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_018889	Listeria monocytogenes SLCC2372 plasmid pLM1-2cUG1, complete sequence	0 crisprs	csa3,cas5	0	0	1	0
NC_018588	Listeria monocytogenes SLCC2372, complete genome	4 crisprs	DinG,cas3,WYL,casR,DEDDh,csa3	0	1	6	0

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

23685 : 32530

Streptococcus_phage(33.33%)

transposase

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_003728469.1\|23685_26601_-\|transposase	Tn3 family transposase	A0A1B0V7H9	Salmonella_phage	1.9e-174	36.7
WP_003728468.1\|26604_27159_-	recombinase family protein	A0A0F7LA37	Escherichia_phage	7.0e-38	53.4
WP_003728467.1\|27438_27798_+	Cd(II)-sensing metalloregulatory transcriptional repressor CadC	E4ZFI8	Streptococcus_phage	3.1e-26	50.0
WP_003728466.1\|27797_29933_+	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	1.6e-247	64.5
WP_003728465.1\|30125_30467_-	type II toxin-antitoxin system PemK/MazF family toxin	NA	NA	NA	NA
WP_003728464.1\|30460_30703_-	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	NA	NA	NA	NA
WP_003728463.1\|30763_31015_-	hypothetical protein	NA	NA	NA	NA
WP_003728462.1\|31145_31472_+	hypothetical protein	A0A2K9V3N4	Faecalibacterium_phage	3.2e-06	40.8
WP_003731676.1\|31471_32134_+	DUF2786 domain-containing protein	NA	NA	NA	NA
WP_003769263.1\|32152_32530_+	DUF3850 domain-containing protein	C9E2N9	Enterococcus_phage	2.2e-14	55.1

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_018588

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CRISPR-Cas detection and classification

Crispr_ID: NC_018588_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018588_1

210264-210415

Unclear

Consensus_repeat	Method
CCAATGCTTCTTGGTTTTAATGCTCCTGCTACATCAGAACCGAGCTC	CRISPRCasFinder

1 spacers

cas3

The CRISPR arrays of NC_018588_1

>merge|NC_018588|1|210264-210415|CRISPRCasFinder
CCAATGCTTCTTGGTTTTAATGCTCCTGCTACATCAGAACCGAGCTCATTCGAATTTCCACCACCACCTACGGATGAAGAGTTAAGACTTGCTTTGCCAGAGACGCCAATGCTTCTTGGTTTTAATGCTCCTGCTACATCGGAACCGAGCTC

>NC_018588|1|1|210264-210415|CRISPRCasFinder
CCAATGCTTCTTGGTTTTAATGCTCCTGCTACATCAGAACCGAGCTC	ATTCGAATTTCCACCACCACCTACGGATGAAGAGTTAAGACTTGCTTTGCCAGAGACG
CCAATGCTTCTTGGTTTTAATGCTCCTGCTACATCGGAACCGAGCTC

Protein	Signature genes	Signature genes Name	Protein_function
NC_018588.1\|WP_003722725.1\|200044_200353_+\|septation-regulator-SpoVG	unknown	unknown	gnl\|CDD\|237321
NC_018588.1\|WP_003722729.1\|203590_204304_-\|listeriolysin-O-transcriptional-regulator-PrfA	unknown	unknown	gnl\|CDD\|223736
NC_018588.1\|WP_009924872.1\|212316_212640_+\|DUF5502-family-protein	unknown	unknown	gnl\|CDD\|340321
NC_018588.1\|WP_003722731.1\|205769_207359_+\|cholesterol-dependent-cytolysin-listeriolysin-O	unknown	unknown	gnl\|CDD\|366559
NC_018588.1\|WP_003722728.1\|202591_203548_+\|ribose-phosphate-diphosphokinase	unknown	unknown	gnl\|CDD\|234929
NC_018588.1\|WP_003722736.1\|212774_213236_+\|YehR-family-lipoprotein	unknown	unknown	gnl\|CDD\|227145
NC_018588.1\|WP_014930057.1\|217751_221291_+\|transcription-repair-coupling-factor	cas3	cd09639_cas3_CAS-I	gnl\|CDD\|224118
NC_018588.1\|WP_003722742.1\|217076_217637_+\|aminoacyl-tRNA-hydrolase	unknown	unknown	gnl\|CDD\|235457
NC_018588.1\|WP_014930056.1\|214436_215378_-\|L-lactate-dehydrogenase	unknown	unknown	gnl\|CDD\|178836
NC_018588.1\|WP_009930501.1\|216385_216970_+\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|379228
NC_018588.1\|WP_009931069.1\|198152_199361_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|182528
NC_018588.1\|WP_003722740.1\|215672_216296_+\|50S-ribosomal-protein-L25/general-stress-protein-Ctc	unknown	unknown	gnl\|CDD\|235534
NC_018588.1\|WP_003722726.1\|200472_200781_+\|septation-regulator-SpoVG	unknown	unknown	gnl\|CDD\|237321
NC_018588.1\|WP_009930499.1\|213685_214360_-\|DNA-alkylation-repair-protein	unknown	unknown	gnl\|CDD\|378033
NC_018588.1\|WP_009931068.1\|201167_202541_+\|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU	unknown	unknown	gnl\|CDD\|184643
NC_018588.1\|WP_010989373.1\|207689_209222_+\|zinc-metalloproteinase-Mpl	unknown	unknown	gnl\|CDD\|225768
NC_018588.1\|WP_003722723.1\|197463_198156_+\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213222
NC_018588.1\|WP_003725735.1\|213286_213619_-\|putative-heavy-metal-binding-protein	unknown	unknown	gnl\|CDD\|179228
NC_018588.1\|WP_003733144.1\|204574_205528_-\|phosphatidylinositol-specific-phospholipase-C	unknown	unknown	gnl\|CDD\|176497
NC_018588.1\|WP_010989375.1\|211375_212245_+\|phosphatidylcholine-phospholipase-C	unknown	unknown	gnl\|CDD\|214813

Protein	Function_ID	Function_description	E-value
NC_018588.1\|WP_003722725.1\|200044_200353_+\|septation-regulator-SpoVG	gnl\|CDD\|237321	PRK13259, PRK13259, septation regulator SpoVG.	2.92652e-53
NC_018588.1\|WP_003722729.1\|203590_204304_-\|listeriolysin-O-transcriptional-regulator-PrfA	gnl\|CDD\|223736	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].	9.59942e-12
NC_018588.1\|WP_009924872.1\|212316_212640_+\|DUF5502-family-protein	gnl\|CDD\|340321	pfam17606, DUF5502, Family of unknown function (DUF5502). This is a family of unknown function found in Listeria.	9.06348e-49
NC_018588.1\|WP_003722731.1\|205769_207359_+\|cholesterol-dependent-cytolysin-listeriolysin-O	gnl\|CDD\|366559	pfam01289, Thiol_cytolysin, Thiol-activated cytolysin.	1.50399e-178
NC_018588.1\|WP_003722728.1\|202591_203548_+\|ribose-phosphate-diphosphokinase	gnl\|CDD\|234929	PRK01259, PRK01259, ribose-phosphate diphosphokinase.	0
NC_018588.1\|WP_003722736.1\|212774_213236_+\|YehR-family-lipoprotein	gnl\|CDD\|227145	COG4808, COG4808, Uncharacterized protein conserved in bacteria [Function unknown].	5.22035e-59
NC_018588.1\|WP_014930057.1\|217751_221291_+\|transcription-repair-coupling-factor	gnl\|CDD\|224118	COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription].	0
NC_018588.1\|WP_003722742.1\|217076_217637_+\|aminoacyl-tRNA-hydrolase	gnl\|CDD\|235457	PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.	4.98809e-109
NC_018588.1\|WP_014930056.1\|214436_215378_-\|L-lactate-dehydrogenase	gnl\|CDD\|178836	PRK00066, ldh, L-lactate dehydrogenase; Reviewed.	0
NC_018588.1\|WP_009930501.1\|216385_216970_+\|GNAT-family-N-acetyltransferase	gnl\|CDD\|379228	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions.	7.52035e-10
NC_018588.1\|WP_009931069.1\|198152_199361_+\|ABC-transporter-permease	gnl\|CDD\|182528	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB.	2.47504e-62
NC_018588.1\|WP_003722740.1\|215672_216296_+\|50S-ribosomal-protein-L25/general-stress-protein-Ctc	gnl\|CDD\|235534	PRK05618, PRK05618, 50S ribosomal protein L25/general stress protein Ctc; Reviewed.	2.38585e-63
NC_018588.1\|WP_003722726.1\|200472_200781_+\|septation-regulator-SpoVG	gnl\|CDD\|237321	PRK13259, PRK13259, septation regulator SpoVG.	5.03804e-54
NC_018588.1\|WP_009930499.1\|213685_214360_-\|DNA-alkylation-repair-protein	gnl\|CDD\|378033	pfam08713, DNA_alkylation, DNA alkylation repair enzyme. Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.	1.81561e-21
NC_018588.1\|WP_009931068.1\|201167_202541_+\|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU	gnl\|CDD\|184643	PRK14354, glmU, bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU.	0
NC_018588.1\|WP_010989373.1\|207689_209222_+\|zinc-metalloproteinase-Mpl	gnl\|CDD\|225768	COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid transport and metabolism].	7.98048e-139
NC_018588.1\|WP_003722723.1\|197463_198156_+\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213222	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.	7.27113e-121
NC_018588.1\|WP_003725735.1\|213286_213619_-\|putative-heavy-metal-binding-protein	gnl\|CDD\|179228	PRK01119, PRK01119, putative heavy metal-binding protein.	8.98192e-61
NC_018588.1\|WP_003733144.1\|204574_205528_-\|phosphatidylinositol-specific-phospholipase-C	gnl\|CDD\|176497	cd00137, PI-PLCc, Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C. This subfamily corresponds to the catalytic domain present in prokaryotic and eukaryotic phosphoinositide-specific phospholipase C (PI-PLC), which is a ubiquitous enzyme catalyzing the cleavage of the sn3-phosphodiester bond in the membrane phosphoinositides (phosphatidylinositol, PI; Phosphatidylinositol-4-phosphate, PIP; phosphatidylinositol 4,5-bisphosphate, PIP2) to yield inositol phosphates (inositol monosphosphate, InsP; inositol diphosphate, InsP2; inositol trisphosphate, InsP3) and diacylglycerol (DAG). The higher eukaryotic PI-PLCs (EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. They play a critical role in most signal transduction pathways, controlling numerous cellular events, such as cell growth, proliferation, excitation and secretion. These PI-PLCs strictly require Ca2+ for their catalytic activity. They display a clear preference towards the hydrolysis of the more highly phosphorylated PI-analogues, PIP2 and PIP, to generate two important second messengers, InsP3 and DAG. InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. In contrast, bacterial PI-PLCs contain a single catalytic domain. Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. They participate in Ca2+-independent PI metabolism. They are characterized as phosphatidylinositol-specific phospholipase C (EC 4.6.1.13) that selectively hydrolyze PI, not PIP or PIP2. The TIM-barrel type catalytic domain in bacterial PI-PLCs is very similar to the one in eukaryotic PI-PLCs, in which the catalytic domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. The catalytic mechanism of both prokaryotic and eukaryotic PI-PLCs is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes a distinctly different type of eukaryotic PLC, glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC), an integral membrane protein characterized in the protozoan parasite Trypanosoma brucei. T. brucei GPI-PLC hydrolyzes the GPI-anchor on the variant specific glycoprotein (VSG), releasing dimyristyl glycerol (DMG), which may facilitate the evasion of the protozoan to the host#s immune system. It does not require Ca2+ for its activity and is more closely related to bacterial PI-PLCs, but not mammalian PI-PLCs.	8.10719e-115
NC_018588.1\|WP_010989375.1\|211375_212245_+\|phosphatidylcholine-phospholipase-C	gnl\|CDD\|214813	smart00770, Zn_dep_PLPC, Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. Structure information: PDB 1ca1.	4.70099e-87

