348e-119
NC_004088.1\|WP_138921619.1\|1281054_1283367_-\|penicillin-binding-protein-1C	gnl\|CDD\|273954	TIGR02073, Includes:_Penicillin-insensitive_transglycosylase, penicillin-binding protein 1C. This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].	0
NC_004088.1\|WP_002223323.1\|1298796_1300344_+\|sugar-ABC-transporter-ATP-binding-protein	gnl\|CDD\|224053	COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism].	0
NC_004088.1\|WP_002210296.1\|1291753_1292608_-\|MurR/RpiR-family-transcriptional-regulator	gnl\|CDD\|224651	COG1737, RpiR, Transcriptional regulators [Transcription].	1.17523e-68
NC_004088.1\|WP_002209746.1\|1278673_1279075_-\|DUF1240-domain-containing-protein	gnl\|CDD\|336520	pfam06836, DUF1240, Protein of unknown function (DUF1240). This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Yersinia pestis. The function of this family is unknown.	5.05571e-40
NC_004088.1\|WP_002210294.1\|1284185_1290164_-\|alpha-2-macroglobulin-family-protein	gnl\|CDD\|225248	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only].	0
NC_004088.1\|WP_002209749.1\|1277455_1278028_+\|Hcp-family-type-VI-secretion-system-effector	gnl\|CDD\|213799	TIGR03344, VI_effect_Hcp1, type VI secretion system effector, Hcp1 family. This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens. [Cellular processes, Pathogenesis].	2.31704e-76
NC_004088.1\|WP_002210304.1\|1302572_1304543_+\|5-dehydro-2-deoxygluconokinase	gnl\|CDD\|378281	pfam09863, DUF2090, Uncharacterized protein conserved in bacteria (DUF2090). This domain, found in various prokaryotic carbohydrate kinases, has no known function.	0
NC_004088.1\|WP_002223316.1\|1290570_1291119_-\|DUF1440-domain-containing-protein	gnl\|CDD\|226008	COG3477, COG3477, Predicted periplasmic/secreted protein [Function unknown].	1.03166e-68

>NC_004088.1|WP_002223316.1|1290570_1291119_-|DUF1440-domain-containing-protein
MSEKRVNLQVIAWATIIGGFVSSLVKSGTEVNMPPRVVGEISPPAANIDAWLGWLGINSHSMDYVYQGVTISGAVVLYHWLFSFVFAFVYVLLSAYWPKVRLWYSAAYGLSITVAIHGVLIPALGFRHPAYLAGETGWLWNLNGYELWSEIIGHLCWSASLEICLVAVLAFFSKPIKGIWAN
>NC_004088.1|WP_002210294.1|1284185_1290164_-|alpha-2-macroglobulin-family-protein
MDLLRFLLISPFALIKGLYRLSAYLLRLVGRLLRPVVGNLNWRAPQWMTKTANGLHCAFNRSEQWVAKHPKGISAAIVLLMAAASAAFYGYHWYLNRPQPIEPAPMVYQETSIRVSAPRTVNYQAQKPEAQPLSLNFMHSAAPITAMGQVVDQGISLTPAIEGEWKWATERTLVFTPKKAWPMGANYQITIDTEKLLAPQIKLNQTELNFTTPAFAYQLEKAEYYQDPQEAQKRSTIFHVQFNAPVDVASFEKQILLGLVEGKSKSEKKLNFSVVYDEKKLNAWIHSQPLMPMDKGGSVHLSINKGVNASVAATPTTQAQNKWVSVPNLYSLAVNSINATLVESDNNNGERALIIAISDAVKDKEIKNAVKAWLLPQHNFQAKESAKTSTDFYPWDMDDIDDNLLQQSTPLALTLNEAEQEYQPIFSFKFDAPSYRTLLIEVNNSLTSVGGYKMPEKIYQIVRVPDYPKTLRFMSQGSLLSMQGDKQISVAARNMTGMKLDIKRVIPSQLQHIVSFKSSEYSSAHFNRLSDEYFTEHFQYQTALNNDNPGEINYQGVDLSRYLANNPSARRGVFLLTLSAWDPEKRDNQQHSEEDYDEDQEWVGDSRFVVITDLGIITKQSQDRSRDVFVQSIHSGLPAADAKVSVVAKNGVVLLSQITDSKGHVHFPALDAFKNERQPVMFLVEKEGDVSFLPTRATYDRNLDFSRFDIDGEETPSDPRTLSSYLFSDRGVYRPGDRFNIGLITRTANWATALDGVPLRAEIRDPRDTLMSTLPITLDSSGFNELSYTTGENSPTGEWNVYLYLVGKNNETSMLLGHTTVNVKEFEPDRLKVQLQLTPERQQGWVKPQELQANINVQNLFGTPAQERRVTSRLILRPMYPSFAPFPDYLFYENRHNSDGFETELEEQTTDLQGMATIPLDLKSYADATYQLQLLSEAFEAGGGRSVAATARVLVSPYDSLVGVKADGDLSYINRDAVRKLNIIAVDPSLNKIALPDLSLSLIEQKYISVLTKQDSGVYKYQSRLKEQLVSEQPLQISPTGTDFTLVTQQPGDFILVVKDSQGQVLNRISYTVAGNANLTRSLDRNTELKLKLNQAEYLQGEEIEIAINAPYAGSGLITIEKDKVYSWQWFHSDTTSSVQRIRIPPAMEGNGYINVQFVRDVNSDEIFMSPLSYGVMPFKISTKARQAAIELASPSVIKPGEVLPIKVTTDSPQRVVVFAVDEGILQVARYRLKDPLDYFFRKRELSVQSAQILDLILPEFSKLMALTSAPGGDAGEGLDLHLNPFKRKQDKPVAYWSGITEVNGETTFNYPIPDYFNGKIRVMAISATPDRIGKVQTSTTVRDNFILTPNVPAMVAPGDEFDVTVGVSNNLQGLKGKAVDITVRLTPPPQLEVVGEAQHSLSLAEKRETLVSFRLRARSALGDAPLVFDASYGSQSSRRTVSTSVRPAMPFRTQSVMGRMEGNKHTVTNLRQMFDNYAQRQATASHSPLVLTQGLARYLADYPYYSSEQIVSRSIPLIMQSKHPEMDSALNQNEVRDQLKNMLRILSSRQNSTGAIGLWHASPTPDPFVTPYVVQFLLEAKSAGYSLPNDILEGANNALRLLAARPYDDLYSLRLRAFAVYLLTLQGEITTNTLASVQSTLQQLYPDSWQTDLSAIYLASSYRLLKMDDEANKLLQPTWKQLGKAYSKAWWTQNYFDPLVQDATRLYLITRHFPEKVSSIPPQALENMVLALRDEHYTTYSSAMSILALESYTSQVAAQQDTPETLQIIEISKSKGIDPNVISTLNGLFVQGDFTGEAKAIQFNNYASAPAWYVVNQSGYDLQPPKDAISNGLEISRSYTDEQGKPVTQVTLGQKVNVHLKIRANAKQGQNNLAIVDLLPGGFEVVQQTAPEPEFYDNQDDQDEETGSGWQSPLMVSGSSWYPDYSDIREDRVIIYGSASTDVKEFIYQIKSTNTGRFVVPPAYGEAMYDRNVQALSVGKGHILVVPPEAK
>NC_004088.1|WP_002213775.1|1283612_1284071_+|IS200/IS605-like-element-IS1541B-family-transposase
MRDEKSLAHTRWNCKYHIVFAPKYRRQVFYREKRRAIGSILRKLCEWKNVNILEAECCVDHIHMLLEIPPKMSVSGFMGYLKGKSSLMLYEQFGDLKFKYRNREFWCRGYYVDTVGKNTARIQEYIKHQLEEDKMGEQLSIPYPGSPFTGRK
>NC_004088.1|WP_138921619.1|1281054_1283367_-|penicillin-binding-protein-1C
MALFLLALLVIGFRLWPHPPLSQGLPLSTAYYDRHGTLLRLSLANDDRYRLWTPLEEISPLVIQGIQLHEDRGFYYHPGVNPISLLRGFWQSYVQGGRQQGGSTLTMQLARMHWHLNTRSPTGKLRQIARAIQLELSYSKHDILEAYLNYAPYGRNIESIAAASLIYFDKKPQQLTLPEALTLAVLPQSPSYRIDPTTGVLGSALTQARNRLFVRWQQTYPTDSSQMALFQLPLSLRQPEKMPYIAPHFIEQIRRQNQQLANTQSQVDTTLDANLQQLVEKQVEAFIRRNNSRGIHNAAVLLLDTRDMGVRALVGSANYYDREIQGQVNGTNAKRSPGSTLKPFIYALGLEQGILHPMTILKDVPSSFGAYAPENFDHRFLGPVTATDALNFSRNIPAVYVASRLRQPTLYQFLRLSGVTNMASENHYGLSLVLGGGEITLQELARLYAMLANRGTLHPIQMVQTDKTLPSIRLLSEAASFITLDMLRQHRRPGDTLAQSPTSLPVYWKTGTSWGFRDAWSAGIFGPYVLIVWEGNFAGKGNSAFVGADAAAPLFFNIIDSIQANYPALREPKHPWPPQLKRVAICLASGNLPTPWCQQQGKTWFIPGKSPIKVDTVYRPVVIDINSGQAACLPYDRSQTRTEVFEFWPSDLANVFAQAGLPKRQPPDRSHCKEGNTLASGNAPRITSPLRNTTYTLRQSQQGRDQIVFSATLDADSTTTYWFVDDIYLGSSTSKKSIDWHPTRSGQYRIRAIDDHGRADSRLIRVEKVD
>NC_004088.1|WP_002209745.1|1280596_1280842_+|helix-turn-helix-domain-containing-protein
MDKQDWHPADILAGLKKRGTTMAALSRKSGLASSTLANTLLRPWPKGERLIAEVLELHPAEIWPSRYLKPKKSPAESVNPG
>NC_004088.1|WP_002209746.1|1278673_1279075_-|DUF1240-domain-containing-protein
MVKINRPLVGAFAILLFFLSSWGCWFSLSGYLAFFKLSDVIIFSWKVGFVIFAVPLLFYFSYLAFFSAIKNKPAIMNNKLANALAILAILGSIISLFSSAYISYSLTEYSYKSCPRSSWMSPNKYVKDIKLCP
>NC_004088.1|WP_002209748.1|1278039_1278441_-|DUF1240-domain-containing-protein
MVKINRPLFGAFAVFLLFLSCWVSWFSLNGYWDFFKLSDVIIFSWKVGVMIFGAPVLFYFSYLAFYCAIKNKPAKVNNKLANTFAMLAMLGVVISFFSSVYIGYSLTEYGYKLCSRSSWMSPNEYVKDIKLCP
>NC_004088.1|WP_002209749.1|1277455_1278028_+|Hcp-family-type-VI-secretion-system-effector
MSNLIYASVNGKKQGLISAGCSSLNSIGNRCQAGHEDQIQVLSLNHSISRQQNVAHHPVHFVKPIDKSSPLLGVAISENERINVVFYFYRVNSAGQLELYYEVKLTDASIVDITSVYPHSIDNNEMIPYEKIQLKYKSIAWDHKSAGTSGYSVWEDRVYSFLISSTLFQVCLNIFIFFNWLVYQNYFWEK
>NC_004088.1|WP_002227852.1|1277180_1277432_+|hypothetical-protein
MMKNNKNINKDEFSDKLSQQIKEMINNSQLDSVEILSVVMESIFSLFSETEGHLAEMKFIDSAGEDYRFILRLEVPPILERQH
>NC_004088.1|WP_002209751.1|1276902_1277142_+|hypothetical-protein
MEKEKKTLFGHKTPAMMQLSEQLESSLHNSPLVPEEKLALIMKLCVLLFRENKTDAAEMKVSDGRILKLTLEKTSSVLH
>NC_004088.1|WP_002210296.1|1291753_1292608_-|MurR/RpiR-family-transcriptional-regulator
MTTASNLSELQQQIRDRYDNLSKRLQQVSRYVLDNTNSVAFDTVAVIAERADVPPSTLIRFANAFDFSGFNEMKQLFRMNLVEETASYTDRARLFRAMESEAVPETPLGILQEFARSNAQALQQLAARTEPEMLQRAVELLAQADTIYVVGLRRSFSVAAYLTYALSHLECRPVQLHGLGGMLREQVNSIKARDIVVSISFSPYAEETVMVSEIAASAGARQIVITDSQISPLATFSDLCFVVKEAQVDAFRSQSATLCLVQSLVVALAYQQEAQAGAALAHRQ
>NC_004088.1|WP_002210297.1|1292945_1294472_+|CoA-acylating-methylmalonate-semialdehyde-dehydrogenase
METVANFINGKCVFSCGNSVTSGSPRAQAIFNSATGEPIRQVMMSTAQETEQAITAAQQAFASWSRQAPLKRARVMFRFKSLLEQHLDALAQLISEEHGKVYSDAVGELTRGLEVVEFACGIPHLQKGEHSANVGTGVDNHSLMQPLGVCVGITPFNFPAMVPMWMFPIALATGNTFVLKPSEKDPSLAVRLAQLLTEAGLPDGVFNVVQGDKTAVDVLLTDPRVQAVSFVGSTPIAEYIYQTASAHGKRCQALGGAKNHCILMPDADMDMAASAIMGAAYGAAGERCMALSVVLAVGDETADNLCARLEQQISTLRVGPGLAQEPENDMGPLISAPHRAKVLGYIDSGVAQKATLRIDGRGLKVAGHEQGYFVGPTLFDHVTPAMTIYQEEIFGPVLSVVRIADYRSAVDLINRHEYGNGTAIFTRDGGTARRFCEEVQVGMVGVNVPIPVPVAFHSFGGWKRSIFGPLNVHGNDGVRFYTRMKTITARWPEAQHDQGAAFSMPTLG
>NC_004088.1|WP_002359655.1|1294506_1296432_+|3D-(3,5/4)-trihydroxycyclohexane-1,2-dione-acylhydrolase-(decyclizing)
MKTVRMTMAQALVRFLNQQYVAIDGQEVAFVHGVMTIFGHGNVLGIGQALEENPGHLQVHQGCNEQGMAHMAIGFAKQYRRQRIYAVSSSIGPGAANMVTAAATATANRIPLLLLPGDIYASRQPDPVLQQIEQYHDLSISTNDCFRPVSRYWDRINRPEQLMSAMLSAMRVLTDPADTGAVTLCLPQDVQGEAWDYPASFFERRVHRIERRPPDTRRLSDALSLIARKRRPLVVCGGGVRYSGAHEAFRAFVENAQLPFTETQAGKGALPSDHPLNLGGIGVTGGLAANRLAPQADLVIGIGTRLTDFTTGSKALFSHPEVAFLLLNVAEFDALKLDATALIADARVGLEALTEGLAGYRTAWQGDIIEAKAAWCDECQRLWSRTWRPDEVPEVAGHLDDSLQEYAEVLNTTLTQTRVLGLINQHIEDDAIVVGAAGSLPGDLQRLWQVKTADTYHLEYGYSCMGYEIAAAIGAKIAMPHQPVYAMVGDGSYMMLHSELHTAVQEGLKITVLLFDNAGFGCINNLQMGHGMGSFCTESRHRNHESGQLNGPLICVDFAQNAESYGCRAWRVHDEPSLLAALAASRDHPGPVLLDIKVLPKSMTHDYASWWRTGDAQIARSPAVQQAAERTQMKVKRARQY
>NC_004088.1|WP_002223320.1|1297818_1298748_+|substrate-binding-domain-containing-protein
MKKLILAALIVFTSGVAFAENEQIVFSTPNLAMPFEVHMQRTAVKTAKALGVKLQVLDGQGSSPKQVADLENAITRGAQGFIVSPNDINAISSAVEEIQQAKLPVVTLDRSVESEKKVPHFGANNYKGGEAIANYVKSMFPNGAEIVLLTGQLGSSSNIERTKGIRDSLKTGGDKYRIVVDQTGNWMRSEGMRIIESVLPSLPKPPQVILSANDDMALGAIEALQSHGMKPGEIMVTGFDAVPEALARVREGWMAVTADQRPGYAVTTAMNQLVANIRDQKAITGADFLPTMITKENLDQAERVSEAGK
>NC_004088.1|WP_002223323.1|1298796_1300344_+|sugar-ABC-transporter-ATP-binding-protein
MSQPLLKITDMAKSFSGVWALSNVQLTLEQGEIHALLGENGAGKSTLLKALSGAQPQTHGEIWFNGEMLALDDSPVERQNKGIITIYQEVNLLPNMTVAENMFLGREPRRRQVFVDEKAVNQEAQAILDYLQLNVSPTTAVARLSIAQQQMVEIARALTLNAKLIVMDEPSAALSDSEVESLHRVVRELKGRGVSIIYVTHRLHEVFQLCDRFTVFQDGRYTGSDEVAGTNVEKIIRLMVGRDVVFNRRPASETHHQDQPIRLSVQGLCREKPPLDPHGVALKDISFHVHAGEVLGIAGLVGAGRTEVARCLFGAGAFTSGNFEIDGVPYQPRDPMFALEQGIALVPEDRKKEGAVQGLSIRDNLTLSSLAGLLQWRFFVNTRKEDQLIETYRLALQIKMVNSEQAVRKLSGGNQQKVILARCMALNPRILIVDEPTRGIDVGTKSEVHQVLFDMAKQGVAVIVISSDLPEVLAVSDRIITLSEGRVTGEIHGDDASEERLMTMMTINHNALNAA
>NC_004088.1|WP_002210302.1|1300355_1301384_+|ABC-transporter-permease
MLQPLSKPQASVKSAMRFDPITFFERFGVLIFMFLLLIFFQLQNSNFLSERNIFNILTEVSIYGIMAVGMTFVILTAGIDLSVGSILAVSAMTAAYVIKGDNFTTIDPNAWGGMSWLIGLSICLAMGTLIGFLQGLGVTRLRLPPFIVTLGGMTIWRGLTLVINDGAPIAGFDAGYRWWGRGDLLGISIPIWIFAIVAIAGYLALHKTRWGRFVYAIGGNPEAARLAGVNVKRVLVSVYVVIGCLAGLAGFILSARLGSAEAVAGISFELRVIASVVIGGTSLMGGYGRIGGTIIGSIIMGILINGLVLMNVSAYYQQIITGLIIVLAVAFDTYAKNRRGAL
>NC_004088.1|WP_002210303.1|1301407_1302541_+|Gfo/Idh/MocA-family-oxidoreductase
MKEVRIGLIGTGYIGKAHAIAYAQAPTVFELRGKLVREMVAEVSPALAAQRAQAFGFNRFTCDWRELVADPAIDVVDICSPNYLHKEMALAAIHHGKHVYAEKPLALNARDASEMAAAATRAGVKTLVGFNYIKNPSAKLAKEIIERGEIGEVIHFYGTHNEDYMADPNTPIHWHCLHATAGLGALGDLAAHIVSMAQYLVGEITQVCGDLKTVVVTRPASVGSSARVAVENEDQAHAMVRFVNGAQGVIEASRVACGRKMGLSYMITGTQGAISFTQERMAELKLYLHNDPVNRQGFRTLLVGPAHPEYAAFCMAAGHGIGFNDQKTVEVRDLIDGIAMDTPLWPDFAEGWKVSRILDAIALSHQDSRWVNVTDIV
>NC_004088.1|WP_002210304.1|1302572_1304543_+|5-dehydro-2-deoxygluconokinase
MSVEKQFSVSAEKTCNTENKCNTEKKFDVICMGRIAVDLYGQQIGARLEDVASFAKYLGGSSGNVAYGSARQGLRSSMLARVGDEHMGRFLREELHQVGCDTSHLTTDKKRLTALVLLSIKDRDTFPLIFYRDNCADMAITAQDFSEQYIASARSLAITGTHLSHPNTREAVLTALRYARRNGVRTVLDIDYRPVLWGLTSLGDGETRFIESHQVTAELLAVFNLFDVIVGTEEEFHIAGGSTNTLDALRGVREVSDAALVCKRGALGCSVYTEAIPQTLDEGLTVSGVRVKVLNVLGAGDAFMSGLLRGYLNDEGWPQACRYANACGALVVSRHGCAPAMPSKIELDNYLARADAVVRPDLDVHLNHLHRVTTRRRQWPELCVMAFDHRSQLEEMALQCGADLCHISTLKTLILQASREAVHTAGLQGKAGLLCDGTFGQDALNAITGAGWWIGRPIELPGSRPLAMEHGNIGSQLIGWPQEHIVKCLVFFHPEDAYSLRLEQEQKIIEVYRACCQSGHELLLEVILPAGMPRSDELYLRAISRFYNLGVYPDWWKLPPLASEGWAALNKLIERRDPHCRGVVILGLDASLEALRTGFNAAAGYPIVKGFAVGRTLFGDASLAWLKRDIDDTQLIARIRDNYLQLITLWRERGQK
>NC_004088.1|WP_002214721.1|1304557_1305616_+|myo-inosose-2-dehydratase
MTMVDQRTAVEPKTAVDQTTEVVRKAEVNQKIGIVRKIDIVRKTETVRKTEADRHTTAVQLGINPLTWTNDDLPSLGAETSLETCLSEGKEAGFAGFELGNKFSREAGVLGPILEHHQLKLVSGWYSGRLLERSVEEEIVAVRSHLALLRELGAKVMVFAEVSGCIHGEQQTPVHLRPRFPPARWAEYGAKLTAFARYTQALGVQIAYHHHMGTVIESAQDIDNLMIHTGEEVGLLLDTGHLTFAGADPLAVAQRWIARINHVHCKDVRTSVLADVKNRKTSFLDAVLSGVFTVPGDGGVDYPPIMALLKQHGYQGWLVVEAEQDPNVAHPMTYARMGYHNLSRLAHNAGLI
>NC_004088.1|WP_002210306.1|1305625_1306441_+|5-deoxy-glucuronate-isomerase
MSRLLSRRQAPDERGLTQRITPAQAGWGYVGFEVYELNEGQPLTLTAVPDERCLVLIAGRASISTPSAQFPNIGDRMSPFERHKPWAVYVTPGEAVQVQAITPLELAVCSAPGKGTYPTRLISPEDIGAEARGKGHNQRYVHNILPEDHPADSLLVVEVYTNEGASSSYPSHKHDTDNPPHETYLEETYYHRLNPEQGFCMQRVYTDDRSLDECMAVYNREVVMVPRGYHPVATMAGYDSYYLNVMAGPVRKWIFSWENDHVWINHNYPIT

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Crispr_ID: NC_004088_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_3

1902328-1902537

TypeI-F

I-F

Consensus_repeat	Method
TGTTCACTGCCGCACAGGCAGCTTAGAAAA	CRISPRCasFinder
GTTCACTGCCGCACAGGCAGCTTAGAAAATC	PILER-CR
GTTCACTGCCGCACAGGCAGCTTAGAAAA	CRT

3 spacers

cas1,cas3f,cas8f,cas5f,cas7f,cas6f

The CRISPR arrays of NC_004088_3

>merge|NC_004088|3|1902328-1902537|CRISPRCasFinder,PILER-CR,CRT
TGTTCACTGCCGCACAGGCAGCTTAGAAAATCTGCGCCAAAGAAAATGCCATTCAGATAATGTTCACTGCTGCACAGGCAGCTTAGAAAAACTACTAGAAGCTTGCCCATCTTACCTTTTCGTTCACTGCCGCACAGGCAGCTTAGAAAATCATGAAAGACATTGTTCGCCAGTCCCCTGAGTTCACTGCCGCACAGGCAATAATCAAAT

>NC_004088|3|3|1902328-1902537|CRISPRCasFinder
TGTTCACTGCCGCACAGGCAGCTTAGAAAA	TCTGCGCCAAAGAAAATGCCATTCAGATAA
TGTTCACTGCTGCACAGGCAGCTTAGAAAA	ACTACTAGAAGCTTGCCCATCTTACCTTTT
CGTTCACTGCCGCACAGGCAGCTTAGAAAA	TCATGAAAGACATTGTTCGCCAGTCCCCTG
AGTTCACTGCCGCACAGGCAATAATCAAAT

>NC_004088|3|2|1902329-1902479|PILER-CR
GTTCACTGCCGCACAGGCAGCTTAGAAAATC	TGCGCCAAAGAAAATGCCATTCAGATAAT
GTTCACTGCTGCACAGGCAGCTTAGAAAAAC	TACTAGAAGCTTGCCCATCTTACCTTTTC
GTTCACTGCCGCACAGGCAGCTTAGAAAATC

>NC_004088|3|2|1902329-1902537|CRT
GTTCACTGCCGCACAGGCAGCTTAGAAAA	TCTGCGCCAAAGAAAATGCCATTCAGATAAT
GTTCACTGCTGCACAGGCAGCTTAGAAAA	ACTACTAGAAGCTTGCCCATCTTACCTTTTC
GTTCACTGCCGCACAGGCAGCTTAGAAAA	TCATGAAAGACATTGTTCGCCAGTCCCCTGA
GTTCACTGCCGCACAGGCAATAATCAAAT