>NC_018588.1|WP_010989373.1|207689_209222_+|zinc-metalloproteinase-Mpl
MKSKLICIIMVIAFQAHFTMTVKADSVGEEKLQNNTQAKKTPADLKALPDSCEAKDFYKNFKILDMTKDKLGVTHYTLALSSGGYLTDNDEIKVHVTPDNKITFINGDLQQGQLRITNQIKITEKNAIEKAFEAIGQSEAHVKSYVGNPVKEKEIILNSRTKRLVYNIKLIFAEPEVASWIVQVDVETGAILKKQNMLSEVERADTHKDFQALGKGANRLLQRPLHVMKINDLFYLVDRTHKGLIRTFDLKHNTDTSFGKVVSNKTNMFTDPEFSSAVDAHFYASEVYEYYKNVHQLESLDGKGGEIDSFVHYGLNCNNAFWDGQEILYGDGDKKNFKPFSCAKTIVGHELTHAVIQYSAGLEYEGQSGALNESFADVFGYFIAPNHWLIGEDVCVRGSRDGRIRSIKDPDKYNQAAHMKDYESLPLTEEGDWGGVHYNSGIPNKAAYNTITKLGKEKTEQLYFRALKYYLTKKSQFTDAKKALQQAAKDLYGEDASKKVAEAWEAVGVN
>NC_018588.1|WP_003722731.1|205769_207359_+|cholesterol-dependent-cytolysin-listeriolysin-O
MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDNPIE
>NC_018588.1|WP_003733144.1|204574_205528_-|phosphatidylinositol-specific-phospholipase-C
MYKNYLQRTLVLLLCFILYFFTFPLGGKAYSLNNWNKPIKNSVTTKQWMSALPDTTNLAALSIPGTHDTMSYNGDITWTLTKPLAQTQTMSLYQQLEAGIRYIDIRAKDNLNIYHGPIFLNASLSGVLETITQFLKKNPKETIIMRLKDEQNSNDSFDYRIQPLINIYKDYFYTTPRTDTSNKIPTLKDVRGKILLLSENHTKKPLVINSRKFGMQFGAPNQVIQDDYNGPSVKTKFKEIVQTAYQASKADNKLFLNHISATSLTFTPRQYAAALNNKVEQFVLNLTSEKVRGLGILIMDFPEKQTIKNIIKNNKFN
>NC_018588.1|WP_003722729.1|203590_204304_-|listeriolysin-O-transcriptional-regulator-PrfA
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
>NC_018588.1|WP_003722728.1|202591_203548_+|ribose-phosphate-diphosphokinase
MSNEYFDPKLKIFSLNSNRELAEEIAKEVGIELGKSSVTHFSDGEIQINIEESIRGCHVYVIQSTSNPVNQNLMELLIMIDALKRASAATINIVMPYYGYARQDRKARSREPITAKLVANLIETAGATRMITLDMHAPQIQGFFDIPIDHLNAVRLLSDYFSERHLGDDLVVVSPDHGGVTRARKMADRLKAPIAIIDKRRPRPNVAEVMNIVGNVEGKVCIIIDDIIDTAGTITLAAKALREAGATKVYACCSHPVLSGPAMKRIEESPIEKLVVTNSIALPEEKWIDKMEQLSVAALLGEAIVRVHENASVSSLFE
>NC_018588.1|WP_009931068.1|201167_202541_+|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU
MSKRYAVVLAAGQGTRMKSKLYKVLHPVCGKPMVEHVVDQISTLNVDKVVTIVGHGAEKVQEHLAGKSEFVKQDEQLGTAHAVLQAKAELAGKDGVTLVVCGDTPLIEASTMEALLKYHHEKRAKATILTTVIEDPTGYGRIIRDDLGIVEKIVEHKDATEKEQRISEINTGTYCFDNKALFEALENVSNDNVQGEYYLPDVIKILKDSDEVVAAYRMESFEESLGVNDRIALAEASKLMQRRINENHMRNGVTLVNPESTYIDIDVKIGQDTVIEPGVMLRGKTVIGDDCVVTSGSEIVNSVIGERVHVRTSSIFESKVGDDVQIGPYAHLRPESDIHDHVKIGNYVETKKAVVGEGTKLPHFIYMGDAEIGKNVNVGCGSIAVNYDGKNKAKTIIGDNVFVGCNSNLIAPVKVGDRAFIAAGSTITKDVPEDALGIARAKQDNKLGYAKHLNHSK
>NC_018588.1|WP_003722726.1|200472_200781_+|septation-regulator-SpoVG
MQVTDVRLRRVETDGRMRAIASITLDEEFVVHDIRVIDGNNGLFVAMPSKRGVDGEFRDIAHPINSDTRAKIQEVVLAEYERVGEEEATAVTEEESESVSAE
>NC_018588.1|WP_003722725.1|200044_200353_+|septation-regulator-SpoVG
MEITDVRLRRVETDGRMKAISSITIDGEFVIHDIRVIDGNEGLFVAMPSKRTPDGEFRDIAHPINSGTRAKIQEAVLAAYEVADEPAVNEESSADESIVEEN
>NC_018588.1|WP_009931069.1|198152_199361_+|ABC-transporter-permease
MNVLQSMKMAWKQLKASKLRSFLTMLGIIIGVASVILLVSLGNGVTQEVDDQMGDLGSNLITVVNSSVNPNDKYTYDEVMKYQNIDGVKSVSPELSGQVNATFDYKNSSNKVIGTNDQYKAARSLEMKEGRFLLPIDTEYGQKVAVIGSTVASDLFGFGDPIGETIRLNGMPYKVVGVLKEKGASMMGSSDDQIFIPISSAQRLLKDTNVRTIYVETKSAEDVDFVVNTLESRLAIKFGDEKEQEKNASSAQMGPSYQVINQQEILNAFNTISTTLTTALGAIAAISLVVGGIGIMNIMLVSVSERTREIGIRKALGAKKRAILLQFLIESIVISVCGGVIGIIIGVSGALIFGSVAGISSGITAGTIIFSFVFSLCIGVIFGIAPANKASKLRPIDALRSE
>NC_018588.1|WP_003722723.1|197463_198156_+|ABC-transporter-ATP-binding-protein
MPKPLIDMKNLTKTYTLGGETFKALDDVTFTVEQGEFLSIVGPSGSGKSTLMNMIGCLDVPDEGSYHLDDVDVFKLSDNKLSEIRNKKIGFIFQQFNLLPKLSAFENVELPLIYAGLSVSAREKAAIECLEKVGLLEKRRNLPTQLSGGQQQRVAIARALAGKPQILLADEPTGALDSKTGKEVMGILQELNRAGNTIVMITHDPTIASYGTRSIRIQDGKLFHEEATQA
>NC_018588.1|WP_010989375.1|211375_212245_+|phosphatidylcholine-phospholipase-C
MKFKKVVLGMCLIASVLVFPVTIKANACCDEYLQTPAAPHDIDSKLPHKLSWSADNPTNTDVNTHYWLFKQAEKILAKDVNHMRANLMNELKKFDKQIAQGIYDADHKNPYYDTSTFLSHFYNPDRDNTYLPGFANAKITGAKYFNQSVTDYREGKFDTAFYKLGLAIHYYTDISQPMHANNFTAISYPPGYHCAYENYVDTIKHNYQATEDMVAKRFCSDDVKDWLYENAKRAKADYPKIVNAKTKKSYLVGNSEWKKDTVEPTGARLRDSQQTLAGFLEFWSKKTNE
>NC_018588.1|WP_009924872.1|212316_212640_+|DUF5502-family-protein
MYIKGRLIFFFVVLVIALCSVLILLIIKISVWKDEPFHLSDAKEIECLGSCEIKNTNQKIHFFSIKENLFEEKGDIAGILNEDEQKVADKSIFIVILDDEKGIANEE
>NC_018588.1|WP_003722736.1|212774_213236_+|YehR-family-lipoprotein
MKMLKKGTAVLFVMIMAVMLVACGDKEETKTYTLSQNGVDSKLTYTYKGDKVTKQTAENTMSYASLGVASKEDAEKMLKATSDKFQGIDGLKEKIEYKDDKAIETLEVDYTKISSEDMNKIPGMSSNGDTSKGISMEESAKMLESQGYKEVSK
>NC_018588.1|WP_003725735.1|213286_213619_-|putative-heavy-metal-binding-protein
MIVTTSPNIEGKQIIEYKKIVFGEVITGVNFMKDIGAGLRNFFGGRSQGYEDELINAREEAIREMEQRAKDIGANAVIGVDIDYEVLGADNGMLMVTASGTAVVIEAQDY
>NC_018588.1|WP_009930499.1|213685_214360_-|DNA-alkylation-repair-protein
MITFDQLDTELQALENPNTIKIFRNHGCPDSLDLYGLKIGDLKKIIRREKLTKNHELAVKLIESNNSDLIYLGLLAINPNKITTEQIEKWNIAFRETWSQLTFGLASIVSKRDDALLFAKTWIESDYDLTKSMGWQIYSEHINNLPEAETLLQRAKETLQTETNRTRYSMNGFIITCGIYKDDLHEKAMEAAKSVGKVHVNLGNTACKVPDAISYIEKARNRTK
>NC_018588.1|WP_014930056.1|214436_215378_-|L-lactate-dehydrogenase
MKDHQKIILVGDGAVGSSYAFACVNLSIGQEFGIIDIDKDRTIGDAMDLSHAVPFSTPKKIYSANYSDCHDADLVVVTAGTAQKPGETRLDLVNRNIKIMKGIVDEVMASGFDGIFLIASNPVDILTYATWKFSGLPKERVIGSGTSLDTARFRMSIADYLKVDARNVHGYILGEHGDTEFPAWSHTTVGGLPITEWISEDEQGAMDTILVSVRDAAYEIINKKGATFYGVAAALARITKAILNNENAILPLSVYLDGHYGMNDIYIGAPAVVNRQGVRHIVEMNLNDKEKEQMKNSADTLKKVLDDAMKQID
>NC_018588.1|WP_003722740.1|215672_216296_+|50S-ribosomal-protein-L25/general-stress-protein-Ctc
MATTLEVQKRETTQHSEVTRLRSEGKVPGIIYGYKSENVPVSVDSLELIKAVRDNGRNAVFSVTVDGKKLNVLLHEYQVDPLKDVLVHVDLLAVDMNEEVETDVRVVLVGDAPGVKAGGVLQQIIHDVKVSATPEKLPETIELDISSLEIGDVLTTNDLPENKDYVVQAEEEETVVTVSAPRAEEEPTTTEAPEPEAVHGKDEEPVE
>NC_018588.1|WP_009930501.1|216385_216970_+|GNAT-family-N-acetyltransferase
MLDKSVPHISVIMVNHDATNYPEFHLPAGYSFCFYKDGLEEDWCRLQLETGQVLSMDSIRARFETEFGNEKEKLTKRCIFVKAPNGEIIGTAMLWDGNTFGKIESRIHWVAVLDSHGGKGIAKALLSKILGLNKSKFVYLTTQTGSYQAIYLYRKFGFEKYVGKTPENWKTVNFQEEKETAWQIIENKIAEHQA
>NC_018588.1|WP_003722742.1|217076_217637_+|aminoacyl-tRNA-hydrolase
MKLIAGLGNPGKKYERTRHNVGFMVVDELSFRHQTPWKKSKFNGMTSEIIVGGEKMILVKPLTFMNASGECIRPLMDYYNIPIEDVVIVYDDLDLPVGKIRLRQKGSAGGHNGMKSIIQHVKTQEFNRIRVGVSRPLKGEVINYVLGDFPKAEQPDIIAAIQKSADAIEDFAQTPFIEVMNKYNQK
>NC_018588.1|WP_014930057.1|217751_221291_+|transcription-repair-coupling-factor
MKGLQQLIYEQKDIRAVLNALDEKEKAQLVTGLTGSSRALFASVVEGASKRPVVFVTHNLYHAQKLYDDLLSLMDVDRLFLYPADELISSELSISSPELRGQRVEALDFLLSGKPGIVIVPVAGLRKMLPPVSLWKHFNISIVEGEEIDPDVLRQKLVTMGYTMSGMVNTPGEFSVRGGIIDIYPITEEFPIRIELFDTEVDSLRFFDVETQRSTTRVEEFRLLPATEIILDQSYYPDIVKRLEKKMMLTLNELKEQEDKQALIENLEEDLEMLRSGVKPDMFFKYIGLAYPDPASLFDYLPKNTAILLDEFGRILETEESLEREEAEWQTETLSRMETVRDVQVSHSFKKLLEGNHSPKIYLSLFQKQMASMRVSKTTNIVYKQMQQFHGQMNVLKTELESWHKNNYAVVILAPNLERAEKMQQTLTDYDMESTILKKESDVPKYGIVQFVIGTFQNGFELPLAKVAIISETELFNKKIKKVKKRQKLSNAERIQSYSELKVGDYVVHVNHGIARYVGMETLDINGVHKDYLLLVYQGEDKLFIPVDQLDLVQKYVGAEGKSPRLNKLGGAEWKRVKKKVQASVQDIADDLIKLYAEREAEKGYAFSADDEMQREFEEAFPYQETEDQLRSISEIKKDMERPRPMDRLLVGDVGYGKTEVALRAAFKAIMDGKQVAFLVPTTILAQQHFETMKERFQGFPIEIGLLSRFRTKKQQTETLKGMKNGTVDVVVGTHRLLSKDVEYQDLGLLIVDEEQRFGVTHKEKIKQMRSKIDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRFPVQTYVAEQNNVLVREAIERELARDGQVYYLYNRVESITQKADEISAMVPDARVATAHGQMGESELESVILSFLEGEFDVLVTTTIIETGVDIPNVNTLFVQDADRMGLSQLYQLRGRVGRWNRIAYAYFMYQKDKILREEAEKRLSAIKEFTELGSGFKIAMRDLSIRGAGNILGAQQHGFIDSVGFDLYSQMLKEAIEAKKPKEEQKQIVPVEIDIQADAYIPEYYITDGRQKIEMYKRFRNIETLSELEDLQSDMIDRFGEYPEEVEYLFTMTELKVRALEVGIESVKQEQNKITMLFSESGTAGIRGDIVMQIIGEFGRMVGVGMEGTQLKITINVQNKPLKEWLYQVKSLAEKLRGAMKEKASTEN

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Crispr_ID: NC_018588_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018588_2

497544-498128

Orphan

Consensus_repeat	Method
GATGTAAGTNATTTTGATACNAGTTCAGTAACTNATATG	CRT

7 spacers

The CRISPR arrays of NC_018588_2

>merge|NC_018588|2|497544-498128|CRT
GATTTGAGTGGTCTTGATACTAGTGCGGTAACTACTATGTGGGATATGTTTAACAGCTGTAGGGCACTTGAGGAACTGGATGTAAGTCATTTTGATACAAGTTCAGTAACTAATATGTCTTACATGTTTTATGATAATAGAAATCTTGAGGTGCTGGATGTAAGCAACCTTGATACCAGTTCAGTAACTAATATGTATGCCATGTTTGAAGATTGTACTAGTCTTGAAGAGCTGGATGTAAGTCATTTTGATACGAGTTCAGTAACTGATATGTATAGAGTGTTTAATGGCTGTGAAAAACTGAAGAAACTAGATGTAAGTAATTTCGATACCAGTTCCGCTACTGCAATGGTTCAAATGTTTAGAAATTGTAGCGCCCTTGAGAAGTTGGATGTAAGTAATTTTAATACGAGCTTAGTAACTGATATGCGTGCCATGTTTGCTGGTTGTACTAGTCTTGAAGCGTTAGATGTAAGTAATTTTGATACGAGTTCAGTAACTAATATGGCTGCCATGTTTTCTGATAATGAAAAAGTGGAGAAGCTTGATTTAAGTACCTTTGATACCAGTTCAGTGACTAACATG

>NC_018588|2|1|497544-498128|CRT
GATTTGAGTGGTCTTGATACTAGTGCGGTAACTACTATG	TGGGATATGTTTAACAGCTGTAGGGCACTTGAGGAACTG
GATGTAAGTCATTTTGATACAAGTTCAGTAACTAATATG	TCTTACATGTTTTATGATAATAGAAATCTTGAGGTGCTG
GATGTAAGCAACCTTGATACCAGTTCAGTAACTAATATG	TATGCCATGTTTGAAGATTGTACTAGTCTTGAAGAGCTG
GATGTAAGTCATTTTGATACGAGTTCAGTAACTGATATG	TATAGAGTGTTTAATGGCTGTGAAAAACTGAAGAAACTA
GATGTAAGTAATTTCGATACCAGTTCCGCTACTGCAATG	GTTCAAATGTTTAGAAATTGTAGCGCCCTTGAGAAGTTG
GATGTAAGTAATTTTAATACGAGCTTAGTAACTGATATG	CGTGCCATGTTTGCTGGTTGTACTAGTCTTGAAGCGTTA
GATGTAAGTAATTTTGATACGAGTTCAGTAACTAATATG	GCTGCCATGTTTTCTGATAATGAAAAAGTGGAGAAGCTT
GATTTAAGTACCTTTGATACCAGTTCAGTGACTAACATG

Protein	Signature genes	Signature genes Name	Protein_function
NC_018588.1\|WP_009932195.1\|501614_503345_+\|DUF4365-domain-containing-protein	unknown	unknown	gnl\|CDD\|379535
NC_018588.1\|WP_014601344.1\|500913_501078_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_072217966.1\|504021_504939_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|379523
NC_018588.1\|WP_009931585.1\|499021_499495_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_009931584.1\|499514_500000_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_003733941.1\|500027_500333_+\|LPXTG-cell-wall-anchor-domain-containing-protein	unknown	unknown	gnl\|CDD\|273478
NC_018588.1\|WP_010989473.1\|486364_487513_-\|DUF58-domain-containing-protein	unknown	unknown	gnl\|CDD\|224635
NC_018588.1\|WP_010989474.1\|487517_488465_-\|MoxR-family-ATPase	unknown	unknown	gnl\|CDD\|223786
NC_018588.1\|WP_010989475.1\|488620_490216_+\|PucR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225306
NC_018588.1\|WP_010989479.1\|501139_501376_-\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_009932193.1\|503389_503713_+\|AP2-domain-containing-protein	unknown	unknown	unknown
NC_018588.1\|WP_010989471.1\|482649_483315_-\|DUF1275-domain-containing-protein	unknown	unknown	gnl\|CDD\|226146
NC_018588.1\|WP_003721244.1\|490349_491633_+\|cytosine-permease	unknown	unknown	gnl\|CDD\|271377
NC_018588.1\|WP_010989480.1\|503687_503993_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_010989476.1\|492726_494277_+\|hydantoinase/oxoprolinase-family-protein	unknown	unknown	gnl\|CDD\|223223
NC_018588.1\|WP_014601342.1\|495096_496635_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|368260
NC_018588.1\|WP_009930718.1\|484208_486368_-\|transglutaminase	unknown	unknown	gnl\|CDD\|376628
NC_018588.1\|WP_003721255.1\|500408_500675_+\|transposase	unknown	unknown	unknown
NC_018588.1\|WP_003721245.1\|491633_492734_+\|DUF917-domain-containing-protein	unknown	unknown	gnl\|CDD\|226065
NC_018588.1\|WP_009930717.1\|483335_484091_-\|DUF4866-domain-containing-protein	unknown	unknown	gnl\|CDD\|379782

Protein	Function_ID	Function_description	E-value
NC_018588.1\|WP_072217966.1\|504021_504939_+\|hypothetical-protein	gnl\|CDD\|379523	pfam14253, AbiH, Bacteriophage abortive infection AbiH. This family of proteins confers resistance to bacteriophage.	0.00778454
NC_018588.1\|WP_009932195.1\|501614_503345_+\|DUF4365-domain-containing-protein	gnl\|CDD\|379535	pfam14280, DUF4365, Domain of unknown function (DUF4365). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 182 and 530 amino acids in length. There is a single completely conserved residue D that may be functionally important.	5.7395e-10
NC_018588.1\|WP_003733941.1\|500027_500333_+\|LPXTG-cell-wall-anchor-domain-containing-protein	gnl\|CDD\|273478	TIGR01167, Zinc_metalloprotease_ZmpB, LPXTG-motif cell wall anchor domain. This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region. [Cell envelope, Other].	4.04229e-05
NC_018588.1\|WP_010989473.1\|486364_487513_-\|DUF58-domain-containing-protein	gnl\|CDD\|224635	COG1721, COG1721, Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only].	2.48336e-53
NC_018588.1\|WP_010989474.1\|487517_488465_-\|MoxR-family-ATPase	gnl\|CDD\|223786	COG0714, COG0714, MoxR-like ATPases [General function prediction only].	1.51988e-102
NC_018588.1\|WP_010989475.1\|488620_490216_+\|PucR-family-transcriptional-regulator	gnl\|CDD\|225306	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism].	1.08474e-59
NC_018588.1\|WP_010989471.1\|482649_483315_-\|DUF1275-domain-containing-protein	gnl\|CDD\|226146	COG3619, COG3619, Predicted membrane protein [Function unknown].	6.55182e-68
NC_018588.1\|WP_003721244.1\|490349_491633_+\|cytosine-permease	gnl\|CDD\|271377	cd11484, SLC-NCS1sbd_CobB-like, nucleobase-cation-symport-1 (NCS1) transporter CobB-like; solute-binding domain. This NCS1 subfamily includes Escherichia coli CodB (cytosine permease), and the Saccharomyces cerevisiae transporters: Fcy21p (Purine-cytosine permease), and vitamin B6 transporter Tpn1. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and solute carrier 6 family neurotransmitter transporters (SLC6s).	6.12636e-95
NC_018588.1\|WP_010989476.1\|492726_494277_+\|hydantoinase/oxoprolinase-family-protein	gnl\|CDD\|223223	COG0145, HyuA, N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism].	1.31898e-105
NC_018588.1\|WP_014601342.1\|495096_496635_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|368260	pfam05043, Mga, Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.	1.11775e-19
NC_018588.1\|WP_009930718.1\|484208_486368_-\|transglutaminase	gnl\|CDD\|376628	pfam01841, Transglut_core, Transglutaminase-like superfamily. This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.	5.52486e-28
NC_018588.1\|WP_003721245.1\|491633_492734_+\|DUF917-domain-containing-protein	gnl\|CDD\|226065	COG3535, COG3535, Uncharacterized conserved protein [Function unknown].	0
NC_018588.1\|WP_009930717.1\|483335_484091_-\|DUF4866-domain-containing-protein	gnl\|CDD\|379782	pfam16160, DUF4866, Domain of unknown function (DUF4866). This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various human gut Firmicute species and abundant in human gut metagenomic datasets. The function of this family is unknown.	3.03926e-122

>NC_018588.1|WP_014601342.1|495096_496635_+|helix-turn-helix-domain-containing-protein
MREYLDSKSQKKVALLEKIFYAENHTSTQEELLNDLNITYPTLISTIKTINFDIERFGYKAFSIVHSAPNLSYTLKISDNCSIQLIINAYIRESPKFQILETLLLASFPNLQALAKKVHVSYSGIKKEIKELNEELRERNLSISTGNQVEITGDEFSLRIFYAFLFLVTYSGDRWPFSFVQYDEITDLLESCPKEIYRANSIDKGMMIHYYVAMHLLRDRMNCQIDTTRQFKVALYKACTEESKKSESAFIKKVAKQLPNRNYKEITYTTQIILSTIVAFGSYSSIEKMPSFFYMDEQLEEMGFMKLVDFASERVNDNLSIPFSEKEMELLRYSFASINYRYFLLDNLINKFNNIVPGYTDLDRNIRKIHKVNHLEPLISQLVNLKEMRLLKPFEERLASDYLIILDKRIDFSIHTLPIKVTILSTISNETAVFDFMRYFSSYYNLEIINQVDPVVDLYISDFSVSPEVLTSLRINQPIVYVNTRWLESDYVKINDNLAKIARKKFIANKKD
>NC_018588.1|WP_010989476.1|492726_494277_+|hydantoinase/oxoprolinase-family-protein
MYKIGIDVGGTNTDAVILDENQQLIHSVKMPTSEDIETGITESLHRVLSETGIDRSKVTHAMLGTTQCTNAIVERKKLAKVGVLRLGYPATASVLPYTAWPEDMVGFLSGKYKLTGGGYEYDGQVLSEINEAEIRETLASWKGEVESVAVVGVFSSLKNDQELAVQKIIEEELGADIPVSISSSVGSVGLIERENATILNAALFKVIAATSDGFEKALEQEGIEHAEIYLCQNDGTLMSLNYARQFPILTIACGPTNSIRGASYLAGLKDAMVLDVGGTTSDIGVLTDGFPRESSLAVDVGGVRTNFRMPDIISIGLGGGSIVREKDGDITIGPDSVGYRISEEALVFGGKTMTTTDIAVRLGMAEIGNPELVAHIPTDFAEKAYKKIADMTEDAIDKMKTSSGSVSLVLVGGGSVIIPDEISGVAQIFRDKNGPVANAIGASISQISGQYEQIYIYSQIEREEALQDAEQKAREQATLAGAVTDSIEVVEVEEIPLAYHPGNATRLRVKVVGNLV
>NC_018588.1|WP_003721245.1|491633_492734_+|DUF917-domain-containing-protein
MRYLDEQAIENIAIGAAFLGTGGGGDPYIGKMMALTAIKKHGPIKLLSPEEIADDDYFIPAAMMGAPSVLIEKFPKGDEFVRVFEKLGRYVGKEVKGTFPMEAGGVNSMIPIVVAAQLGLPMVDCDGMGRAFPELQMVTFHLDGISATPMAITDEKGNIGIMETIDNKWTERLARVTTVEMGASSLVSLYPCNGAQIKQSSIKNIVTLSEEIGKVIRETSMDEAEKLQKLLDVTHGYHLFEGKITDVVRETRAGFNFGRVKIDGLNKDTNSEVIVHFQNENLVAEKNGEPIAITPDLICMVDLETLMPVTTEALKYGKRVRVMALPADDAWRTDKGIETVGPRYFGYDVDFEPLEELVKKEERRHV
>NC_018588.1|WP_003721244.1|490349_491633_+|cytosine-permease
MTEKKTVEQAQSWQSLAFVWTGAMICVPSLLVGGTLISGMPLWEAILIALLGYGVIVVFMIYQGMQSSDLGIPAVSVASQVFGEQGSKKIISILLAIACLGWFGIQANVCGAAFSQFLGIYGINLPVPVSSLIWGVIMLLSAIYGIRILSILNYIAVPILLFVCIYGLVVSLNNGGLAVVENYKPAGSMSFMTGLAITIGSFALGAVIAGDYSQYTKSRKDVVKAAIVGILPSGVLMIAVGAILALTAGTADISVVFTNLGLPVLGIIGLILAAWTTNAVNAFSGGIAIINVFNISEKYHKVAVAIAGGLGTVLAVIGILNHFVPIMSVLSAMVPPVAGVMIASYWIVQKGDKSKWAPVPGVNWLGVTSWLVGAVIAGIPVILTFFPALPQLPNQPLIGIILSLAVYLVGAKVLSGKTNNVENLEGK
>NC_018588.1|WP_010989475.1|488620_490216_+|PucR-family-transcriptional-regulator
MSVKLADLMKLPSLKEAKVVSGKSGLSKLVSSISVLEYTEVALLEDDLFDNDEFYGSEIVVSAFVNIRDDVEAQCRTIERLHKVGEVALILYYVGIFVPKMDQKLIDFANELDFTIIVMPENEMSLRYSEVIYEVVEAIVKQEMTDTNFVTESLEQISSVRPPQRNIDTTLKILSDRTHSSLVLTDNSFQVINSITWPRTRHWDFERVIETSKQIDEHELVQLHLDERDFYTARKPIFQDGMQAMHLFMMKEKGALTADVVMQITEVVQVFMNLWGRNYVEISTAELMKAILNDESVKMRRLGKILNVDVSSIKWMWLVKTEEIRNNEQVLAELKSFVASHFQVSLIDLFEDNIVVLLDNSVGQRDRTHTANEFAMMMKEHGIDLKITVCQGMEQTSDVQSAYSLVNEYKNAANAIYANKSIYSLQEIDFAAKCVEIVDRGELAIAEQMRPLKSLEDNDELIETLSVFLLEGESNYNQAAELLFLHKNTIKYRIQRINELLQYPATKIPESYNLYLAVAIRRLLGGNNNNK
>NC_018588.1|WP_010989474.1|487517_488465_-|MoxR-family-ATPase
MSIEPSIKINEIINEVEKVIVGKRHVVKLSLTALLAGGHVLLEDVPGVGKTMMVRTLSKTIGVSFKRIQFTPDLLPADVTGVSIFNPETRDFEFRPGPVMGNIVLADEINRTAPRTQAALLEGMAENSVTVDGITRKLANPFFVMATQNPIEYEGTYALPEAQLDRFLLKINIGYPTVEEEMQLLTLKQYQDPLDQTKQVVTLSELLDLKNKAKQVFIDDVLKNYIIRLVDATRKHPSVALGISPRGSLAFMQAAQAFALIEGRDYVIPDDIQYLAPYIFTHRLILKSEAYYNEETAESIIASILKNTSVPVEKR
>NC_018588.1|WP_010989473.1|486364_487513_-|DUF58-domain-containing-protein
MLKKRLLLASRWIIMLIIYAGLWTYTLFQGDTASWFLTYFFSFILLLLFLSSIYPLKAWKVNRSFVKNTYHDGDLIDMQVSFTRKSRYPVGYLLFQQKIPATFGKVRARQQVVYPLFKKQFTVTLAGFVGVRGIHSFPPVDVETSDAFGLLERSRQLSSEKSLTIYPTYFPNVLEKISEASPENERNAAYWTLKKNSNLHSLREFSSGDRISLIDWKSSAKSDQLMTREFENSATSRLSVIFYGASHPNFELSLRAAYSFIRKISEENGEIRVTLLGDQTSKFAPAKGTSRLQDISTAFAEIAPVDSLTLQESLDSNLHSGEKILLFTPCMDTMLMQKVTRLTDNKQLQIITFQSEHSKAMDAPAIFLEQASLLSRWERETK
>NC_018588.1|WP_009930718.1|484208_486368_-|transglutaminase
MKRYLTLVMLFILSVLLISEWIYPFAELTELSTATWIILFITLSLGSFFLRLKYYWTIPLHVVMIIIVSGIYYAKGGILAGNWLGSFFQITFNGFRDMVQFRSSDISMDFILIVFLIALWLLSYITTYSILRKQRIMSVLVLTVAYLAVINTFTDYNSNWAIVRTVLEGFLLLHLALASRIATPNRISADSLKRNGLFYHGFVILLLAVFVFSSLMLPKKAPIFPDPIPTIKNALGINTTRTVGYSEDDTTLGGALKKDNATVFTAQAEKGHYWRVESKTVYTGTGWANANSGDVISFSSGDNFPIQLTEQTTGATNTAEISFASSSDYMPYPYGTQAVNGAVDSFSANLTIERVGPVDTIKNYTVQLKTPVYNIEKMQNADFSTLSNAFVSQYTQTPKDLPDRVTKLANKVTKDADSIYDKTKAIESYLSTSGTFTYSTDDAKETPMGADYVDQFLFETQIGYCDNFSTSMVVMLRSLGIPARWAKGYTPGEGEKKENDAKTTYTITNNNAHSWPEVFFPGTGWVPFEPTATFSNPENFQEPTTETANKPETPNDSTSTPETPNTPDKTPEQDNGSSSTGETPKKEEPKTETATSNVEIPSWVWWIPAGLVVALLALAIVFRRRIRGYLLLRSLRNSPEFGKTYHRLMKLLASYGYVRESSETLRHFSARVDADLTTSEFSRLTKMYETQLYSKNLTEKVIAAEETQLVQQIIARLTK
>NC_018588.1|WP_009930717.1|483335_484091_-|DUF4866-domain-containing-protein
MTTIFPKEQNVTPLFEQILANPTACRRFKDVFLDNLESYQETRGFEKDDTLFAKIILSAYRQSDVSALLLGVCGRTLFELLRQAFLIPKKLTVDNPFFLTDKEGNFIAKKDDISNREQEKFQEIYQSDLHHSETTIFLVDDDDIVHSYEPDFSISTKRINKKRGILVLYSLPDTLKSGMTESEVYAFIWKTFLHIQEIIPSSRIFYGQETSENADELGVFLPIHHFEKKMLQNIEQVNELVDALREQMVNK
>NC_018588.1|WP_010989471.1|482649_483315_-|DUF1275-domain-containing-protein
MARTRQISESIGLGLLLALAGGFMDAYSYIERGQVFANAQTGNILLFGINISEGNWAIAIQYFWPVVSFTVGIALSEVIHRRDIRRLHWRQLSVLIEAVILIGVAFIPLDHNLIANSLISFVCGIQVESFRKMHGRGVATTMCIGNLRSATQNLCDYFEYKEKQYLHNSFLYFSVILSFIIGAVVGNFFIQLFAQYAILVCAFLQLIAFMMMFIDRESKII
>NC_018588.1|WP_009931585.1|499021_499495_+|hypothetical-protein
MKKKKVVVISLLLLLVSVIGISSYFLFKDKINLLDVDPSAVEWNGKKQKDTSGEENTIAIPGFEKVTLYANETKQAVNFHNPEINDCYFKISLIHPDGSVLWRSDLIEPGKGMYSIELEKTLAVGEYENAVLKYECFSLNDQSPLNGSEINLKLVVV
>NC_018588.1|WP_009931584.1|499514_500000_+|hypothetical-protein
MNKLVLSTLSVAAMGMVIFSGGTAYAADKEGNTVVEYSVEGDYTLVVPEKVNLSNDNATEMSVKTINRNLEPGKEVEVTLSSGLSADGEIELERVGATSDVITSSFKSNNSTVTMANPVIGSFSGYAIEETEVSKIQIGSPQGDKKAGAYQTTLTFTAAFK
>NC_018588.1|WP_003733941.1|500027_500333_+|LPXTG-cell-wall-anchor-domain-containing-protein
MKRKLVLAMVLISFCGMFLLSPERVQASQTVVEVFISEDDLDVSEENIQEIPKKELAASSDKDNKQHMLPKAGDTVTNYTLLGLVLVLIWLIMQRKRKKKE
>NC_018588.1|WP_003721255.1|500408_500675_+|transposase
MARIEYGEEIQKSLLVLYSRGSTIDSICKEYGIPRYEFHKWMKLHDADKLETKEVKTLLQIRELKQQKNKLEEEILFLNEAINLLESP
>NC_018588.1|WP_014601344.1|500913_501078_+|hypothetical-protein
MYVESKEELEKIIYQQLINNINVKPDPWKWEERNALIVEIEVKAVLEKYGSTPI
>NC_018588.1|WP_010989479.1|501139_501376_-|hypothetical-protein
MSLKKILESDESIEKKEQQIDSYYQSELITRVEACELLDVSTKSLDRYIKQNKLSFQLNSLLIPHFCLIVLLMPLAIL
>NC_018588.1|WP_009932195.1|501614_503345_+|DUF4365-domain-containing-protein
MVKYTNPKIEKLGVNAVSNYIVESDYLSDFLAQQSTEPATDGTIRIYNGPGERKRDLIGIVPVQVKGTTTKNIIKYNRHEIDIVDLTYYYKVGGVVYFVVYVTNKVPKIYYRDLLRIDIKEILKKNEKLRGKKEKGTITIDFREVPVNVEDFRTVLLNFHKDQDYQTKDYVELGSINEISRDLTFTIIAPNSNIVEALKYVSPVLYKNEGDLKIPVRRFKIGELSVFTKSEFSIGIKGANSYIATVMEGEEETEIQIGSLQQLIVKFKEGRFKVDFEAKGKIQETIELLEILLGIVTGVNLYIDNKPVTEFFIEEVNEDFISRVNHALESFKKTQEALNHCKVPSNFHYEELTENDIDVINSIMELYQTSIDNTWGKFEFNNRLVYLLKHKGTIYNLLDSNVALEINFWSKREDGIQYTTTPLILIDDFSKMNDTEICNIKGPIEKLIPIHEKACSDINLICVRLIDAYDQTNNNQFLLVAFELLELIIPFTTNNEIHLIYLNKYQIKKRWDNLVMEDINHLVSIQKEFEEDKRIHLATLILLSAKNDAAQLLSELKNNEGFSLEDMPILNLLEKN
>NC_018588.1|WP_009932193.1|503389_503713_+|AP2-domain-containing-protein
MYQKASEKMKETMKANIALVESIRISSISNKKLQSDNKSGHTVVTFKDNKWVARICVSGVEHQLGSFVTKEEAIDARIEGEKYFQPLINKYNNRLDVFYSERRPFWT
>NC_018588.1|WP_010989480.1|503687_503993_+|hypothetical-protein
MNVDPFGRKVELMIIGNGLDVKANLASTFVDYYKHRCKLMRLEYNEDDFYRLKSKNYFPMKVKMQQFPSIRRCNIEILSIDAETAINENITFWDLVLFFCL
>NC_018588.1|WP_072217966.1|504021_504939_+|hypothetical-protein
MESKIERVLNKLGGYLSDPINIILNNCGFGENLEDEQENDLYNLMEERLEEKDKYVLSVAFIHKLNSYSNCSLEEFLMLELNKYEKYFSDYIKTEVTNKYEEYHKTRNNILTKLSGGLGATHSISVMNFNFTPNQFSDSVKLNEKIGLAHVNVHGSYLANSIFGIDTKSLEDIDTIGSGYRFTKTYRKLTLKTKRSTEILYHDITDIIFYGHSLGQADYAYFQSIFDYLDIYNNTIVLTFYYSDYKENVREEQTIAVRNLIEEYGKTFDNKHKGKNLLHKLLLEERISVTDLEIYEEDYSSKDMK