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002211863.1\|1913106_1914465_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|340874
NC_004088.1\|WP_002211866.1\|1910894_1911449_+\|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4	cas6f	cd09674_cas6f_CAS-I-F	gnl\|CDD\|378224
NC_004088.1\|WP_002211868.1\|1908911_1909862_+\|type-I-F-CRISPR-associated-protein-Csy2	cas5f	cd09676_cas5f_CAS-I-F	gnl\|CDD\|187807
NC_004088.1\|WP_002210199.1\|1892320_1893607_+\|carbohydrate-ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|224567
NC_004088.1\|WP_002210192.1\|1900746_1901991_-\|mechanosensitive-ion-channel-family-protein	unknown	unknown	gnl\|CDD\|223740
NC_004088.1\|WP_002210197.1\|1894591_1895416_+\|carbohydrate-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223472
NC_004088.1\|WP_002216551.1\|1914588_1914798_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002211865.1\|1911526_1912546_-\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|381305
NC_004088.1\|WP_002210198.1\|1893715_1894591_+\|sugar-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224096
NC_004088.1\|WP_002211864.1\|1912556_1913060_-\|formaldehyde-activating-enzyme	unknown	unknown	gnl\|CDD\|224708
NC_004088.1\|WP_002210200.1\|1891008_1892049_-\|LacI-family-DNA-binding-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380502
NC_004088.1\|WP_002211867.1\|1909879_1910884_+\|type-I-F-CRISPR-associated-protein-Csy3	cas7f	cd09677_cas7f_CAS-I-F	gnl\|CDD\|378222
NC_004088.1\|WP_002210196.1\|1895562_1896618_+\|glycoside-hydrolase-family-130-protein	unknown	unknown	gnl\|CDD\|350124
NC_004088.1\|WP_002210194.1\|1897705_1898821_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002222491.1\|1907568_1908915_+\|type-I-F-CRISPR-associated-protein-Csy1	cas8f	cd09675_cas8f_CAS-I-F	gnl\|CDD\|274203
NC_004088.1\|WP_002221142.1\|1903872_1907160_+\|type-I-F-CRISPR-associated-helicase-Cas3	cas3f	cd09673_cas3f_CAS-I-F	gnl\|CDD\|187804
NC_004088.1\|WP_002210201.1\|1889603_1890992_-\|phosphomannomutase/phosphoglucomutase	unknown	unknown	gnl\|CDD\|185312
NC_004088.1\|WP_002210191.1\|1902895_1903876_+\|type-I-F-CRISPR-associated-endonuclease-Cas1	cas1	cd09718_cas1_CAS-I-F	gnl\|CDD\|132676
NC_004088.1\|WP_002210193.1\|1898859_1900134_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002213840.1\|1896644_1897583_+\|DUF1861-family-protein	unknown	unknown	gnl\|CDD\|378102

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002211863.1\|1913106_1914465_-\|MFS-transporter	gnl\|CDD\|340874	cd17316, MFS_SV2_like, Metazoan Synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters of the Major Facilitator Superfamily. This family is composed of metazoan synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters including those that transport inorganic phosphate (Pht), aromatic compounds (PcaK and related proteins), proline/betaine (ProP), alpha-ketoglutarate (KgtP), citrate (CitA), shikimate (ShiA), and cis,cis-muconate (MucK), among others. SV2 is a transporter-like protein that serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. Also included in this family is synaptic vesicle 2 (SV2)-related protein (SVOP) and similar proteins. SVOP is a transporter-like nucleotide binding protein that localizes to neurotransmitter-containing vesicles. The SV2-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	3.50877e-50
NC_004088.1\|WP_002211866.1\|1910894_1911449_+\|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4	gnl\|CDD\|378224	pfam09618, Cas_Csy4, CRISPR-associated protein (Cas_Csy4). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4.	1.71931e-94
NC_004088.1\|WP_002210199.1\|1892320_1893607_+\|carbohydrate-ABC-transporter-substrate-binding-protein	gnl\|CDD\|224567	COG1653, UgpB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism].	2.85244e-50
NC_004088.1\|WP_002210192.1\|1900746_1901991_-\|mechanosensitive-ion-channel-family-protein	gnl\|CDD\|223740	COG0668, MscS, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].	2.65074e-32
NC_004088.1\|WP_002210197.1\|1894591_1895416_+\|carbohydrate-ABC-transporter-permease	gnl\|CDD\|223472	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism].	4.72016e-69
NC_004088.1\|WP_002211865.1\|1911526_1912546_-\|aldo/keto-reductase	gnl\|CDD\|381305	cd19079, AKR_EcYajO-like, Escherichia coli YajO and similar proteins. Escherichia coli YajO is the prototype of this family. It is an uncharacterized aldo/keto reductase family oxidoreductase.	6.34333e-143
NC_004088.1\|WP_002210198.1\|1893715_1894591_+\|sugar-ABC-transporter-permease	gnl\|CDD\|224096	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism].	2.26211e-58
NC_004088.1\|WP_002211864.1\|1912556_1913060_-\|formaldehyde-activating-enzyme	gnl\|CDD\|224708	COG1795, COG1795, Formaldehyde-activating enzyme nesessary for methanogenesis [Energy production and conversion].	1.50048e-90
NC_004088.1\|WP_002210200.1\|1891008_1892049_-\|LacI-family-DNA-binding-transcriptional-regulator	gnl\|CDD\|380502	cd06279, PBP1_LacI-like, ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.	1.56156e-83
NC_004088.1\|WP_002211867.1\|1909879_1910884_+\|type-I-F-CRISPR-associated-protein-Csy3	gnl\|CDD\|378222	pfam09615, Cas_Csy3, CRISPR-associated protein (Cas_Csy3). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2463 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy3, for CRISPR/Cas Subtype Ypest protein 3.	0
NC_004088.1\|WP_002210196.1\|1895562_1896618_+\|glycoside-hydrolase-family-130-protein	gnl\|CDD\|350124	cd18612, GH130_Lin0857-like, Glycoside hydrolase family 130 such as Listeria innocua beta-1,2-mannobiose phosphorylase. This subfamily contains the glycosyl hydrolase family 130 (GH130), as classified by the carbohydrate-active enzymes database (CAZY), enzymes that are phosphorylases and hydrolases for beta-mannosides, and includes Listeria innocua beta-1,2-mannobiose phosphorylase (Lin0857). hey possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Structure of Lin0857 shows beta-1,2-mannotriose bound in a U-shape, interacting with a phosphate analog at both ends. Lin0857 has a unique dimer structure connected by a loop, with a significant open-close loop displacement observed for substrate entry. A long loop, which is exclusively present in Lin0857, covers the active site to limit the pocket size.	9.75278e-165
NC_004088.1\|WP_002211868.1\|1908911_1909862_+\|type-I-F-CRISPR-associated-protein-Csy2	gnl\|CDD\|187807	cd09676, Csy2_I-F, CRISPR/Cas system-associated RAMP superfamily protein Csy2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas5 ortholog.	1.12008e-157
NC_004088.1\|WP_002221142.1\|1903872_1907160_+\|type-I-F-CRISPR-associated-helicase-Cas3	gnl\|CDD\|187804	cd09673, Cas3_Cas2_I-F, CRISPR/Cas system-associated protein Cas3/Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas3/Cas2 fusion; This protein includes both DEAH and HD motifs for helicase and N-terminal domain corresponding to Cas2 RNAse; signature gene for Type I and subtype I-F.	0
NC_004088.1\|WP_002222491.1\|1907568_1908915_+\|type-I-F-CRISPR-associated-protein-Csy1	gnl\|CDD\|274203	TIGR02564, conserved_hypothetical_protein, CRISPR type I-F/YPEST-associated protein Csy1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1.	0
NC_004088.1\|WP_002210191.1\|1902895_1903876_+\|type-I-F-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|132676	TIGR03637, cas1_YPEST, CRISPR-associated endonuclease Cas1, subtype I-F/YPEST. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the YPEST subtype of CRISPR/Cas system.	0
NC_004088.1\|WP_002210201.1\|1889603_1890992_-\|phosphomannomutase/phosphoglucomutase	gnl\|CDD\|185312	PRK15414, PRK15414, phosphomannomutase.	0
NC_004088.1\|WP_002213840.1\|1896644_1897583_+\|DUF1861-family-protein	gnl\|CDD\|378102	pfam08950, DUF1861, Protein of unknown function (DUF1861). This hypothetical protein, found in bacteria and in the eukaryote Leishmania, has no known function.	6.29599e-176

>NC_004088.1|WP_002210192.1|1900746_1901991_-|mechanosensitive-ion-channel-family-protein
MQQRISQWLERLGMEFSDVMSLTMVIGLILLISVMIHLVLHRVVLAALQRRGQQSQRIWQQAITKHKLFQRVALLLQGIIINLQAVLWLQNGSQTQAVIVTAAQVWIMAFALLALFSLLDTLLALLRQSSVAHQLPLRGICQGLKLVAAIFIGIMIVSLLMGRSPLLLLSGLGAMTAVLMLVFKDPILGLVAGIQLSANDMLKIGDWLEMPKYGADGAVTDIGLTTVKVRNWDNTVTTIPTYALISDSFKNWRSMSESGGRRIKRSINIDTTSVHFLSEQEQQRLTLNPLLQHYLSEKSQELNQYNQQIALDLSSPLNGRRLTNIGTLRAYLVAYLRAHLGIHQSMTLMVRQLAPTPEGLPLEVYAFTNTTIWAEYEGIQADIFDHIFAVVSEFDLRIHQTPSGNDMRSMLAKV
>NC_004088.1|WP_002210193.1|1898859_1900134_+|hypothetical-protein
MKLLNTLVCIIGLTSFSSSAKLVNAEHLDALYQKVTVANKTELGLIHIYSEFPDYRWVKDPIEGVSAIDDVARAAIFYQRQYQATGSAADLEKVKSLVEFILYQRADNGYFYNFIYPDHSINKEYKTSVAEPNWWTWRALWALTQVYPTLVKTDNALAQRTRETIFATIDVIYKDFNFKQTRGEKEGVAVPEWLPHTAGDQASVLLMALSDAQALEAKPEIEKMMRSLAAGIMLMQVKDTSSPVNGAFLSWQNLWHGYGNSQAYALLVAGNRLGDRDMIKAAFNELDHFHPWLISNGLLNEFTVRQQGEKVTLIEQKKFSQIAYIIRPMVFANIKAWEISRDAVYLERAVDLSLWFFKNNPAQAQMYYPVTGIAFDGIDSATTVNKNSGAESTIEALLTLQLIESIPDAKRMLESALEKRNIKQ
>NC_004088.1|WP_002210194.1|1897705_1898821_+|hypothetical-protein
MKHKKYLPLFLMAGICSVAQADNSPDVVSANNMDNRTFFAGDKIRIVKDGGETIEAVVELSDDNIGIVRIPKDEKAYFHGNWLAEYKIEHFRNEGRSTNSRPVHEIVFADGRVNFGDTGWNTGFLLKQVRFTSDSRNESNHKVDFRMVEMEIRPAWSKSIDKHWFMFEGIYLGKTGYEKNRTTGGDNNIGGDGYGFRPYYRYQVSDRLSVNTDVKMLVEDKDARGADNGRFQFYEALVNVNYRVADNVHVGIEVFRKEGQDFNHNGTKTANVLEQELRPWVAWNMGKNNFLFKMEPQLRRIGGQDGYRETSKAQKYIFNYSYPIADRVYLVAEYFYRVEHDKKFWDRGVRDNKSYSDTTTHFGKLGINYIF
>NC_004088.1|WP_002213840.1|1896644_1897583_+|DUF1861-family-protein
MMRHAPPASVAQLFADYQKRTAHNTFSTGRLEFTGVGDKDVYNITAPFTSAGQVVIAGRVEARDSEHSTIVFFSEQQGQWAPVENAPTFQLQDPFFTRIEDELILGGVEINPHPDNPRQLIWHTVFFRGRDIHSLTRFASGPPGMKDIRLCHIQQGRIGVFTRPQGKIGGRGTIGYVEINNLEALTPETITSAELFEQQFNSEEWGGVNETHLLCDGTIGLLSHIACFDQHGRRHYYPGVFIFNPDTKNYTPIKIIAARDNFLPGATKRPDLVDVIFPGGLIVLPNNGWRLYVGASDAEAHWIDIEDPFSGF
>NC_004088.1|WP_002210196.1|1895562_1896618_+|glycoside-hydrolase-family-130-protein
MMRYSGNPLITPQDITPSHPGFKVECAFNAGITKLGDETIMLIRIAESVIPESEGITVVPLLMEISGHWQVTTRVFKHDDPAYDFSDPRLISDIADPSTVYLTSLSHLRVARSHDGVTFVVDDQPFIFPANGDEAFGCEDARITQIDGAYYINYSAVSAKGICTALAVTQDFTDVKRLGLIFCPDNRDACLFPEKINGKYMTLHRPAPKHFGKPEIWLASSLDLLHWGDHRHLLGTSQDPWDALKLGGGAQMLKTEKGWLQIYHGVDATQRYSLGALLLDLEQPTKILAKSPVPLLQPQAPYELHGFFGNVVFTCGALIENDSLRVYYGAADECMCLAEMPLAQLWQHLSV
>NC_004088.1|WP_002210197.1|1894591_1895416_+|carbohydrate-ABC-transporter-permease
MKKNINSLIIHLVMFSLALSWLYPYIWMVLSSFKQSADIYTTGLFGSAYSLDNYRFLFENSGRVEKPFLKTLFNSLFISTVVTVAVTLSSMFIGFALAKMQFKGQSLFRNLLFLQMVFPASMFIIPQFVLVRELGLLNTYSAMIVPFLMSSWGIFMISQSFQGTPNDYIHAAKIDNASLWQIMIYLMMPLNKAIIAIVALFTFVGTWDNFLWPLIVIQDESKMPLSVLLATFSKSYGVYVGPVIAGAVIQTIPIVVLFILFRKYFMQGMSLSLK
>NC_004088.1|WP_002210198.1|1893715_1894591_+|sugar-ABC-transporter-permease
MTFLKLKDKQVGSVLAASYLGYTSIFWFYPFIWLAVLSLTEWRFVGIPTFNGLNNFILVMQDPLFWKSMLNVMRFLMYYLPIVFISSFLFAFGLQKLKHGRTFVALSFLLANVSSGVAYSIVFSKIFSQNGPLNTFLYDWFGFTLPWLTSPDFAMLSIALVVTWKFVGYYGLILFSGLNSIPKEIYSAAELDNTRTIKRLFHITLPMINPQLIMVLVLAITVSFAIFTEPYLITGGGPLNSTTTPMIVMYETAFMKMQPSWAATMSIFIALISFGIILGVRKLLERKVEIV
>NC_004088.1|WP_002210199.1|1892320_1893607_+|carbohydrate-ABC-transporter-substrate-binding-protein
MLEKMKNTLISLAIASSCVVFTGCDNDTASAKNEKQDITLWIAPNNVQEAFWSEVVGEWNKQPDKKKVVFSTIPAAGSSEEAIMNAIASDRAPDISENIFTGFGSQLADLGQVVDLSTLDGYENLISTRQMTDIMDNWRYNGKNYILPIYMNPVLFWWRGDLLKEQGFSEVPKTYDEVYALSEKYTIPDKRYAIQATSGRNWWDRWFDFIALYYAQSDGKPYIANQQASYDNQAGRDVLDFMHTLFSKKWTLYDFGQDDPLVTGKVLGAVRGPWDISRYQQQYPEILKHIKMGPMLVKEQQDKPHTFADGKGLVLFSHSKVKPEAWEFIQWVFSQPKFDKRWMELTGMPPARADLLTNPFFAEYYQEHPYAAAYAEYVNVAIPPVSSGETVEIQRSMTQMIEKTAFNTATPDEALQQSIKEVNAILKP
>NC_004088.1|WP_002210200.1|1891008_1892049_-|LacI-family-DNA-binding-transcriptional-regulator
MTTGKKRETLKTIAETLNVTHTTVSNVFNRPEKVSPELREKILAYAESINYHGPAGAGRFLRTGKCGTLGVIFNDNLSYVFSDRHDIALMRGIAEECEKNGINIALMPLKTNNALKKRMMGALVDGYILNATYNNDEVVQAALTSGLPVITTDIKLQNFTCVSIDDGAAMQAICHHLLAAGHKKFGIVSFPVKRLPGELTSLAEFSTDYDNGVAFGRISACITALSDAGIDLHTSYVAEQPHSETGGEKAAKALLAKEPGISAIICLSDRFAFGVYQFCQDHNIPVPGQIAITGFDDIDIQDPPVGLTTIRQPTVLKGREAARALISGQLDNDISLDFELVVRDSA
>NC_004088.1|WP_002210201.1|1889603_1890992_-|phosphomannomutase/phosphoglucomutase
MEKLTCFKAYDIRGKLGSELNEEIAYRIGRAYCQWLKPAKVVVGGDARATSVELKNALAKGLMDGGADVIDIGMVGTEEVYFATRFYGVDGGIQVTASHNPIDYNGMKLVKKDAQPISGDNGLYEIQRLAQDNHFAPPGVRGQLETQLVREHYVEHLLSYIDLNALLPMKIVVNAGNGAAGPTLDALEAALAKRKVPISFIKINHQPDSSFPNGIPNPMLPENQWSTRQAVCEHQADLGIAWDGDFDRCFFFDHLGNFIEGYYIVGLLAEKFLLTNNMGKATHNTDKIIHDPRLTWNTIDIVQTLNGTAIESKTGHAFIKDAMRHHDAVYGGEMSAHHYFREFGYCDSGMIPWLLVIELLSKKTTSLFSLIESRKAKFPVSGELNFTVSDPKTKIQQIKQFYADSAIHVTGIDGLSMEFEHWRFNLRSSNTEPLVRLNIETRGDVTLLEQKTAQLTQLLYPK
>NC_004088.1|WP_002210191.1|1902895_1903876_+|type-I-F-CRISPR-associated-endonuclease-Cas1
MENAIHSSDLKTILHSKRSNIYYLEYCRVLVNGGRVEYVTDEGKQSLYWNIPIANTTVIMLGTGTSVTQAAMREFARAGVLVGFCGGGGTPLFAANDVEVNVSWLTAQSEYRPTEYLHDWVSFWFDDEKRLAAAVAFQRIRIAQIQQHWLSSHIQRESLFPVNHDQLLFILTRFEQNLANCLTSNDLMVQEAVLTKALYKLAANTVNYGDFTRAKRGGGIDLANRFLDHGNYLAYGLAATATWVIGLPHGLSVLHGKTRRGGLVFDVADLIKDALVLPQAFIAAMQGEEEQEFRQRCISGFQRTEALDVMIDGIKETAALCSQVPR
>NC_004088.1|WP_002221142.1|1903872_1907160_+|type-I-F-CRISPR-associated-helicase-Cas3
MNILLISQCHKRALNETRRILDQFAERKGDRTWQTAITQEGLNTLRKLLRRTARRNSAVACHWIKSNNQSELLWIVGNLRRFNAEGTVPTNTTQRDILRSQDENNWHSVETIALLAGIAGLFHDFGKANVLFQQGLQGQGKTYQPYRHEWVSLRLFQAFVEQKNDIQWLTALSQINPADETTLMSNLVKDGLDDYTNPLAALPPLAKTIAWLILSHHRLPVYPSKDYHRPPKVEEIDDWLHQQLMPVWNSTNMDSGDWREKDKLDVWRFPHGTPLQSAEWCKKAQKFAKRALRQPSLVNDGHLNQRFTSHMARLVLMLADHHYSSLPATPGWQDKNYQVFANTHNKMRDANAHSKTIEMKQRLDEHNIGVGQNALLLGRSLPHIRKTLPAITRHKGFKQRSVQEKYRWQDKAFDLAVTLRERSLQQGFFGVNMASTGCGKTFANARIMYGLSDEKQGCRFSVALGLRTLTLQTGTALQQKLTLQKDDLAVLIGSQSVLQLYQLNNDKLEPRGTGSQSADKFFSEHQYVSYDGSLDDGRLSTWLSNNDRLKRLLCAPVLVCTIDHLIPATESLRGGKQIAPMLRLLTSDLVLDEPDDFDRNDLPALCRLVNWAGMLGSRVLLSSATLPPALVQALFNAYRAGRADYQQASGQPDTPVNICCAWFDEHGVAQQDIQQSKDFIQHHGDFITRRVGKLSTAEVLRRAELIPVSSASVKNGSVLDAMAAVMRDSMLRLHQAHHQTHPSEKTVSVGVVRMANIDPLVAIAQRLYAMAAPENYRIHYCVYHSQHPLAVRSAIERRLDVTLTRYQPNALWQVAEIEHALQHHPEQHHLFVVLATSVVEVGRDHDYDWALAEPSSMRSFIQLAGRVQRHRQVAPQMANMHILQKNFKALTQKDPAIPVYCKPGFETTRCRLNTHDLDKLLLPSQYKVINAISRIQERTKLEPRDNFVDLEHLSLRLILQGSAEPLKYYAALWWRKQATWSGEQQRCTPFRQSSPDEQHNLWIDDEADKPVFKRLDSDQIEWKVSDGFQDVELTLAAGNSAWIDTDCLRIYQWLAESLNKELNEVSRQFGEVRLPKKDGERWHYHPLLGVFGALD
>NC_004088.1|WP_002222491.1|1907568_1908915_+|type-I-F-CRISPR-associated-protein-Csy1
MSDEGLAAFIVSYIKSREQPKLEAFDKEAEKRLAGLTQAEDIALAQQEIAQQRQELIARYEVRNWLTDAANRAGQIKLATHAPKYTHSDSKSSGILNIELQSKKKDYFSSVDLAEQASDVIGNAAVFDLVKLLQSECEGGSLIKCLEQGDNSVLKLFSNDDELVEEWTTKFKSILNNEKFTSHKLAKQFYFPVGPDQYHLLSPLFSSSLAQAMHQRIIEARFSDQSKEAKAAHKAGRWHPTVRVLYLDTAVQHIGGTKPQNISYLNSVRGGKVWLLPCGAPSWKNIQKPPIKYRSIFHDRSEFTVLARNNLWQMQLYLLGVKPLSNTMDIRAARLACCDEIIDILFNYVAEIQNLDGTNGWSDAEDCKLKRSEQLWLDPTRAMDDPVFKLEREKEDWKQEVSQDFGYWLNRWLQHDELVFGYVEQREWSSLFKQRLREFEQGSLETSS
>NC_004088.1|WP_002211868.1|1908911_1909862_+|type-I-F-CRISPR-associated-protein-Csy2
MSSLIVLHQVRVENANAIAGLTYGFPAITHFLGYSHALSRKLQSSHGLTLRGCAVICHYQQVHAYLSGWDYVFSLTRNPLTKEAKTAAFNEEGRMHMTVSLVIECDGTIANGDDGANALEKHLASLCLTQRLAGGTITNIRRVKVINYPETEVATRRLLCRLLPGFALLDRSELLAEHLNRLRQTNPQAEMLDAWLDFSALKIQAIPPQSDTPVESGAPAPWGYVGKPAAGYLVPIVTGYRAISPLYAPGEVDKTRDPHTPFRFVESLYGIGEWRGLHRITDLRQLLWGYHQEGDNYLCRCALPASVDTYLLNDEE
>NC_004088.1|WP_002211867.1|1909879_1910884_+|type-I-F-CRISPR-associated-protein-Csy3
MAKATIKTASVLAFERKLSNSDAMMYAGNWGQTDNWQPIIIKEKAVRGTISNRLKNALASDPAKLDAEIQKANLQRVDVAALPFDTDTLKMSFTLRVLGNLATPSVCNDQEYQAELASVINGYISEQSFSVLAARYAENLANGRFLWRNRVGAEDIKVCITSQTKSYQFDSNEFSLRQFSQPSKELTALAQEIEQGLAGNGFAFFTVDAFVRLGNGQEVFPSQELVLDSNSKKSKVLYQIDGIAALHSQKVGNALRTIDDWYPDATELALGPIAVEPYGSVTSRGKAYRQPKQKMDFYTLLDNWVTKGTVPAVEQQHYVMATLIRGGVFGEKGE
>NC_004088.1|WP_002211866.1|1910894_1911449_+|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4
MDHYLDIRVLPDPEFSAQTLLEALFAKLHRALVATIPGRVGVSFPTAGKTLGSQLRLHGSRGDLLELQSAGWLKGLQDYCECSEILPVPADVKHRTIRRVQVKSSAQRLRRRSVSKGWLTEEQARLRIPDSHDKRCDLPFLRLKSRSSEQYFLLFIEQGTLQASATTGEFSAYGLSVNATIPWF
>NC_004088.1|WP_002211865.1|1911526_1912546_-|aldo/keto-reductase
MDYIKLGHCGLQVSRLCLGTMNMGSKQWKPWVFDKAESTPLIKHALDCGINFIDLADFYSAGVGEEVVGRIVKNLMSRDELVLTTKVGYPIGHGPNNQGHSRKHIMASIDASLKRLGTDYIDIYMLHYFDINTPVEETWSAMNDIIHSGKARYTGVSTMFTWQLSKILWCCERNGFAKPINMQLQLNCAYREEEREMIPQCRDQGLGISAFSPLARGLLSCDFSSVRNKTDFFTQEMYADVTSLNIAQSVERVAKNRGITPAQVAQAWVLNHPGTDCMLVGADTIEQINSAVTALRISLNAEEHFELERNYTPCDVINDYTAGQRIAREARPPSGIFAP
>NC_004088.1|WP_002211864.1|1912556_1913060_-|formaldehyde-activating-enzyme
MQMYIGEGFAGNGVNAAHINIMIGPRDGVVGQAFAASLASPSQGHYPFIVVIKPNVAAKPMTLYVNKAEIRSELHGRATWGASQAAVAKAVAEALLANLFPPEAEDDWCIITANWVNIDCDDIDEVYRNNYRACTTALHAAMAKTPKRDQLTHALTQLSNPFFTPKA
>NC_004088.1|WP_002211863.1|1913106_1914465_-|MFS-transporter
MQTLPSEKIRMDDVPLNRFHIRIAGLTFGAHFIDGYILGLIGFALIQLKPIMALTPLWEGLLGSAALIGLFLGSLILGWISDYIGRQKIFSFSFVIITLASALQFFASTPEQLFILRVIVGIGIGGDYSVGHTLLAEFSPRKHRGVLLGAFSVIWTFGYVSASFVGHYLSMVSPEAWRWLLSSAALPALLILLVRIGTPESPRWLMGKGREDDAMAIVHKYFGPNVTLIDEEPATSTRRFLSLFGRKYWRRTAFNSLFFVCLVIPYFAIYTFLPSILNVMALSQNFATDLLLNGLLVVGALVGIVLTAFCSRRSFLISSFIFLATCLLLLSILPSNQTFWLIALFAAFTLVMSAVSNLVGVFPAESFPTEVRSMGVGFATSMSRLGSAIGTSLLPLAIVNYGMPVTTTLLAFVLIIGAIVSIAWAPETKGLTLVDASQSATTPRPPSSIIPN
>NC_004088.1|WP_002216551.1|1914588_1914798_+|hypothetical-protein
MVIGDLLTETDRLFQKRTAAMDDLFSSPGPVRLILFVMAMCQPKYKAASAFYAYPSEKKVRDPPLNSYK

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Crispr_ID: NC_004088_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_4

2875721-2875930

Orphan

I-F

Consensus_repeat	Method
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	CRISPRCasFinder
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	CRT
AGGTTCACTGCCGCACAGGCAGCTTAGAAAAT	PILER-CR