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Crispr_ID: NC_018588_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018588_3

543092-543380

Orphan

I-A

Consensus_repeat	Method
GTTTTAGTTACTTATTGTGAAATGTAAAT	PILER-CR
GTTTTAGTTACTTATTGTGAAATGTAAAT	CRISPRCasFinder
GTTTTAGTTACTTATTGTGAAATGTAAAT	CRT

4 spacers

The CRISPR arrays of NC_018588_3

>merge|NC_018588|3|543092-543380|PILER-CR,CRISPRCasFinder,CRT
GTTTTAGTTACTTATTGTGAAATGTAAATCGATAAAAAAGATATTAGTAATTTATTTGCAATTTAGTTTTAGTTACTTATTGTGAAATGTAAATTGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGCGTTTTAGTTACTTATTGTGAAATGTAAATGCGATTTTTGTCAAAGGGACAGCGATGGGTTACAAGTTTTAGTTACTTATTGTGAAATGTAAATTTACCACCAAAGTCCCTACACTCAATACCACCAAAGCGTTTTAGTTACTTATTGTGAAATATAAAT

>NC_018588|3|1|543092-543380|PILER-CR
GTTTTAGTTACTTATTGTGAAATGTAAAT	CGATAAAAAAGATATTAGTAATTTATTTGCAATTTA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTACCACCAAAGTCCCTACACTCAATACCACCAAAGC
GTTTTAGTTACTTATTGTGAAATATAAAT

>NC_018588|3|2|543092-543380|CRISPRCasFinder
GTTTTAGTTACTTATTGTGAAATGTAAAT	CGATAAAAAAGATATTAGTAATTTATTTGCAATTTA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTACCACCAAAGTCCCTACACTCAATACCACCAAAGC
GTTTTAGTTACTTATTGTGAAATATAAAT

>NC_018588|3|2|543092-543380|CRT
GTTTTAGTTACTTATTGTGAAATGTAAAT	CGATAAAAAAGATATTAGTAATTTATTTGCAATTTA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTACCACCAAAGTCCCTACACTCAATACCACCAAAGC
GTTTTAGTTACTTATTGTGAAATATAAAT

Protein	Signature genes	Signature genes Name	Protein_function
NC_018588.1\|WP_003721298.1\|545030_545390_-\|Lin0512-family-protein	unknown	unknown	gnl\|CDD\|131113
NC_018588.1\|WP_003721303.1\|550183_550999_-\|histidine-phosphatase-family-protein	unknown	unknown	gnl\|CDD\|223483
NC_018588.1\|WP_003721293.1\|540199_540493_+\|PTS-sugar-transporter-subunit-IIB	unknown	unknown	gnl\|CDD\|99908
NC_018588.1\|WP_003721294.1\|540507_541779_+\|PTS-galactitol-transporter-subunit-IIC	unknown	unknown	gnl\|CDD\|226298
NC_018588.1\|WP_003721290.1\|538081_538480_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_009930754.1\|543639_544218_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_009931217.1\|553340_554345_+\|ROK-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224851
NC_018588.1\|WP_003733192.1\|536967_537570_+\|SIS-domain-containing-protein	unknown	unknown	gnl\|CDD\|223865
NC_018588.1\|WP_003727296.1\|551279_551648_-\|DUF1304-domain-containing-protein	unknown	unknown	gnl\|CDD\|226282
NC_018588.1\|WP_009930756.1\|539137_540184_+\|galactitol-1-phosphate-5-dehydrogenase	unknown	unknown	gnl\|CDD\|176198
NC_018588.1\|WP_010989501.1\|548632_550063_-\|CapA-family-protein	unknown	unknown	gnl\|CDD\|225399
NC_018588.1\|WP_014930080.1\|537597_538065_+\|PTS-sugar-transporter-subunit-IIA	unknown	unknown	gnl\|CDD\|238129
NC_018588.1\|WP_010989498.1\|534903_536964_+\|BglG-family-transcription-antiterminator	unknown	unknown	gnl\|CDD\|226234
NC_018588.1\|WP_010989497.1\|534144_534795_+\|transaldolase	unknown	unknown	gnl\|CDD\|223254
NC_018588.1\|WP_010989499.1\|544325_545006_+\|type-1-glutamine-amidotransferase	unknown	unknown	gnl\|CDD\|153212
NC_018588.1\|WP_003733190.1\|541918_542854_+\|ribose-phosphate-pyrophosphokinase	unknown	unknown	gnl\|CDD\|234929
NC_018588.1\|WP_003721291.1\|538490_539141_+\|ribulose-phosphate-3-epimerase	unknown	unknown	gnl\|CDD\|223114
NC_018588.1\|WP_003721301.1\|548154_548586_+\|universal-stress-protein	unknown	unknown	gnl\|CDD\|366180
NC_018588.1\|WP_009932856.1\|545396_545855_-\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|378956
NC_018588.1\|WP_009931218.1\|551794_553210_+\|multidrug-efflux-MFS-transporter	unknown	unknown	gnl\|CDD\|129794

Protein	Function_ID	Function_description	E-value
NC_018588.1\|WP_003721298.1\|545030_545390_-\|Lin0512-family-protein	gnl\|CDD\|131113	TIGR02058, lin0512_fam, conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus. [Hypothetical proteins, Conserved].	5.62162e-67
NC_018588.1\|WP_003721303.1\|550183_550999_-\|histidine-phosphatase-family-protein	gnl\|CDD\|223483	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only].	5.01016e-50
NC_018588.1\|WP_003721293.1\|540199_540493_+\|PTS-sugar-transporter-subunit-IIB	gnl\|CDD\|99908	cd05566, PTS_IIB_galactitol, PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.	3.06007e-27
NC_018588.1\|WP_003721294.1\|540507_541779_+\|PTS-galactitol-transporter-subunit-IIC	gnl\|CDD\|226298	COG3775, GatC, Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism].	7.01085e-178
NC_018588.1\|WP_003721301.1\|548154_548586_+\|universal-stress-protein	gnl\|CDD\|366180	pfam00582, Usp, Universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity.	4.03126e-27
NC_018588.1\|WP_009931217.1\|553340_554345_+\|ROK-family-transcriptional-regulator	gnl\|CDD\|224851	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism].	1.11713e-20
NC_018588.1\|WP_003733192.1\|536967_537570_+\|SIS-domain-containing-protein	gnl\|CDD\|223865	COG0794, GutQ, Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane].	1.15952e-75
NC_018588.1\|WP_003727296.1\|551279_551648_-\|DUF1304-domain-containing-protein	gnl\|CDD\|226282	COG3759, COG3759, Predicted membrane protein [Function unknown].	2.33548e-41
NC_018588.1\|WP_009930756.1\|539137_540184_+\|galactitol-1-phosphate-5-dehydrogenase	gnl\|CDD\|176198	cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Related proteins include threonine dehydrogenase, formaldehyde dehydrogenase, and butanediol dehydrogenase. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Horse liver alcohol dehydrogenase is a dimeric enzyme and each subunit has two domains. The NAD binding domain is in a Rossmann fold and the catalytic domain contains a zinc ion to which substrates bind. There is a cleft between the domains that closes upon formation of the ternary complex.	0
NC_018588.1\|WP_010989501.1\|548632_550063_-\|CapA-family-protein	gnl\|CDD\|225399	COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane].	2.95496e-100
NC_018588.1\|WP_014930080.1\|537597_538065_+\|PTS-sugar-transporter-subunit-IIA	gnl\|CDD\|238129	cd00211, PTS_IIA_fru, PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.	4.3046e-37
NC_018588.1\|WP_010989498.1\|534903_536964_+\|BglG-family-transcription-antiterminator	gnl\|CDD\|226234	COG3711, BglG, Transcriptional antiterminator [Transcription].	5.36772e-80
NC_018588.1\|WP_010989497.1\|534144_534795_+\|transaldolase	gnl\|CDD\|223254	COG0176, MipB, Transaldolase [Carbohydrate transport and metabolism].	5.85703e-62
NC_018588.1\|WP_010989499.1\|544325_545006_+\|type-1-glutamine-amidotransferase	gnl\|CDD\|153212	cd01741, GATase1_1, Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase.	9.06055e-60
NC_018588.1\|WP_003733190.1\|541918_542854_+\|ribose-phosphate-pyrophosphokinase	gnl\|CDD\|234929	PRK01259, PRK01259, ribose-phosphate diphosphokinase.	1.26262e-153
NC_018588.1\|WP_003721291.1\|538490_539141_+\|ribulose-phosphate-3-epimerase	gnl\|CDD\|223114	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism].	4.74405e-108
NC_018588.1\|WP_009932856.1\|545396_545855_-\|MarR-family-transcriptional-regulator	gnl\|CDD\|378956	pfam12802, MarR_2, MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.	9.15558e-13
NC_018588.1\|WP_009931218.1\|551794_553210_+\|multidrug-efflux-MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	3.18163e-80