3 spacers

DEDDh

The CRISPR arrays of NC_004088_4

>merge|NC_004088|4|2875721-2875930|CRISPRCasFinder,CRT,PILER-CR
TTATTGGGCTGCCTGTGCGGCAGTGAACGTTATACCCCGCGCAGGGAGTGAAGCGTTGACTTTCTAAGCTGCCTGTGCGGCAGTGAACTTAAGTTCTTTTTGTCAGCATCTTTAATAAATTTTCTAAGCTGCCTGTGCGGCAGTGAACCTGAAATACAAATAAAATAAATCGTCGAACATTTTCTAAGCTGCCTGTGCGGCAGTGAACGT

>NC_004088|4|4|2875721-2875928|CRISPRCasFinder
TTATTGGGCTGCCTGTGCGGCAGTGAAC	GTTATACCCCGCGCAGGGAGTGAAGCGTTGAC
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	TTAAGTTCTTTTTGTCAGCATCTTTAATAAAT
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	CTGAAATACAAATAAAATAAATCGTCGAACAT
TTTCTAAGCTGCCTGTGCGGCAGTGAAC

>NC_004088|4|3|2875721-2875928|CRT
TTATTGGGCTGCCTGTGCGGCAGTGAAC	GTTATACCCCGCGCAGGGAGTGAAGCGTTGAC
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	TTAAGTTCTTTTTGTCAGCATCTTTAATAAAT
TTTCTAAGCTGCCTGTGCGGCAGTGAAC	CTGAAATACAAATAAAATAAATCGTCGAACAT
TTTCTAAGCTGCCTGTGCGGCAGTGAAC

>NC_004088|4|3|2875781-2875930|PILER-CR
TTTCTAAGCTGCCTGTGCGGCAGTGAACTTAA	GTTCTTTTTGTCAGCATCTTTAATAAAT
TTTCTAAGCTGCCTGTGCGGCAGTGAACCTGA	AATACAAATAAAATAAATCGTCGAACAT
TTTCTAAGCTGCCTGTGCGGCAGTGAACGT

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002211902.1\|2876422_2877814_-\|APC-family-permease	unknown	unknown	gnl\|CDD\|223605
NC_004088.1\|WP_157131899.1\|2882570_2882861_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|374732
NC_004088.1\|WP_002211904.1\|2874255_2875686_+\|exodeoxyribonuclease-I	DEDDh	cd06127_DEDDh_CAS-I	gnl\|CDD\|236979
NC_004088.1\|WP_002211911.1\|2865079_2866384_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|340877
NC_004088.1\|WP_002217522.1\|2872102_2872420_-\|DUF496-family-protein	unknown	unknown	gnl\|CDD\|180070
NC_004088.1\|WP_002209743.1\|2870523_2871732_-\|IS256-family-transposase	unknown	unknown	gnl\|CDD\|225865
NC_004088.1\|WP_002211905.1\|2872853_2873963_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187547
NC_004088.1\|WP_002211912.1\|2864648_2865071_+\|thiol-disulfide-oxidoreductase-DCC-family-protein	unknown	unknown	gnl\|CDD\|225556
NC_004088.1\|WP_002211896.1\|2884548_2885448_+\|ATP-phosphoribosyltransferase	unknown	unknown	gnl\|CDD\|234781
NC_004088.1\|WP_002231208.1\|2884218_2884266_+\|his-operon-leader-peptide	unknown	unknown	unknown
NC_004088.1\|WP_002211917.1\|2861300_2862578_-\|L-fuconate-dehydratase	unknown	unknown	gnl\|CDD\|239440
NC_004088.1\|WP_002211916.1\|2862609_2863452_-\|fumarylacetoacetate-hydrolase-family-protein	unknown	unknown	gnl\|CDD\|223257
NC_004088.1\|WP_002216312.1\|2878272_2879364_-\|oxidoreductase	unknown	unknown	gnl\|CDD\|182570
NC_004088.1\|WP_002216393.1\|2863499_2864240_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187626
NC_004088.1\|WP_002211895.1\|2885451_2886783_+\|histidinol-dehydrogenase	unknown	unknown	gnl\|CDD\|234853
NC_004088.1\|WP_002211900.1\|2881186_2882182_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224093
NC_004088.1\|WP_002211898.1\|2883015_2883843_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187576
NC_004088.1\|WP_002216311.1\|2879649_2880543_+\|sugar-ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224053
NC_004088.1\|WP_002216310.1\|2880500_2881190_+\|sugar-ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224053
NC_004088.1\|WP_002216388.1\|2867408_2870561_+\|inverse-autotransporter-beta-barrel-domain-containing-protein	unknown	unknown	gnl\|CDD\|378762

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002211902.1\|2876422_2877814_-\|APC-family-permease	gnl\|CDD\|223605	COG0531, PotE, Amino acid transporters [Amino acid transport and metabolism].	3.72025e-45
NC_004088.1\|WP_157131899.1\|2882570_2882861_+\|hypothetical-protein	gnl\|CDD\|374732	pfam16695, Tai4, Type VI secretion system (T6SS), amidase immunity protein. Tai4 is a new form of autoimmunity protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein. The effector is Tae4, pfam14113.	4.0065e-14
NC_004088.1\|WP_002211904.1\|2874255_2875686_+\|exodeoxyribonuclease-I	gnl\|CDD\|236979	PRK11779, sbcB, exonuclease I; Provisional.	0
NC_004088.1\|WP_002211911.1\|2865079_2866384_-\|MFS-transporter	gnl\|CDD\|340877	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily. This family is composed of predominantly bacterial transporters for hexuronate (ExuT), glucarate (GudP), galactarate (GarP), and galactonate (DgoT). They mediate the uptake of these compounds into the cell. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	1.17308e-74
NC_004088.1\|WP_002217522.1\|2872102_2872420_-\|DUF496-family-protein	gnl\|CDD\|180070	PRK05423, PRK05423, DUF496 family protein.	5.26004e-59
NC_004088.1\|WP_002209743.1\|2870523_2871732_-\|IS256-family-transposase	gnl\|CDD\|225865	COG3328, COG3328, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	1.39969e-152
NC_004088.1\|WP_002211905.1\|2872853_2873963_-\|SDR-family-oxidoreductase	gnl\|CDD\|187547	cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended (e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding proteins, many of which may function as fatty acyl CoA reductases (FAR), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. This N-terminal domain shares the catalytic triad (but not the upstream Asn) and characteristic NADP-binding motif of the extended SDR family. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	1.89947e-61
NC_004088.1\|WP_002211912.1\|2864648_2865071_+\|thiol-disulfide-oxidoreductase-DCC-family-protein	gnl\|CDD\|225556	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function prediction only].	5.0494e-57
NC_004088.1\|WP_002211896.1\|2884548_2885448_+\|ATP-phosphoribosyltransferase	gnl\|CDD\|234781	PRK00489, hisG, ATP phosphoribosyltransferase; Reviewed.	6.63843e-161
NC_004088.1\|WP_002211917.1\|2861300_2862578_-\|L-fuconate-dehydratase	gnl\|CDD\|239440	cd03324, rTSbeta_L-fuconate_dehydratase, Human rTS beta is encoded by the rTS gene which, through alternative RNA splicing, also encodes rTS alpha whose mRNA is complementary to thymidylate synthase mRNA. rTS beta expression is associated with the production of small molecules that appear to mediate the down-regulation of thymidylate synthase protein by a novel intercellular signaling mechanism. A member of this family, from Xanthomonas, has been characterized to be a L-fuconate dehydratase. rTS beta belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.	0
NC_004088.1\|WP_002211916.1\|2862609_2863452_-\|fumarylacetoacetate-hydrolase-family-protein	gnl\|CDD\|223257	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism].	8.96038e-107
NC_004088.1\|WP_002216312.1\|2878272_2879364_-\|oxidoreductase	gnl\|CDD\|182570	PRK10586, PRK10586, putative oxidoreductase; Provisional.	0
NC_004088.1\|WP_002216393.1\|2863499_2864240_-\|SDR-family-oxidoreductase	gnl\|CDD\|187626	cd05368, DHRS6_like_SDR_c, human DHRS6-like, classical (c) SDRs. Human DHRS6, and similar proteins. These proteins are classical SDRs, with a canonical active site tetrad and a close match to the typical Gly-rich NAD-binding motif. Human DHRS6 is a cytosolic type 2 (R)-hydroxybutyrate dehydrogenase, which catalyses the conversion of (R)-hydroxybutyrate to acetoacetate. Also included in this subgroup is Escherichia coli UcpA (upstream cys P). Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. Note: removed : needed to make this chiodl smaller when drew final trees: rmeoved text form description: Other proteins in this subgroup include Thermoplasma acidophilum aldohexose dehydrogenase, which has high dehydrogenase activity against D-mannose, Bacillus subtilis BacC involved in the biosynthesis of the dipeptide bacilysin and its antibiotic moiety anticapsin, Sphingomonas paucimobilis strain B90 LinC, involved in the degradation of hexachlorocyclohexane isomers...... P).	1.05065e-117
NC_004088.1\|WP_002211895.1\|2885451_2886783_+\|histidinol-dehydrogenase	gnl\|CDD\|234853	PRK00877, hisD, bifunctional histidinal dehydrogenase/ histidinol dehydrogenase; Reviewed.	0
NC_004088.1\|WP_002211900.1\|2881186_2882182_+\|ABC-transporter-permease	gnl\|CDD\|224093	COG1172, AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism].	1.22935e-72
NC_004088.1\|WP_002211898.1\|2883015_2883843_-\|SDR-family-oxidoreductase	gnl\|CDD\|187576	cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; however, the upstream Ser is present at the usual place, and some potential catalytic residues are present in place of the usual YXXXK active site motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	2.54107e-68
NC_004088.1\|WP_002216311.1\|2879649_2880543_+\|sugar-ABC-transporter-ATP-binding-protein	gnl\|CDD\|224053	COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism].	3.90601e-98
NC_004088.1\|WP_002216310.1\|2880500_2881190_+\|sugar-ABC-transporter-ATP-binding-protein	gnl\|CDD\|224053	COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism].	1.76633e-90
NC_004088.1\|WP_002216388.1\|2867408_2870561_+\|inverse-autotransporter-beta-barrel-domain-containing-protein	gnl\|CDD\|378762	pfam11924, IAT_beta, Inverse autotransporter, beta-domain. This is a family of beta-barrel porin-like outer membrane proteins from enteropathogenic Gram-negative bacteria. Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They carry C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal beta domains that are embedded in the outer membrane. This family represents the beta-barrel porin-like domain in the outer membrane that can be found in intimins, invasins and some inverse autotransporters.	1.47456e-126

>NC_004088.1|WP_002211904.1|2874255_2875686_+|exodeoxyribonuclease-I
MSDKNKQPTFYVHDYETFGQRPALDRPAQFAGVRTDLDFNLVEEPLVIYCKPADDYLPQPEAVMITGITPQHALANGVNEAEFSRQIHQAFSVPGTCILGYNNIRFDDEVSRNIFYRNFYDPYAYSWQGGNSRWDLLDVMRACYALRPEGIVWPENDDGLPSFKLEHLTKANGVEHLQAHDAMSDVYATIAMAKLVKQAQPRLFDYLYQHRSKHKINALIDIAEMTPLVHVSGMFGAARGNTSWVAPLAWHPENKNAVIMCDLAGDMSPLLELDSDTLRERLYTRRDKLQAQESAIPIKLVHINKCPVLAPAKTLLPENADRLGIDRQRCLQNLQLLRQNPQVREKVVALFAQAEPFAVTDDVDTQLYNGFFSDADRATIKIIQQTESQNLPALDLTFQDPRLEALLFRFRARNYPNTLNDSEQQRWLQHRREALSPERVQDYVLQLEQFYNQYEDDKEKLALLKALFEYAKGLVS
>NC_004088.1|WP_002211905.1|2872853_2873963_-|SDR-family-oxidoreductase
MKKLLLTGATGFLGGAVLEKLLLASSDFNYLLLVRANTPEQGLMRIRENLEKFYLPNELINKININHVLLGDLAEPDSFINDVRIDDVTHVINCAAIASFGNNPLIWKVNVEGTLAFGKRMAQVAGLQRFVHVGTAMACTPEADTVVDERVLSTENDAHLVEYTKSKSAIECLLAEHCPTLPLVFARPSIVVGHTRLGCQPSSSIFWVFRMALMLRKFMCSLDDHIDVIPVDYCADALLYILEYPNLPDDIYHISAGEKGSVSFSEIDQAMSVAAKQKPVGVNYSQVEYTALVQMRNQLKGIFGPCNERLMLKAMRLYGSFAMLNVRFSNERLLSLGMPRTPRFTDYIARCVESSHGMTIQQQMAVDFK
>NC_004088.1|WP_002217522.1|2872102_2872420_-|DUF496-family-protein
MDNASKPTFQDVLEFVRMFRRKNKLQREIVDNEKKIRDNQKRVLLLDNLSEYIKPGMSIEEVQAIIANMRGDYEDRVDDYIIKNADLSKERRELSKKLKAMGEVK
>NC_004088.1|WP_002209743.1|2870523_2871732_-|IS256-family-transposase
MDEKKLKALAAELAKGLKTEADLNAFSRMLTKLTVETALNAELTEHLGHEKNTPKSGSNTRNGYSSKTLLCDDGEIELNTPRDRENTFEPQLIKKNQTRITQMDSQILSLYAKGMTTREIVATFKEMYDADVSPTLISKVTDAVKEQVAEWQNRQLDALYPIVYMDCIVVKVRQNGSVINKAVFLALGINTEGQKELLGMWLAENEGAKFWLSVLTELKNRGLQDILIACVDGLKGFPDAINSVYPQTHIQLCIIHMVRNSLKYVSWKDYKAVTSGLKMVYQAPTEEAALMALDKFAEAWDDKYPQISKSWRTHWENLNTFFGYPPDIRKAIYTTNAIESVNSVIRAAIKKRKVFPTDDSVRKVVYLAIKDASKKWSMPIQNWRLAMSRFIIEFGDRLSDHL
>NC_004088.1|WP_002216388.1|2867408_2870561_+|inverse-autotransporter-beta-barrel-domain-containing-protein
MSLYRISSLHQAKQLNKNKQLNKTRISKSVVWANIVIQAIFPLSIAFTPAVMAAETVGASDEKPRSASQAEQSTANAATRLASILTNDDSAKQASSIARGTAANAGNEALQKWFNQFGSAKVQLNLDEKLSLKGSQLDVLLPLTDSPDLLTFTQLGGRYIDDRVTLNVGLGQRHFFAQQMLGYNLFIDHDASYSHTRIGVGAEYGRDFINLAANGYFGVSGWKNSPDLDKYDEKVANGFDLRSEAYLPTLPQLGGKLIYEQYFGDEVGLFGVDNRQKNPLAVTLGVNYTPIPLFTVGVDHKMGRAGMNDTRFNLGFNYAFGTPLTHQLDSDAVAIKRSLMGSRYNLVDRNNQIVMKYRKQNRVTLELPARVSGAARQTMPLVANATAQQGIDRLEWEASALTLAGGKITGSGNNWQITLPSYLSGGEGNNTYRISAIAYDTLGNASPVAYSDLVVDSHGVNTNASGLTAAPEILPANASASSVIEFNIKDNANQPITGIADELAFSLELVELPEELAKAKARSVPLKTVSHTLTKITESAPGIYQATLTSGSKPQLINITAQINGVPLADVQTKVTLIADESTATLQTSSLQIITNGSLADDTDANQIRAVVVDAYGNKLSGVQVNFTVGNNAKITETTLSDKQGGVTAAITSTKAGTYTVTAELNGVTQQIDVNFIPDAGTATLDDSDEYKLQWVTNGQVADGESTNSVQLTVVDKFGNTVPGVDVAFTTDIGAIISEVTPTDANGVATAKIISSQAKSHTVKATLNRKEQTVEVNFIADTATAEITANNFTVEVDGQVAGSGTNQVQALVVDKKGNPVANMTVNFTATNGVVVETTSAKTDENGKVTTNLSMTNVGGTISTVTATMINSANVTSTQDKPVIFYPDFTKATLNTPANTYSGFNINSGFPTTGFKNTHFQLSPHGITGANSDYDWVSSHPNVSVSNTGAITLQDNPGGKVTITATWKHDSSKVFTYDFTLNYWVGLYSSTNLSWAQANASCINAGMRLPTNREVSAGQDVRGVGSLLSLSIILCNCHRIKGDRSGGHRTR
>NC_004088.1|WP_002211911.1|2865079_2866384_-|MFS-transporter
MSNFNHYPDPTLNSAIKKAWYRLMPLMFIMYFVAFIDRINVGFAKDAMSADIGLSQSAFALGAGIFFAAYALFGIPANLMMNKLGAKVWLSSTTVVWGLLSAGTGLVSNEYQFVILRFLLGVAEAGFYPGILLLASIYFPNKIRASVIGIFVLGVPAALTLGSPISGALLDMQGFLGQPGWFWMFLLEGLPAVGLGIFAFFYLDDSPATARYLNPEEKQALLTQLSIEQSDTESSSVKAVLLSPKVWHLALIYGTIQVGVYGLIFFLPSQVATLLGSTLGFKESLVAAIPWAFSALGVYYIPRYADRKTHRRNPIATLNLVVAAIGLIISAYASPVLAIAALCLCAIGFLAVQPIFWTFPAQILSGKALAAGIGFCTTMGAFFSFLAPIIRVEAESQFNSPPAGLITLALFSLLSATLIFSLKFWPAKATAEVI
>NC_004088.1|WP_002211912.1|2864648_2865071_+|thiol-disulfide-oxidoreductase-DCC-family-protein
MSAPLPYIKPGERVIIYDGVCALCTGWVNFLIRHDRRHTVRLSAVQSKKGHALLEWAGLPTDKINTLVLIENQQVYLRSEAIFRVIANLPWPWRILGVLRIFPRPLRDRCYDGIALNRYRLFGRYDAVRKLKADHERRFL
>NC_004088.1|WP_002216393.1|2863499_2864240_-|SDR-family-oxidoreductase
MNLKGKKALVTAAGQGIGFNTATLFARKGAEVIASDINIAALSNIPGITAVSLDVTDTLAINDVAQAIGPIDVLFNCAGVVHSGDILTCSEQEWQFALDLNVTAMFHMIRAFLPGMIACQQGSIINMSSVASSIKGVPNRFAYSTSKAAVIGLTRSVAADYVTQGIRCNAICPGTVESPSLRQRIAVQAHAEGRSEADVFQAFAARQPIGRIGKAEEIAQLALYLASDASAYTTGTIHIIDGGWSN
>NC_004088.1|WP_002211916.1|2862609_2863452_-|fumarylacetoacetate-hydrolase-family-protein
MKLLRYGPVGEERPALLDELGEIRDLSAHIEDISGKFLLPATLYKLRQLDSASLPLVRGEQRLGACVGHVGKFICVGLNYADHAAETGAEIPQEPVIFNKWTSAIIGPNDDIEIPRNSVKTDWEVELGVVIGTGGRYIGEANAMSYVAGYCVVNDISEREFQLEHGGTWDKGKGCDTFGPIGPWLVTRDEIPDPHQLGLWLDVDGRRYQNGSTRTMIFKIPQIISYLSRFMSLQSGDVISTGTPPGVGLGQKPPVYLHAGQIMRLGIEGLGEQCQKTIQA
>NC_004088.1|WP_002211917.1|2861300_2862578_-|L-fuconate-dehydratase
MTIITALRTEDVRFPTSLELDGSDAMNPDPDYSAAYVILDTDNPALSGHGLTFTIGRGNEICCVAIHALEHLIVGRDLASMTANMGKFWREFTSDSQLRWIGPEKGAIHLATGAVINAVWDLWSKAEGKPLWRLVADMSPEELVRCIDFRYITDCITPEEALTLLQQRAHNKALRLEKLQDEGYPCYTTSAGWLGYPDDKLRRLCQDAVDAGFDYLKLKVGRDLEDDIRRVRITREVLGPDRKLMIDANQIWETNEAIPWVNQLAFANPWFIEEPTNPDDIEGHRRIRQGVAPVKVATGEMCQNRIMFKQFIMREAIDVVQIDACRLGGVNEVLAVMLMAAKYDLPVCPHAGGVGLCEYVQHLAMIDYLCIAGTDKGRVIEYVDHLHEHFVHPCVIKNAAYMPPEQPGFSIEMHQSSIEKYRFRV
>NC_004088.1|WP_002211902.1|2876422_2877814_-|APC-family-permease
MAHDATVAVGTNQTGTNNRVQLRKTLTLVQVVMMGLAYLQPMTIFDTFGIVSGLTDGHVATSYAIALIAVLFTAVSYGKLVKRFPSAGSAYTYAQKSISPNVGFMVGWSSLLDYLFMPMINILLAKIYLEAIFPGVPSWIFVGALVSLMTLFNLRGINIVANLNSVIVVVQVAIMVVFMGLLIHGVYQGEGAGTLVSARPFYSENAHLVPMITGATILCFSFLGFDGISSLSEETPNAGKVIPKAIFLTALIGGIIFIAVSYCLQLYFPDISRFTDPEASQPEIMLFVAGKFFQSVILCFSCVTVLASGMAAHAGVSRLLYVMGRDGVFPEKVFGYVHPKWRTPAINVLLVGGVALSAISFDLVTATALINFGALVAFTFVNLSVIAQFYVRERRNSTFKDHFNYLILPMIGAGTVGVLWVNLESSSMTLGLVWGAIGLSYMVWKTRAFRRALPQFTEEPAQL
>NC_004088.1|WP_002216312.1|2878272_2879364_-|oxidoreductase
MSANAIRVQVGPANYFSFPGAIDKLSEFYPQAALDKALWIYGERALAAAQDYLPKAFHGPQAVRAKFSTHCSQSTVADLVSAAGGDRQVVIGIGGGAVLDTAKVVARQLGVPLVAIPTIAATCAAWTPLSVWYNEAGQALNFEIFNDANHLVLVEPRIMLHAPVEYLLAGIGDTLAKWYEAVVLSPQPETLSLTVRLGLQAALEIRNVLLKQSEAALQAVAQGELTQDFLDVVDAIIAGGGMVGGLGERYTRVAAAHAVHNGLTLLPQTEHFLHGTKVAYGILVQTALLGQDEVLRSLIVAFNQLGLPTHLAALDVDINDREAIDRVIGRILKPGESIHYLPIALNSEKVWAAIEQVEIAAQH
>NC_004088.1|WP_002216311.1|2879649_2880543_+|sugar-ABC-transporter-ATP-binding-protein
MSSIPPSRLEMRNISISFSGFHALQEVDFTLEGGSTHALIGANGAGKSTLMAILSGAHNHYRGEIFIDGQPIDIHSPRQARQHGIHVVQQEVDVALIPTLSVAENIMLDELADRGHLFNWPQLYRQAEALLEQLELKLNVRQRLESCTLAEKQQVLLARALSHQCRFLILDEPTAPLDQEESARLFRVVRRLQSEGIGIVFISHRIHELREVCDQLTVLRDGRRVSHDTMEGMSGEQIVEKMLGHTLEDISPLGERQSAAKHGCRKHYCRKHCYRSAAYMISISCAISPSHYIRAKF
>NC_004088.1|WP_002216310.1|2880500_2881190_+|sugar-ABC-transporter-ATP-binding-protein
MRDISLTLHQGEILGIAGLAGAGKTELCKALFGDTPSTLERGELSGKAWRPRSPDRSVAQGLALVPEERRKEGIFIDEGIPMNLSVAADDSFSRWSLFSRRQELSWAKELIERLGIRTSSPQQKLAHLSGGNQQKVAIGKWLRGDAQVLIFDEPTKGVDIKAKQDLFSLIDQLAQQGKGIIYASGEFSELVGLCDRICVLWDGRIVAELNAAEVDEETLLLFSTGGTPQ
>NC_004088.1|WP_002211900.1|2881186_2882182_+|ABC-transporter-permease
MSKELPLPDVQPWRHQLFDFLYKWGMLLTVVALIALFGLASDNFLDPNNIINILRSIAIVTVIAIGVSISLSIGGFDLSVGSTASLANAVVVSLFVWYGFGTTGAIILTLLICTLVGLFNAFLIVVLKIPDMLATLASLFVIQGVAMTYSRGGSITQSMLLPSGDMAEGVIPEIFSALGQVPVIVLIMLAVTVVVQLYLSLTKHGRRMYAIGGNPQAARLAGIRTVRYRVLAYVLSAQLAALGGILLASRIGSSQVNAGSGYLMDAVAAAYIGFSLAGSGKPNAFGTLIGAIILGVLQNGLVMLSVPYYAMDIIKGLVLAMALALTYIQKR
>NC_004088.1|WP_157131899.1|2882570_2882861_+|hypothetical-protein
MQQKNNLENFALSICLAEGFPDGEINSEAFSAVGAYVELGAYPVEAYEEVSELAKKFLEKKYISKNGESKLTVMKCIDLSQSSELSAIKDKYTRHI
>NC_004088.1|WP_002211898.1|2883015_2883843_-|SDR-family-oxidoreductase
MKKVAIIGLGWLGMPLAQSLSRRGIDVVGSKTTPDGVDAARMSGINCYPLVLTPELICEPDDLAQLMAVDALVITLPASRTTAGGDHYFQAVQQVVDSALAFGVPRIIFTSSTSVYGETRGRIKESSPLQPVTVAGKTLMALEQWLHQLPHTSVDILRLAGLVGTDRHPGRFLAGKTGVKGGSQGVNLVHQEDVIAAIELLLNRPKGGHLYNLCAPIHPRKRDFYPACARALQLTPPEFAVEEQEGANREIDGSKICSELGFEYLYPDPSRMPLN
>NC_004088.1|WP_002231208.1|2884218_2884266_+|his-operon-leader-peptide
MNRVQFNHHHHHHPD
>NC_004088.1|WP_002211896.1|2884548_2885448_+|ATP-phosphoribosyltransferase
MLDKTRLRIAMQKSGRLSDESQELLSRCGIKINLQQQRLIAFAENMPIDILRVRDDDIPGLVMDGVVDLGIIGENVLEEELLNRRAQGDDPRYFTLRRLDFGGCRLSLAAPLDAEYTGPQCLQDTRIATSYPHILKQYLDKQGVRFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEANGLREVEVIYRSKACLIQRDGEMSVDKQQLIDRLMTRIQGVIQARESKYIMMHAPSERLDEIITLLPGAERPTILPLAGDKSRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME
>NC_004088.1|WP_002211895.1|2885451_2886783_+|histidinol-dehydrogenase
MQPTNFNTLINWQQCSEEQQKALLSRPAINASERITAAVSDILDRVKAEGDSALRDFSQRFDHVQVADIRITASEIAAASARLSDDVKHAMAQAVRNIEIFHNAQKMPVVDVETQPGVRCQQITRPIASVGLYIPGGSAPLPSTVLMLGTPARIAGCQRVVLCSPPPIADEILYAAQLCGIQEVFQIGGAQAIAAMAFGSESVPKVHKIFGPGNAYVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPAFIAADLLSQAEHGPDSQVILLTPDAAIAQAVAVEVEQQLALLSRADIARQALESSRLIVTNDLQQCIDISNAYGPEHLILQIRQPEEIIDQIDNAGSVFMGDWSPESAGDYASGTNHVLPTYGYTSTYSSLGLADFVKRMTVQQLTPQGLLGLASTIETLAQAEQLTAHKNAVTLRVTALNNALTAVNKE

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Crispr_ID: NC_004088_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_5

3000867-3000988

Orphan

Consensus_repeat	Method
CAATTGATTATATCGATTAATATTGGCATTAAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_004088_5

>merge|NC_004088|5|3000867-3000988|CRISPRCasFinder
CAATTGATTATATCGATTAATATTGGCATTAAGAGATTTAATACTGCAATATGTTTTTTTGGAAAAAACTCAATCCTCCCCCTCCACTACAATTGATTATGTCGATTAATATTGGCATTAAG

>NC_004088|5|5|3000867-3000988|CRISPRCasFinder
CAATTGATTATATCGATTAATATTGGCATTAAG	AGATTTAATACTGCAATATGTTTTTTTGGAAAAAACTCAATCCTCCCCCTCCACTA
CAATTGATTATGTCGATTAATATTGGCATTAAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002213017.1\|2993167_2993416_-\|acyl-carrier-protein	unknown	unknown	gnl\|CDD\|180851
NC_004088.1\|WP_002213046.1\|3008202_3008532_+\|sulfurtransferase-TusE	unknown	unknown	gnl\|CDD\|225472
NC_004088.1\|WP_002213052.1\|3008955_3010146_+\|23S-rRNA-(cytosine(1962)-C(5))-methyltransferase-RlmI	unknown	unknown	gnl\|CDD\|185082
NC_004088.1\|WP_002213025.1\|2994771_2995524_-\|enoyl-CoA-hydratase/isomerase-family-protein	unknown	unknown	gnl\|CDD\|235936
NC_004088.1\|WP_002213026.1\|2995525_2996245_-\|enoyl-CoA-hydratase/isomerase-family-protein	unknown	unknown	gnl\|CDD\|223955
NC_004088.1\|WP_002213060.1\|3012223_3012688_+\|methylglyoxal-synthase	unknown	unknown	gnl\|CDD\|179969
NC_004088.1\|WP_002221095.1\|3012748_3014803_-\|DNA-helicase-IV	unknown	unknown	gnl\|CDD\|182930
NC_004088.1\|WP_002213024.1\|2993980_2994769_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|212491
NC_004088.1\|WP_002213030.1\|2997491_2998229_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187594
NC_004088.1\|WP_002213032.1\|2998230_2999514_-\|beta-ketoacyl-[acyl-carrier-protein]-synthase-family-protein	unknown	unknown	gnl\|CDD\|238430
NC_004088.1\|WP_002213039.1\|3002140_3004558_+\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|366708
NC_004088.1\|WP_002213028.1\|2996237_2997476_-\|hydroxymethylglutaryl-CoA-synthase-family-protein	unknown	unknown	gnl\|CDD\|225959
NC_004088.1\|WP_002228570.1\|2993453_2993894_-\|lipocalin-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|372819
NC_004088.1\|WP_002213036.1\|3000291_3000510_-\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002213054.1\|3010206_3010524_+\|heat-shock-protein-HspQ	unknown	unknown	gnl\|CDD\|184526
NC_004088.1\|WP_002213056.1\|3010632_3011049_-\|CoA-binding-protein	unknown	unknown	gnl\|CDD\|224745
NC_004088.1\|WP_002213058.1\|3011364_3012045_+\|DUF2057-family-protein	unknown	unknown	gnl\|CDD\|179619
NC_004088.1\|WP_002213049.1\|3008583_3008862_-\|acylphosphatase	unknown	unknown	gnl\|CDD\|184675
NC_004088.1\|WP_002213038.1\|3001240_3001987_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|180440
NC_004088.1\|WP_002213034.1\|2999503_3000028_-\|beta-hydroxyacyl-ACP-dehydratase	unknown	unknown	gnl\|CDD\|223835

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002213017.1\|2993167_2993416_-\|acyl-carrier-protein	gnl\|CDD\|180851	PRK07117, PRK07117, acyl carrier protein; Validated.	4.77778e-09
NC_004088.1\|WP_002213052.1\|3008955_3010146_+\|23S-rRNA-(cytosine(1962)-C(5))-methyltransferase-RlmI	gnl\|CDD\|185082	PRK15128, PRK15128, 23S rRNA (cytosine(1962)-C(5))-methyltransferase RlmI.	0
NC_004088.1\|WP_002213026.1\|2995525_2996245_-\|enoyl-CoA-hydratase/isomerase-family-protein	gnl\|CDD\|223955	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism].	1.17502e-35
NC_004088.1\|WP_002213025.1\|2994771_2995524_-\|enoyl-CoA-hydratase/isomerase-family-protein	gnl\|CDD\|235936	PRK07110, PRK07110, polyketide biosynthesis enoyl-CoA hydratase; Validated.	2.57932e-133
NC_004088.1\|WP_002213060.1\|3012223_3012688_+\|methylglyoxal-synthase	gnl\|CDD\|179969	PRK05234, mgsA, methylglyoxal synthase; Validated.	2.55286e-93
NC_004088.1\|WP_002213028.1\|2996237_2997476_-\|hydroxymethylglutaryl-CoA-synthase-family-protein	gnl\|CDD\|225959	COG3425, PksG, 3-hydroxy-3-methylglutaryl CoA synthase [Lipid metabolism].	1.57028e-141
NC_004088.1\|WP_002213024.1\|2993980_2994769_-\|SDR-family-oxidoreductase	gnl\|CDD\|212491	cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.	5.49415e-40
NC_004088.1\|WP_002213030.1\|2997491_2998229_-\|SDR-family-oxidoreductase	gnl\|CDD\|187594	cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs. This subgroup includes the Escherichai coli K12 BKR, FabG. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet) NAD(P)(H) binding region and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H) binding pattern: TGxxxGxG in classical SDRs. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P) binding motif and an altered active site motif (YXXXN). Fungal type type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P) binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr-151 and Lys-155, and well as Asn-111 (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs.	2.26541e-68
NC_004088.1\|WP_002213032.1\|2998230_2999514_-\|beta-ketoacyl-[acyl-carrier-protein]-synthase-family-protein	gnl\|CDD\|238430	cd00834, KAS_I_II, Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP.	2.93328e-136
NC_004088.1\|WP_002221095.1\|3012748_3014803_-\|DNA-helicase-IV	gnl\|CDD\|182930	PRK11054, helD, DNA helicase IV; Provisional.	0
NC_004088.1\|WP_002213039.1\|3002140_3004558_+\|GNAT-family-N-acetyltransferase	gnl\|CDD\|366708	pfam01565, FAD_binding_4, FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.	1.41205e-31
NC_004088.1\|WP_002228570.1\|2993453_2993894_-\|lipocalin-like-domain-containing-protein	gnl\|CDD\|372819	pfam13924, Lipocalin_5, Lipocalin-like domain. This family includes domains distantly related to lipocalins. However, they do contain the important GXW motif in the first strand. The protein in this family include aln5, which is involved in biosynthesis of alnumycin. The family also includes the ZFK protein from Trypanosoma brucei which is a protein kinase. This domain is at the C-terminus of that protein. The domain is also found as the C-terminal domain in StiJ a protein involved in producing stigmatellin. This domain has been assumed to catalyze a final cyclisation reaction.	5.67247e-46
NC_004088.1\|WP_002213046.1\|3008202_3008532_+\|sulfurtransferase-TusE	gnl\|CDD\|225472	COG2920, DsrC, Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism].	2.4785e-71
NC_004088.1\|WP_002213054.1\|3010206_3010524_+\|heat-shock-protein-HspQ	gnl\|CDD\|184526	PRK14129, PRK14129, heat shock protein HspQ; Provisional.	3.64231e-72
NC_004088.1\|WP_002213056.1\|3010632_3011049_-\|CoA-binding-protein	gnl\|CDD\|224745	COG1832, COG1832, Predicted CoA-binding protein [General function prediction only].	1.53332e-71
NC_004088.1\|WP_002213058.1\|3011364_3012045_+\|DUF2057-family-protein	gnl\|CDD\|179619	PRK03641, PRK03641, DUF2057 family protein.	4.09411e-122
NC_004088.1\|WP_002213049.1\|3008583_3008862_-\|acylphosphatase	gnl\|CDD\|184675	PRK14426, PRK14426, acylphosphatase; Provisional.	1.02172e-54
NC_004088.1\|WP_002213038.1\|3001240_3001987_+\|SDR-family-oxidoreductase	gnl\|CDD\|180440	PRK06172, PRK06172, SDR family oxidoreductase.	1.01866e-70
NC_004088.1\|WP_002213034.1\|2999503_3000028_-\|beta-hydroxyacyl-ACP-dehydratase	gnl\|CDD\|223835	COG0764, FabA, 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Lipid metabolism].	1.09929e-42

>NC_004088.1|WP_002213036.1|3000291_3000510_-|hypothetical-protein
MYLLQQIELCPDQILHAWKISQNPQVSEVFEIEVVSSEEDAEEAVLFWKAYFSSLGETVIDGRHVGDTFSRF
>NC_004088.1|WP_002213034.1|2999503_3000028_-|beta-hydroxyacyl-ACP-dehydratase
MKNTELNFLKTNFLFNQDITNELNTSFGQDIIKKMIPHREPFLMVDNVELINIECRLIKAIRRVDEKDPVFGGHFPNDPIYPGVLQQESMFQTALILMYFLLNETAIPPAEENIIHAVGTRVYDVFHLSAVRPGELMTIRCCITEYDTFLATAIVQITVNDQIVTVGKGEFHVF
>NC_004088.1|WP_002213032.1|2998230_2999514_-|beta-ketoacyl-[acyl-carrier-protein]-synthase-family-protein
MSSDRIVITGVAINTPIGDTLDLVGNNLLSGKSAIGYWRNFDTSNIYSKIGGQIPEYDIEGKLHAFSNRIPDIVLSRAEKVFKQTTKGVQLSVLMAMEAWLDAGLFEHIIDPFDCGIICGGHNLSDKYLLDQQKIFSDEPEFIDAFSGLNSLDTDHSSSVAQVLNTKGFAYLVGGTCATGNIAIQTAINAIKVDKKQVVAVVCPMASFHPMMLHSLTILEAICYSQYQDTPTKASRPYDINRSGFLPSEGGAVLIFEQAEHAKNRGAKIYAELLGASVNSDANHLGDPSHEGQVRVIQDVLKKCNISPEQVDYVSAHATSTKLGDIVELKSIKRVFGSHAEKLIINAPKSLLGHTMWASGVVEAAIAIWQMRQGEFHQSHNIETLDPAVELNVCASGNVKKEVNIFLNNSFGMGGINSASLFSRYHG
>NC_004088.1|WP_002213030.1|2997491_2998229_-|SDR-family-oxidoreductase
MNLFISGGASGIGRSVVIAALSKGWNVGFSYHNNKEGAQQLLDIAVAEFPRQLCRAYQLDVIDSGAVEYVGDRLLVDFSNIDAVVCNAGIDLPGNLVSMTDEDWALVLNTNLTGTFYLIRYFLPLFLANKYGRIVTLSSLAKDGSSGQAAYAASKAGLVGLTKTTAKEYGHFGITANVVVPGLINTEIIGDDIKGIKNFFAQYAPVGRLGSPSEVAEAILFLVAKESSYVNGAVFNVTGGIDWVY
>NC_004088.1|WP_002213028.1|2996237_2997476_-|hydroxymethylglutaryl-CoA-synthase-family-protein
MNSIGIEKISIYPSSLALKLSELAQARGGDNKYIQESLMVIKRSLVPQWEDAVTLAVNSAKDMLNDQDRSDIGLFIIATESGLDQEKAISTWAHRYLGLPATCRVFELKSACHAGAAALKMAESWISSGLNRGKKVLLINVDISNNMICHGKMEYSLGAGAIALLISDNPVFAVIETGKSGIHTHEVTDVIRPLPWKEVAFDVEASLFSYMDGLENAFEEYCHQTPEARESTYFNYNLYHVPFPGISKEAHKVLLELQGLFGKEALATSFKQKVMPSLYYAQKIGATYCGSIFLSLFSLMVKAPEIKSGDRIGVYSYGSGSCAEYFSMQVGDQAVEIAQQQGAALDILLTQRKILDVAAYEQLENARSAQMQGKDYRLDGDNLQDWYTHHYSGSGLLILERIDNHLRRYRYA
>NC_004088.1|WP_002213026.1|2995525_2996245_-|enoyl-CoA-hydratase/isomerase-family-protein
MHEYVTVPIKFSPDSLADFENRFISALNDERYKVIVLIGGPTYFSMGMDLTYISTHYDADFVSQFCHILKMVRNSHKPVLAKVEGNVIAGGLALLSVVDFILSSDSASFSLPEVTFGITPTIAMSCLLERIRPHHLKYFVWSSSVISAKQALKWGLIDQINTLENLDQDIQVISNKLSRIPKSAIRESKLLLAEQYSFEESLDLGSHLLVERLNDAQTIEKIRHYLEDIKLFNDEYADD
>NC_004088.1|WP_002213025.1|2994771_2995524_-|enoyl-CoA-hydratase/isomerase-family-protein
MKKIYLRKSDEGIAFMHINDPVNKNAIDDEFCLQLHGIVDTIKQDKTIKVLILVGLPDIFCTGGTEAFLQSLITHYKTNIEHEYANHLKHFLNIPIPVIAAMEGSATGGGLVLGLYADILVAAEESRYGMSFMNMGFTPGMGSTAMSKEAFGYYTGFEMMVTGNYIRGSELKGKCCFNYILPRAMVMEKAIELATSIAEKPRHSLELLKKYMSIDRRKMLEETSTIEAFMHHIAFNQSNIEQQIQDNYTG
>NC_004088.1|WP_002213024.1|2993980_2994769_-|SDR-family-oxidoreductase
MLNNLSEMTVLVTGGTKGIGRATVESFVKAGAKVYGTYFWGDNLDELENHFSQYLNRPVFLQADISDEEITTQLIEKIAQENKKIDILILNAAFAPQFKDTYKFRGLLDSIEHNSWPLITYIDCIKQHFGQYPGYVVAITSEGHRSCHITGYDYVAASKAVLETLTKYIGARENIIINCISPGVVDTEAFELVFGKKAQAFIRKFDPDFIVSPEAVGNVSVALCSGLMDAVRGQVITVDNGRMFTDNFTKWIDMIETNFIEK
>NC_004088.1|WP_002228570.1|2993453_2993894_-|lipocalin-like-domain-containing-protein
MSNPNRNLFLGRWKLESCIGNSGGIHIYPIGREPFGMLIYTEQYMMVFISSVERTQFSTEDIRAIPSEQIVADFPKFETYCGHYIVNHDEKIVTHFIDNSKIPNQIGTQFRRYFSFEHEKLVLKSIDSLLLNDESWLFELVWNKQE
>NC_004088.1|WP_002213017.1|2993167_2993416_-|acyl-carrier-protein
MDRDHIASIVKKHIVNSIDGAKEHEIDLQKSMADYGASSLDIVSVVSGVMRELKIKIPRTELKNIKSINGLIDLFVTSSSES
>NC_004088.1|WP_002213038.1|3001240_3001987_+|SDR-family-oxidoreductase
MKKTILITGALSGIGNTATKLFSEMGYNVVFSGRRPEEGRVILDDLKRINKDVLYVNADMNSESDIKHLIEMTLERFGSLDVAVNCAGTVGETAEIQAVTQDNFHLVFNTNVLGTLLAMKYQIPVMVERGKGSIINISSIAGLVGLPSTGIYVASKHAIEGLTKTAALEVATTGVRINSISPGPVEGKMFDRFLGHDENNKKAFIEMMPNKRFTTQEEVAHTIVFLAEDNVTAITGQTITIDGGYTAQ
>NC_004088.1|WP_002213039.1|3002140_3004558_+|GNAT-family-N-acetyltransferase
MTTTLDIINSAKDLDPAEYRAFFLQSKAPLFYDLRFLIAAEQSPLLNVSKIFYLLARDEGRLIALVPLYLQEFRSADPLGLLISSAKLSIESEERGLFSHIIHCTDTTIPTLSHDPSLYARIFDAITAIAQAELARYFCFLNVQDGVLLREAQRNGLNINYMVDKFSIELDAFPDFDSFAQALPKYRRYEMVRQLRIFNRSDAKVRILAPPFDNEIEKLARLYYLTTQRLGTPYYWPESQLAVFCRLCGDLVRLIVVEQNGQIVSGFICFEEDGALHFWSAGMDDESSDFSPYTLGVSAVYRYAFEKGINLIECGRLNSHIKTRLGFKPKRLYSIVSQDLGIPAATQTSLSQLKLASQLDGEVRLASHPAFDEWYLTSVWNGRGPTRRPAGIVRAATEADVIRTIVFAKERGMEVSVRGSGHNYVGCFLRVDTLMLDISGLKGLDIDSRHKRAIVESGVSSGQLCHALAAKGLAFPTGHVKEVGISGFLLGGGLGINCSQWGGMSVFNVQALDIVTADGHLRHVSETQEPDLFWAARGAGPCSFFVVTRFYLSCYSLPRVITNSLYTLPFTYLHDLLARLEDASPPTNLQVMVSVSPPTSGDTPAVLLNILAFTDSPQEAQALCESFETRLELPLTALAINQPSNFETIYEQFSSMVVSKRFYADNILTDNTQELVSILSRYLSDAPSRGALTTIFWRGVTTYPQAAFSAHGKFFVSTYAQWDDAKDDSVNKYWLKRMYDELQEIARSRYINEYDLETRAGETSKCFAAENWERLQRLRLEYDPDGVFVDVQQLEEHGDQPGANN
>NC_004088.1|WP_002213046.1|3008202_3008532_+|sulfurtransferase-TusE
MLEFEGRIIDTDAQGYLKNSTDWSEALAPVLAEQEGITLTEPHWEVVRFVRAFYQEFNTSPAIRMLVKAMAQKYGEEKGNSRYLYRLFPKGPAKQATKIAGLPKPVKCI
>NC_004088.1|WP_002213049.1|3008583_3008862_-|acylphosphatase
MSKIYIVAYVYGVVQGVGFRYSTQRQAQQLGVTGYAKNCDDGSVEVVASGNPQAVERLMEWIRQGGPRGARVDRLLTEPYPPTPFETFSIRY
>NC_004088.1|WP_002213052.1|3008955_3010146_+|23S-rRNA-(cytosine(1962)-C(5))-methyltransferase-RlmI
MTVRLILAKGREKSLLRRHPWIFSGAVQRLEGDALSGETIDILDSQGKWLARAAYSPESQILARVWTFQQDEVIDCAFFIRRLQQAQNWRDWLAQRDGLNGYRLIAGESDGLPGITIDRFQNFLVLQLLSAGAEYQRETLVSALQHCYPECSIYDRSDVSVRKKEGLPLTQGLICGEMPPALLPISENGMQLFVDIQQGHKTGFYLDQRDSRLAARNYANGRRVLNCFSYTGAFAVAALMGNCQQVISVDTSQSVLDIAKQNIELNQLDLSKTEFVRDDVFQLLRSYRAQGEKFDLIIMDPPKFVENKSQLASACRGYKDINMLAIQLLRPGGILLSFSCSGLMPVDLFQKILADAALDAGHDIQFIEQFRQAADHPVIAAYPEGLYLKGFACRVM
>NC_004088.1|WP_002213054.1|3010206_3010524_+|heat-shock-protein-HspQ
MIASKFGIGQQVRHSLHGYLGVVIDIDPEYSLAPPEPDEVANNKTLRSSPWYHVVIEDDDGQPVHTYLAEAQLTYEDVDAHPEQPSLDELAASIRHQLQAPHLRN
>NC_004088.1|WP_002213056.1|3010632_3011049_-|CoA-binding-protein
MHDKDIADILKKVKTIALVGASDIPSRPSYRVMAYLLQQGYQVTPVNPKLAGELLLGQLVYAELADIPHAIDMVDVFRNSDAAYCIAQDAIAIGAKVLWLQIGVINEQAAILATDAGLQVVMDRCPKIELPRLGLEKG
>NC_004088.1|WP_002213058.1|3011364_3012045_+|DUF2057-family-protein
MKLGLVAGMLAVCFSFSSVAMTLKLTPEIDLLVVDGKNMSGSLLKGADSLELNSGMHQILFKVIKPLPTDPLVLYSSPPLIVVFNAHNTRSVAIKLPVINTLRDGHQFSKNPLYQLIGDNGHPLSVRHDVLRQDHLNNSTTLETVMAAYNVGKYNASVPAFAAIPPSPVSAVPGTTIPVAGVNTPHKTASLQGENVTEQMLQYWFLQANPETQKRFLIWAKKQPIH
>NC_004088.1|WP_002213060.1|3012223_3012688_+|methylglyoxal-synthase
MELTTRTIAARKHIALVSHDHCKKSLLAWVMENRDLLAQHELYATGTTGNLVQKATGIDVHCLLSGPMGGDQEVGALISEKKIDILIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNRSTADFLIGSTLFSSEVTIAIPDYDRYMQQRLDLK
>NC_004088.1|WP_002221095.1|3012748_3014803_-|DNA-helicase-IV
MELKATSFGKHLSQHPYNRVRLLNAGIEVCGDKHQYLIPFNQLVSIQCKRGIVWGELEFELPQQKVVRLHGTEWQETQHFYHYLLGVWQQWSEEMSQVCAEVLHKQVESIKRIEQQDKWFKRSELGQIQVMIREAFSALPMPVERLAAFESCRADYECCLRWLQQGRHSVERCNQQWTARMLEEYQDFFQNVETSPLNASQSRAVVNGEDSVLVLAGAGSGKTSVLVARAGWLLRRNEALPEQILLLAFGRQAADEMNSRIKQRLGVDSIQAKTFHALALHIIQQGSRKTPVISKLESDSQARRALLIQHWQQQCSEKKAQAKGWREWLTDELEWDVADGDFWQDKRLAARLASRLERWVGLMRMYGGSQAEMIEQANDEVRDLFQKRIRLMAPLLKAWKTALKDEGAVDFSGLIHQAVNLLEKGRFVSPWKHVLVDEFQDISPQRAMLLAALRKQNKQTCLFAVGDDWQAIYRFSGAELSLTTAFSEHFGEGAECALDTTYRFNDRIGDIANRFIQQNPYQLKKPLNSLSKGNKKSVMILPDEQLEALLDKLSGFVKDGERILILARYHHLRPEVLQKAATRWPKLTIDFMTIHASKGQQADYVIIVGLHEGNDGFPAAARESVLEDVLLPPPEDFPDAEERRLLYVAITRAKHQVWLLQDTARPSIFVSQLSELGALVQRKP

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Crispr_ID: NC_004088_6

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_004088_6

3917689-3917768

Orphan

Consensus_repeat	Method
CAGCCGCAGCCACGCTCAGCCATTC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_004088_6

>merge|NC_004088|6|3917689-3917768|CRISPRCasFinder
CAGCCGCAGCCACGCTCAGCCATTCGACACCCATATCAGAATGACTGCGGCAACGCAGCCGCAGCCACGCTCAGCCATTC

>NC_004088|6|6|3917689-3917768|CRISPRCasFinder
CAGCCGCAGCCACGCTCAGCCATTC	GACACCCATATCAGAATGACTGCGGCAACG
CAGCCGCAGCCACGCTCAGCCATTC

Protein	Signature genes	Signature genes Name	Protein_function
NC_004088.1\|WP_002214241.1\|3926902_3927133_-\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002212196.1\|3913059_3913683_+\|SH3-domain-containing-protein	unknown	unknown	gnl\|CDD\|182809
NC_004088.1\|WP_002212199.1\|3916408_3916768_-\|bifunctional-dihydroneopterin-aldolase/7,8-dihydroneopterin-epimerase	unknown	unknown	gnl\|CDD\|183219
NC_004088.1\|WP_002210361.1\|3924908_3925379_-\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002212192.1\|3905570_3906821_-\|L-methionine/branched-chain-amino-acid-transporter	unknown	unknown	gnl\|CDD\|236823
NC_004088.1\|WP_002212194.1\|3908422_3911278_-\|bifunctional-[glutamate--ammonia-ligase]-adenylyl-L-tyrosine-phosphorylase/[glutamate--ammonia-ligase]-adenylyltransferase	unknown	unknown	gnl\|CDD\|236836
NC_004088.1\|WP_002212197.1\|3913842_3915081_+\|multifunctional-CCA-addition/repair-protein	unknown	unknown	gnl\|CDD\|182810
NC_004088.1\|WP_002210360.1\|3924426_3924882_-\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002210359.1\|3921447_3923286_+\|RNA-polymerase-sigma-factor-RpoD	unknown	unknown	gnl\|CDD\|235549
NC_004088.1\|WP_002212193.1\|3906857_3908288_-\|bifunctional-D-glycero-beta-D-manno-heptose-7-phosphate-kinase/D-glycero-beta-D-manno-heptose-1-phosphate-adenylyltransferase-HldE	unknown	unknown	gnl\|CDD\|183085
NC_004088.1\|WP_002212201.1\|3917771_3918785_-\|tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-transferase-subunit-TsaD	unknown	unknown	gnl\|CDD\|236585
NC_004088.1\|WP_002231433.1\|3911586_3912756_-\|inorganic-triphosphatase	unknown	unknown	gnl\|CDD\|225569
NC_004088.1\|WP_002210366.1\|3928805_3929738_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176161
NC_004088.1\|WP_002210363.1\|3927688_3927847_+\|hypothetical-protein	unknown	unknown	unknown
NC_004088.1\|WP_002212198.1\|3915316_3916135_-\|undecaprenyl-diphosphate-phosphatase	unknown	unknown	gnl\|CDD\|234712
NC_004088.1\|WP_002210362.1\|3925387_3926770_-\|HNH-endonuclease	unknown	unknown	gnl\|CDD\|238038
NC_004088.1\|WP_001144069.1\|3919190_3919406_+\|30S-ribosomal-protein-S21	unknown	unknown	gnl\|CDD\|234707
NC_004088.1\|WP_002210358.1\|3919541_3921290_+\|DNA-primase	unknown	unknown	gnl\|CDD\|235551
NC_004088.1\|WP_002212191.1\|3904964_3905246_+\|accessory-factor-UbiK-family-protein	unknown	unknown	gnl\|CDD\|225508
NC_004088.1\|WP_002217581.1\|3916875_3917526_+\|glycerol-3-phosphate-1-O-acyltransferase-PlsY	unknown	unknown	gnl\|CDD\|234691