>NC_018588.1|WP_003733190.1|541918_542854_+|ribose-phosphate-pyrophosphokinase
MAGKMKLFSVTSERPLATKIADYLDIPLCEVELQKFSDGEVKINIEESIRGTNAYVVQSMNSNVNERLMELLIMVDALKRASVHSINIIMPYYGYARQDRKARSREPITAKLMANLIQRAGANRLITVDLHAAQIQGFFNIPIDHLSAIPLIGDYLIENYGEKDVVVVAPDHSGVVRARRIADRLNAPIAILNRKPRPHEDEIMSVIGDVKGKVAIVVDDIIDTGVRATTSADILLEKGAVEVIACATHSVMAGNATERLQNSNIKEVITSDSIDLPEDKQFDKLTTISIGRILGRAIEGVQENRSLHPLF
>NC_018588.1|WP_003721294.1|540507_541779_+|PTS-galactitol-transporter-subunit-IIC
MDIILDFFKYIIGLGVTVMMPIIITILGVIFRKKISVAFKAGLTVGVGFVGLGVITSLMLTTITPVTKALVENYNFKLTATDIGWGVGSSLAWGTEVVPFVFVAIIATNILMIAFKWTKTMDVDIWNYWQPLFIASALYLTTGSMIIAVLSSIINMAIIFKIADWTQKDVEDVLGLEGISLPQIQTTGWALVGYPMNWLLGKIPGVRKINWSTEKVQSRLGIFGEPMLMGLIIGGGLAAIAQMPLSQVLQTGVTIAASLVLIPRMVSLLMDGLTVISEAAHEFMEKRFPGRELFIGLDSAVGIGHPFVLSLGLLMIPITLILAFILPGNKVLPLADLTALPFYMIFAIVPSKGNLFRGIFTGIVIVIITLYLSGAAAPLMTELAGQIGYNIPKDAVEVTSLAVGTQWYTWIVYYGLHWFGGIL
>NC_018588.1|WP_003721293.1|540199_540493_+|PTS-sugar-transporter-subunit-IIB
MKKKRIYVCCGTGIATSTVISKKVRAVLDEKRIPYEISQCTVQEVASKVSTSKPDIIVSSTTVTGDVGDVPVVIGRSFLTGLKKQETIDEILAILQD
>NC_018588.1|WP_009930756.1|539137_540184_+|galactitol-1-phosphate-5-dehydrogenase
MKALKLYGKRDLRYEEADMPTIEEPDDVILKVKTVGICGSDISRYSKLGPYVPGMVWGHEFSGEVIEVGSEVTDIEIGDRAAGCPALYCGECEYCKKGEFARCRKLTVIGARHPGAYAEYIKLPAENVVKIPNELDYEAAALVEPSAVVVHGFYHTKLQAGDDVVVVGSGNIGLLAIQWAKVFGARRVIAIDVDDKKLALAKEVGADVVINSLKEDPLEVVAAHTDGLNADLVVEAAGSPITSAQVFAYAKKGGGVVFLGIPYADVTIERFYFEKIVRSELTVWGSWNAISAPFPGKEWQTTIHFLANKQINIEPMITHRLSLAEGPEVFERIYERNEFFGKVLFFPE
>NC_018588.1|WP_003721291.1|538490_539141_+|ribulose-phosphate-3-epimerase
MAKIVPSVFGADIGRINEQLQVLEKNDIDLLHVDMMDGSFVPNIAFGPDQIKMMKKGTKLQFDVHMMVYEPDRYIPRLVEAGAHMITVHQEATTHLHRTIQLIKSYGVRAGVVLNPGTPPSTLEYVLDDIDCILLMTVNPGLGGQKFFQSSLEKIRKTKAYIGNRPIQIEVDGGVNDELAKECTLAGADLIVVGSYLFEGDIEANLEKLAKGVLTE
>NC_018588.1|WP_003721290.1|538081_538480_+|hypothetical-protein
MGSFFASFVDWLIGSPGRFVVNLIEDNMLIFMVVVMIYATTILYAKWTLAYYLPKKMSQLAEMKTWELDELYAAWQTEKKALPWYILVPSRNEFWVKSARNAPESTKLLHFSQQKLKLSDKEKLQKIIEIQS
>NC_018588.1|WP_014930080.1|537597_538065_+|PTS-sugar-transporter-subunit-IIA
MDVLEYCKEEMVRFSNEQNKEKLLAEMAEQLCEVGAVKPSYKDAVIKREKVFPTGLLTAHAGVAIPHTDSEHVIRPVVAVRILKKPVSFIEMASDNEAIDVRIVFMMALRSADEQLDMLQTLIQLIQDEEVMTTLLKAQETGDVLSAIEHFSKNN
>NC_018588.1|WP_003733192.1|536967_537570_+|SIS-domain-containing-protein
MDKQAILNNIHQTWQEEANAISRLPEVTSEEALVKTVEKIAECTGKIVVAGCGTSGVAAKKLVHSFNCIERPAVFLTPSDAVHGTLGVLQKEDILILISKGGNTGELLNLIPACKTKGSTLIGVTENPDSVIAKEADIFFPVSVSKEPDPFNMLATASTMAVIASFDAVIVCLMTYMNYTKEQFSVIHPGGAVGNKLLNK
>NC_018588.1|WP_010989498.1|534903_536964_+|BglG-family-transcription-antiterminator
MYLDNRSKTLFQEVIKNPNITNKQLEVKYKLSRYQISYSFQKVNEWLKWKNYPEVKRSKNGRFILEPELTALFSEKETRDPSVEYLPSENERANLILLMLLTSKEELSLAHFTTKIQVSKNTILRDLKVAQKLLPKETTVTYSRASGYQLAGSEWELRKVLTQVVSSVKEMFRGEHYFLSYSGIEKVQLMEIRRTLEEAEAMMQIKFTYEQIELLPYLLSVMFLRIRDRRLIDTAFHIDEKSLSDTREYHITDILLEKTGPVPEQERLFITLQLLTTNIFSGEILTEKLTEDLEKVVLTCLDLFEKKALVSLKNKHILIEKLLLHLKPAYYRIKYQMNLEDTLYEKFNQEFEALNFIVKEAFDPLAKFIGREIPAGEIFFISLFIGSDMIPQNDIYHKQKRAIVLCPSGVTFSKIMENILVKLFPEIHFYPTISVREYAFFKAEVDIVFSSIPLKDGENVFVVQPFMNDIEKTQLRQHVLQNLFGMGNQLTSIDKIMEVVERNADIKDPNAIRDGIIDILSANIATDENKRVKKVYLHDLITEDNIMICEDVKNYQEAIRLASQPLLLQQAITANYVKTMIDNHKFHDPYIIIGEDIAIPHAMPNAGVNRLAMSLLVVKNGVYFSETEQVHFVIVIAPVDKEQHIEALYQIVHLAENHQILDDLLENVTKEKIMQTINQLVIREDE
>NC_018588.1|WP_010989497.1|534144_534795_+|transaldolase
MHLDSANLDDVKKIQASSIFKGITTNPTILVKEKCNRQTAINRILELTDKQVFVQTVGFTYEEILADARMLLTMFGKDKIAIKIPAHEAGTNVIDTLKKEDKTIQILGTAIYSADQAITAALAGADFVAPYVNRMSAANIDPFKEITQMRHFFDKKALKTQIMAASFKHSGQVMQAYESGADTVTIPYEIYSQMTNKVLAVEAIRVFNEDAVLYEK
>NC_018588.1|WP_009930754.1|543639_544218_+|hypothetical-protein
MKKILVPILLLATILASCSSPNEKITKDTKISKTITIRADYKVPKDIKELEDDSANIVKVKFLQNKTIGKDGSTISEIEILTSYKGNLEKGSKVDISEPWYLSDGKYVAVENYIALDKEQEYTIFLGEKDKDTYPLSSLGYGKFGGSLKEDQAVLADFNILGEVQKFDFISENTEEVKNYQLIKEQVAGKYK
>NC_018588.1|WP_010989499.1|544325_545006_+|type-1-glutamine-amidotransferase
MIIDVLQHVPHEGPGLIANWARENQHQLKIHSLFEENAHVPNDSDFLIVLGGPMGINDTAEFPWLKDERKLIKRLSEQHKPVFGVCLGAQQIAATFGSEITVNKEKEVGWFPVKRTSDKLLFFPKSLNVFHWHQDTFALPTGSTRLFASEGCLNQAFLYGENIIGLQFHFEMEKAGIETILRIDEAFITPGKYVQSVEVMREKDVPEDNKQMLEAILDYLINPKTI
>NC_018588.1|WP_003721298.1|545030_545390_-|Lin0512-family-protein
MEQILFIQTGFGVDVHGQNITKAAERAVRNAIFTNSMPGIQGLLPDGDLQNMVVNIKLALPCDADQLDEDTIRAIIPYGTVTIEKMAGGMMTTSGIFLEDKEDKNDLMYIVNASVETGY
>NC_018588.1|WP_009932856.1|545396_545855_-|MarR-family-transcriptional-regulator
MNNEQNMNQQIALFYFGYKAFTETADLIIAKHSLKRLHHRILFFTARMPGLTINELLTFLEISKQALHQPLAELKERELLTIEQGRRDKRQRCIFLTSAGKELENELGAAQRKQMSEIFTNSADTDGMHFTEVMEGYAKNRPGAAFIKDFKE
>NC_018588.1|WP_003721301.1|548154_548586_+|universal-stress-protein
MEKYHRILVAVDGSEPAKLAFEKGLELALKLDGVLGIASIVDLRAFSPNVSYDGSLEEKAELELKTSVNEYAEKARTAGVKQVETFVAKGNPKILLSTDIPAEFQADLIICGATGMNRVEKLVLGSVSSYIMAHAICDTLIAR
>NC_018588.1|WP_010989501.1|548632_550063_-|CapA-family-protein
MKKLTYVIITGLVLVFIAGAFWITNSTNQSDQKATQTEPIKKISPANVKTISSEAKKTLNSLASSGADKASISDLKQLIKELKSYPTEKNDSGVYLQNLTACLEAVKSYTTGKADEKTLGKVYPAFLASEQKLSAIEKTNQYDWFYAAAATNQQGLKEKGVVTLTMVGDNSFGTYPETPEHLKFDNVFQKNNGNNTYVYKNCLPWFKSDDYTIINAESAFTNATKAENKMWRIKSDPAHVAFLPASGVDAANLANNHTMDYFQVGYDDTLKAFKENNIPVFNADAPLETTIKGMKTVLLGYDCRMSQQSPAYLERIVKDVKKYKKEDTLVIVNMHWGVEYRETPTDYQTQFGHAILDAGADIIMGSHPHRLESVEKYKDKYIVYSMGDFAFGADPTLLSRMTSMFQLRFTKEDNKIVLKDISIVPTYENSDGSTTENNYQPLPVFGDDAKKIVDELNRISKPIEGGVTEYTYFDPF
>NC_018588.1|WP_003721303.1|550183_550999_-|histidine-phosphatase-family-protein
MKKNIFKLLMALCAVLLIAGCGNSTSADKKETKETKEDGTVTFYVVRHGKTMLNTTDRVQGWSDAVLTPAGEEVVKSAGKGLKDVDFSAAYSSDSGRAIQTANLILKESDKSADKEVQTDPRFREFNFGSYEGDLNENMWTDIAKSQGKTLEEWQKAGLSPKDFANSVAALDKTRVKEGENWPAEDYATIQARLKEGLTDVAKKESKNGDSNVLLVSHGLSIGALLDTIEPGYKLPAEGIKNASVTKITYKDGKFTIGDVNDLSYVEKGSK
>NC_018588.1|WP_003727296.1|551279_551648_-|DUF1304-domain-containing-protein
MAILAFILTFIVMIEHIYIMILEMFFANTKLAAKTFGVEKELLANKKVQTLFANQGLYNGFLAAGLVWGLFFAGAGFAETVQIFFLSCVVVAALFGGATSSKGILVKQGLPAVLALVAVLLV
>NC_018588.1|WP_009931218.1|551794_553210_+|multidrug-efflux-MFS-transporter
MQQEATGGQKIRPIPIIASFLMAGFIGLFSETALNMALSDLIQVFDISSATVQWLTTGYLLTLGILVPISGLLLQWFTTRGLFFTAVSFSIAGTLIAALSPTFAMLMIGRVVQAVGTALLLPLMFNTILLIFPEHKRGSAMGMIGLVIMFAPAVGPTISGLILENLTWNWIFWISLPFLIIALLFGMKFMQNVSVVTKPKIDILSIILSTLGFGGVVFAFSSAGESGWGSATVLVSIIVGGIALGLFVWRQLTMEKPLMDLKVFKYPMFTLGLILVFISFMMILSTMILLPLYLQNSLALAAFSAGLVLLPGGVLNGLMSPFTGRLFDAYGPRALVIPGFIVAVVALFFLTRIEVGTSALTIIVLHSVLMIGISMVMMPAQTNGLNQLPPKLYPDGTAIMNTLQQVSGAIGTAVAITIMSAGQKAYMETAQGVGPEQMVASLTAGIQNAFVFGLIMACIGLLCSLFIRKAK
>NC_018588.1|WP_009931217.1|553340_554345_+|ROK-family-transcriptional-regulator
MAIPRDLKELNKKNIKSILRQQGAMTKAEIAEVTGLSVVTVNKLIRDLVENEEILEQDNSVATGGRRAVSYEINPNFQQVLVISLQEKWKKITYSFSVYNLLGEPEFVEDMSGEDLDITALKRNTKDIICAFPKISCVVIGVPGIEIGGKLRAMDFPLLLNVQLRETLEAEVNLPVLVETDTNAAILGYKNRPMKEENIVGLYYPERFPPGAGLLMNGEILKGQNGLAGEIKHMPLQVDWDNFDFSVDEIKAHIRKMALLTMSFYDPETIVLYTNFYFGQKDFMEELKEELKQVYPYAVLPEIVLSRKFTTDYRIGLLAFGIDYLENNMTDWRI

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Crispr_ID: NC_018588_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018588_4

2807979-2808089

Orphan

Consensus_repeat	Method
AGCGATGATTTAATCCTTCCCAGAACTTTCAAAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_018588_4

>merge|NC_018588|4|2807979-2808089|CRISPRCasFinder
AGCGATGATTTAATCCTTCCCAGAACTTTCAAAATGTACTTTATTTTGATTTAGTTCTTCAATATAAATCTGAGCAAAGCGATGATTTAATCCTTCCCAGAACTTTCAAAA

>NC_018588|4|3|2807979-2808089|CRISPRCasFinder
AGCGATGATTTAATCCTTCCCAGAACTTTCAAAA	TGTACTTTATTTTGATTTAGTTCTTCAATATAAATCTGAGCAA
AGCGATGATTTAATCCTTCCCAGAACTTTCAAAA

Protein	Signature genes	Signature genes Name	Protein_function
NC_018588.1\|WP_003732088.1\|2814716_2815655_-\|GW-domain-containing-glycosaminoglycan-binding-protein	unknown	unknown	gnl\|CDD\|226309
NC_018588.1\|WP_003732084.1\|2806125_2807865_-\|DNA-polymerase-III-subunit-gamma/tau	unknown	unknown	gnl\|CDD\|235505
NC_018588.1\|WP_009931588.1\|2811020_2811176_+\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_003722067.1\|2808858_2809080_-\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_003732087.1\|2813086_2814601_-\|gluconokinase	unknown	unknown	gnl\|CDD\|212659
NC_018588.1\|WP_003722062.1\|2805073_2805670_-\|recombination-protein-RecR	unknown	unknown	gnl\|CDD\|234616
NC_018588.1\|WP_003722074.1\|2815697_2816645_-\|LPXTG-cell-wall-anchor-domain-containing-protein	unknown	unknown	gnl\|CDD\|273478
NC_018588.1\|WP_003722056.1\|2800915_2801512_+\|dihydroxyacetone-kinase-subunit-L	unknown	unknown	gnl\|CDD\|274099
NC_018588.1\|WP_003722065.1\|2808191_2808656_-\|DUF3284-domain-containing-protein	unknown	unknown	gnl\|CDD\|378692
NC_018588.1\|WP_003722061.1\|2804813_2805059_-\|YaaL-family-protein	unknown	unknown	gnl\|CDD\|378478
NC_018588.1\|WP_003722063.1\|2805778_2806096_-\|YbaB/EbfC-family-nucleoid-associated-protein	unknown	unknown	gnl\|CDD\|234669
NC_018588.1\|WP_009925039.1\|2811747_2812389_-\|hypothetical-protein	unknown	unknown	unknown
NC_018588.1\|WP_009930438.1\|2801515_2801890_+\|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM	unknown	unknown	gnl\|CDD\|184702
NC_018588.1\|WP_009930437.1\|2799904_2800894_+\|dihydroxyacetone-kinase-subunit-DhaK	unknown	unknown	gnl\|CDD\|237724
NC_018588.1\|WP_003725004.1\|2809214_2810579_-\|PTS-sugar-transporter-subunit-IIC	unknown	unknown	gnl\|CDD\|224372
NC_018588.1\|WP_009931159.1\|2803925_2804768_+\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|223729
NC_018588.1\|WP_003727657.1\|2808673_2808856_-\|DUF3188-domain-containing-protein	unknown	unknown	gnl\|CDD\|371501
NC_018588.1\|WP_010990044.1\|2801995_2802847_+\|MurR/RpiR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224651
NC_018588.1\|WP_014601547.1\|2816785_2818525_-\|thiol-reductant-ABC-exporter-subunit-CydC	unknown	unknown	gnl\|CDD\|227320
NC_018588.1\|WP_010990045.1\|2802965_2803805_+\|Cof-type-HAD-IIB-family-hydrolase	unknown	unknown	gnl\|CDD\|319818