Protein	Function_ID	Function_description	E-value
NC_004088.1\|WP_002212196.1\|3913059_3913683_+\|SH3-domain-containing-protein	gnl\|CDD\|182809	PRK10884, PRK10884, SH3 domain-containing protein; Provisional.	4.34503e-147
NC_004088.1\|WP_002212199.1\|3916408_3916768_-\|bifunctional-dihydroneopterin-aldolase/7,8-dihydroneopterin-epimerase	gnl\|CDD\|183219	PRK11593, folB, bifunctional dihydroneopterin aldolase/7,8-dihydroneopterin epimerase.	2.02028e-82
NC_004088.1\|WP_002212192.1\|3905570_3906821_-\|L-methionine/branched-chain-amino-acid-transporter	gnl\|CDD\|236823	PRK11021, PRK11021, putative transporter; Provisional.	0
NC_004088.1\|WP_002212194.1\|3908422_3911278_-\|bifunctional-[glutamate--ammonia-ligase]-adenylyl-L-tyrosine-phosphorylase/[glutamate--ammonia-ligase]-adenylyltransferase	gnl\|CDD\|236836	PRK11072, PRK11072, bifunctional [glutamate--ammonia ligase]-adenylyl-L-tyrosine phosphorylase/[glutamate--ammonia-ligase] adenylyltransferase.	0
NC_004088.1\|WP_002212197.1\|3913842_3915081_+\|multifunctional-CCA-addition/repair-protein	gnl\|CDD\|182810	PRK10885, cca, multifunctional CCA addition/repair protein.	0
NC_004088.1\|WP_002210359.1\|3921447_3923286_+\|RNA-polymerase-sigma-factor-RpoD	gnl\|CDD\|235549	PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.	0
NC_004088.1\|WP_002212193.1\|3906857_3908288_-\|bifunctional-D-glycero-beta-D-manno-heptose-7-phosphate-kinase/D-glycero-beta-D-manno-heptose-1-phosphate-adenylyltransferase-HldE	gnl\|CDD\|183085	PRK11316, PRK11316, bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase HldE.	0
NC_004088.1\|WP_002212201.1\|3917771_3918785_-\|tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-transferase-subunit-TsaD	gnl\|CDD\|236585	PRK09604, PRK09604, tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD.	0
NC_004088.1\|WP_002231433.1\|3911586_3912756_-\|inorganic-triphosphatase	gnl\|CDD\|225569	COG3025, COG3025, Uncharacterized conserved protein [Function unknown].	1.28142e-177
NC_004088.1\|WP_002210366.1\|3928805_3929738_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176161	cd08472, PBP2_CrgA_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	8.91117e-86
NC_004088.1\|WP_002212198.1\|3915316_3916135_-\|undecaprenyl-diphosphate-phosphatase	gnl\|CDD\|234712	PRK00281, PRK00281, undecaprenyl-diphosphate phosphatase.	5.08833e-116
NC_004088.1\|WP_002210362.1\|3925387_3926770_-\|HNH-endonuclease	gnl\|CDD\|238038	cd00085, HNHc, HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.	2.83623e-06
NC_004088.1\|WP_001144069.1\|3919190_3919406_+\|30S-ribosomal-protein-S21	gnl\|CDD\|234707	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.	8.25342e-17
NC_004088.1\|WP_002210358.1\|3919541_3921290_+\|DNA-primase	gnl\|CDD\|235551	PRK05667, dnaG, DNA primase; Validated.	0
NC_004088.1\|WP_002212191.1\|3904964_3905246_+\|accessory-factor-UbiK-family-protein	gnl\|CDD\|225508	COG2960, COG2960, Uncharacterized protein conserved in bacteria [Function unknown].	1.21559e-35
NC_004088.1\|WP_002217581.1\|3916875_3917526_+\|glycerol-3-phosphate-1-O-acyltransferase-PlsY	gnl\|CDD\|234691	PRK00220, PRK00220, glycerol-3-phosphate 1-O-acyltransferase PlsY.	6.06402e-111

>NC_004088.1|WP_002217581.1|3916875_3917526_+|glycerol-3-phosphate-1-O-acyltransferase-PlsY
MSAIALGMIIFAYLCGSISSAILVCRVARLPDPRTHGSGNPGATNVLRIGGRTAAVAVLLFDILKGMLPVWIAYLLHIPPLYLGLTAIAACLGHIYPVFFHFKGGKGVATAFGAIAPIGWDLTGLMTGTWLLTVLLSGYSSLGAIVSALIAPFYVWWFKPQFTFPVAMLSCLILMRHHDNIQRLWRGKEGKIWDKLRKKKQKTPAEEAAELEEKED
>NC_004088.1|WP_002212199.1|3916408_3916768_-|bifunctional-dihydroneopterin-aldolase/7,8-dihydroneopterin-epimerase
MDIVFIEELSVITTIGVYDWEQTIQQKLVFDIEMGWDNRKAAGSDDVNDCLSYADISEAVIQHVGSQRFALVERVAEEVAELLLRRFNSPWVRIKVSKPGAVAQAKNVGVIIERGQRLS
>NC_004088.1|WP_002212198.1|3915316_3916135_-|undecaprenyl-diphosphate-phosphatase
MTDMYSLFVAFILGVVEGLTEFLPVSSTGHMIIVGELLGFTGDKAKTFEVIIQLGSILAVVVVFWRRLFGLIGIHFGAVPHEGKTNGHLTLGHILLAMIPAVILGLAFHDVIKALFDPKSVMYALVAGGVLLLAAEWLKPKNPKAVGLDDITYRQAFAIGCFQCLALWPGFSRSGATISGGMLVGVNRYAASEFSFILAVPMMIGASGLDLYKSLHFLTLGDLPMFAVGFITAFIVALIAIKTFLSLIKRISFVPFAIYRFIVAAVVYWVFM
>NC_004088.1|WP_002212197.1|3913842_3915081_+|multifunctional-CCA-addition/repair-protein
MNIYLVGGAVRDSLLNLPVTEQDWVVVGATPEQLLKLGYQQVGKDFPVFLHPVSHEEYALARTERKSGQGYTGFTCYAAPDVTLEDDLLRRDLTVNAIARSADGEFIDPYHGKQDLENRVLRHVSDAFGEDPLRVLRVARFAARFAYLGFTIAPETMSLMSNMAQSGELSALTPERVWKETEKALKTQSPHVYFQVLRDCGALAVLFPEIERLFGVPAPEKWHPEIDTGIHTLMTLAIAAQLSPEVDIRFAALCHDLGKGLTPKEHWPHHHGHGPAGVKLVEQLCQRLRIPNPVRDLAKLVAEYHDLIHTVNKLRPETLLKLFNAIDVWRKPERLEQMIMTSEADARGRTGFENNPYPQGDYLRAAFQIANGVSIQEVVASGLQGLAIRDELQRRRQQALAEWKQTQETASI
>NC_004088.1|WP_002212196.1|3913059_3913683_+|SH3-domain-containing-protein
MQKLRLICLTILSVSLSWGAQAEEKRYISDELDTYVHSGPGNQYRIVGTLKGGDEVTLISVDNGTNYGQIRDSKGKTTWIPLNQLSETPSLRVRVPDLEQQVKTLTDKLANIDNSWNQRTAEMQQKVAASDSVISELQKENESLKNQLIVAQKKVNAVNLQLDDKQRTIILQWFMYGGGVAGIGLLLGLVLPHLIPSRKKNNRWMNC
>NC_004088.1|WP_002231433.1|3911586_3912756_-|inorganic-triphosphatase
MTVEIELKFIATPAAIAALPEWIESQKNQHFPPQTLANIYFDTADKRLRQNDIGLRIRGYDGRYEMTVKTGGKVVGGLHQRPEYNVDIDSDQLDLARFPQDIWPEGWAVDLLQAELQPLFRTDFTREKWVITYGESEIELALDQGSISADTLSEPLSEIELELKQGTQGDLLALAAELAKMGGLRQSNLSKAARGYHLAQGNPPRELRPFLVFQPVAKSTVEQGMAGGLESILEHWQYHEELWLRGEPAAKTMIIDALAMVRQSLAIFGGLVPRKASTELRALLIALEPQLEPKSVDAALLCYSVDYLKCKLALTSWLITAGWRPFMDAKAQAKFDGSFKRFCDIMLSRSAADLKEAFGHNLDDDGYLAQLPRLNRQLIAFQLLSGFYP
>NC_004088.1|WP_002212194.1|3908422_3911278_-|bifunctional-[glutamate--ammonia-ligase]-adenylyl-L-tyrosine-phosphorylase/[glutamate--ammonia-ligase]-adenylyltransferase
MLPLPSELQIQAQSIKQRFSELPAPPDLRDEDIAVLALSDFVSDMLLIHPQWLEELHQQPPQPQEWQYYSQWLSQALAGVQDEAALLTALRLFRRRVMVRIAWSQVLQTSGTAETLQQLSTLAESMIIAARDWLYQVCCRELGTPCNRQGVPQPLLILGMGKLGGGELNFSSDIDLIFAYPENGQTQGGRRELDNAQFFTRLGQRLIKALDQHTIDGFVYRVDMRLRPFGDSGPLVLSFAALEDYYQEQGRDWERYAMVKARLMGGADDPYSQELRQMLRPFVFRRYIDFSVIQSLRNMKGMIAREVRRRGLKDNIKLGAGGIREIEFITQVFQLIRGGREPRLQERALLPTLQAVAELGLLPEQQVADLSGSYLFLRRLENLLQAIADEQTQTLPNDPLNQARLAWGMGYADWAAMSTALENHMQAVRVVFDDLIGDETPDIGEDPSHGLYKSLWQDVLEESDLAPLTPHLEEAARRQLLATISGFRHDVDKRTIGPRGREVLDQLMPRLFAEVCPRPDANVALSRLILLLLSIVTRTTYLELLVEYHAALKHVIRLCSASPMVASQLARYPLLLDELLDPQSLYQPLAPSAYRDELRQYLLRVPEDDEEQQLEALRQFKQAQQLRIAAGDITEALPVMKVSDHLTYLAEAIIDAVIQQAWNQMVARYGQPSHLQQSEGRGFAVIGYGKLGGWELGYSSDLDLVFLLDCPLDVMTDGDRSIDGRQFYLRLAQRIMHLFSTRTSSGILYEVDARLRPSGEAGMLVSTIEAFADYQRNEAWTWEHQALVRARIVYGSPKLHQQFDAIRQQILCRHREDPQLQQEVREMREKMRNHLGSKQRDIFDIKADAGGITDIEFIAQYLVLRYAASEPRLTRWSDNVRIFESMAHYDIMSPEEAAALTRAYVTMRDEIHHLALQEQSSKVAADSFIAEREQVAASWHKWLAANDANVS
>NC_004088.1|WP_002212193.1|3906857_3908288_-|bifunctional-D-glycero-beta-D-manno-heptose-7-phosphate-kinase/D-glycero-beta-D-manno-heptose-1-phosphate-adenylyltransferase-HldE
MKVTLPDFRRAGVLVVGDVMLDRYWYGPTCRISPEAPVPVVKVDTIEERPGGAANVAMNIASLGAVARLVGLTGIDDAARALICKLSEVRVRCDFVSVPTHPTITKLRVLSRNQQLIRLDFEEGFDGVDPTPIFERIQLALPQIGALVLSDYAKGALNSVQPMIQLARKANVPVLIDPKGSDFERYRGATLLTPNLSEFEAVVGRCKNEEELVNRGMQLVADFELSALLVTRSEQGMTLLQLGKPPLHLPTQAKEVFDVTGAGDTVIGVLAAALAAGNSLEESCFLANAAAGVVVGKLGTSTVSPIELENAIRGRAETGFGVMDEQQLKIAVAQARQRGEKVVMTNGIFDILHAGHVSYLANARKLGDRLIVAVNSDASTKRLKGEKRPVNPLEQRMVVLGALEAVDWVVPFEEDTPQRLIADILPDLLVKGGDYKPHEIAGSEEVWAAGGEVKVLNFEDGVSTTNIIQSIKNGRG
>NC_004088.1|WP_002212192.1|3905570_3906821_-|L-methionine/branched-chain-amino-acid-transporter
MGGLKQELSLAQGVGLLSTSLLGTGVFAVPALAAMLAGHDSLWAWPVLIVLVFPIAIAFAALGRHFPSAGGAAHFVAIAFGPKLGKVTGWLFLSVIPVGLPAALQIAAGFWQAMFGWSDTGLLMVQLVTLLVIWLLGTRSAGSSANLQTVIALLVIALVAAIWWQGDIRLSQIPWPALQDVSPPNIFNALAVMFWCFVGLEAFAHLATEFRHPERDFPRALIVGLLVAGAVYWGCTVAVLHFQAYGESQAAAASLPGIVVQLFGEHALWIACIIGYLACFASVNIYTQSFARMVWSQSQVRPQSKLARLSAGQTPVNALTAVVGSCLVFALLIYWLALPLDLLIVYANGIFVLIYLLCMLAGIRLLSGRARVMSVIGSLLCCVLLVMIGWKSVYALLMFALLWMLMSKPKTQLTQP
>NC_004088.1|WP_002212191.1|3904964_3905246_+|accessory-factor-UbiK-family-protein
MIDPKKIEQIARQVHESMPKGIREFGEDVEKKIRLILQSQLTRLDLVNREEFDVQTQVLLRTREKLALLEQRVGALEAKFNSAPADHGEKTGE
>NC_004088.1|WP_002212201.1|3917771_3918785_-|tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-transferase-subunit-TsaD
MRVLGIETSCDETGIAVYDDKAGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEANLSAKDIDAVAYTAGPGLVGALLVGATIGRALAFAWGVPAVPVHHMEGHLLAPMLEENAPEFPFVALLVSGGHTQLISVTGIGEYLLLGESVDDAAGEAFDKTAKLLGLDYPGGPMLSRMAQQGTVGRFTFPRPMTDRPGLDFSFSGLKTFAANTIRANGDDDQTRADIARAFEDAVVDTLAIKSKRALDQTGFKRLVIAGGVSANQTLRLKLADMMQKRGGEVFYARPEFCTDNGAMIAYAGMVRLRSNLNSELSVSVRPRWPLSELPKV
>NC_004088.1|WP_001144069.1|3919190_3919406_+|30S-ribosomal-protein-S21
MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY
>NC_004088.1|WP_002210358.1|3919541_3921290_+|DNA-primase
MAGRIPRVFINDLLARTDIIDLIDARVKLKKQGKNYHACCPFHHEKTPSFTVNGEKQFYHCFGCGAHGNAVDFLMNYDRLEFVESIEELATMHGLEVPYEAGSGTTQIERHQRQSLYQLMESLSAFYQQSLKGQNAKQAREYLKHRGLSEEIIQHFAIGFAPPGWDNALKRFGRDGESRTALNDAGMLVTNDTGRTYDRFRERVMFPIRDKRGRVIAFGGRILGDGVPKYLNSPETEIFHKGRQLYGLYEAQVNHPNPTRLLVVEGYMDVVALAQFGIDYAVASLGTATTAEHIQLLFRATDNVICCYDGDRAGRDAAWRALETALPYLNDGRQLRFMFLPDGEDPDTLVRKEGKDAFEQRMEAAQPLSTFLFETLMPQVDLSSPDGRAKLSTLALPLISQVPGEALRLYLRQQLGNKLGLLDDSQLDKLMPKQIDNANTYQPPQLKRTTMRILIGLLVQNPQLATLIPSLQGLEQAKLAGLPLFIELVETCLAQPGLTTGQLLELYRDNKFSQQLETLATWNHMIVEDMVEPTFVDTLASLYDSILEQRQETLIARDRTHGLNAEERKELWSLNLALARKK
>NC_004088.1|WP_002210359.1|3921447_3923286_+|RNA-polymerase-sigma-factor-RpoD
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYENARMEIKKNGRNHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD
>NC_004088.1|WP_002210360.1|3924426_3924882_-|hypothetical-protein
MANLEKAVNEFTRISKSMGYNINPPYTGKLETYDFGRDISPEQPDFWKQYGSFLRISNGSFADGCVFYGMSGGEDDAGLIEFNNALNIPDFKDETMTGLIVIGGNNTDTFYYDPRTGKWEACDRIGTDRVWESCDSLAELIETQIKMLENG
>NC_004088.1|WP_002210361.1|3924908_3925379_-|hypothetical-protein
MTDIEKAVTTFQAYRAAIGYPKIPPYEGEVIEYDFGRKIESNQPDFWTQYHEFLRLSDGLAADGVYFYGIACEGKLIGNRLIDNNDALRDGEMYDESMDGLIAIGSSNSDIFVYDTNTHKWESRDRIAIDDINESYDTLAELIDSQLQRINIGDAF
>NC_004088.1|WP_002210362.1|3925387_3926770_-|HNH-endonuclease
MSFNLPGMYLYYLSRDNLAPEEYERIISPHAAWARICREYEFDDSHNTSRYLINMREREQRSSPDQPRPGGIREKEKLEKLVFSGDVVMLSDMYGPARLFYINGEGQLMSTDPHAFRFEGAAKIIKAFDDSVKCRNYQRTGGKPRSTQTRRLKSTTNTIPDRSMVTRASDESGRVLSAKWQSVTDSAKTLWEATPFTHDKATTEAARGRIADGAVGTLEGLGTLMGPSAQEYMAGAFNPEQAAINKVRQQNQQAAGKAIYDNTKGAVTDAYQRNGLAGAAAMVVTASVAELAGTKGLGTVEKVGTLGDVAKLGKAVELEKLEGYLGTYKGQKVLLQNVDVVKMDYVRRSTADRNLLRKEFDNGVRKKFLKDIANNPEVVKRLDAFDRSVLAKGVVPDGYQVHHKLPLDDSGNNNFDNLVLISTRPEHAAFTTTQKHITKNLTPTGTNIVLWPKPQGIIYP
>NC_004088.1|WP_002214241.1|3926902_3927133_-|hypothetical-protein
MDTLTTATPSVHRKYFRHILGACGSCYFERQAGKFILGEEGDQFFSAYVREDSAYRIERMESESPLGYQTSGAIPV
>NC_004088.1|WP_002210363.1|3927688_3927847_+|hypothetical-protein
MTKKTAHSQITKTQIYRAVASSTAIETGVSVQKIEQQLKQNLAQAKAVGLAR
>NC_004088.1|WP_002210366.1|3928805_3929738_-|LysR-family-transcriptional-regulator
MDKFSAMTTFAKVVETGSFTRAADVLALPKARVSQRVSDLERHLGVRLLNRTTRSLNLTEDGQAYFAKCQVILQEIDELEGALKGGSVEPRGKLRVEALVSVARWVIAPSLHEFQARYPNISVRLGGSDRISHLLDNGIDCAIRGGHLEDSSQIARHVCDVHLGLYAAPAYLEAAGAVTHPQELSVHRRISWFTGQRNPFIWSLQSASDAFELPAEEGLLFDDPDVALASCMAGSGICPGAPFAVESWVRAGALVPVLPHWRFKARPIHIIYPSNRHLSARVRCFVDWSLEMMQANTSMRITPWELAERI

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_004088_2	2.4\|1291691\|32\|NC_004088\|CRISPRCasFinder,CRT	1291691-1291722	32	NC_004088.1	2439155-2439186	0	1.0

1. spacer 2.4|1291691|32|NC_004088|CRISPRCasFinder,CRT matches to position: 2439155-2439186, mismatch: 0, identity: 1.0

agactgatgcaagatggcggtatgcgtacaga	CRISPR spacer
agactgatgcaagatggcggtatgcgtacaga	Protospacer
********************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_004088_2	2.4\|1291691\|32\|NC_004088\|CRISPRCasFinder,CRT	1291691-1291722	32	MT374852	Yersinia phage vB_YpM_3, complete genome	12-43	0	1.0
NC_004088_3	3.3\|1902478\|30\|NC_004088\|CRISPRCasFinder	1902478-1902507	30	NZ_CP054046	Yersinia massiliensis strain 2011N-4075 plasmid unnamed1, complete sequence	2177-2206	3	0.9
NC_004088_4	4.4\|2875813\|28\|NC_004088\|PILER-CR	2875813-2875840	28	MH616963	CrAssphage sp. isolate ctbg_1, complete genome	86944-86971	5	0.821
NC_004088_4	4.4\|2875813\|28\|NC_004088\|PILER-CR	2875813-2875840	28	MT774386	CrAssphage cr110_1, complete genome	42860-42887	5	0.821
NC_004088_3	3.3\|1902478\|30\|NC_004088\|CRISPRCasFinder	1902478-1902507	30	CP049262	Cronobacter sakazakii strain CS-09 plasmid pCsaCS09b, complete sequence	69637-69666	6	0.8
NC_004088_4	4.4\|2875813\|28\|NC_004088\|PILER-CR	2875813-2875840	28	NZ_CP028934	Campylobacter jejuni strain FORC_083 plasmid pFORC_083_2, complete sequence	25851-25878	6	0.786
NC_004088_3	3.1\|1902358\|30\|NC_004088\|CRISPRCasFinder	1902358-1902387	30	NZ_CP013487	Vibrio alginolyticus strain ATCC 33787 plasmid pMBL287, complete sequence	166773-166802	7	0.767
NC_004088_3	3.2\|1902418\|30\|NC_004088\|CRISPRCasFinder	1902418-1902447	30	NZ_CP031943	Nostoc sphaeroides strain Kutzing En plasmid p2, complete sequence	4007-4036	7	0.767
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	MF679145	Escherichia coli plasmid pBJ114-96, complete sequence	37586-37614	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_KP453775	Klebsiella pneumoniae strain ST11 plasmid pKP12226, complete sequence	60831-60859	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP021340	Escherichia coli strain 95NR1 plasmid p95NR1A, complete sequence	67671-67699	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP021336	Escherichia coli strain 95JB1 plasmid p95JB1A, complete sequence	67672-67700	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP040920	Escherichia coli strain FC853_EC plasmid p853EC1, complete sequence	33438-33466	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP024832	Escherichia coli strain CREC-532 plasmid pCREC-532_2, complete sequence	33830-33858	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP024817	Escherichia coli strain CREC-629 plasmid pCREC-629_2, complete sequence	62769-62797	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP029117	Escherichia coli strain AR435 plasmid unnamed4	15616-15644	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP029117	Escherichia coli strain AR435 plasmid unnamed4	112580-112608	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP023961	Escherichia coli strain FDAARGOS_448 plasmid unnamed2, complete sequence	16858-16886	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	AP023222	Escherichia coli M505 plasmid pM505-b DNA, complete genome	93737-93765	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	AP023233	Escherichia coli YJ4 plasmid pYJ4-b DNA, complete genome	47570-47598	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP019075	Escherichia coli strain CRE1493 plasmid p1493-4, complete sequence	16520-16548	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP015837	Escherichia coli strain MS6198 plasmid pMS6198C, complete sequence	3287-3315	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NZ_CP011063	Escherichia coli str. Sanji plasmid pSJ_98, complete sequence	37637-37665	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	JF974294	Aeromonas phage pIS4-A genomic sequence	21968-21996	7	0.759
NC_004088_3	3.4\|1902360\|29\|NC_004088\|PILER-CR	1902360-1902388	29	NC_021534	Vibrio phage pYD38-A genomic sequence	3299-3327	7	0.759
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NC_021534	Vibrio phage pYD38-A genomic sequence	3299-3329	7	0.774
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	JF974294	Aeromonas phage pIS4-A genomic sequence	21966-21996	7	0.774
NC_004088_3	3.8\|1902478\|31\|NC_004088\|CRT	1902478-1902508	31	CP049262	Cronobacter sakazakii strain CS-09 plasmid pCsaCS09b, complete sequence	69637-69667	7	0.774
NC_004088_4	4.2\|2875809\|32\|NC_004088\|CRISPRCasFinder,CRT	2875809-2875840	32	MH616963	CrAssphage sp. isolate ctbg_1, complete genome	86942-86973	7	0.781
NC_004088_4	4.4\|2875813\|28\|NC_004088\|PILER-CR	2875813-2875840	28	MK415408	CrAssphage GF1-2_000079F, complete genome	71106-71133	7	0.75
NC_004088_3	3.3\|1902478\|30\|NC_004088\|CRISPRCasFinder	1902478-1902507	30	NZ_CP041669	Legionella israelensis strain L18-01051 plasmid unnamed, complete sequence	43412-43441	8	0.733
NC_004088_3	3.5\|1902420\|29\|NC_004088\|PILER-CR	1902420-1902448	29	AP014500	Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S32-C79, * SEQUENCING IN PROGRESS *, 2 ordered pieces	26489-26517	8	0.724
NC_004088_3	3.7\|1902418\|31\|NC_004088\|CRT	1902418-1902448	31	NZ_CP031943	Nostoc sphaeroides strain Kutzing En plasmid p2, complete sequence	4007-4037	8	0.742
NC_004088_4	4.2\|2875809\|32\|NC_004088\|CRISPRCasFinder,CRT	2875809-2875840	32	NZ_CP010358	Acinetobacter johnsonii XBB1 plasmid pXBB1-8, complete sequence	46720-46751	8	0.75
NC_004088_4	4.2\|2875809\|32\|NC_004088\|CRISPRCasFinder,CRT	2875809-2875840	32	NC_019694	Oscillatoria acuminata PCC 6304 plasmid pOSCIL6304.02, complete sequence	20911-20942	8	0.75
NC_004088_2	2.3\|1291630\|33\|NC_004088\|PILER-CR,CRISPRCasFinder,CRT	1291630-1291662	33	NZ_CP040366	Bacillus flexus isolate 1-2-1 plasmid punnamed3, complete sequence	923-955	9	0.727
NC_004088_3	3.2\|1902418\|30\|NC_004088\|CRISPRCasFinder	1902418-1902447	30	AP014500	Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S32-C79, * SEQUENCING IN PROGRESS *, 2 ordered pieces	26487-26516	9	0.7
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	MF679145	Escherichia coli plasmid pBJ114-96, complete sequence	37586-37616	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_KP453775	Klebsiella pneumoniae strain ST11 plasmid pKP12226, complete sequence	60831-60861	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP021340	Escherichia coli strain 95NR1 plasmid p95NR1A, complete sequence	67671-67701	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP021336	Escherichia coli strain 95JB1 plasmid p95JB1A, complete sequence	67672-67702	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP024832	Escherichia coli strain CREC-532 plasmid pCREC-532_2, complete sequence	33830-33860	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP024817	Escherichia coli strain CREC-629 plasmid pCREC-629_2, complete sequence	62769-62799	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP029117	Escherichia coli strain AR435 plasmid unnamed4	15616-15646	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP029117	Escherichia coli strain AR435 plasmid unnamed4	112580-112610	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP023961	Escherichia coli strain FDAARGOS_448 plasmid unnamed2, complete sequence	16858-16888	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	AP023233	Escherichia coli YJ4 plasmid pYJ4-b DNA, complete genome	47570-47600	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP019075	Escherichia coli strain CRE1493 plasmid p1493-4, complete sequence	16520-16550	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP015837	Escherichia coli strain MS6198 plasmid pMS6198C, complete sequence	3287-3317	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP011063	Escherichia coli str. Sanji plasmid pSJ_98, complete sequence	37637-37667	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	NZ_CP040920	Escherichia coli strain FC853_EC plasmid p853EC1, complete sequence	33436-33466	9	0.71
NC_004088_3	3.6\|1902358\|31\|NC_004088\|CRT	1902358-1902388	31	AP023222	Escherichia coli M505 plasmid pM505-b DNA, complete genome	93735-93765	9	0.71
NC_004088_4	4.2\|2875809\|32\|NC_004088\|CRISPRCasFinder,CRT	2875809-2875840	32	MT774386	CrAssphage cr110_1, complete genome	42858-42889	9	0.719
NC_004088_4	4.2\|2875809\|32\|NC_004088\|CRISPRCasFinder,CRT	2875809-2875840	32	NZ_CP028934	Campylobacter jejuni strain FORC_083 plasmid pFORC_083_2, complete sequence	25849-25880	9	0.719

1. spacer 2.4|1291691|32|NC_004088|CRISPRCasFinder,CRT matches to MT374852 (Yersinia phage vB_YpM_3, complete genome) position: , mismatch: 0, identity: 1.0

agactgatgcaagatggcggtatgcgtacaga	CRISPR spacer
agactgatgcaagatggcggtatgcgtacaga	Protospacer
********************************

2. spacer 3.3|1902478|30|NC_004088|CRISPRCasFinder matches to NZ_CP054046 (Yersinia massiliensis strain 2011N-4075 plasmid unnamed1, complete sequence) position: , mismatch: 3, identity: 0.9

tcatgaaagacattgttcgccagtcccctg	CRISPR spacer
tcatgaaagacattgtgcgccagtcacccg	Protospacer
**************** ******** **.*

3. spacer 4.4|2875813|28|NC_004088|PILER-CR matches to MH616963 (CrAssphage sp. isolate ctbg_1, complete genome) position: , mismatch: 5, identity: 0.821

aagttctttttgtcagcatctttaataa	CRISPR spacer
ataatctttttatcagcatcttttataa	Protospacer
* . *******.*********** ****

4. spacer 4.4|2875813|28|NC_004088|PILER-CR matches to MT774386 (CrAssphage cr110_1, complete genome) position: , mismatch: 5, identity: 0.821

aagttctttttgtcagcatctttaataa	CRISPR spacer
agtttctttttatcagcatcttcaatag	Protospacer
*. ********.**********.****.

5. spacer 3.3|1902478|30|NC_004088|CRISPRCasFinder matches to CP049262 (Cronobacter sakazakii strain CS-09 plasmid pCsaCS09b, complete sequence) position: , mismatch: 6, identity: 0.8

tcatgaaagacattgttcgccagtcccctg	CRISPR spacer
tcatgaaagagattgttcgccagcgcgacg	Protospacer
********** ************. *  .*

6. spacer 4.4|2875813|28|NC_004088|PILER-CR matches to NZ_CP028934 (Campylobacter jejuni strain FORC_083 plasmid pFORC_083_2, complete sequence) position: , mismatch: 6, identity: 0.786

aagttctttttgtcagcatctttaataa	CRISPR spacer
actttctttttgtcagcgtctgtaatgt	Protospacer
*  **************.*** ****.

7. spacer 3.1|1902358|30|NC_004088|CRISPRCasFinder matches to NZ_CP013487 (Vibrio alginolyticus strain ATCC 33787 plasmid pMBL287, complete sequence) position: , mismatch: 7, identity: 0.767

tctgcgccaaagaaaatgccattcagataa	CRISPR spacer
tctgtgccaaagaaaatgccactgaacaag	Protospacer
****.****************.* *.  *.

8. spacer 3.2|1902418|30|NC_004088|CRISPRCasFinder matches to NZ_CP031943 (Nostoc sphaeroides strain Kutzing En plasmid p2, complete sequence) position: , mismatch: 7, identity: 0.767

actactagaagcttgcccatcttacctttt	CRISPR spacer
accactaaaagcttgcccatctttctcata	Protospacer
**.****.*************** *.. *

9. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to MF679145 (Escherichia coli plasmid pBJ114-96, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

10. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_KP453775 (Klebsiella pneumoniae strain ST11 plasmid pKP12226, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

11. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP021340 (Escherichia coli strain 95NR1 plasmid p95NR1A, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

12. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP021336 (Escherichia coli strain 95JB1 plasmid p95JB1A, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

13. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP040920 (Escherichia coli strain FC853_EC plasmid p853EC1, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

14. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP024832 (Escherichia coli strain CREC-532 plasmid pCREC-532_2, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

15. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP024817 (Escherichia coli strain CREC-629 plasmid pCREC-629_2, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

16. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP029117 (Escherichia coli strain AR435 plasmid unnamed4) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

17. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP029117 (Escherichia coli strain AR435 plasmid unnamed4) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

18. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP023961 (Escherichia coli strain FDAARGOS_448 plasmid unnamed2, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

19. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to AP023222 (Escherichia coli M505 plasmid pM505-b DNA, complete genome) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

20. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to AP023233 (Escherichia coli YJ4 plasmid pYJ4-b DNA, complete genome) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

21. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP019075 (Escherichia coli strain CRE1493 plasmid p1493-4, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

22. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP015837 (Escherichia coli strain MS6198 plasmid pMS6198C, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

23. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NZ_CP011063 (Escherichia coli str. Sanji plasmid pSJ_98, complete sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
acagttaaagaaactgccaatcagataat	Protospacer
   *..******* ***** *********

24. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to JF974294 (Aeromonas phage pIS4-A genomic sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
aggcataaagcaaatgccattcaggtaat	Protospacer
 *   .**** *************.****

25. spacer 3.4|1902360|29|NC_004088|PILER-CR matches to NC_021534 (Vibrio phage pYD38-A genomic sequence) position: , mismatch: 7, identity: 0.759

tgcgccaaagaaaatgccattcagataat	CRISPR spacer
aggcataaagcaaatgccattcaggtaat	Protospacer
 *   .**** *************.****

26. spacer 3.6|1902358|31|NC_004088|CRT matches to NC_021534 (Vibrio phage pYD38-A genomic sequence) position: , mismatch: 7, identity: 0.774

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
tcaggcataaagcaaatgccattcaggtaat	Protospacer
** *   .**** *************.****

27. spacer 3.6|1902358|31|NC_004088|CRT matches to JF974294 (Aeromonas phage pIS4-A genomic sequence) position: , mismatch: 7, identity: 0.774

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
tcaggcataaagcaaatgccattcaggtaat	Protospacer
** *   .**** *************.****

28. spacer 3.8|1902478|31|NC_004088|CRT matches to CP049262 (Cronobacter sakazakii strain CS-09 plasmid pCsaCS09b, complete sequence) position: , mismatch: 7, identity: 0.774

tcatgaaagacattgttcgccagtcccctga	CRISPR spacer
tcatgaaagagattgttcgccagcgcgacgt	Protospacer
********** ************. *  .*

29. spacer 4.2|2875809|32|NC_004088|CRISPRCasFinder,CRT matches to MH616963 (CrAssphage sp. isolate ctbg_1, complete genome) position: , mismatch: 7, identity: 0.781

ttaagttctttttgtcagcatctttaataaat	CRISPR spacer
taataatctttttatcagcatcttttataatt	Protospacer
* * . *******.*********** **** *

30. spacer 4.4|2875813|28|NC_004088|PILER-CR matches to MK415408 (CrAssphage GF1-2_000079F, complete genome) position: , mismatch: 7, identity: 0.75

aagttctttttgtcagcatctttaataa	CRISPR spacer
ataagacttttatcagcatctttaataa	Protospacer
* .   .****.****************

31. spacer 3.3|1902478|30|NC_004088|CRISPRCasFinder matches to NZ_CP041669 (Legionella israelensis strain L18-01051 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.733

tcatgaaagacattgttcgccagtcccctg	CRISPR spacer
tcatgaaagacattgttcgacaaaaaacac	Protospacer
******************* **.    *

32. spacer 3.5|1902420|29|NC_004088|PILER-CR matches to AP014500 (Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S32-C79, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces) position: , mismatch: 8, identity: 0.724

tactagaagcttgcccatcttaccttttc	CRISPR spacer
tactagaagcttgcacatcttctacaacc	Protospacer
************** ****** . .  .*

33. spacer 3.7|1902418|31|NC_004088|CRT matches to NZ_CP031943 (Nostoc sphaeroides strain Kutzing En plasmid p2, complete sequence) position: , mismatch: 8, identity: 0.742

actactagaagcttgcccatcttaccttttc	CRISPR spacer
accactaaaagcttgcccatctttctcataa	Protospacer
**.****.*************** *.. *

34. spacer 4.2|2875809|32|NC_004088|CRISPRCasFinder,CRT matches to NZ_CP010358 (Acinetobacter johnsonii XBB1 plasmid pXBB1-8, complete sequence) position: , mismatch: 8, identity: 0.75

ttaagttctttttgtcagcatctttaataaat	CRISPR spacer
gtgccatattttcgtcagcatcattaataaat	Protospacer
 *.   * ****.********* *********

35. spacer 4.2|2875809|32|NC_004088|CRISPRCasFinder,CRT matches to NC_019694 (Oscillatoria acuminata PCC 6304 plasmid pOSCIL6304.02, complete sequence) position: , mismatch: 8, identity: 0.75

ttaagttctttttgtcagcatctttaataaat	CRISPR spacer
ttgatgctcttttggcagcttctttaataaat	Protospacer
**.*  ...***** **** ************

36. spacer 2.3|1291630|33|NC_004088|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP040366 (Bacillus flexus isolate 1-2-1 plasmid punnamed3, complete sequence) position: , mismatch: 9, identity: 0.727

ccgaaatcatcagatgtaattaagatttttgct	CRISPR spacer
aatggattatcagatgtaattaagtttttttcc	Protospacer
   ..**.**************** ***** *.

37. spacer 3.2|1902418|30|NC_004088|CRISPRCasFinder matches to AP014500 (Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S32-C79, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces) position: , mismatch: 9, identity: 0.7

actactagaagcttgcccatcttacctttt	CRISPR spacer
attactagaagcttgcacatcttctacaac	Protospacer
*.************** ****** . .  .

38. spacer 3.6|1902358|31|NC_004088|CRT matches to MF679145 (Escherichia coli plasmid pBJ114-96, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

39. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_KP453775 (Klebsiella pneumoniae strain ST11 plasmid pKP12226, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

40. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP021340 (Escherichia coli strain 95NR1 plasmid p95NR1A, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

41. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP021336 (Escherichia coli strain 95JB1 plasmid p95JB1A, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

42. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP024832 (Escherichia coli strain CREC-532 plasmid pCREC-532_2, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

43. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP024817 (Escherichia coli strain CREC-629 plasmid pCREC-629_2, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

44. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP029117 (Escherichia coli strain AR435 plasmid unnamed4) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

45. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP029117 (Escherichia coli strain AR435 plasmid unnamed4) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

46. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP023961 (Escherichia coli strain FDAARGOS_448 plasmid unnamed2, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

47. spacer 3.6|1902358|31|NC_004088|CRT matches to AP023233 (Escherichia coli YJ4 plasmid pYJ4-b DNA, complete genome) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

48. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP019075 (Escherichia coli strain CRE1493 plasmid p1493-4, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

49. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP015837 (Escherichia coli strain MS6198 plasmid pMS6198C, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

50. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP011063 (Escherichia coli str. Sanji plasmid pSJ_98, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

51. spacer 3.6|1902358|31|NC_004088|CRT matches to NZ_CP040920 (Escherichia coli strain FC853_EC plasmid p853EC1, complete sequence) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

52. spacer 3.6|1902358|31|NC_004088|CRT matches to AP023222 (Escherichia coli M505 plasmid pM505-b DNA, complete genome) position: , mismatch: 9, identity: 0.71

tctgcgccaaagaaaatgccattcagataat	CRISPR spacer
aaacagttaaagaaactgccaatcagataat	Protospacer
     *..******* ***** *********

53. spacer 4.2|2875809|32|NC_004088|CRISPRCasFinder,CRT matches to MT774386 (CrAssphage cr110_1, complete genome) position: , mismatch: 9, identity: 0.719

ttaagttctttttgtcagcatctttaataaat	CRISPR spacer
caagtttctttttatcagcatcttcaatagca	Protospacer
. *. ********.**********.****.

54. spacer 4.2|2875809|32|NC_004088|CRISPRCasFinder,CRT matches to NZ_CP028934 (Campylobacter jejuni strain FORC_083 plasmid pFORC_083_2, complete sequence) position: , mismatch: 9, identity: 0.719

ttaagttctttttgtcagcatctttaataaat	CRISPR spacer
taactttctttttgtcagcgtctgtaatgtgc	Protospacer
* *  **************.*** ****. ..

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

143870 : 197973

uncultured_Mediterranean_phage(18.18%)

transposase,protease,holin,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002216203.1\|143870_144386_-\|protease	ClpXP protease specificity-enhancing factor	A0A1S5R3H3	Pseudomonas_phage	3.6e-28	55.6
WP_002210135.1\|144391_145033_-	stringent starvation protein A	NA	NA	NA	NA
WP_002230558.1\|145212_145410_+	hypothetical protein	NA	NA	NA	NA
WP_002210133.1\|145406_145799_-	30S ribosomal protein S9	NA	NA	NA	NA
WP_002210132.1\|145813_146242_-	50S ribosomal protein L13	NA	NA	NA	NA
WP_002210131.1\|146555_147683_-	cell division protein ZapE	NA	NA	NA	NA
WP_002210130.1\|147906_148311_+	DUF1043 family protein	NA	NA	NA	NA
WP_002218066.1\|148581_149955_+\|protease	serine endoprotease DegQ	A0A1B1IT49	uncultured_Mediterranean_phage	7.4e-20	28.2
WP_002213775.1\|150071_150530_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002210128.1\|150755_151844_+	outer membrane-stress sensor serine endopeptidase DegS	A0A1B1IRD3	uncultured_Mediterranean_phage	2.1e-09	31.8
WP_002210127.1\|152024_153287_-	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	NA	NA	NA	NA
WP_002210126.1\|153440_153695_-	BolA family iron metabolism protein IbaG	NA	NA	NA	NA
WP_002210125.1\|153841_154144_-	lipid asymmetry maintenance protein MlaB	NA	NA	NA	NA
WP_002210124.1\|154179_154803_-	phospholipid-binding protein MlaC	NA	NA	NA	NA
WP_002210123.1\|154815_155373_-	outer membrane lipid asymmetry maintenance protein MlaD	NA	NA	NA	NA
WP_002210122.1\|155377_156160_-	lipid asymmetry maintenance ABC transporter permease subunit MlaE	NA	NA	NA	NA
WP_002210121.1\|156377_157196_-	phospholipid ABC transporter ATP-binding protein MlaF	G3M9Y6	Bacillus_virus	2.2e-19	31.7
WP_002210120.1\|157460_158435_+	calcium/sodium antiporter	NA	NA	NA	NA
WP_002210119.1\|158545_159532_+	arabinose-5-phosphate isomerase KdsD	A0A2P0VNK5	Tetraselmis_virus	6.0e-40	30.8
WP_002228203.1\|159780_160344_+	3-deoxy-manno-octulosonate-8-phosphatase KdsC	A0A140XBD6	Dickeya_phage	9.6e-59	83.0
WP_002218352.1\|160340_160904_+	LPS export ABC transporter periplasmic protein LptC	NA	NA	NA	NA
WP_002210117.1\|160887_161433_+	lipopolysaccharide ABC transporter substrate-binding protein LptA	NA	NA	NA	NA
WP_002210116.1\|161439_162165_+	LPS export ABC transporter ATP-binding protein	A0A2H4PQG7	Staphylococcus_phage	1.4e-22	28.4
WP_002210115.1\|162226_163660_+	RNA polymerase factor sigma-54	NA	NA	NA	NA
WP_002213952.1\|164088_164571_+	PTS IIA-like nitrogen regulatory protein PtsN	NA	NA	NA	NA
WP_002210113.1\|164876_165731_+	RNase adapter RapZ	A0A0R8VB27	Thermobifida_phage	3.2e-05	30.0
WP_002210112.1\|165727_166000_+	PTS phosphocarrier protein NPr	NA	NA	NA	NA
WP_002210111.1\|166337_167273_+	aspartate carbamoyltransferase	M1HWF9	Paramecium_bursaria_Chlorella_virus	1.5e-48	38.5
WP_002210110.1\|167284_167749_+	aspartate carbamoyltransferase regulatory subunit	NA	NA	NA	NA
WP_002210109.1\|167886_168273_+	2-iminobutanoate/2-iminopropanoate deaminase	NA	NA	NA	NA
WP_002210107.1\|168571_169048_+	PliI family lysozyme inhibitor of I-type lysozyme	NA	NA	NA	NA
WP_002210106.1\|169281_170235_+	HTH-type transcriptional regulator TreR	NA	NA	NA	NA
WP_002215779.1\|170645_172061_+	PTS trehalose transporter subunit IIBC	NA	NA	NA	NA
WP_002210104.1\|172155_173823_+	alpha,alpha-phosphotrehalase	NA	NA	NA	NA
WP_002210103.1\|174175_174586_+	nucleoside diphosphate kinase regulator	NA	NA	NA	NA
WP_002210102.1\|174817_175204_-	cytochrome b562	NA	NA	NA	NA
WP_011055205.1\|175411_176056_-	hypothetical protein	A0A1B0VBK8	Salmonella_phage	3.4e-52	49.0
WP_002210100.1\|176304_177645_-\|protease	metalloprotease PmbA	NA	NA	NA	NA
WP_002210099.1\|177825_178374_+	ribosome-associated protein	NA	NA	NA	NA
WP_002210098.1\|178485_178767_-	ribonuclease inhibitor	NA	NA	NA	NA
WP_002214288.1\|178771_179245_-	ribonuclease Ba	NA	NA	NA	NA
WP_002210095.1\|181174_183130_-	p-hydroxybenzoic acid efflux pump subunit AaeB	NA	NA	NA	NA
WP_002210094.1\|183131_184067_-	p-hydroxybenzoic acid efflux pump subunit AaeA	NA	NA	NA	NA
WP_002210093.1\|184074_184278_-	AaeX family protein	NA	NA	NA	NA
WP_002210092.1\|184580_185492_+	HTH-type transcriptional activator AaeR	NA	NA	NA	NA
WP_002214297.1\|185752_186619_+	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002210090.1\|186854_189356_+	toxin	NA	NA	NA	NA
WP_002220204.1\|189396_192990_+\|tail	phage tail tape measure protein	NA	NA	NA	NA
WP_002210089.1\|193046_197537_+	toxin	NA	NA	NA	NA
WP_002214300.1\|197670_197973_+\|holin	phage holin family protein	NA	NA	NA	NA

DBSCAN-SWA_2

507057 : 574426

Escherichia_phage(35.29%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_000255944.1\|507057_508080_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|508079_508859_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002211540.1\|508897_509233_+	TatD family hydrolase	NA	NA	NA	NA
WP_002211541.1\|509247_510270_+	porphobilinogen synthase	NA	NA	NA	NA
WP_002211542.1\|510379_510868_-	transcription/translation regulatory transformer protein RfaH	NA	NA	NA	NA
WP_002215917.1\|511115_512612_+	4-hydroxy-3-polyprenylbenzoate decarboxylase	NA	NA	NA	NA
WP_002215918.1\|512666_513368_+	NAD(P)H-flavin reductase	NA	NA	NA	NA
WP_002211545.1\|513527_514691_-	acetyl-CoA C-acyltransferase FadA	NA	NA	NA	NA
WP_002211546.1\|514702_516892_-	fatty acid oxidation complex subunit alpha FadB	NA	NA	NA	NA
WP_002211547.1\|517218_518550_+	Xaa-Pro dipeptidase	NA	NA	NA	NA
WP_002211548.1\|518549_518759_+	YigZ family protein	NA	NA	NA	NA
WP_002213759.1\|518863_519322_+\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002211550.1\|519910_521362_+	Trk system potassium transporter TrkH	NA	NA	NA	NA
WP_002215920.1\|521383_521917_+	menaquinone-dependent protoporphyrinogen IX dehydrogenase	NA	NA	NA	NA
WP_002212288.1\|528053_529091_+	UDP-N-acetylmuramate dehydrogenase	NA	NA	NA	NA
WP_002212289.1\|529087_530047_+	bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA	NA	NA	NA	NA
WP_002212290.1\|530081_531032_-	type I pantothenate kinase	A0A1B1ISL9	uncultured_Mediterranean_phage	8.7e-28	31.2
WP_002355327.1\|531242_531701_-	GNAT family N-acetyltransferase	NA	NA	NA	NA
WP_000255944.1\|531883_532906_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|532905_533685_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002210669.1\|534741_535926_+	elongation factor Tu	A0A2K9L516	Tupanvirus	2.0e-13	26.9
WP_002210670.1\|536176_536560_+	preprotein translocase subunit SecE	NA	NA	NA	NA
WP_002210671.1\|536561_537107_+	transcription termination/antitermination protein NusG	A0A291AUS6	Sinorhizobium_phage	5.9e-13	28.3
WP_002210672.1\|537297_537726_+	50S ribosomal protein L11	NA	NA	NA	NA
WP_002210673.1\|537729_538434_+	50S ribosomal protein L1	NA	NA	NA	NA
WP_002210674.1\|538798_539296_+	50S ribosomal protein L10	NA	NA	NA	NA
WP_002210675.1\|539362_539731_+	50S ribosomal protein L7/L12	NA	NA	NA	NA
WP_002210676.1\|540073_544102_+	DNA-directed RNA polymerase subunit beta	A0A0N9R0J7	Chrysochromulina_ericina_virus	1.2e-22	29.0
WP_002210677.1\|544230_548451_+	DNA-directed RNA polymerase subunit beta'	A0A2I7QNZ7	Vibrio_phage	8.5e-67	27.0
WP_002213759.1\|548577_549036_-\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002210678.1\|549467_550598_-	2-iminoacetate synthase ThiH	NA	NA	NA	NA
WP_002228257.1\|550590_551406_-	thiazole synthase	NA	NA	NA	NA
WP_002217275.1\|551407_551623_-	sulfur carrier protein ThiS	NA	NA	NA	NA
WP_002210680.1\|551619_552417_-	HesA/MoeB/ThiF family protein	A0A1V0SAV8	Catovirus	1.6e-11	27.8
WP_002210681.1\|552406_553081_-	thiamine phosphate synthase	NA	NA	NA	NA
WP_002210682.1\|553067_555113_-	phosphomethylpyrimidine synthase ThiC	NA	NA	NA	NA
WP_002210683.1\|555488_555998_-	sigma D regulator	NA	NA	NA	NA
WP_002210684.1\|556094_556877_+	NAD(+) diphosphatase	NA	NA	NA	NA
WP_002210685.1\|556969_557755_+	hypothetical protein	NA	NA	NA	NA
WP_002210686.1\|557873_558941_+	uroporphyrinogen decarboxylase	NA	NA	NA	NA
WP_002210687.1\|558970_559711_+	deoxyribonuclease V	NA	NA	NA	NA
WP_002210688.1\|559756_560347_+	YjaG family protein	NA	NA	NA	NA
WP_002210689.1\|560535_560811_+	DNA-binding protein HU-alpha	A7KV42	Bacillus_phage	3.6e-19	55.6
WP_002355296.1\|560860_561514_+	DUF1481 domain-containing protein	NA	NA	NA	NA
WP_002210691.1\|561661_562948_-	phosphoribosylamine--glycine ligase	NA	NA	NA	NA
WP_002210692.1\|563007_564597_-	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	Q58MG4	Prochlorococcus_phage	2.2e-68	49.4
WP_086016626.1\|570860_571959_+\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	2.2e-46	39.2
WP_001297096.1\|572624_573404_-	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_000255944.1\|573403_574426_-\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0