Protein	Function_ID	Function_description	E-value
NC_018588.1\|WP_003732088.1\|2814716_2815655_-\|GW-domain-containing-glycosaminoglycan-binding-protein	gnl\|CDD\|226309	COG3786, COG3786, Uncharacterized protein conserved in bacteria [Function unknown].	3.04876e-98
NC_018588.1\|WP_003732084.1\|2806125_2807865_-\|DNA-polymerase-III-subunit-gamma/tau	gnl\|CDD\|235505	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated.	0
NC_018588.1\|WP_003732087.1\|2813086_2814601_-\|gluconokinase	gnl\|CDD\|212659	cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY family of carbohydrate kinases. This subfamily is composed of a group of gluconate kinases (GntK, also known as gluconokinase; EC 2.7.1.12) encoded by the gntK gene, which catalyzes the ATP-dependent phosphorylation of D-gluconate and produce 6-phospho-D-gluconate and ADP. The presence of Mg2+ might be required for catalytic activity. The prototypical member of this subfamily is GntK from Lactobacillus acidophilus. Unlike Escherichia coli GntK, which belongs to the superfamily of P-loop containing nucleoside triphosphate hydrolases, members in this subfamily are homologous to glycerol kinase, xylulose kinase, and rhamnulokinase from Escherichia coli. They have been classified as members of the FGGY family of carbohydrate kinases, which contain two large domains separated by a deep cleft that forms the active site. This model spans both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. Some uncharacterized homologous sequences are also included in this subfamily. The Lactobacillus gnt operon contains a single gntK gene. The gnt operons of some bacteria, such as Corynebacterium glutamicum, have two gntK genes. For example, the C. glutamicum gnt operon has both a gluconate kinase gntV gene (also known as gntK) and a second hypothetical gntK gene (also known as gntK2). Both gluconate kinases encoded by these genes belong to this family, however the protein encoded by C. glutamicum gntV is not included in this model as it is truncated in the C-terminal domain.	0
NC_018588.1\|WP_003722062.1\|2805073_2805670_-\|recombination-protein-RecR	gnl\|CDD\|234616	PRK00076, recR, recombination protein RecR; Reviewed.	7.77001e-132
NC_018588.1\|WP_003722074.1\|2815697_2816645_-\|LPXTG-cell-wall-anchor-domain-containing-protein	gnl\|CDD\|273478	TIGR01167, Zinc_metalloprotease_ZmpB, LPXTG-motif cell wall anchor domain. This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region. [Cell envelope, Other].	1.13667e-05
NC_018588.1\|WP_003722056.1\|2800915_2801512_+\|dihydroxyacetone-kinase-subunit-L	gnl\|CDD\|274099	TIGR02365, dha_L_ycgS, dihydroxyacetone kinase, phosphoprotein-dependent, L subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the subunit homologous to the E. coli YcgS subunit.	3.29756e-82
NC_018588.1\|WP_003722065.1\|2808191_2808656_-\|DUF3284-domain-containing-protein	gnl\|CDD\|378692	pfam11687, DUF3284, Domain of unknown function (DUF3284). This family of proteins with unknown function appears to be restricted to Firmicutes.	5.35099e-31
NC_018588.1\|WP_003722061.1\|2804813_2805059_-\|YaaL-family-protein	gnl\|CDD\|378478	pfam10704, DUF2508, Protein of unknown function (DUF2508). This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known.	2.68189e-15
NC_018588.1\|WP_003722063.1\|2805778_2806096_-\|YbaB/EbfC-family-nucleoid-associated-protein	gnl\|CDD\|234669	PRK00153, PRK00153, YbaB/EbfC family nucleoid-associated protein.	3.53269e-41
NC_018588.1\|WP_009930438.1\|2801515_2801890_+\|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM	gnl\|CDD\|184702	PRK14484, PRK14484, phosphotransferase mannnose-specific family component IIA; Provisional.	1.1917e-48
NC_018588.1\|WP_009930437.1\|2799904_2800894_+\|dihydroxyacetone-kinase-subunit-DhaK	gnl\|CDD\|237724	PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK; Provisional.	0
NC_018588.1\|WP_003725004.1\|2809214_2810579_-\|PTS-sugar-transporter-subunit-IIC	gnl\|CDD\|224372	COG1455, CelB, Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism].	3.47828e-162
NC_018588.1\|WP_009931159.1\|2803925_2804768_+\|aldo/keto-reductase	gnl\|CDD\|223729	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only].	6.97706e-130
NC_018588.1\|WP_003727657.1\|2808673_2808856_-\|DUF3188-domain-containing-protein	gnl\|CDD\|371501	pfam11384, DUF3188, Protein of unknown function (DUF3188). This bacterial family of proteins has no known function.	1.21027e-11
NC_018588.1\|WP_010990044.1\|2801995_2802847_+\|MurR/RpiR-family-transcriptional-regulator	gnl\|CDD\|224651	COG1737, RpiR, Transcriptional regulators [Transcription].	6.1079e-63
NC_018588.1\|WP_014601547.1\|2816785_2818525_-\|thiol-reductant-ABC-exporter-subunit-CydC	gnl\|CDD\|227320	COG4987, CydC, ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones].	0
NC_018588.1\|WP_010990045.1\|2802965_2803805_+\|Cof-type-HAD-IIB-family-hydrolase	gnl\|CDD\|319818	cd07516, HAD_Pase, phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily. Escherichia coli Cof is involved in the hydrolysis of HMP-PP (4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate, an intermediate in thiamin biosynthesis), Cof also has phosphatase activity against the coenzymes pyridoxal phosphate (PLP) and FMN. Thermotoga maritima TM0651 acts as a phosphatase with a phosphorylated carbohydrate molecule as a possible substrate. Escherichia coli YbhA is also a member of this family and catalyzes the dephosphorylation of PLP, YbhA can also hydrolyze erythrose-4-phosphate and fructose-1,6-bis-phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.	1.49073e-86

>NC_018588.1|WP_003732084.1|2806125_2807865_-|DNA-polymerase-III-subunit-gamma/tau
MAYQALYRVFRPQSFQDVVGQEHVTKTLKNAIVQNKTSHAYLFSGPRGTGKTSAAKIFAKAINCEHGHDGEPCNECEICKGTTDGSIPDVLEIDAASNNGVEEIRDIREKVKYAPTVAKYKVYIIDEVHMLSTGAFNALLKTLEEPPKHVIFILATTEPHKLPLTIISRVQRFDFKRITTQDIIGRLKFILEEEKIPYDEKALMIVARAAEGGMRDALSLLDQVISYGSEEVTVEDALEITGSVAQNLLTKLVSAAFDGDAAEAISTLTALLAEGKDPVRLVEDLLVFFRDVLLYQKAPNLEETMERALIDDDFVALAKRADSLKVYEFVKILNTAQQQMRFSNHPGIYVEVALVQLTQAGQSVAGGGNVPADAASGSDVSDLKRQMEQMHQEIQTLKKQIASGAGAAPADKPTQNRGGSKKAINNGKQFKAPIGKINHVLGEAKKENLQLIRGCWGELLSMLMASQAALLNDAEPVAASQDTFVLKFKHEIHCQMAMDNPNFVETITSSIARLTQVNYTFIGIPEDQWADVRENFLHSHGSDADAEDGANPEAKKPAEDPFVAEAAKLVGEDLLEIKD
>NC_018588.1|WP_003722063.1|2805778_2806096_-|YbaB/EbfC-family-nucleoid-associated-protein
MRGMGNMQGMMKQMQKMQKEMAKAQADLEAQEFTGTAGGGMVTVKATGKRVITDVVINEEVVDPEDIEMLQDLVLAATNDVLKQIEDTTSQTMGKFTQGLNIPGM
>NC_018588.1|WP_003722062.1|2805073_2805670_-|recombination-protein-RecR
MHYPEPITKLIDSFMKLPGIGPKSAARLAFYVLDMKEDDVLDFAKALVDAKRNLSFCSVCGHITDKDPCYICADTSRDRSVICVVQESKDVIAMEKMRDFHGLYHVLHGTISPMDGIGPEDINIPDLLKRLQDDTIEEVILATNPNVEGEATAMYISRLLKPSGIKVTRIAHGLPVGGDLEYADEVTLSKAMEGRREV
>NC_018588.1|WP_003722061.1|2804813_2805059_-|YaaL-family-protein
MESRSNKFGRKKNKKIGKLHKSYDAYLMELIEVTQENWHKQKVLMRKSFEYDPNLEYEEKKAEARYFYLFKEARTRQLKNK
>NC_018588.1|WP_009931159.1|2803925_2804768_+|aldo/keto-reductase
MTLSFSDTYRLNNGIEMPRHGFGVYKLTDEARMRTALETAVDVGYRLFDTASFYHNEKELGDFFASSGLKRDEFFVTTKMWNTEQGYDETLRAFEKSQKKLQLDQIDLYLVHWPKQDTFFDTWRAVEKLYDEGLVRAIGVSNFEAHHLDRLRTSANVLPVVDQLETHPHFPNHLLHRYLEELHIVHQAWSPLGRGGVLQEQILIDLAEKHGKSPAQIVLRWHLQNNISIIPKSETPSRIRENAAIYDFELSEADMRQVERLNTGERVSHAPDVMYVRSEI
>NC_018588.1|WP_010990045.1|2802965_2803805_+|Cof-type-HAD-IIB-family-hydrolase
MTTQAIILDIDGTLLNDDKQISPETKKALITAQENGVKLILASGRPTTGMHVYAEQLEMEKHHGLLVSYNGAKVVDCATNEELFNQALTVEEGKAVLEHMKQFEVKVMIDKEDYMYTNDVYDCYVPYRGEEINIIQYESRGGNFKLCEKDDLAAFLDYRLSKILTAGDPAYMQKNYQAMMAPFKDTLNCVFTADFYFEFTAQGIDKAKALDTVLTPMGIHAENVIAFGDGHNDITMVEYAGTGIAMQNAVPELKAAASSVTLSNNEDGIAHVLNSLIPS
>NC_018588.1|WP_010990044.1|2801995_2802847_+|MurR/RpiR-family-transcriptional-regulator
MNILIKIRELTNLTNSEKELANYILANPKKTLQFKPKELATAAFVSAATIYRLINKLGLNGIGELKIEIASSLRETSEEKDLNYDYPILESDTPYQIMTNLHQIYKGTIDETLNNADPEELVKIGEKLIQAKTIDVYAASANLFFAQNFKFQMQEIGVLVNVPEEDYIQSLSAANSDENHIAIVVSYGGRSRTLQRVVKILSENNVDIILITSMQDNPLVEFATHKIYMASAENHYNKVSSFSTRQSLLSIFDTLYSIYFNQNYEKNIQYKTTNYQKMNTELE
>NC_018588.1|WP_009930438.1|2801515_2801890_+|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM
MAKPYGVVIISHSKDVAKGVHDIIKEIAPDVSITHAGGTEDGRIGTSFDAVNEAIENNEANKVYTFYDLGSAKMNIETVEEISEKEIILFNAPILEGAYATAAQVQMDEKPEVIAANLKTIEIK
>NC_018588.1|WP_003722056.1|2800915_2801512_+|dihydroxyacetone-kinase-subunit-L
MTYDKDWALRWLNDFGERVQENKQLLSDLDQAIGDGDHGINMARGLGELKKAFTEKEPADLKDVFKTAGMTMVSKVGGASGPLYGTAFLNMSKAVDADTIDAVGLTKVIEAGLEGIEKRGKSHAGEKTMIDVWEPVVHALHQEDLTDDVVDAALQKTKDLKATKGRASYLGERSIGHLDPGAYSSALLFHAMLQTEVS
>NC_018588.1|WP_009930437.1|2799904_2800894_+|dihydroxyacetone-kinase-subunit-DhaK
MKKILNGTDQVVEQMVEGLVKSHADVVHRVEGTRVIARNDKRPGKVGLVSGGGSGHEPAHAGYVGRGMLSAAVCGDVFTSPTPDQIYEGIKAADQGAGVLLIVKNYTGDVMNFEMAADLADADDIKVEQIVVDDDIAVEDSTFTTGRRGVAGTVLVHKIIGAAAEAGASLDELKALGEKVIASVKTLGVALSPCTVPEVGHPGFELGDDEIELGIGIHGEPGFTREKIMPSASLAKQLYERISNESKLLAGDKVVVLVNGMGATPLMEQYVFANDVHELLKNAGVQVEKTLVGDYMTSLEMAGLSLTILKLEDEKWVDMLKLPVDTIAW
>NC_018588.1|WP_003722065.1|2808191_2808656_-|DUF3284-domain-containing-protein
MNVTQKLYISQKECFDTLVSSAIYDVKNATGKTLQVRKLEGYKYQRTMSNGALATTKIVKVQPNELYQFETSSRVNTHTTTYTIKSTSETTCEVTYNELIETEKALNKMNNIIVGFMFGFFRKKRVKNLLKSIELSVINESKQKQEKLAAKSEQ
>NC_018588.1|WP_003727657.1|2808673_2808856_-|DUF3188-domain-containing-protein
MKIVNALFLISIGLIIIMFSPSYGKDGMASVPLLVTGLAVVLIGCVFIVLKIRKDKKEKN
>NC_018588.1|WP_003722067.1|2808858_2809080_-|hypothetical-protein
MIILNCPMKRDYITELLETYDKDGVTFKKIDEKGMKLTFETNIEDEEKAAKIAKETIKATEIGSVLYFQVSVG
>NC_018588.1|WP_003725004.1|2809214_2810579_-|PTS-sugar-transporter-subunit-IIC
MNGLTAFLEKYFVPVAAKIGSQKHLVALRDAFISTMPITMAGSIAVLLNAFFRDFPTDWGWTGFVEAMQPLIGINGYVYNGTLAIVSIIFAFSLGYNLSKAYEVDRLAGGLVSLAAFVMNLTVTVSLDAVKAAIAASNANFDVATLPKEFAGIYGFFSLSQVNGTGLFTAMIFGFISTIIYAKLMRRNIIIKMPDSVPPAVSKAFAAIIPALVALYVVGIIDWAFFKITNMDVITWISKTIQEPLLSLSQGYGAVLLVTFLVQLLWFFGIHGPNVLAPVLESLWGTAQLQNISAAQEGAKLPFEWVRGSFDAYVWMGGSGGTLVLIIALLMFSKRADARTVAKLSLAPGIFNINEPIMFGLPIVLNTIYLIPFLIAPMVMVTIAYFATTLGIVGPVKIAVVWVMPPLLNSFLATGGDWMAPVISLINMVVAFLIWVPFVITANRVGVPEEEMKA
>NC_018588.1|WP_009931588.1|2811020_2811176_+|hypothetical-protein
MAVKRDMPEESKNSKVVKKEHFSIVFPDDIKEPATVEEKKKQDAEKKTDDN
>NC_018588.1|WP_009925039.1|2811747_2812389_-|hypothetical-protein
MQQLKSKKKWLPALIVAVFVGIIVILAIMFGFFQRQEVFDKYEVAYEIDGKLYEVFPISATDIGVDKKSKDKNLYFRVNSYYNIDYLFRLAYKQYEINEPSTNKYYSGLIDYSVADNAYVTQKDVYITNNESYATYDFFDKNGKKIYTYNPEETSNDDYIVRIKPTILQGYEKSDIGSYDDYLNITALFKDKLGMDVNVRIDEDKEMVIFSIK
>NC_018588.1|WP_003732087.1|2813086_2814601_-|gluconokinase
MTSKPYIMGVDIGTSSTKAVLFNQRGEVIFRQATHYELITDETGKAEESPTEIFDAVLTSIQAVMKNINTEELAGISFSSAMHSLIMVGSNGELLTECITWADGRSSETLEKVKRDNYLFQLYEATGTPIHPMSPFAKICWLKEEKPTLFKRTEKFVDIKSYILYRLFGVWVMDESLASGTGLYNIMEHDWEFEAMEIVKLTPDFLPKVVPETYQLAGVKKEYAELMGIPENLPFIIGGSDGALANIGIQATGQNDVTITVGTSGAVRKLTDQFQIDSRGRTFCYGAGDGYFIAGGAVNNGGKVVEWGLQQFGSEAEISRRDFASFIAKIEEVPPGAAGLLFQPYLLGERAPFWTNDIRGGFVGLTINHTKAHFIRAILEGVAFNLAEVYEAVSAPDDIIYVTGGISAHDAWCKLLADILNREIRVPHTIEGSSLGAAIIGMRSLGILKDLNLKHTLPIKAVYHPSENVLKYAELRLIFKQVTTQLMSSYSQLNSWQKKFDINS
>NC_018588.1|WP_003732088.1|2814716_2815655_-|GW-domain-containing-glycosaminoglycan-binding-protein
MKKLLSGLIVVLMVSLLGHSFNAEAASYEKIIYDKAVNLKGVVNQSKRNDGINSKMYKTSSSVKYLGSAKKYDKKTLIITREGKTARAKWYYCKLGNTTIGWIDSRAFTNIGKPTIADAVPALWNSKKAIITTKPKSTTATTYFFQKNSAGNWYEVRHFTSHIGKWGFDPKFSEKSSGTPVGVYRTGIAFGQKGNPGTKLTFRAITNRSYWISNSNDKAYNTWQERNSSSSADEKMKIPQYKYGMEVKYNAKRVKGKGSAVFYHVDSPKYNYTLGCVAQSEANTKEVLKFADKNTLIVLGEESRIKTFYGIN
>NC_018588.1|WP_003722074.1|2815697_2816645_-|LPXTG-cell-wall-anchor-domain-containing-protein
MKKFHGLILTALVTCLIIPFSLAASAETNENGNNSTPTEEKTTDTTENIITEEKTEPAEPTKDTTVTPPQKSKVQTTIDITDSQEVYSYEQNSKIDLKDFTATLTDYTDTKLTNYRLAANSKLSTAQTGIQEVTLLGDNEDGKTTAVKLNYLVKEKTAQLTITDMNFDLETKIFTGKTKPFASVYMSSPADENFGEGTTTADKDGYFYAEWATTPKQITAYAFDESGNYSEEVTYQVPAKKQNEAVVTAPDKVKKIETKNAVKSATTKPTDVTKVTKDDKTDLPSTGDKGTEWIFVVAGVIVILVAVLLLRKRKK
>NC_018588.1|WP_014601547.1|2816785_2818525_-|thiol-reductant-ABC-exporter-subunit-CydC
MRKSSWIIPYIKENRGLFLLVIFLGTLTFASAGALMFTSGHLISKSSLMPESIMAVYISTVGVRAFGIMRSVSRYVERLSSHSLVLRILEKMRVRLYRLLEPQALLLKSRYKTGDILGLLAGDIEHLQNFYLTTMLPAIVSLVLYAGVVIALGAFSIPFAALFVLLIGLLVLVLPWVSLLYARGKNAYLKQGRNSLYQKFTDAVFGISDWKFSGREKTFISNYEKDEADMLRTENKQFHFVNWRDFFSQLVVGFMVIVMVYWSTAESRDGAFSGTLIAAFVLAIMALAEAFVPVSSAISDKSLYQDSLARLDKIEDPALPTFEEETKEIERINTENVVLKAENLTFAYNEKSPEILNGFDFTLQQGEKVAIIGRSGTGKSTFLKLVQGALLPTAGKVTMNDVEVEKLRPQIPELTSMLNQKAHLFSTTVLNNIRLGNQDASDEEVYEAAKKVQLHDFIMSMPDGYHTQMSEMGERFSGGERGRIALARILLQNTPIVILDEPTVGLDPITERDLLATIFETLADKSLIWVTHHLVGAEKMDRVLFLEEGKTLMEGPHAELMAEEPRYKRLYQLDRPIEL