DBSCAN-SWA_3

1229316 : 1284071

uncultured_virus(16.67%)

transposase,protease,tRNA,integrase

attL 1224654:1224672|attR 1300649:1300667

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1224654:1224672	attL	NA	NA	NA	NA
WP_002208581.1\|1229316_1229796_-\|tRNA	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK	NA	NA	NA	NA
WP_002208580.1\|1230059_1230869_-	TraB/GumN family protein	NA	NA	NA	NA
WP_002223301.1\|1231389_1234275_-	copper-exporting P-type ATPase CopA	A0A218MNH6	uncultured_virus	1.0e-111	36.8
WP_002208578.1\|1234481_1234901_+	Cu(I)-responsive transcriptional regulator	NA	NA	NA	NA
WP_002208577.1\|1235009_1235459_-	NfeD family protein	NA	NA	NA	NA
WP_002208576.1\|1235461_1236376_-	SPFH/Band 7/PHB domain protein	NA	NA	NA	NA
WP_002208575.1\|1236570_1237440_-	co-chaperone YbbN	NA	NA	NA	NA
WP_002208574.1\|1237516_1238293_-	SDR family oxidoreductase	NA	NA	NA	NA
WP_002208573.1\|1238679_1239315_-\|protease	multifunctional acyl-CoA thioesterase I/protease I/lysophospholipase L1	NA	NA	NA	NA
WP_002208572.1\|1239285_1239972_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	1.6e-31	34.2
WP_002208571.1\|1239968_1242398_+	ABC transporter permease	NA	NA	NA	NA
WP_002208570.1\|1242441_1243506_-	5-(carboxyamino)imidazole ribonucleotide synthase	NA	NA	NA	NA
WP_002208569.1\|1243502_1244027_-	5-(carboxyamino)imidazole ribonucleotide mutase	NA	NA	NA	NA
WP_002208568.1\|1244322_1245045_-	UDP-2,3-diacylglucosamine diphosphatase	NA	NA	NA	NA
WP_002208567.1\|1245055_1245550_-	peptidylprolyl isomerase B	NA	NA	NA	NA
WP_002222677.1\|1245760_1247146_+\|tRNA	cysteine--tRNA ligase	A0A0G2Y344	Acanthamoeba_polyphaga_mimivirus	2.2e-40	28.5
WP_002213775.1\|1247492_1247951_+\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002209775.1\|1248097_1248310_-	ribosome-associated protein YbcJ	NA	NA	NA	NA
WP_002209774.1\|1248324_1249191_-	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD	A0A249XZQ2	Enterococcus_phage	2.2e-30	34.1
WP_002215270.1\|1249545_1249728_-	AlpA family phage regulatory protein	NA	NA	NA	NA
WP_002215268.1\|1249986_1250187_-	hypothetical protein	NA	NA	NA	NA
WP_002228356.1\|1250300_1250798_-	hypothetical protein	NA	NA	NA	NA
WP_002215266.1\|1250933_1251272_-	hypothetical protein	NA	NA	NA	NA
WP_079866998.1\|1251354_1251633_-\|integrase	tyrosine-type recombinase/integrase	A0A192Y6Q1	Salmonella_phage	4.2e-31	73.5
WP_002354559.1\|1251844_1252051_+	hypothetical protein	NA	NA	NA	NA
WP_002209770.1\|1252450_1253053_+	CDP-alcohol phosphatidyltransferase family protein	NA	NA	NA	NA
WP_002209769.1\|1253045_1253975_+	phosphatidate cytidylyltransferase	NA	NA	NA	NA
WP_002209768.1\|1253984_1254617_+	1-acyl-sn-glycerol-3-phosphate acyltransferase	NA	NA	NA	NA
WP_002209767.1\|1254613_1256377_+	bifunctional alpha/beta hydrolase/class I SAM-dependent methyltransferase	NA	NA	NA	NA
WP_002209766.1\|1256369_1257689_+	phosphatase PAP2/dual specificity phosphatase family protein	NA	NA	NA	NA
WP_002209765.1\|1257670_1258072_+	hypothetical protein	NA	NA	NA	NA
WP_002215253.1\|1258168_1258474_+	hypothetical protein	NA	NA	NA	NA
WP_001297096.1\|1258840_1259620_-	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_000255944.1\|1259619_1260642_-\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_002209764.1\|1260735_1261629_+	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002209763.1\|1261683_1262673_-	aldo/keto reductase	NA	NA	NA	NA
WP_002209762.1\|1262698_1263550_-	aldo/keto reductase	A0A2H4PQR8	Staphylococcus_phage	1.2e-49	41.1
WP_002209759.1\|1264022_1265651_+	hypothetical protein	NA	NA	NA	NA
WP_002209758.1\|1265729_1268111_-	glycoside hydrolase family 3 C-terminal domain-containing protein	NA	NA	NA	NA
WP_002209757.1\|1268269_1268800_-	GDYXXLXY domain-containing protein	NA	NA	NA	NA
WP_002209756.1\|1268792_1271000_-	DUF4401 domain-containing protein	NA	NA	NA	NA
WP_002209743.1\|1271451_1272660_+\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002209753.1\|1273061_1273643_-	AbiEi antitoxin N-terminal domain-containing protein	NA	NA	NA	NA
WP_002224869.1\|1273931_1274054_-	hypothetical protein	NA	NA	NA	NA
WP_002209752.1\|1274177_1276094_-	autotransporter adhesin YapC	NA	NA	NA	NA
WP_002209751.1\|1276902_1277142_+	hypothetical protein	NA	NA	NA	NA
WP_002227852.1\|1277180_1277432_+	hypothetical protein	NA	NA	NA	NA
WP_002209749.1\|1277455_1278028_+	Hcp family type VI secretion system effector	NA	NA	NA	NA
WP_002209748.1\|1278039_1278441_-	DUF1240 domain-containing protein	NA	NA	NA	NA
WP_002209746.1\|1278673_1279075_-	DUF1240 domain-containing protein	NA	NA	NA	NA
WP_002209745.1\|1280596_1280842_+	helix-turn-helix domain-containing protein	A0A2I7S995	Vibrio_phage	7.2e-19	64.2
WP_138921619.1\|1281054_1283367_-	penicillin-binding protein 1C	NA	NA	NA	NA
WP_002213775.1\|1283612_1284071_+\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
1300649:1300667	attR	NA	NA	NA	NA

DBSCAN-SWA_4

1648080 : 1717076

Escherichia_phage(33.33%)

transposase,plate,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002213759.1\|1648080_1648539_+\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002208491.1\|1648681_1649191_-	PTS glucose transporter subunit IIA	NA	NA	NA	NA
WP_002208490.1\|1649239_1650967_-	phosphoenolpyruvate-protein phosphotransferase PtsI	A0A1V0SGR7	Hokovirus	3.0e-18	33.3
WP_002208488.1\|1651015_1651273_-	phosphocarrier protein Hpr	NA	NA	NA	NA
WP_002222180.1\|1651771_1652740_-	cysteine synthase A	A0A1X9I5F1	Streptococcus_phage	4.8e-74	51.8
WP_002213487.1\|1652896_1653631_-	sulfate transporter CysZ	NA	NA	NA	NA
WP_002227089.1\|1653879_1654866_+	cell division protein ZipA	NA	NA	NA	NA
WP_002213368.1\|1654956_1656969_+	NAD-dependent DNA ligase LigA	A0A0K2QQN8	Ralstonia_phage	1.7e-142	42.2
WP_002213369.1\|1656988_1657204_+	DUF3820 family protein	NA	NA	NA	NA
WP_002213372.1\|1657304_1657652_-	FlxA-like family protein	NA	NA	NA	NA
WP_002213374.1\|1657783_1658389_-	nucleotidyltransferase family protein	NA	NA	NA	NA
WP_002213775.1\|1659102_1659561_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002222185.1\|1659753_1661169_-\|tRNA	glutamate--tRNA ligase	NA	NA	NA	NA
WP_002211622.1\|1662402_1663587_-	NupC/NupG family nucleoside CNT transporter	NA	NA	NA	NA
WP_002211621.1\|1664037_1665267_+	Nramp family divalent metal transporter	NA	NA	NA	NA
WP_002216909.1\|1665359_1665773_-	DUF2502 domain-containing protein	NA	NA	NA	NA
WP_002232425.1\|1665943_1666933_-	aldo/keto reductase	NA	NA	NA	NA
WP_002211617.1\|1667068_1667947_-	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002211616.1\|1668049_1668526_+	multidrug/biocide efflux PACE transporter	NA	NA	NA	NA
WP_002211615.1\|1668706_1669678_+	glucokinase	NA	NA	NA	NA
WP_002211614.1\|1669755_1671003_-	DUF1479 domain-containing protein	NA	NA	NA	NA
WP_002211613.1\|1671268_1672504_+	alanine transaminase	NA	NA	NA	NA
WP_002211611.1\|1672767_1673292_+	cytochrome b	A0A0U2QLA7	Escherichia_phage	9.3e-24	47.1
WP_002211610.1\|1673386_1673818_-	hypothetical protein	Q7Y3V7	Yersinia_phage	2.4e-25	48.2
WP_002215847.1\|1674407_1675079_+	lipoprotein	NA	NA	NA	NA
WP_002215846.1\|1675105_1675462_+	DUF4810 domain-containing protein	NA	NA	NA	NA
WP_002211607.1\|1675458_1676115_+	DUF799 domain-containing protein	NA	NA	NA	NA
WP_002211606.1\|1676360_1676930_-	4Fe-4S binding protein	NA	NA	NA	NA
WP_002228419.1\|1676926_1677523_-	molecular chaperone	A0A077SLS7	Escherichia_phage	9.2e-44	49.2
WP_002211604.1\|1678004_1678781_-	dimethyl sulfoxide reductase anchor subunit family protein	A0A077SK59	Escherichia_phage	3.9e-42	41.4
WP_002211603.1\|1678782_1679400_-	dimethylsulfoxide reductase subunit B	A0A077SL61	Escherichia_phage	1.1e-87	68.3
WP_002228420.1\|1679411_1681838_-	dimethyl sulfoxide reductase subunit A	A0A077SK27	Escherichia_phage	6.9e-255	54.3
WP_002211601.1\|1682668_1683517_+	DUF4225 domain-containing protein	NA	NA	NA	NA
WP_002354621.1\|1683746_1684226_-	Hcp family type VI secretion system effector	NA	NA	NA	NA
WP_002211599.1\|1684692_1685217_+	DUF2127 domain-containing protein	NA	NA	NA	NA
WP_002211598.1\|1685289_1686339_-	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	3.9e-21	32.4
WP_002215840.1\|1686335_1687922_-	iron ABC transporter permease	NA	NA	NA	NA
WP_002211596.1\|1687977_1688997_-	iron ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_002211594.1\|1689325_1690420_+	lytic murein transglycosylase B	NA	NA	NA	NA
WP_002211590.1\|1691685_1692288_+	LuxR family transcriptional regulator	NA	NA	NA	NA
WP_002215321.1\|1692645_1693128_-	DcrB-related protein	NA	NA	NA	NA
WP_002211588.1\|1693124_1694807_-	OmpA family protein	NA	NA	NA	NA
WP_002224806.1\|1694807_1695509_-	hypothetical protein	NA	NA	NA	NA
WP_002211586.1\|1695505_1696843_-	glycosyl transferase	A0A292GJ55	Xanthomonas_phage	2.0e-70	32.8
WP_002215319.1\|1696882_1697914_-	fimbrial protein	NA	NA	NA	NA
WP_002211584.1\|1697920_1699102_-	ImpA family type VI secretion system protein	NA	NA	NA	NA
WP_002211583.1\|1699200_1700226_-\|plate	type VI secretion system baseplate subunit TssG	NA	NA	NA	NA
WP_002211582.1\|1700225_1702106_-\|plate	type VI secretion system baseplate subunit TssF	NA	NA	NA	NA
WP_002215317.1\|1702888_1705564_+	type VI secretion system ATPase TssH	A0A223W0B1	Agrobacterium_phage	1.0e-81	32.3
WP_002211580.1\|1705764_1706310_+	type 1 fimbrial protein	NA	NA	NA	NA
WP_002211579.1\|1706466_1707228_+	fimbria/pilus periplasmic chaperone	NA	NA	NA	NA
WP_002215157.1\|1707355_1708906_+	fimbrial biogenesis outer membrane usher protein	NA	NA	NA	NA
WP_002209743.1\|1708927_1710136_-\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211577.1\|1710160_1711351_+	fimbrial biogenesis outer membrane usher protein	NA	NA	NA	NA
WP_002211576.1\|1711335_1711944_+	type 1 fimbrial protein	NA	NA	NA	NA
WP_002211575.1\|1712048_1712573_+	type VI secretion system contractile sheath small subunit	NA	NA	NA	NA
WP_002211574.1\|1712596_1714099_+	type VI secretion system contractile sheath large subunit	NA	NA	NA	NA
WP_002211573.1\|1714424_1714910_+	type VI secretion system tube protein Hcp	NA	NA	NA	NA
WP_002211572.1\|1715183_1715723_+	type VI secretion system lipoprotein TssJ	NA	NA	NA	NA
WP_002211571.1\|1715726_1717076_+\|plate	type VI secretion system baseplate subunit TssK	NA	NA	NA	NA

DBSCAN-SWA_5

2045058 : 2063010

Escherichia_phage(50.0%)

coat,transposase,protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_000255944.1\|2045058_2046081_-\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_002215943.1\|2046487_2046877_+	ASCH domain-containing protein	NA	NA	NA	NA
WP_002210859.1\|2046986_2047226_-	YebV family protein	NA	NA	NA	NA
WP_002210858.1\|2047433_2048423_-\|coat	spore coat U domain-containing protein	NA	NA	NA	NA
WP_002210857.1\|2048628_2051076_-	fimbrial biogenesis outer membrane usher protein	NA	NA	NA	NA
WP_002210856.1\|2051246_2051999_-	molecular chaperone	NA	NA	NA	NA
WP_002216611.1\|2052029_2052587_-\|coat	spore coat U domain-containing protein	NA	NA	NA	NA
WP_002216613.1\|2052607_2053138_-\|coat	spore coat U domain-containing protein	NA	NA	NA	NA
WP_002210852.1\|2053143_2053698_-\|coat	spore coat U domain-containing protein	NA	NA	NA	NA
WP_002216616.1\|2054176_2056828_-	PqiB family protein	NA	NA	NA	NA
WP_002367629.1\|2056796_2058044_-	membrane integrity lipid transport subunit YebS	NA	NA	NA	NA
WP_002210850.1\|2058275_2058773_+	GAF domain-containing protein	NA	NA	NA	NA
WP_002210849.1\|2058868_2059582_+	RNA chaperone ProQ	NA	NA	NA	NA
WP_002210848.1\|2059601_2061674_+	carboxy terminal-processing peptidase	A0A0R6PIZ1	Moraxella_phage	4.0e-86	34.8
WP_002210847.1\|2062128_2063010_+\|protease	protease HtpX	NA	NA	NA	NA

DBSCAN-SWA_6

2367649 : 2467075

102

Escherichia_phage(15.09%)

holin,tail,integrase,transposase,tRNA,lysis

attL 2415479:2415509|attR 2456493:2456523

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002223594.1\|2367649_2368072_-\|transposase	IS200/IS605 family transposase	A0A1S5RHE3	Helicobacter_phage	5.8e-08	32.5
WP_000255944.1\|2368130_2369153_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|2369152_2369932_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002210659.1\|2370300_2370891_-	thymidine kinase	A0A1Z1LYD5	Serratia_phage	1.5e-54	55.8
WP_002223593.1\|2371640_2372048_+	DNA-binding transcriptional regulator H-NS	NA	NA	NA	NA
WP_002210664.1\|2372482_2373829_-	UDP-glucose/GDP-mannose dehydrogenase family protein	A0A127AXI2	Bacillus_phage	1.9e-81	38.3
WP_002210665.1\|2374135_2375152_-	two-component system response regulator RssB	NA	NA	NA	NA
WP_002210666.1\|2376485_2376950_+	YchJ family protein	NA	NA	NA	NA
WP_002209743.1\|2377867_2379076_-\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211665.1\|2379947_2380808_-	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002211667.1\|2381617_2382424_+	exodeoxyribonuclease III	NA	NA	NA	NA
WP_002211668.1\|2382521_2382908_+	pyrimidine (deoxy)nucleoside triphosphate diphosphatase	NA	NA	NA	NA
WP_002211669.1\|2382920_2383211_-	DUF1496 domain-containing protein	NA	NA	NA	NA
WP_002211670.1\|2383207_2385133_-	DNA topoisomerase III	A0A1X9I6W8	Streptococcus_phage	4.2e-37	30.4
WP_002211671.1\|2385179_2386226_-	selenide, water dikinase SelD	NA	NA	NA	NA
WP_002211673.1\|2386450_2387002_-	NAD(P)H nitroreductase	NA	NA	NA	NA
WP_002211674.1\|2387164_2389015_+	signal peptide peptidase SppA	NA	NA	NA	NA
WP_002211675.1\|2389131_2390148_+	asparaginase	NA	NA	NA	NA
WP_002211676.1\|2390162_2390810_+	bifunctional nicotinamidase/pyrazinamidase	A0A2K9L6K4	Tupanvirus	1.8e-21	33.0
WP_002217933.1\|2390943_2391216_-	YeaC family protein	NA	NA	NA	NA
WP_002211677.1\|2391286_2391700_-	peptide-methionine (R)-S-oxide reductase MsrB	NA	NA	NA	NA
WP_002224141.1\|2392047_2393043_+	glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA
WP_002211679.1\|2393356_2394232_+	D-hexose-6-phosphate mutarotase	NA	NA	NA	NA
WP_002430110.1\|2394304_2395054_-	MipA/OmpV family protein	NA	NA	NA	NA
WP_002211681.1\|2395497_2397432_+	protein kinase YeaG	NA	NA	NA	NA
WP_002216501.1\|2397581_2398856_+	YeaH/YhbH family protein	A0A140HLI1	Bacillus_phage	1.5e-11	37.1
WP_002211683.1\|2398963_2400082_+	DMT family transporter	NA	NA	NA	NA
WP_002211684.1\|2400116_2401022_-	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002211685.1\|2401219_2402089_+	pirin family protein	NA	NA	NA	NA
WP_002216508.1\|2402353_2403556_+	multidrug effflux MFS transporter	S4TR35	Salmonella_phage	7.6e-29	29.1
WP_002211686.1\|2403571_2404876_-	D-amino acid dehydrogenase	NA	NA	NA	NA
WP_002211687.1\|2405341_2406877_+	SpoVR family protein	NA	NA	NA	NA
WP_002211688.1\|2407094_2407814_-	fatty acid metabolism transcriptional regulator FadR	NA	NA	NA	NA
WP_002227934.1\|2409867_2410398_+	disulfide bond formation protein DsbB	NA	NA	NA	NA
WP_002214494.1\|2410814_2411171_-	hypothetical protein	NA	NA	NA	NA
WP_002211692.1\|2412262_2413003_+	hypothetical protein	NA	NA	NA	NA
WP_002211693.1\|2413019_2414219_+	cysteine desulfurase	A0A1X7QGF3	Faustovirus	2.4e-38	29.6
WP_002214492.1\|2414222_2415395_+	MFS transporter	NA	NA	NA	NA
2415479:2415509	attL	NA	NA	NA	NA
WP_002209743.1\|2415699_2416908_+\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211695.1\|2417128_2417548_-\|tail	tail fiber assembly protein	B6SCW7	Bacteriophage	5.7e-08	42.0
WP_002211696.1\|2417558_2418476_-	hypothetical protein	NA	NA	NA	NA
WP_002211697.1\|2418492_2419491_-	hypothetical protein	NA	NA	NA	NA
WP_002211698.1\|2419490_2422694_-	host specificity protein J	F1C571	Cronobacter_phage	0.0e+00	60.5
WP_002359202.1\|2422869_2423091_+	hypothetical protein	NA	NA	NA	NA
WP_002211699.1\|2423059_2423224_-	hypothetical protein	NA	NA	NA	NA
WP_002211700.1\|2423265_2423886_-\|tail	tail assembly protein	K7PGY0	Enterobacteria_phage	3.2e-55	57.0
WP_002211701.1\|2423941_2424157_-	hypothetical protein	NA	NA	NA	NA
WP_002214482.1\|2424299_2424851_-	zinc ribbon domain-containing protein	S4TR42	Salmonella_phage	9.5e-27	58.0
WP_002211704.1\|2424949_2425957_-	Bro-N domain-containing protein	A0A2H4J0P1	uncultured_Caudovirales_phage	4.1e-36	33.0
WP_002211705.1\|2426030_2426198_-	hypothetical protein	G9L6D7	Escherichia_phage	5.2e-13	61.8
WP_002211706.1\|2426321_2426753_+	Arc family DNA-binding protein	G9L6D6	Escherichia_phage	2.5e-30	58.4
WP_002211707.1\|2426831_2427464_-	hypothetical protein	NA	NA	NA	NA
WP_002211708.1\|2427724_2428435_-	C40 family peptidase	K7P6F5	Enterobacteria_phage	1.3e-108	76.8
WP_002211709.1\|2428437_2429190_-\|tail	phage minor tail protein L	A0A1W6JNX9	Morganella_phage	9.4e-102	67.7
WP_002211710.1\|2429363_2429705_-\|tail	phage tail protein	Q6UAW6	Klebsiella_phage	1.7e-21	50.0
WP_002211711.1\|2429707_2433211_-\|tail	phage tail tape measure protein	K7PMB9	Enterobacterial_phage	5.2e-118	33.2
WP_071530527.1\|2433211_2433472_-	DUF1799 domain-containing protein	A0A0S2SY90	Pseudomonas_phage	4.1e-12	48.6
WP_002211712.1\|2433519_2433831_-	hypothetical protein	I6PDG2	Cronobacter_phage	1.4e-30	58.3
WP_002211713.1\|2433843_2434764_-	Ig-like domain-containing protein	I6PBN6	Cronobacter_phage	4.4e-61	49.1
WP_002211714.1\|2434829_2435237_-	DUF4128 domain-containing protein	NA	NA	NA	NA
WP_002211715.1\|2435233_2435818_-	hypothetical protein	G8C7Q1	Escherichia_phage	3.6e-48	52.1
WP_002211716.1\|2435819_2436170_-	hypothetical protein	I6PD77	Cronobacter_phage	6.9e-31	56.0
WP_002211717.1\|2436171_2436426_-	hypothetical protein	J9Q7U0	Salmonella_phage	2.2e-18	53.1
WP_002211718.1\|2436422_2436905_-	hypothetical protein	G8C7P9	Escherichia_phage	6.4e-27	46.1
WP_002211719.1\|2436952_2438158_-	Ig-like domain-containing protein	A0A1B0VMF8	Pseudomonas_phage	1.8e-142	79.2
WP_002211720.1\|2438171_2438945_-	hypothetical protein	A0A1B0VMG1	Pseudomonas_phage	2.8e-69	62.3
WP_002211721.1\|2439066_2440179_-	hypothetical protein	I6PD76	Cronobacter_phage	6.0e-121	58.2
WP_002228446.1\|2440179_2440821_-	DUF4055 domain-containing protein	A0A1B0VMH0	Pseudomonas_phage	3.8e-59	54.1
WP_002228445.1\|2440839_2441568_-	hypothetical protein	A0A1B0VMH0	Pseudomonas_phage	4.6e-61	51.4
WP_002211722.1\|2441567_2442542_-	hypothetical protein	A0A1W6JNY3	Morganella_phage	2.3e-153	81.1
WP_002209743.1\|2442546_2443755_-\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211723.1\|2443802_2444387_-	hypothetical protein	A0A0R6PHH0	Moraxella_phage	4.8e-69	70.7
WP_002211724.1\|2444390_2444840_-	DUF2280 domain-containing protein	I6S1P9	Salmonella_phage	1.0e-47	72.9
WP_002211725.1\|2444870_2445506_-	hypothetical protein	I6S676	Salmonella_phage	7.2e-87	71.4
WP_002211727.1\|2445962_2446676_-	phage antirepressor KilAC domain-containing protein	Q5MBW0	Stx1-converting_phage	7.6e-69	60.2
WP_002211729.1\|2447221_2447680_-\|lysis	lysis protein	A0A2H4JHL8	uncultured_Caudovirales_phage	4.9e-21	45.3
WP_002211730.1\|2447664_2448177_-	lysozyme	I6PBN2	Cronobacter_phage	9.7e-50	61.6
WP_002430108.1\|2448207_2448405_-\|holin	phage holin family protein	B6SD15	Bacteriophage	4.9e-18	64.4
WP_002215644.1\|2448650_2448926_+	hypothetical protein	NA	NA	NA	NA
WP_002211731.1\|2448922_2449132_-	hypothetical protein	NA	NA	NA	NA
WP_002393183.1\|2449294_2449471_+	hypothetical protein	NA	NA	NA	NA
WP_002211732.1\|2449555_2450119_-	Bro-N domain-containing protein	B6SD63	Bacteriophage	9.4e-30	58.0
WP_002215638.1\|2450167_2450386_-	ash family protein	NA	NA	NA	NA
WP_002215636.1\|2450389_2450779_-	antitermination protein	A0A1W6JNX1	Morganella_phage	1.4e-45	68.8
WP_002211735.1\|2450779_2451385_-	recombination protein NinG	A0A1P8DTE0	Proteus_phage	2.8e-56	56.9
WP_002211736.1\|2451458_2451905_-	recombination protein NinB	A0A2H4J8D9	uncultured_Caudovirales_phage	3.9e-47	62.5
WP_002215632.1\|2452929_2453190_+	excisionase family protein	Q859D3	Escherichia_coli_phage	1.7e-10	42.9
WP_001297096.1\|2453357_2454137_-	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_000255944.1\|2454136_2455159_-\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_002211738.1\|2455228_2456467_+\|integrase	site-specific integrase	Q20GI2	Phage_258-320	2.3e-121	53.3
WP_002211739.1\|2456493_2456940_-	YcgN family cysteine cluster protein	NA	NA	NA	NA
2456493:2456523	attR	NA	NA	NA	NA
WP_002211740.1\|2457042_2457699_-	fumarylacetoacetate hydrolase family protein	NA	NA	NA	NA
WP_002215627.1\|2457769_2458855_-	lytic murein transglycosylase	NA	NA	NA	NA
WP_002211743.1\|2458995_2459268_-	YcgL domain-containing protein	NA	NA	NA	NA
WP_002220631.1\|2459988_2460675_+	septum site-determining protein MinC	NA	NA	NA	NA
WP_002211179.1\|2460699_2461512_+	septum site-determining protein MinD	NA	NA	NA	NA
WP_002211180.1\|2461515_2461785_+	cell division topological specificity factor MinE	NA	NA	NA	NA
WP_002211181.1\|2462021_2463143_-	ribonuclease D	NA	NA	NA	NA
WP_002220632.1\|2463302_2464991_-	long-chain-fatty-acid--CoA ligase FadD	A0A2H4PQM9	Staphylococcus_phage	3.0e-31	28.9
WP_087768167.1\|2465526_2465634_+	gluconate 5-dehydrogenase	NA	NA	NA	NA
WP_002211183.1\|2465634_2466240_-	Slp family lipoprotein	NA	NA	NA	NA
WP_002211184.1\|2466376_2467075_-\|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB	NA	NA	NA	NA

DBSCAN-SWA_7

2918400 : 2989133

Indivirus(10.0%)

transposase,plate,tRNA,lysis

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002211870.1\|2918400_2920428_+\|tRNA	methionine--tRNA ligase	A0A1V0SDF2	Indivirus	8.0e-55	27.1
WP_002213775.1\|2920591_2921050_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002228565.1\|2921267_2921930_-	hypothetical protein	NA	NA	NA	NA
WP_002211975.1\|2922627_2923704_+	sugar ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_002211974.1\|2923721_2924975_+	LVIVD repeat-containing protein	NA	NA	NA	NA
WP_002211973.1\|2925307_2926489_+	MFS transporter	NA	NA	NA	NA
WP_002211971.1\|2926730_2927138_+	CidA/LrgA family protein	NA	NA	NA	NA
WP_002211970.1\|2927134_2927830_+\|lysis	CidB/LrgB family autolysis modulator	NA	NA	NA	NA
WP_002211969.1\|2928155_2929040_+	cytidine deaminase	NA	NA	NA	NA
WP_002211968.1\|2929395_2931093_+	NAD-dependent malic enzyme	NA	NA	NA	NA
WP_002211966.1\|2931373_2932111_+	outer membrane permeability protein SanA	NA	NA	NA	NA
WP_002211965.1\|2932555_2933566_-	galactose/methyl galactoside ABC transporter permease MglC	NA	NA	NA	NA
WP_002211964.1\|2933586_2935107_-	galactose/methyl galactoside ABC transporter ATP-binding protein MglA	F2Y2R6	Organic_Lake_phycodnavirus	2.6e-10	29.9
WP_002211963.1\|2935336_2936329_-	galactose/glucose ABC transporter substrate-binding protein MglB	NA	NA	NA	NA
WP_002211961.1\|2937076_2938243_-	DUF418 family protein	NA	NA	NA	NA
WP_002211960.1\|2938297_2938960_-	GTP cyclohydrolase I FolE	R9TJA5	Vibrio_phage	5.8e-55	53.5
WP_002211959.1\|2939143_2940295_-	YbfB/YjiJ family MFS transporter	NA	NA	NA	NA
WP_002211958.1\|2940430_2941300_+	LysR family transcriptional regulator	NA	NA	NA	NA
WP_002211957.1\|2941573_2942713_+	S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase	E3SJ82	Synechococcus_phage	5.2e-35	29.9
WP_002211956.1\|2942733_2943576_+	S-formylglutathione hydrolase	NA	NA	NA	NA
WP_002227980.1\|2943832_2944045_+	peptide antibiotic darobactin C	NA	NA	NA	NA
WP_002215886.1\|2944128_2946489_+	darobactin export ABC transporter permease subunit	NA	NA	NA	NA
WP_002211952.1\|2946490_2947753_+	darobactin export ABC transporter periplasmic adaptor subunit	NA	NA	NA	NA
WP_002211951.1\|2947754_2948423_+	darobactin export ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	1.4e-35	40.0
WP_002211950.1\|2948432_2949743_+	darobactin maturation radical SAM/SPASM protein DarE	NA	NA	NA	NA
WP_002211949.1\|2950277_2951552_+	molybdopterin molybdotransferase MoeA	NA	NA	NA	NA
WP_002211948.1\|2951553_2952324_+	molybdopterin-synthase adenylyltransferase MoeB	NA	NA	NA	NA
WP_002209743.1\|2952459_2953668_+\|transposase	IS256 family transposase	A0A218MNI5	uncultured_virus	5.4e-51	50.8
WP_002211947.1\|2953711_2954365_-	hypothetical protein	NA	NA	NA	NA
WP_002227996.1\|2954592_2956188_-	ABC-F family ATPase	A0A2K9L0W2	Tupanvirus	6.1e-58	28.5
WP_002211945.1\|2956870_2957494_+	hypothetical protein	NA	NA	NA	NA
WP_002211944.1\|2957705_2959073_-	ImpA family type VI secretion system protein	NA	NA	NA	NA
WP_002214552.1\|2959550_2960132_-	type VI secretion system lipoprotein TssJ	NA	NA	NA	NA
WP_002211941.1\|2960106_2961192_-\|plate	type VI secretion system baseplate subunit TssG	NA	NA	NA	NA
WP_002211940.1\|2961155_2962919_-\|plate	type VI secretion system baseplate subunit TssF	NA	NA	NA	NA
WP_002211939.1\|2963139_2963595_-	hypothetical protein	NA	NA	NA	NA
WP_002211938.1\|2963609_2964668_-	PAAR domain-containing protein	NA	NA	NA	NA
WP_002211937.1\|2964685_2966287_-	type VI secretion system protein TssA	NA	NA	NA	NA
WP_002211936.1\|2966330_2969753_-	type VI secretion system membrane subunit	NA	NA	NA	NA
WP_002211935.1\|2969749_2970982_-	hypothetical protein	NA	NA	NA	NA
WP_002214564.1\|2973146_2973617_-	hypothetical protein	NA	NA	NA	NA
WP_041175909.1\|2973789_2975973_-	M23 family metallopeptidase	NA	NA	NA	NA
WP_002211931.1\|2975988_2976249_-	DUF2345 domain-containing protein	NA	NA	NA	NA
WP_002211930.1\|2976402_2977176_-	hypothetical protein	NA	NA	NA	NA
WP_011055627.1\|2977172_2979473_-	M23 family metallopeptidase	NA	NA	NA	NA
WP_002231240.1\|2979488_2981837_-	type VI secretion system tip protein VgrG	A0A2H4JCD4	uncultured_Caudovirales_phage	4.5e-17	32.1
WP_002223447.1\|2981839_2984479_-	type VI secretion system ATPase TssH	K4FB40	Cronobacter_phage	1.5e-90	31.5
WP_002210014.1\|2984866_2985358_-	Hcp family type VI secretion system effector	NA	NA	NA	NA
WP_002228049.1\|2985361_2987098_-	OmpA family protein	NA	NA	NA	NA
WP_002210015.1\|2987097_2987784_-	DotU family type IV/VI secretion system protein	NA	NA	NA	NA
WP_002211664.1\|2987780_2989133_-\|plate	type VI secretion system baseplate subunit TssK	NA	NA	NA	NA

DBSCAN-SWA_8

3020691 : 3094065

Escherichia_phage(21.05%)

transposase,protease,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002213775.1\|3020691_3021150_+\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002226586.1\|3021318_3021774_-	macrodomain Ter protein MatP	NA	NA	NA	NA
WP_002224683.1\|3021984_3023736_+\|protease	Lon protease family protein	NA	NA	NA	NA
WP_002220006.1\|3023804_3024323_+	bifunctional 3-hydroxydecanoyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase	NA	NA	NA	NA
WP_002211286.1\|3024588_3024777_-	hypothetical protein	NA	NA	NA	NA
WP_000255944.1\|3025410_3026433_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|3026432_3027212_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002213775.1\|3028372_3028831_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002228015.1\|3029028_3029196_-	ribosome modulation factor	NA	NA	NA	NA
WP_002211289.1\|3029465_3030044_-	membrane integrity-associated transporter subunit PqiC	NA	NA	NA	NA
WP_002211290.1\|3030040_3031693_-	intermembrane transport protein PqiB	NA	NA	NA	NA
WP_002211291.1\|3031679_3032966_-	membrane integrity-associated transporter subunit PqiA	NA	NA	NA	NA
WP_002211292.1\|3033094_3035008_-	ABC transporter ATP-binding protein	A0A2K9L3Z8	Tupanvirus	1.5e-47	28.9
WP_002211293.1\|3035013_3037134_-	bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL	NA	NA	NA	NA
WP_002211294.1\|3037233_3038346_+	YcbX family protein	NA	NA	NA	NA
WP_002211295.1\|3038371_3038923_-	cell division protein ZapC	NA	NA	NA	NA
WP_002211296.1\|3039105_3040116_-	quinone-dependent dihydroorotate dehydrogenase	NA	NA	NA	NA
WP_002220013.1\|3040769_3043385_-	aminopeptidase N	NA	NA	NA	NA
WP_002228013.1\|3044100_3045306_+	nicotinate phosphoribosyltransferase	NA	NA	NA	NA
WP_002211301.1\|3045804_3047205_+\|tRNA	asparagine--tRNA ligase	A0A167RLM0	Powai_lake_megavirus	6.5e-80	35.2
WP_002354007.1\|3047505_3048585_+	porin OmpF	Q1MVN1	Enterobacteria_phage	3.2e-111	56.5
WP_002211303.1\|3048841_3050032_+	aspartate/tyrosine/aromatic aminotransferase	NA	NA	NA	NA
WP_002430096.1\|3050185_3050302_+	hypothetical protein	NA	NA	NA	NA
WP_002211304.1\|3050455_3051103_-	MBL fold metallo-hydrolase	A0A1X9I5D3	Streptococcus_phage	2.2e-22	32.3
WP_002211305.1\|3051163_3051712_-	YcbK family protein	A0A0K1LLY2	Rhodobacter_phage	7.8e-05	34.7
WP_002217987.1\|3051935_3053792_-	L,D-transpeptidase	NA	NA	NA	NA
WP_002213759.1\|3054075_3054534_-\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002211308.1\|3054749_3059207_-	chromosome partition protein MukB	NA	NA	NA	NA
WP_002211309.1\|3059203_3059932_-	chromosome partition protein MukE	NA	NA	NA	NA
WP_002211310.1\|3059912_3061235_-	chromosome partition protein MukF	NA	NA	NA	NA
WP_002211311.1\|3061231_3062017_-\|tRNA	tRNA uridine 5-oxyacetic acid(34) methyltransferase CmoM	NA	NA	NA	NA
WP_002211313.1\|3062789_3063683_-	YcbJ family phosphotransferase	NA	NA	NA	NA
WP_002211314.1\|3064045_3064798_-	3-deoxy-manno-octulosonate cytidylyltransferase	NA	NA	NA	NA
WP_002211315.1\|3064794_3064977_-	hypothetical protein	NA	NA	NA	NA
WP_002211317.1\|3065524_3065734_-	cold-shock protein	A0A1W6JNX5	Morganella_phage	3.0e-10	50.0
WP_002216263.1\|3066460_3067897_+	VOC family protein	NA	NA	NA	NA
WP_002211319.1\|3067904_3068891_-	tetraacyldisaccharide 4'-kinase	NA	NA	NA	NA
WP_002211320.1\|3068887_3070636_-	lipid A ABC transporter ATP-binding protein/permease MsbA	W8CYL7	Bacillus_phage	8.7e-66	31.5
WP_002211321.1\|3070671_3072963_-	ComEC family protein	NA	NA	NA	NA
WP_002211322.1\|3073509_3073794_-	integration host factor subunit beta	A7KV42	Bacillus_phage	2.4e-10	40.2
WP_002211323.1\|3073854_3075528_-	30S ribosomal protein S1	NA	NA	NA	NA
WP_002211324.1\|3075701_3076394_-	(d)CMP kinase	NA	NA	NA	NA
WP_002211325.1\|3076706_3077993_-	3-phosphoshikimate 1-carboxyvinyltransferase	NA	NA	NA	NA
WP_002211326.1\|3078155_3079241_-	3-phosphoserine/phosphohydroxythreonine transaminase	M1Q1P2	Streptococcus_phage	4.4e-84	46.1
WP_002211327.1\|3079607_3081455_-	YadA-like family protein	NA	NA	NA	NA
WP_002211328.1\|3081475_3082570_-	YadA-like family protein	B0FIT1	Escherichia_phage	3.7e-06	32.7
WP_002211329.1\|3082838_3083876_-	L-asparaginase 2	NA	NA	NA	NA
WP_002211330.1\|3084024_3085791_+	30S ribosomal protein S12 methylthiotransferase accessory protein YcaO	NA	NA	NA	NA
WP_002211331.1\|3086488_3087346_+	formate transporter FocA	NA	NA	NA	NA
WP_002211332.1\|3087401_3089684_+	formate C-acetyltransferase	A0A2P0VNR5	Tetraselmis_virus	1.6e-157	41.2
WP_002211333.1\|3089801_3090476_-	glycosyltransferase family 25 protein	A0A2H4UUT1	Bodo_saltans_virus	7.8e-31	40.5
WP_002211334.1\|3091462_3092197_+	pyruvate formate lyase 1-activating protein	A0A2P0VNQ0	Tetraselmis_virus	3.6e-21	27.4
WP_000255944.1\|3093042_3094065_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0

DBSCAN-SWA_9

3107892 : 3117529

Brazilian_cedratvirus(16.67%)

transposase,protease,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002211344.1\|3107892_3109617_+	cysteine/glutathione ABC transporter ATP-binding protein/permease CydC	A0A2R8FG22	Brazilian_cedratvirus	3.3e-17	31.8
WP_002211346.1\|3109835_3110546_+\|tRNA	leucyl/phenylalanyl-tRNA--protein transferase	NA	NA	NA	NA
WP_002211347.1\|3110711_3110930_+	translation initiation factor IF-1	NA	NA	NA	NA
WP_002213759.1\|3111301_3111760_-\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002211348.1\|3112052_3114329_-\|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	A0A223W0B1	Agrobacterium_phage	7.4e-166	41.7
WP_002211349.1\|3114354_3114675_-\|protease	ATP-dependent Clp protease adapter ClpS	A0A1B1IT64	uncultured_Mediterranean_phage	8.2e-15	42.7
WP_002211350.1\|3115035_3115299_+	cold shock-like protein CspD	A0A2H4N7Y6	Lake_Baikal_phage	3.6e-16	59.7
WP_002211351.1\|3115579_3117529_-	macrolide ABC transporter ATP-binding protein/permease MacB	G9BWD6	Planktothrix_phage	8.8e-35	37.7

DBSCAN-SWA_10

3227059 : 3245423

Vibrio_phage(25.0%)

coat,transposase,plate,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002213775.1\|3227059_3227518_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002208835.1\|3227718_3228723_-	nucleoid-associated protein YejK	A0A1V0E8C0	Vibrio_phage	3.1e-84	47.7
WP_002208836.1\|3228900_3229128_+	YejL family protein	NA	NA	NA	NA
WP_002208837.1\|3229155_3230952_+	DUF3413 domain-containing protein	NA	NA	NA	NA
WP_002208839.1\|3231921_3233070_+	HNH endonuclease	NA	NA	NA	NA
WP_002208840.1\|3233082_3233571_+	hypothetical protein	NA	NA	NA	NA
WP_002208841.1\|3234270_3234633_+	hypothetical protein	NA	NA	NA	NA
WP_002208842.1\|3234758_3236195_-	6-phospho-beta-glucosidase	NA	NA	NA	NA
WP_002208843.1\|3236485_3237226_-	MurR/RpiR family transcriptional regulator	NA	NA	NA	NA
WP_002208845.1\|3237523_3238303_-\|tail	tail fiber protein	Q9MCR6	Enterobacteria_phage	7.1e-52	52.4
WP_002208846.1\|3238399_3238747_-	DUF2313 domain-containing protein	A0A2P9JZK7	Alteromonadaceae_phage	6.4e-21	41.3
WP_002215458.1\|3238743_3239004_-	DUF2313 domain-containing protein	NA	NA	NA	NA
WP_002208847.1\|3239000_3240137_-\|plate	baseplate J/gp47 family protein	B5TK75	Pseudomonas_phage	4.5e-31	30.5
WP_002208848.1\|3240140_3240596_-	phage GP46 family protein	A0A0C4UR04	Shigella_phage	4.3e-17	43.8
WP_002215460.1\|3240592_3241189_-\|plate	phage baseplate assembly protein	NA	NA	NA	NA
WP_002208850.1\|3241204_3242260_-\|tail	tail protein	M1PVV2	Vibrio_phage	1.3e-37	27.2
WP_002208852.1\|3242256_3243663_-	DNA circularization protein	Q8SBG8	Shigella_phage	2.1e-17	33.7
WP_002208853.1\|3243929_3245423_-\|coat	coat protein	NA	NA	NA	NA

DBSCAN-SWA_11

3396305 : 3402477

Escherichia_phage(33.33%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002210709.1\|3396305_3396506_+	AlpA family transcriptional regulator	A0A1V0E8E5	Vibrio_phage	1.6e-08	51.7
WP_002215949.1\|3396505_3397048_+	ash family protein	NA	NA	NA	NA
WP_002215950.1\|3397040_3398000_+	toprim domain-containing protein	A0A1W6JPG0	Morganella_phage	1.6e-50	41.0
WP_002210707.1\|3397996_3399085_+	AAA family ATPase	A0A2H4JFA4	uncultured_Caudovirales_phage	1.4e-114	60.4
WP_002210705.1\|3399433_3399748_-	putative addiction module antidote protein	NA	NA	NA	NA
WP_002215951.1\|3399753_3400071_-	type II toxin-antitoxin system RelE/ParE family toxin	A0A141GEX6	Brucella_phage	2.0e-13	48.1
WP_000255944.1\|3400675_3401698_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|3401697_3402477_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6

DBSCAN-SWA_12

4004050 : 4079739

Escherichia_phage(16.67%)

transposase,holin,plate

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002210419.1\|4004050_4004446_+\|holin	phage holin family protein	NA	NA	NA	NA
WP_002210420.1\|4004442_4004727_+	YqjK-like family protein	NA	NA	NA	NA
WP_002210421.1\|4005030_4005426_+	DoxX family protein	NA	NA	NA	NA
WP_000255944.1\|4005704_4006727_+\|transposase	IS21-like element IS100 family transposase	A0A2L1IVA1	Escherichia_phage	1.9e-201	100.0
WP_001297096.1\|4006726_4007506_+	AAA family ATPase	A0A2L1IVB6	Escherichia_phage	4.5e-139	99.6
WP_002210424.1\|4007767_4008154_-	8-oxo-dGTP diphosphatase MutT	A0A0B5CYJ3	Rhizoctonia_fumigata_mycovirus	8.4e-06	30.4
WP_002210426.1\|4008448_4011163_-	preprotein translocase subunit SecA	NA	NA	NA	NA
WP_002210427.1\|4011240_4011774_-	secA regulator SecM	NA	NA	NA	NA
WP_002210428.1\|4011802_4012327_+	DUF721 domain-containing protein	NA	NA	NA	NA
WP_002228285.1\|4012493_4013414_-	UDP-3-O-acyl-N-acetylglucosamine deacetylase	NA	NA	NA	NA
WP_002210430.1\|4013513_4014665_-	cell division protein FtsZ	NA	NA	NA	NA
WP_002210431.1\|4014737_4015994_-	cell division protein FtsA	NA	NA	NA	NA
WP_002228100.1\|4016020_4016848_-	cell division protein FtsQ	NA	NA	NA	NA
WP_002210432.1\|4016849_4017770_-	D-alanine--D-alanine ligase	NA	NA	NA	NA
WP_002216457.1\|4017762_4019238_-	UDP-N-acetylmuramate--L-alanine ligase	NA	NA	NA	NA
WP_002210434.1\|4019375_4020446_-	undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase	NA	NA	NA	NA
WP_002210435.1\|4020442_4021645_-	cell division protein FtsW	NA	NA	NA	NA
WP_002210436.1\|4021644_4022961_-	UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase	NA	NA	NA	NA
WP_002210437.1\|4022963_4024046_-	phospho-N-acetylmuramoyl-pentapeptide- transferase	NA	NA	NA	NA
WP_002210438.1\|4024039_4025416_-	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase	NA	NA	NA	NA
WP_002210439.1\|4025412_4026900_-	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase	NA	NA	NA	NA
WP_002210440.1\|4026886_4028650_-	peptidoglycan glycosyltransferase FtsI	NA	NA	NA	NA
WP_002210441.1\|4028715_4029033_-	cell division protein FtsL	NA	NA	NA	NA
WP_002210442.1\|4029029_4029992_-	16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH	NA	NA	NA	NA
WP_002210443.1\|4029994_4030453_-	division/cell wall cluster transcriptional repressor MraZ	NA	NA	NA	NA
WP_087768171.1\|4031007_4031097_-	gluconate 5-dehydrogenase	NA	NA	NA	NA
WP_002210446.1\|4031554_4031995_+	L-alanine exporter AlaE	NA	NA	NA	NA
WP_002210447.1\|4032125_4033136_-	catabolite repressor/activator	NA	NA	NA	NA
WP_002213775.1\|4033640_4034099_-\|transposase	IS200/IS605-like element IS1541B family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002210448.1\|4034297_4034792_-	acetolactate synthase small subunit	NA	NA	NA	NA
WP_002228103.1\|4034794_4036522_-	acetolactate synthase 3 large subunit	A0A0P0YLY7	Yellowstone_lake_phycodnavirus	7.8e-59	29.4
WP_002216437.1\|4036981_4038787_-	long-chain fatty acid--CoA ligase	A0A1V0SBX8	Catovirus	3.5e-38	23.2
WP_002216434.1\|4039340_4040297_-	transcriptional regulator LeuO	NA	NA	NA	NA
WP_002210452.1\|4040974_4041190_+	hypothetical protein	NA	NA	NA	NA
WP_002213759.1\|4041618_4042077_+\|transposase	IS200/IS605-like element IS1541A family transposase	I4AZI8	Saccharomonospora_phage	8.5e-13	31.5
WP_002224085.1\|4042223_4043786_+	2-isopropylmalate synthase	NA	NA	NA	NA
WP_002210454.1\|4043788_4044880_+	3-isopropylmalate dehydrogenase	NA	NA	NA	NA
WP_002210455.1\|4044881_4046312_+	3-isopropylmalate dehydratase large subunit	NA	NA	NA	NA
WP_002210456.1\|4046326_4046929_+	3-isopropylmalate dehydratase small subunit	NA	NA	NA	NA
WP_002224086.1\|4047169_4048351_-	MFS transporter	NA	NA	NA	NA
WP_002231469.1\|4049014_4050676_+	HTH-type transcriptional regulator SgrR	NA	NA	NA	NA
WP_002214274.1\|4051615_4052608_+	thiamine ABC transporter substrate binding subunit	NA	NA	NA	NA
WP_002214276.1\|4052583_4054191_+	thiamine/thiamine pyrophosphate ABC transporter permease ThiP	NA	NA	NA	NA
WP_002210464.1\|4054177_4054888_+	thiamine ABC transporter ATP-binding protein ThiQ	G3M9Y6	Bacillus_virus	1.0e-20	34.1
WP_002210465.1\|4054956_4055724_-	DedA family protein	NA	NA	NA	NA
WP_002210466.1\|4055919_4058289_+	DNA polymerase II	A0A0P0YM26	Yellowstone_lake_phycodnavirus	1.5e-31	25.5
WP_002220588.1\|4058749_4061656_+	RNA polymerase-associated protein RapA	A0A1B1IUI1	uncultured_Mediterranean_phage	3.0e-23	37.6
WP_002210468.1\|4061911_4062265_-	hypothetical protein	NA	NA	NA	NA
WP_002210469.1\|4065789_4067400_-	DotU family type IV/VI secretion system protein	NA	NA	NA	NA
WP_002210470.1\|4067396_4068752_-\|plate	type VI secretion system baseplate subunit TssK	NA	NA	NA	NA
WP_002210471.1\|4068871_4069363_-	type VI secretion system lipoprotein TssJ	NA	NA	NA	NA
WP_002214737.1\|4069355_4069721_-	DUF4150 domain-containing protein	NA	NA	NA	NA
WP_002210473.1\|4069726_4070344_-	DUF3540 domain-containing protein	NA	NA	NA	NA
WP_002214739.1\|4070336_4071440_-	pentapeptide repeat-containing protein	NA	NA	NA	NA
WP_002224087.1\|4071465_4073685_-	pentapeptide repeat-containing protein	NA	NA	NA	NA
WP_002210474.1\|4073697_4076046_-	type VI secretion system tip protein VgrG	A0A2H4JCD4	uncultured_Caudovirales_phage	2.1e-14	32.9
WP_002210475.1\|4076149_4078738_-	type VI secretion system ATPase TssH	A0A248SJW6	Salicola_phage	1.9e-77	28.7
WP_002210476.1\|4078755_4079739_-\|plate	type VI secretion system baseplate subunit TssG	NA	NA	NA	NA

Anti-CRISPR protein detection

Acr_ID: NC_004088.1|WP_002214494.1|2410814_2411171_-|hypothetical-protein

Click the colored protein region to show detailed information

Acr_ID: NC_004088.1|WP_002211692.1|2412262_2413003_+|hypothetical-protein

Click the colored protein region to show detailed information

Acr ID

Acr position

Acr size

Homology with known anti

Neighbor HTH/AcRanker

Neighbor Aca

In prophage

Protospacer in prophage

NC_004088.1|WP_002214494.1|2410814_2411171_-|hypothetical-protein

2410814_2411171_-

118 aa aa

2367649-2467075

yes

CRISPR ID	CRISPR type	Spacer info	Spacer location	Spacer length	Protospacer location	Mismatch
NC_004088_2	Orphan	2.4\|1291691\|32\|NC_004088\|CRISPRCasFinder,CRT	1291691-1291722	32	2439186-2439155	0

1. spacer 2.4|1291691|32|NC_004088|CRISPRCasFinder,CRT matches to NC_004088 position: 2439186-2439155, mismatch: 0

agactgatgcaagatggcggtatgcgtacaga	CRISPR spacer
agactgatgcaagatggcggtatgcgtacaga	Protospacer
********************************

NC_004088.1|WP_002211692.1|2412262_2413003_+|hypothetical-protein

2412262_2413003_+

246 aa aa

2367649-2467075

yes

CRISPR ID	CRISPR type	Spacer info	Spacer location	Spacer length	Protospacer location	Mismatch
NC_004088_2	Orphan	2.4\|1291691\|32\|NC_004088\|CRISPRCasFinder,CRT	1291691-1291722	32	2439186-2439155	0

1. spacer 2.4|1291691|32|NC_004088|CRISPRCasFinder,CRT matches to NC_004088 position: 2439186-2439155, mismatch: 0

agactgatgcaagatggcggtatgcgtacaga	CRISPR spacer
agactgatgcaagatggcggtatgcgtacaga	Protospacer
********************************

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_004838

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NC_004088

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information