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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
NC_018588_3	3.3\|543251\|35\|NC_018588\|PILER-CR,CRISPRCasFinder,CRT	543251-543285	35	MH341453	Listeria phage PSU-VKH-LP041, complete genome	10139-10173	1	0.971
NC_018588_3	3.3\|543251\|35\|NC_018588\|PILER-CR,CRISPRCasFinder,CRT	543251-543285	35	NC_009813	Listeria phage B054, complete genome	10139-10173	2	0.943

1. spacer 3.3|543251|35|NC_018588|PILER-CR,CRISPRCasFinder,CRT matches to MH341453 (Listeria phage PSU-VKH-LP041, complete genome) position: , mismatch: 1, identity: 0.971

gcgatttttgtcaaagggacagcgatgggttacaa	CRISPR spacer
gcgatttttgtcaaaggaacagcgatgggttacaa	Protospacer
*****************.*****************

2. spacer 3.3|543251|35|NC_018588|PILER-CR,CRISPRCasFinder,CRT matches to NC_009813 (Listeria phage B054, complete genome) position: , mismatch: 2, identity: 0.943

gcgatttttgtcaaagggacagcgatgggttacaa	CRISPR spacer
gcgatttttgtcaaaggaacggcgatgggttacaa	Protospacer
*****************.**.**************

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

120653 : 127178

Listeria_phage(33.33%)

tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003721739.1\|120653_121106_-	ImmA/IrrE family metallo-endopeptidase	A0A059T7S0	Listeria_phage	4.0e-31	47.9
WP_003721740.1\|121111_121447_-	helix-turn-helix transcriptional regulator	A0A2H4JAR9	uncultured_Caudovirales_phage	4.0e-20	52.5
WP_003732219.1\|121663_122092_+	hypothetical protein	NA	NA	NA	NA
WP_003721742.1\|122103_122520_+	hypothetical protein	A8ASQ1	Listeria_phage	1.3e-20	39.3
WP_009930418.1\|122797_123187_+	DUF5072 family protein	NA	NA	NA	NA
WP_003721744.1\|123199_123712_+\|tail	phage major tail protein, TP901-1 family	A0A097PBF4	Streptococcus_pyogenes_phage	1.2e-47	62.7
WP_003721745.1\|123759_124062_+	hypothetical protein	NA	NA	NA	NA
WP_009930419.1\|124103_124508_+	hypothetical protein	NA	NA	NA	NA
WP_010989347.1\|124494_126363_+	membrane protein	A0A097PAU2	Streptococcus_pyogenes_phage	3.5e-20	45.8
WP_009911828.1\|126359_127178_+\|tail	phage tail family protein	A0A060AFE1	Staphylococcus_phage	7.2e-39	35.0

DBSCAN-SWA_2

1122798 : 1130221

Hokovirus(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003721506.1\|1122798_1123182_+	glycerol-3-phosphate cytidylyltransferase	A0A1V0SGE7	Hokovirus	1.4e-16	40.7
WP_010989659.1\|1123203_1124187_+	glycosyltransferase family 2 protein	A0A1V0SAH6	Catovirus	4.1e-12	34.6
WP_010989660.1\|1124201_1125215_+	glycosyltransferase	A0A1V0SAH6	Catovirus	7.9e-11	32.0
WP_003721509.1\|1125423_1126914_+	nicotinate phosphoribosyltransferase	G3MA18	Bacillus_virus	9.5e-114	49.7
WP_009931487.1\|1126925_1127750_+	ammonia-dependent NAD(+) synthetase	G3MA24	Bacillus_virus	7.4e-68	52.6
WP_009931485.1\|1127762_1128071_+	antibiotic biosynthesis monooxygenase	NA	NA	NA	NA
WP_009931483.1\|1128131_1128536_+	PTS sugar transporter subunit IIB	NA	NA	NA	NA
WP_010989661.1\|1128664_1130221_+	glutamine-hydrolyzing GMP synthase	A0A1V0SH76	Hokovirus	2.3e-17	28.1

DBSCAN-SWA_3

1244271 : 1324817

102

Listeria_phage(76.67%)

portal,holin,protease,tRNA,integrase,terminase,tail,capsid

attL 1244155:1244171|attR 1287114:1287130

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1244155:1244171	attL	NA	NA	NA	NA
WP_014930113.1\|1244271_1245426_-\|integrase	site-specific integrase	A8ATC7	Listeria_phage	2.0e-207	94.8
WP_025283118.1\|1246632_1247085_-	ImmA/IrrE family metallo-endopeptidase	R4IBK9	Listeria_phage	9.7e-78	89.3
WP_014930118.1\|1247105_1247429_-	helix-turn-helix transcriptional regulator	Q8W5Y0	Listeria_phage	8.8e-33	66.4
WP_009931099.1\|1248232_1248556_+	hypothetical protein	NA	NA	NA	NA
WP_009929536.1\|1248570_1248774_+	helix-turn-helix transcriptional regulator	A0A059T5F8	Listeria_phage	3.1e-28	100.0
WP_009931097.1\|1248775_1249018_+	hypothetical protein	A8ATD2	Listeria_phage	5.4e-43	98.8
WP_009931096.1\|1249440_1249593_+	hypothetical protein	A0A059T7S2	Listeria_phage	3.4e-19	98.0
WP_009931094.1\|1249729_1250020_+	hypothetical protein	A0A059T7V3	Listeria_phage	1.8e-40	89.4
WP_031659545.1\|1250037_1250220_+	hypothetical protein	NA	NA	NA	NA
WP_009931092.1\|1250230_1250398_+	hypothetical protein	A8ASN5	Listeria_phage	8.9e-21	92.7
WP_014930119.1\|1250413_1250689_+	hypothetical protein	R4ICD2	Listeria_phage	3.4e-41	94.3
WP_009931089.1\|1250685_1251129_+	hypothetical protein	NA	NA	NA	NA
WP_014930120.1\|1251145_1251454_+	hypothetical protein	NA	NA	NA	NA
WP_014930121.1\|1251450_1252014_+	DUF1642 domain-containing protein	A8ATD8	Listeria_phage	1.6e-58	61.5
WP_157824771.1\|1252185_1252359_+	pentapeptide repeat-containing protein	NA	NA	NA	NA
WP_009932944.1\|1252585_1253215_+	hypothetical protein	A0A191KBJ8	Streptococcus_virus	2.4e-66	57.9
WP_003722554.1\|1253233_1253401_+	hypothetical protein	NA	NA	NA	NA
WP_045131531.1\|1253504_1253681_+	hypothetical protein	A0A076G7F4	Listeria_phage	5.5e-21	86.2
WP_014930124.1\|1253677_1254079_+	hypothetical protein	A8ATD9	Listeria_phage	7.8e-71	95.5
WP_025283119.1\|1254075_1254282_+	hypothetical protein	A0A059T6C7	Listeria_phage	1.7e-29	92.6
WP_154079741.1\|1254308_1254479_+	hypothetical protein	A0A059T654	Listeria_phage	2.4e-21	92.3
WP_023548953.1\|1254475_1254910_+	hypothetical protein	A8ATS7	Listeria_phage	2.5e-38	52.8
WP_009933642.1\|1254942_1255116_+	hypothetical protein	A0A059T5G3	Listeria_phage	5.2e-24	100.0
WP_009933640.1\|1255112_1255313_+	hypothetical protein	A0A059T6A2	Listeria_phage	2.6e-11	58.1
WP_014930125.1\|1255309_1255921_+	hypothetical protein	B6D7K1	Listeria_phage	6.8e-50	49.5
WP_009933853.1\|1255935_1256169_+	hypothetical protein	NA	NA	NA	NA
WP_014930126.1\|1256165_1256936_+	DUF1351 domain-containing protein	B6D7K2	Listeria_phage	3.3e-17	27.4
WP_014930127.1\|1256938_1257574_+	hypothetical protein	NA	NA	NA	NA
WP_014930128.1\|1257646_1259335_+	hypothetical protein	A8ATS1	Listeria_phage	1.6e-125	43.6
WP_014930129.1\|1259337_1261143_+	primase	A8ATS2	Listeria_phage	3.5e-126	40.2
WP_025283122.1\|1261558_1262092_+	DUF3310 domain-containing protein	A8ATF5	Listeria_phage	1.3e-76	79.4
WP_009930672.1\|1262092_1262248_+	hypothetical protein	NA	NA	NA	NA
WP_003731655.1\|1262309_1262537_+	hypothetical protein	NA	NA	NA	NA
WP_009917712.1\|1262549_1262975_+	DUF722 domain-containing protein	A0A059T6H4	Listeria_phage	8.0e-74	100.0
WP_010991275.1\|1263072_1263816_+	DUF559 domain-containing protein	NA	NA	NA	NA
WP_014930130.1\|1264062_1264389_+	hypothetical protein	A0A059T5G5	Listeria_phage	2.2e-55	100.0
WP_009931610.1\|1264388_1264703_+	HNH endonuclease	A8ATF8	Listeria_phage	5.0e-57	98.1
WP_012951543.1\|1264752_1265109_+\|terminase	P27 family phage terminase small subunit	A0A059T7Y1	Listeria_phage	2.0e-46	98.0
WP_012951544.1\|1265105_1266749_+\|terminase	terminase large subunit	A0A059T7Q8	Listeria_phage	0.0e+00	99.3
WP_009917707.1\|1266758_1267148_-	DUF2513 domain-containing protein	A0A1Q1PVT8	Staphylococcus_phage	3.7e-17	39.8
WP_012951545.1\|1267198_1268329_+\|portal	phage portal protein	A0A059T6F0	Listeria_phage	2.8e-214	99.5
WP_012951546.1\|1268325_1269042_+\|protease	Clp protease ClpP	A0A1S5SFF8	Streptococcus_phage	9.3e-67	59.0
WP_012951547.1\|1269068_1270220_+\|capsid	phage major capsid protein	A0A059T678	Listeria_phage	3.1e-213	99.5
WP_012951548.1\|1270226_1270397_+	hypothetical protein	A0A059T7Y2	Listeria_phage	6.3e-22	100.0
WP_009934007.1\|1270406_1270706_+	hypothetical protein	A8ATA0	Listeria_phage	9.9e-47	98.0
WP_009934006.1\|1270689_1271055_+	hypothetical protein	A0A059T6F2	Listeria_phage	1.6e-62	96.7
WP_012951550.1\|1271051_1271453_+	hypothetical protein	A0A059T5F3	Listeria_phage	2.1e-68	100.0
WP_009931623.1\|1271449_1271833_+	hypothetical protein	A0A059T681	Listeria_phage	6.1e-65	96.1
WP_009931624.1\|1271853_1272441_+\|tail	phage tail protein	A0A059T7Y4	Listeria_phage	4.0e-108	100.0
WP_014930131.1\|1272511_1272844_+	hypothetical protein	A0A059T7R2	Listeria_phage	1.1e-51	97.3
WP_009931626.1\|1272894_1273056_+	hypothetical protein	A0A059T6F4	Listeria_phage	4.3e-20	98.0
WP_014930132.1\|1273059_1277991_+\|tail	phage tail tape measure protein	A0A059T5F4	Listeria_phage	0.0e+00	96.5
WP_014930133.1\|1277978_1279628_+\|tail	phage tail family protein	A0A059T682	Listeria_phage	0.0e+00	99.3
WP_012951555.1\|1279640_1281935_+\|tail	phage tail protein	A0A059T7Y6	Listeria_phage	0.0e+00	94.0
WP_031644619.1\|1281924_1283019_+	hypothetical protein	A0A059T7R4	Listeria_phage	2.2e-184	87.9
WP_012951557.1\|1283066_1283369_+	hypothetical protein	A0A059T5E6	Listeria_phage	1.7e-38	93.0
WP_012951558.1\|1283368_1283626_+\|holin	phage holin	A8ATB7	Listeria_phage	3.2e-25	69.0
WP_014930134.1\|1283625_1284468_+	M15 family metallopeptidase	A0A059T7Y8	Listeria_phage	9.5e-127	81.6
WP_012951560.1\|1284571_1285570_+	DUF3644 domain-containing protein	A0A0N9RUA4	Staphylococcus_phage	3.9e-71	44.8
WP_003769913.1\|1285784_1285991_-	hypothetical protein	A0A059T7Z0	Listeria_phage	1.3e-16	82.8
WP_009933529.1\|1286580_1286814_+	hypothetical protein	R4IDW6	Listeria_phage	2.8e-28	78.9
WP_010989715.1\|1287495_1288854_+	DUF1254 domain-containing protein	NA	NA	NA	NA
1287114:1287130	attR	NA	NA	NA	NA
WP_010989716.1\|1288895_1289489_-	DUF1801 domain-containing protein	NA	NA	NA	NA
WP_009914084.1\|1289642_1290050_-	glyoxalase/bleomycin resistance/extradiol dioxygenase family protein	NA	NA	NA	NA
WP_009924169.1\|1290214_1290814_+	histidine phosphatase family protein	A0A1X9IGJ2	Lactococcus_phage	5.8e-30	41.0
WP_003723543.1\|1290845_1291106_-	hypothetical protein	NA	NA	NA	NA
WP_010989717.1\|1291229_1292642_+	ATP-dependent RNA helicase DbpA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	8.3e-51	31.8
WP_003723545.1\|1292666_1292930_+	DUF3116 family protein	NA	NA	NA	NA
WP_003723546.1\|1293097_1293574_+	8-oxo-dGTP diphosphatase	NA	NA	NA	NA
WP_003723547.1\|1293611_1293857_-	hypothetical protein	NA	NA	NA	NA
WP_003723548.1\|1293853_1295059_-	MFS transporter	NA	NA	NA	NA
WP_003723549.1\|1295263_1295923_+	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_003723550.1\|1295964_1296159_-	hypothetical protein	NA	NA	NA	NA
WP_003723551.1\|1296225_1297074_-	YitT family protein	NA	NA	NA	NA
WP_003723553.1\|1297404_1297542_-	hypothetical protein	NA	NA	NA	NA
WP_009931701.1\|1297692_1298406_+	trehalose operon repressor	NA	NA	NA	NA
WP_010989718.1\|1298436_1300083_-	alpha,alpha-phosphotrehalase	NA	NA	NA	NA
WP_003723556.1\|1300101_1301586_-	PTS system trehalose-specific EIIBC component	NA	NA	NA	NA
WP_003723557.1\|1301701_1302154_+	NUDIX domain-containing protein	NA	NA	NA	NA
WP_003723558.1\|1302200_1302665_-	hypothetical protein	NA	NA	NA	NA
WP_003723559.1\|1302853_1303774_+	alpha/beta hydrolase	NA	NA	NA	NA
WP_009932313.1\|1303793_1305041_-	glutamate-5-semialdehyde dehydrogenase	A0A1X9I5D4	Streptococcus_phage	1.2e-106	51.8
WP_003723561.1\|1305024_1305855_-	glutamate 5-kinase	A0A1X9I5D0	Streptococcus_phage	4.3e-47	42.4
WP_003723562.1\|1305990_1307130_-\|protease	PrsW family intramembrane metalloprotease	NA	NA	NA	NA
WP_003723563.1\|1307210_1307606_-	helix-turn-helix transcriptional regulator	A9D9J6	Lactobacillus_prophage	1.3e-14	57.4
WP_003727524.1\|1307756_1307972_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_010989719.1\|1308090_1308624_+\|protease	matrixin family metalloprotease	NA	NA	NA	NA
WP_003732795.1\|1308641_1309307_+	hypothetical protein	NA	NA	NA	NA
WP_003732796.1\|1309568_1310507_+	hypothetical protein	NA	NA	NA	NA
WP_003723884.1\|1310621_1311905_+	trigger factor	NA	NA	NA	NA
WP_003723886.1\|1312090_1313350_+\|protease	ATP-dependent protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	1.4e-145	63.2
WP_003723887.1\|1313468_1314035_+	type I signal peptidase SipX	NA	NA	NA	NA
WP_003723888.1\|1314069_1314639_+	type I signal peptidase SipY	NA	NA	NA	NA
WP_003723889.1\|1314740_1315283_+	type I signal peptidase SipZ	NA	NA	NA	NA
WP_003723890.1\|1315292_1316156_+	ribosome biogenesis GTPase YlqF	NA	NA	NA	NA
WP_003723891.1\|1316152_1316938_+	ribonuclease HII	G4YAY0	Emiliania_huxleyi_virus	3.0e-26	39.2
WP_010989720.1\|1317071_1317932_+	DNA-protecting protein DprA	NA	NA	NA	NA
WP_009924617.1\|1318203_1320282_+	type I DNA topoisomerase	A0A1V0SB35	Catovirus	1.4e-107	37.7
WP_010989721.1\|1320344_1321649_+\|tRNA	FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO	NA	NA	NA	NA
WP_009911635.1\|1321931_1322834_+	tyrosine recombinase XerC	A0A097EYL9	Mycobacterium_phage	1.2e-13	28.6
WP_014601431.1\|1322854_1323394_+\|protease	ATP-dependent protease subunit HslV	NA	NA	NA	NA
WP_010989722.1\|1323407_1324817_+\|protease	ATP-dependent protease ATPase subunit HslU	W6AS21	Erwinia_phage	4.9e-43	27.7

DBSCAN-SWA_4

1858442 : 1866728

Synechococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003722243.1\|1858442_1859009_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	7.0e-25	35.9
WP_009933235.1\|1859005_1860055_-	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	1.0e-61	43.2
WP_010989807.1\|1860073_1861501_-	amidophosphoribosyltransferase	A0A1B1ISH6	uncultured_Mediterranean_phage	8.1e-54	31.9
WP_010989808.1\|1861485_1863705_-	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	2.0e-160	41.2
WP_003733240.1\|1863697_1864381_-	phosphoribosylformylglycinamidine synthase subunit PurQ	NA	NA	NA	NA
WP_003722248.1\|1864384_1864630_-	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA
WP_010989809.1\|1864641_1865355_-	phosphoribosylaminoimidazolesuccinocarboxamide synthase	A0A0E3F9V5	Synechococcus_phage	2.3e-41	38.3
WP_003733238.1\|1865435_1866728_-	adenylosuccinate lyase	A0A1B3B081	Gordonia_phage	7.2e-17	32.6

DBSCAN-SWA_5

2381576 : 2419895

Listeria_phage(89.58%)

tail,terminase,holin

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_014601489.1\|2381576_2382008_+	helix-turn-helix transcriptional regulator	A8ATJ2	Listeria_phage	2.4e-25	81.7
WP_014601490.1\|2382004_2382505_+	AP2 domain-containing protein	A8ATW6	Listeria_phage	3.2e-66	72.4
WP_012951560.1\|2382710_2383709_-	DUF3644 domain-containing protein	A0A0N9RUA4	Staphylococcus_phage	3.9e-71	44.8
WP_014930186.1\|2383811_2384657_-	M15 family metallopeptidase	A0A059T7Y8	Listeria_phage	7.2e-135	86.9
WP_003733521.1\|2384656_2384923_-\|holin	phage holin	A0A059T684	Listeria_phage	9.8e-38	93.1
WP_014930187.1\|2384922_2385225_-	hypothetical protein	A0A059T5E6	Listeria_phage	2.2e-38	92.0
WP_014601493.1\|2385275_2387441_-\|tail	phage tail protein	A8ATW1	Listeria_phage	0.0e+00	94.5
WP_014930188.1\|2387453_2389022_-\|tail	phage tail family protein	A8ATW0	Listeria_phage	2.0e-303	99.0
WP_014930189.1\|2389018_2393818_-\|tail	phage tail tape measure protein	A8ATV9	Listeria_phage	0.0e+00	90.7
WP_072215797.1\|2393822_2394134_-	hypothetical protein	A0A0B5D116	Listeria_phage	2.5e-40	93.4
WP_003725062.1\|2394130_2394562_-	hypothetical protein	A0A0B5D0B8	Listeria_phage	1.1e-73	98.6
WP_014930190.1\|2394617_2395304_-	Ig domain-containing protein	A0A0B5CYK8	Listeria_phage	5.2e-115	98.2
WP_003745007.1\|2395308_2395680_-	hypothetical protein	A0A0B5CTY4	Listeria_phage	1.1e-63	100.0
WP_014930191.1\|2395676_2395994_-	HK97 gp10 family phage protein	A0A0B5CTS1	Listeria_phage	4.4e-53	99.0
WP_014930192.1\|2395983_2396349_-	hypothetical protein	A0A0B5D114	Listeria_phage	1.5e-65	100.0
WP_003745003.1\|2396348_2396702_-	hypothetical protein	A8ATV2	Listeria_phage	2.4e-60	97.4
WP_014930193.1\|2396702_2396882_-	hypothetical protein	A8ATV1	Listeria_phage	1.5e-10	94.1
WP_014930194.1\|2396895_2397768_-	hypothetical protein	A8ATV0	Listeria_phage	4.7e-161	99.3
WP_003744996.1\|2397790_2398345_-	hypothetical protein	A8ATU9	Listeria_phage	1.1e-88	99.5
WP_014930195.1\|2398440_2399484_-	hypothetical protein	A0A0B5D111	Listeria_phage	7.7e-195	96.8
WP_014601502.1\|2399488_2401045_-	hypothetical protein	A0A0B5D0A6	Listeria_phage	7.7e-300	98.8
WP_014930196.1\|2401059_2402379_-\|terminase	PBSX family phage terminase large subunit	A0A0B5CYJ6	Listeria_phage	8.7e-220	82.8
WP_014601504.1\|2402314_2403184_-\|terminase	terminase small subunit	A8ATU5	Listeria_phage	2.6e-10	57.4
WP_014930197.1\|2403372_2403663_-	hypothetical protein	NA	NA	NA	NA
WP_014601506.1\|2403995_2404448_-	hypothetical protein	A8ASQ1	Listeria_phage	4.4e-54	73.4
WP_003733720.1\|2404512_2405010_-	Holliday junction resolvase RecU	A0A1L2JY30	Aeribacillus_phage	1.8e-32	49.3
WP_003733721.1\|2404999_2405182_-	hypothetical protein	A8ASP6	Listeria_phage	1.1e-16	79.4
WP_014930199.1\|2405200_2405683_-	single-stranded DNA-binding protein	A0A059T5E0	Listeria_phage	4.4e-52	66.2
WP_014930200.1\|2405683_2405863_-	hypothetical protein	R4IBL7	Listeria_phage	2.3e-22	98.2
WP_014930202.1\|2406122_2406584_-	hypothetical protein	D9J0I6	Brochothrix_phage	2.6e-14	31.3
WP_014930203.1\|2406580_2407228_-	DUF1642 domain-containing protein	A0A0B5D0I5	Listeria_phage	6.1e-17	31.1
WP_003731843.1\|2407224_2407440_-	hypothetical protein	NA	NA	NA	NA
WP_014930204.1\|2407451_2407619_-	hypothetical protein	A8ASN5	Listeria_phage	1.6e-17	80.0
WP_014930205.1\|2407623_2408079_-	class I SAM-dependent methyltransferase	A8ATY8	Listeria_phage	1.4e-79	89.4
WP_014930206.1\|2408075_2409047_-	phage replisome organizer N-terminal domain-containing protein	A8ASN4	Listeria_phage	5.2e-153	85.9
WP_014601516.1\|2409063_2409702_-	ERF family protein	A8ASN3	Listeria_phage	7.8e-81	76.7
WP_009930471.1\|2409706_2410183_-	siphovirus Gp157 family protein	A8ASN2	Listeria_phage	2.0e-57	94.9
WP_009930470.1\|2410179_2410374_-	hypothetical protein	A0A059T6E8	Listeria_phage	1.8e-28	95.3
WP_014930207.1\|2410679_2410868_-	hypothetical protein	Q9T175	Listeria_phage	2.2e-20	75.8
WP_014601517.1\|2410975_2411191_-	hypothetical protein	Q9T176	Listeria_phage	6.7e-21	69.0
WP_014930208.1\|2411187_2411721_-	hypothetical protein	Q9T177	Listeria_phage	1.2e-82	89.8
WP_014930209.1\|2411844_2412624_-	phage antirepressor Ant	A0A059T6E7	Listeria_phage	1.8e-140	97.7
WP_003725092.1\|2412687_2412891_+	KTSC domain-containing protein	A0A1S5S8T9	Streptococcus_phage	2.0e-14	56.7
WP_003725093.1\|2412891_2413059_-	hypothetical protein	NA	NA	NA	NA
WP_014930210.1\|2413084_2413369_-	hypothetical protein	A0A0B5D168	Listeria_phage	2.5e-47	98.9
WP_003735007.1\|2413380_2413575_-	hypothetical protein	A0A059T6E5	Listeria_phage	1.3e-26	100.0
WP_031645989.1\|2413640_2413898_+	hypothetical protein	NA	NA	NA	NA
WP_014930211.1\|2413894_2414116_-	hypothetical protein	NA	NA	NA	NA
WP_014930212.1\|2414136_2414370_-	helix-turn-helix transcriptional regulator	A8ASM3	Listeria_phage	5.4e-32	97.3
WP_014930213.1\|2414532_2415009_+	helix-turn-helix transcriptional regulator	A8ASM2	Listeria_phage	4.5e-57	80.3
WP_003733638.1\|2415166_2415334_+	hypothetical protein	NA	NA	NA	NA
WP_003733640.1\|2415623_2416346_+	hypothetical protein	A0A059T7P9	Listeria_phage	2.8e-103	97.9
WP_003733641.1\|2416368_2416974_+	hypothetical protein	NA	NA	NA	NA
WP_003749252.1\|2416986_2417409_+	hypothetical protein	NA	NA	NA	NA
WP_014930214.1\|2417463_2417919_+	hypothetical protein	Q6SEA3	Lactobacillus_prophage	1.5e-17	39.0
WP_014930215.1\|2417938_2418340_+	DUF1828 domain-containing protein	NA	NA	NA	NA
WP_014930216.1\|2418536_2419895_+	recombinase family protein	Q8LTD8	Listeria_phage	3.5e-256	99.1

DBSCAN-SWA_6

2564055 : 2571899

Streptococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003722604.1\|2564055_2565027_-	DNA-binding protein WhiA	Q7AWZ3	Streptococcus_phage	5.2e-52	39.4
WP_003722605.1\|2565034_2566003_-	YvcK family protein	A1IMD5	Streptococcus_phage	6.7e-68	43.3
WP_010990001.1\|2566004_2566880_-	RNase adapter RapZ	A0A0R8VB27	Thermobifida_phage	3.2e-08	29.7
WP_010990002.1\|2566987_2568718_-	phospho-sugar mutase	A0A1X9I671	Streptococcus_phage	1.3e-175	54.0
WP_009930954.1\|2568759_2569821_-	galactose mutarotase	NA	NA	NA	NA
WP_009924988.1\|2569837_2570821_-	UDP-glucose 4-epimerase GalE	A0A2K9L1R4	Tupanvirus	2.6e-51	37.2
WP_003722610.1\|2570939_2571899_-	thioredoxin-disulfide reductase	G3MA85	Bacillus_virus	2.0e-88	53.7

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_018889

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_018588

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

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection