CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Target MGE spacer number	Prophage number
NZ_CP025132	Planococcus sp. MB-3u-03 plasmid unnamed9	0 crisprs	NA	0	0
NZ_CP025127	Planococcus sp. MB-3u-03 plasmid unnamed4, complete sequence	0 crisprs	NA	0	0
NZ_CP025123	Planococcus sp. MB-3u-03 plasmid unnamed12	0 crisprs	NA	0	1
NZ_CP025125	Planococcus sp. MB-3u-03 plasmid unnamed2, complete sequence	1 crisprs	NA	1	0
NZ_CP025126	Planococcus sp. MB-3u-03 plasmid unnamed3	0 crisprs	NA	0	0
NZ_CP025130	Planococcus sp. MB-3u-03 plasmid unnamed5, complete sequence	0 crisprs	NA	0	0
NZ_CP025133	Planococcus sp. MB-3u-03 plasmid unnamed10	0 crisprs	NA	0	0
NZ_CP025131	Planococcus sp. MB-3u-03 plasmid unnamed8	0 crisprs	NA	0	0
NZ_CP025124	Planococcus sp. MB-3u-03 plasmid unnamed1, complete sequence	0 crisprs	csa3	0	0
NZ_CP025128	Planococcus sp. MB-3u-03 plasmid unnamed6	0 crisprs	NA	0	0
NZ_CP025134	Planococcus sp. MB-3u-03 plasmid unnamed11	0 crisprs	NA	0	0
NZ_CP025135	Planococcus sp. MB-3u-03 chromosome, complete genome	4 crisprs	csa3,cas3,DinG,DEDDh	0	2
NZ_CP025129	Planococcus sp. MB-3u-03 plasmid unnamed7	0 crisprs	NA	0	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

94052 : 125640

Bacillus_phage(57.14%)

integrase,transposase

attL 92874:92887|attR 96113:96126

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
92874:92887	attL	NA	NA	NA	NA
WP_101189020.1\|94052_95201_-\|integrase	tyrosine-type recombinase/integrase	A0A0K2CP59	Brevibacillus_phage	9.2e-08	23.2
WP_101189021.1\|95498_95795_+	hypothetical protein	NA	NA	NA	NA
WP_101189022.1\|96369_96783_+	hypothetical protein	NA	NA	NA	NA
96113:96126	attR	NA	NA	NA	NA
WP_101189023.1\|96779_97763_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_101189024.1\|97987_98287_+	AbrB family transcriptional regulator	S5MA41	Brevibacillus_phage	1.3e-09	43.1
WP_101189026.1\|98915_99236_-	hypothetical protein	NA	NA	NA	NA
WP_101189049.1\|100342_100504_+	hypothetical protein	NA	NA	NA	NA
WP_157824097.1\|101004_101112_+	hypothetical protein	NA	NA	NA	NA
WP_157824098.1\|101980_102202_+	hypothetical protein	NA	NA	NA	NA
WP_101189028.1\|102640_102874_+	hypothetical protein	NA	NA	NA	NA
WP_157824099.1\|102863_103052_+	hypothetical protein	NA	NA	NA	NA
WP_101189029.1\|103445_103658_+	hypothetical protein	NA	NA	NA	NA
WP_101189030.1\|103923_104166_+	SAM-dependent DNA methyltransferase	NA	NA	NA	NA
WP_157824103.1\|104218_104437_+	N-6 DNA methylase	NA	NA	NA	NA
WP_157824100.1\|104514_104634_+	N-6 DNA methylase	NA	NA	NA	NA
WP_101189050.1\|105309_105471_+	hypothetical protein	NA	NA	NA	NA
WP_101189034.1\|107363_107981_-	recombinase family protein	A0A1V0E035	Clostridioides_phage	1.7e-16	32.8
WP_101189035.1\|108573_109170_-	hypothetical protein	NA	NA	NA	NA
WP_101189036.1\|109408_109657_-	hypothetical protein	NA	NA	NA	NA
WP_101189037.1\|109795_110086_-	hypothetical protein	NA	NA	NA	NA
WP_157824101.1\|111503_111671_+	hypothetical protein	NA	NA	NA	NA
WP_101189039.1\|114117_114252_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_145990581.1\|114399_114606_-\|transposase	transposase family protein	A0A1B1P773	Bacillus_phage	2.1e-08	48.5
WP_157824102.1\|114713_114836_-\|transposase	IS3 family transposase	A0A1B1P773	Bacillus_phage	1.3e-05	59.0
WP_101189041.1\|114943_115507_-\|transposase	transposase	A0A1B1P776	Bacillus_phage	2.9e-15	35.3
WP_101189051.1\|120616_120913_-	cupin domain-containing protein	NA	NA	NA	NA
WP_101805000.1\|122280_123273_-	hypothetical protein	NA	NA	NA	NA
WP_145990577.1\|124758_125640_-\|transposase	IS3 family transposase	A0A1B1P773	Bacillus_phage	1.5e-34	37.9

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. NZ_CP025125

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP025125_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP025125_1

4227-4317

Orphan

Consensus_repeat	Method
ATAGTTCGAATCGAAAAGGTAATAGTT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP025125_1

>merge|NZ_CP025125|1|4227-4317|CRISPRCasFinder
ATAGTTCGAATCGAAAAGGTAATAGTTCGAATCGAAAAGGTAATAGTTTCGAATCGAAAAGGTAATAGTTCGAATCGAAAAGGTAATAGTT

>NZ_CP025125|1|1|4227-4317|CRISPRCasFinder
ATAGTTCGAATCGAAAAGGTAATAGTT	CGAATCGAAAAGGTAATAGTTTCGAATCGAAAAGGTA
ATAGTTCGAATCGAAAAGGTAATAGTT

>NZ_CP025125.1|WP_101189102.1|2945_4112_-|replication-initiation-protein
MNQNYVVTQGNNLIEARHKKPLTAREQKIILTMVSMIEPTDGDFKDYIISVRDFHEMLGLEGREHYTEIKRVVESLMTKVVEIPLEDKGWLMTHWVSTARYVDGSGVIQLRFAPELKPYLLQLKDTFTSYKLNNILSLKSVYAIRLYELMKKWQTVTEWKCSIDSLRGKLGASNKSYNLYGNFKNKILLPAIKELNEQTDLLIQYKEIKKGRKVDAIEFTIRHVPEKKIKVPHLENISASVEELSEMDKLRIRVNELAEGYQFDTAFFAQLHQGASLIWQDDAEQELEFLIRYVNEEKSVKNPLGFIKSKITSAWEIHETGGRITFADLQPVKERWAGREEKLPDWFTSKDEPAEPSESNPELDKEKEKLLKKLAEKKKRAKKDASTS
>NZ_CP025125.1|WP_101189101.1|2198_2513_+|hypothetical-protein
MQQNRGLAQTVPSFFAPLTQFVPVKKVHFGKMIGCFFSKNNPEFNCFFKLKLASKRTETSKIDEKKLVQNCTKRKKSWHKLVPIRKKSGTKLCQNRNLMYPTKH
>NZ_CP025125.1|WP_101189099.1|397_955_-|MerR-family-transcriptional-regulator
MRIPISKLVKELNLEAHQLREWEKRGWLGEVVKDPWQNQQRVYTEEQVERIQSIADIIQSQREKGIKRTDLAEVEAKLLERFGGEVKRIDTDLVVPPQSLNQIVELLMGQNQKINEVQQLMHQQSKKQLPDPVDHTEVLTDLKNQLKKSQEREEQLLAIVQQLQSDMDELKKAPAKSKWKFWGKE
>NZ_CP025125.1|WP_101189104.1|4717_5218_-|tyrosine-type-recombinase/integrase
MKWSLKKWCSERDYILFLLGINSGLRVGDLLTIQTSEIQGKQVVSLREGKTGKRRTIHLGNIYEELDAYIRKLEGTKWLFPSRKGNGPITRVQAYRQLQKAAQMVDISLGIGTHTLRKTFGYWHYKQFKDIAELQNILNHAHPQITLRYIGITDEQIESNLKAFRL
>NZ_CP025125.1|WP_157824107.1|5877_6024_+|hypothetical-protein
MEKHKIGDTNDEGKVWICTPYITKNGVRIYPKGSKVFCFWANPRKEKN

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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
NZ_CP025125_1	1.1\|4254\|37\|NZ_CP025125\|CRISPRCasFinder	4254-4290	37	NZ_CP025125	Planococcus sp. MB-3u-03 plasmid unnamed2, complete sequence	4254-4290	0	1.0

1. spacer 1.1|4254|37|NZ_CP025125|CRISPRCasFinder matches to NZ_CP025125 (Planococcus sp. MB-3u-03 plasmid unnamed2, complete sequence) position: , mismatch: 0, identity: 1.0

cgaatcgaaaaggtaatagtttcgaatcgaaaaggta	CRISPR spacer
cgaatcgaaaaggtaatagtttcgaatcgaaaaggta	Protospacer
*************************************

Prophage detection

Region	Region Position	Protein_number	Hit_taxonomy	Key_proteins	Att_site	Prophage annotation

Anti-CRISPR protein detection

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

3. NZ_CP025135

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP025135_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP025135_1

808194-808290

Orphan

Consensus_repeat	Method
CATAAATGAGAAATTTTGAAAGG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP025135_1

>merge|NZ_CP025135|1|808194-808290|CRISPRCasFinder
CATAAATGAGAAATTTTGAAAGGTATACTATAAAGTTTACAGGAAATCGGGGTGTCTTTCACTTGAGACGCATGCATAAATGAGAAATTTTGAAAGG

>NZ_CP025135|1|1|808194-808290|CRISPRCasFinder
CATAAATGAGAAATTTTGAAAGG	TATACTATAAAGTTTACAGGAAATCGGGGTGTCTTTCACTTGAGACGCATG
CATAAATGAGAAATTTTGAAAGG

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP025135.1\|WP_101192145.1\|800871_801744_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224054
NZ_CP025135.1\|WP_101189744.1\|815539_816724_+\|iron-containing-alcohol-dehydrogenase	unknown	unknown	gnl\|CDD\|341481
NZ_CP025135.1\|WP_101189741.1\|810395_811943_+\|L-aspartate-oxidase	unknown	unknown	gnl\|CDD\|236147
NZ_CP025135.1\|WP_101189742.1\|811942_812797_+\|carboxylating-nicotinate-nucleotide-diphosphorylase	unknown	unknown	gnl\|CDD\|181221
NZ_CP025135.1\|WP_101189733.1\|802193_802631_-\|Na+/H+-antiporter-subunit-G	unknown	unknown	gnl\|CDD\|237147
NZ_CP025135.1\|WP_101189740.1\|808412_809105_+\|universal-stress-protein	unknown	unknown	gnl\|CDD\|238945
NZ_CP025135.1\|WP_101189734.1\|802608_802893_-\|Na(+)/H(+)-antiporter-subunit-F1	unknown	unknown	gnl\|CDD\|183617
NZ_CP025135.1\|WP_101189735.1\|802889_803375_-\|Na+/H+-antiporter-subunit-E	unknown	unknown	gnl\|CDD\|237159
NZ_CP025135.1\|WP_101189731.1\|800156_800870_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101189743.1\|812793_813888_+\|quinolinate-synthase-NadA	unknown	unknown	gnl\|CDD\|236489
NZ_CP025135.1\|WP_101189736.1\|803404_804892_-\|Na+/H+-antiporter-subunit-D	unknown	unknown	gnl\|CDD\|181085
NZ_CP025135.1\|WP_101189739.1\|805638_808041_-\|Na+/H+-antiporter-subunit-A	unknown	unknown	gnl\|CDD\|237155
NZ_CP025135.1\|WP_101189737.1\|804884_805223_-\|Na(+)/H(+)-antiporter-subunit-C	unknown	unknown	gnl\|CDD\|181497
NZ_CP025135.1\|WP_101189732.1\|801743_802118_-\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224639
NZ_CP025135.1\|WP_101189745.1\|816800_817829_-\|NADP-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|176190
NZ_CP025135.1\|WP_101189747.1\|819227_819872_+\|DUF1643-domain-containing-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101189746.1\|817983_819111_+\|NADH-dependent-flavin-oxidoreductase	unknown	unknown	gnl\|CDD\|240086
NZ_CP025135.1\|WP_101189738.1\|805226_805649_-\|Na(+)/H(+)-antiporter-subunit-B	unknown	unknown	gnl\|CDD\|183602
NZ_CP025135.1\|WP_101189748.1\|820833_821187_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|238045
NZ_CP025135.1\|WP_101192146.1\|809157_810294_-\|aminotransferase-class-V-fold-PLP-dependent-enzyme	unknown	unknown	gnl\|CDD\|179511

Protein	Function_ID	Function_description	E-value
NZ_CP025135.1\|WP_101192145.1\|800871_801744_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224054	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms].	7.09351e-52
NZ_CP025135.1\|WP_101189744.1\|815539_816724_+\|iron-containing-alcohol-dehydrogenase	gnl\|CDD\|341481	cd08551, Fe-ADH, iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases, insect-type, or short-chain alcohol dehydrogenases, iron-containing alcohol dehydrogenases, among others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H.	8.90325e-180
NZ_CP025135.1\|WP_101189741.1\|810395_811943_+\|L-aspartate-oxidase	gnl\|CDD\|236147	PRK08071, PRK08071, L-aspartate oxidase; Provisional.	0
NZ_CP025135.1\|WP_101189742.1\|811942_812797_+\|carboxylating-nicotinate-nucleotide-diphosphorylase	gnl\|CDD\|181221	PRK08072, PRK08072, carboxylating nicotinate-nucleotide diphosphorylase.	7.12758e-153
NZ_CP025135.1\|WP_101189733.1\|802193_802631_-\|Na+/H+-antiporter-subunit-G	gnl\|CDD\|237147	PRK12586, PRK12586, Na+/H+ antiporter subunit G.	1.86542e-50
NZ_CP025135.1\|WP_101189740.1\|808412_809105_+\|universal-stress-protein	gnl\|CDD\|238945	cd01987, USP_OKCHK, USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.	3.7421e-45
NZ_CP025135.1\|WP_101189734.1\|802608_802893_-\|Na(+)/H(+)-antiporter-subunit-F1	gnl\|CDD\|183617	PRK12600, PRK12600, Na(+)/H(+) antiporter subunit F1.	4.64819e-27
NZ_CP025135.1\|WP_101189735.1\|802889_803375_-\|Na+/H+-antiporter-subunit-E	gnl\|CDD\|237159	PRK12651, PRK12651, Na+/H+ antiporter subunit E.	1.10985e-46
NZ_CP025135.1\|WP_101189743.1\|812793_813888_+\|quinolinate-synthase-NadA	gnl\|CDD\|236489	PRK09375, PRK09375, quinolinate synthase NadA.	8.36597e-148
NZ_CP025135.1\|WP_101189736.1\|803404_804892_-\|Na+/H+-antiporter-subunit-D	gnl\|CDD\|181085	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed.	0
NZ_CP025135.1\|WP_101189739.1\|805638_808041_-\|Na+/H+-antiporter-subunit-A	gnl\|CDD\|237155	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed.	0
NZ_CP025135.1\|WP_101189737.1\|804884_805223_-\|Na(+)/H(+)-antiporter-subunit-C	gnl\|CDD\|181497	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed.	1.15379e-54
NZ_CP025135.1\|WP_101189732.1\|801743_802118_-\|GntR-family-transcriptional-regulator	gnl\|CDD\|224639	COG1725, COG1725, Predicted transcriptional regulators [Transcription].	3.46505e-30
NZ_CP025135.1\|WP_101189745.1\|816800_817829_-\|NADP-dependent-oxidoreductase	gnl\|CDD\|176190	cd05288, PGDH, Prostaglandin dehydrogenases. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.	3.79373e-176
NZ_CP025135.1\|WP_101189746.1\|817983_819111_+\|NADH-dependent-flavin-oxidoreductase	gnl\|CDD\|240086	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.	4.9324e-163
NZ_CP025135.1\|WP_101189738.1\|805226_805649_-\|Na(+)/H(+)-antiporter-subunit-B	gnl\|CDD\|183602	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B.	1.49819e-54
NZ_CP025135.1\|WP_101189748.1\|820833_821187_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|238045	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.	3.01659e-13
NZ_CP025135.1\|WP_101192146.1\|809157_810294_-\|aminotransferase-class-V-fold-PLP-dependent-enzyme	gnl\|CDD\|179511	PRK02948, PRK02948, IscS subfamily cysteine desulfurase.	7.14779e-138

>NZ_CP025135.1|WP_101189739.1|805638_808041_-|Na+/H+-antiporter-subunit-A
MQLLILSILFPFLAAALIPLIHRRIGDFNIGWLVLSIPVLLFGFFASQIPMVSSRETLLSSVEWIPSLGINFTAYLDGLSLIMALLITGVGSLVVLYSIYYLSPTDSFPHFYAYLLLFMGAMLGVVLSDNLMVLYVFWELTSISSFLLIAFWYHRKNSRYGAQKSLLITVFGGFAMFAGFLMLYAMTGTLSIRETAAAMGQLTEHALFYPAMFLILLGAFTKSAQFPFHIWLPDAMEAPTPVSAYLHSATMVKAGIYLAARFTPIFGGTSAWFWTITIVGLITLFWGAFCAIRQTDLKALLAYSTISQLGLIMSLLGMGSAALHYGNTEAGALYGLAIFAALFHLVNHSTFKGALFMVVGIIDHQVGTRDIRRLGGLMALLPVTFTFAVIGSFSMAGLPLLNGFLSKEMFFTASLNAASMPGLFSTSWGWLIPVIAWLASVLTFIYAMIIVFRTFLGNRDSKAVEKRPVEPPIGMLISPAILSVLIVGLFFAPNLLGDHLLKPALEQLLPGISGASPDSIYAWHGVNTELLMTIGIVLIGSVLFITFDRWKGIFKIQPAGWTFNALYNYALTSSENAASFVTRSYMTGRLHQYFFYILLFFIISTGGTLLLSDALSISFVQDAPVSIYELMLVLVMIITAISILFTRSRLSAILMNGVLGYSISIFFVLFRAPDLALTQLVIETVTTALFLLCFNYLPEWKREPLPKRKKARNAVLAIAGGLVITLTGLSVNSADLFETISSYFQNSYELAGGQNIVNSILGDFRALDTMLEGLVLFIAGIGVYTLIRLKLKKEAGTDGD
>NZ_CP025135.1|WP_101189738.1|805226_805649_-|Na(+)/H(+)-antiporter-subunit-B
MGINDVILKTVAKAVVLIILTFGIYLFLSGHNSPGGGFVGGLVLASAFVLMFLSYDTETVKDAIPIDFKKLSAFGVLLAVLSGLGPLLFGQNFLEQSFDYFNLPIFGKTEIATVLIFEAGIALTVVGVVVNIILSISEDE
>NZ_CP025135.1|WP_101189737.1|804884_805223_-|Na(+)/H(+)-antiporter-subunit-C
MESLIIILVGVLSTVAFYLLLSRNIVRVILGTAILSHAAHLMILAMGGLKIGSAPLLGEEAETYVDALPQALILTAIVISFAVTAFILVLAYRAYQELGTDDLEEMRGTDNE
>NZ_CP025135.1|WP_101189736.1|803404_804892_-|Na+/H+-antiporter-subunit-D
MNNIILIPMILPILAGVLLIFLRTYGRLQAWTSIAVMAVVAAAAVYLLNAIQTDGILRIDFGGWTPPFGISFVADSFAVLLVLTSSVVTVICLLHALVSTDKELVTMYFYPTVLFLIAGINGSFLSGDIFNLFVCFEVMLLSSYILLTLGGSKRQLREAIKYVSINIVSSWFFLIAIAYLYGAVGTLNFAHLSVRVAENGQEPLLTTISIVFLIVFSLKAGLLLYFWLPGSYSSPPVVTSALFGALLTKVGIYAMFRMFTLVFYHEPETTHNIIAVMAVLTLIGGSIGAIAHNDIRQIAAYNVVIAVGFILTGLAIATPDAIEGAIFYLLHDMVVKALLFLLIGTIILLTGTAQIGKMSGIIQNYPILGWSFFIAMLSLAGIPPLSGFVGKVLLSQGAIDSGSYILLAIALGSSLFVLYSLLKIFKNCFWGETIVSKDDQVPLRRGFLVPCLLLVALTIGIGLGAEGLSDYVSDAADTLLNPQVYIDAVLTEDFQ
>NZ_CP025135.1|WP_101189735.1|802889_803375_-|Na+/H+-antiporter-subunit-E
MPAQFLLNIMIGLLWTLLMDETAFYFSTFLTGYLIGLGIIFLMHRFFGTKFYLIRVYSTLKLLLIFIRELFQSSISIMKQILSPKLDIKPGIFTYEHNMEGDYELTTLALLLTLTPGSVILEVSPDNKVFYIHAMDVEKSRESLLSSIKTFETAIMEVTRN
>NZ_CP025135.1|WP_101189734.1|802608_802893_-|Na(+)/H(+)-antiporter-subunit-F1
MIDIILTIALSLFVLAILLALYRIIRGPSMPDRVVALDMIGVNLISAVAVFSVFLKTHVFLEVILVVGILAFISTIALARFVERGDIVEHKHDQ
>NZ_CP025135.1|WP_101189733.1|802193_802631_-|Na+/H+-antiporter-subunit-G
MNISMISEYIGVFLILAGSVMAVISAIGILRFPDAYTRSHAATKSATLAVLLSLIGAFIFFWASENFISVRLLLGIVFVFLTAPVSGHLIMRAAYRSNVKLTSISTEDALAEALNKKNTIEQKKGETALLFIGILSSGTVLKYYS
>NZ_CP025135.1|WP_101189732.1|801743_802118_-|GntR-family-transcriptional-regulator
MVNSTDSAKPLFLQIRELIEDQIVNDQLKEGDQAPSTNQLVNFYKINHATVSKGITQLVDEGILFKKRGIGMFVAEGAKKTLVQQRKKAFVDNYVTGLVQEAEKLGITEQEIIELIKSTKGRDA
>NZ_CP025135.1|WP_101192145.1|800871_801744_-|ABC-transporter-ATP-binding-protein
MAASVQLNHVTLKFKKFEALKDVSLTLEAGKIHGLIGRNGAGKTSLLSLIAAFREPTAGEVFVDGSTVFENPEKMEQVAFVYDKDYKEETEKAKKLIALASHYRPHFDMGYAEQLIERFKLPVNKPVNKLSKGMQSALNVVIGLASRAPITIFDEAYLGMDAPSREIFYKEILQDQEDHPRTFILSTHLVSEMDYLFDNVVIIDQGTVLLHEPYETIEAHGVSVTGAAQEVDIFTAGMKQLNEQQLGGTKSVMIYGNLGDAKRQEARAQGLEIGPVSLQDLFIHLTEEAN
>NZ_CP025135.1|WP_101189731.1|800156_800870_-|hypothetical-protein
MTSPRYRRVAAAVFSDMFKWSLWFFSILFVIHLVRVFWLNGDTNQIEGFFVFSQYSVNIFMLVVGIMSAYVFMSRHIQQGVSRKDSYLGTALAALALSAFATLVPLAVNGLQHLLAETISLPVELDTVSAFETTGGWFAAAIALFLNTLTFFLAGWVISIGYYRFGWIAGFGFIALSFVIFGLNDYLWKPNTADAMEWLPYNPLEANFWLTALGSSVLILLLFSLMRLLTKRVTIKM
>NZ_CP025135.1|WP_101189740.1|808412_809105_+|universal-stress-protein
MKKIRGRMDESILVCVFYGPNGERLIKRGSKLANMLDCPLYILTVDALPYDEFDTGKSAYVEKWGELAEELGAEEFVIRDNEKRPPAKVIAEVANQFNITQIIIGQTARSRWEEITKGSFMNVLLREIPFVDFHVVSVARTVKGNDGDDFEKGVRCYLVQEGEKYKIHFSQTKDCQIEGIFFKEIGTDFNNGIFKFMENNKLHQVEVLDNYIQDTDEIEGCIKKEPAKLS
>NZ_CP025135.1|WP_101192146.1|809157_810294_-|aminotransferase-class-V-fold-PLP-dependent-enzyme
MIYLDSAATAPMRKEAIDAYVETANNAFGNTQSLHDAGSLAADYLASCKKLWGQFLNVRQDGIYFTGNASEANQLAIRSLLKGRPEHYRSIVSTQLEHASVLSVLHELEREGYEITYVPVDCFGRVDLDAYERLVDEETALVVMQLVNSEMGAVQPVEQCTKIALQFGVPLHSDIVQGFGKLPVDIGLWGVASAVCSAHKVGGPKGVGIAYLDPSVHWESVYEGTTHQNGFRAGTIDVPAIVSATIAAKHAVMEQPESYEHARKLQCYLIEQLPAGVIVTGDIKSKSPFIQGLVLPHVEGQWMMLACNRAQIAISTGTACKIGYGEAMSAMLAMGTESDTAKKFIRISFTKHTSSNELDAFIHVLNENQSTQKNRLPI
>NZ_CP025135.1|WP_101189741.1|810395_811943_+|L-aspartate-oxidase
MFDVCIIGGGVAGLMLARSLPDHYSIAVVTKEHAGTGNTSLAQGGIAASLSFDDRPESHATDTLIASADHADAGRVEILVNEGSELMKNLLAHGLPFDGDELGLPALGMEGAHSHRRIVHAGGDQTGKMLMHYLMEETSGKITRFAFHQALELRMESGRCAGVLFSDRFGKRSVIHARHVVLATGGIGQLYSETSNSSVSTGDGLSLAYHAGAVLEDLEFVQFHPTVLTLEGKSCGLISEAVRGEGAVLVDRDGKRIMDGIHPLMELAPRDVVARAIERHWQTEGSVFLDARHLADFHQRFPSIYDNCRNHGIDPTQELLPVRPGAHFHMGGVRTDSCGQTSIPGLYAVGEVASTGVHGANRLASNSLLEGLVFARRLAEQIKGEPQSSEKISSTQVDLVPSTYFGAIDESQLKRHMTEMAGILREPHALQKFLETHPLKTYALKEYKDEIIAQIHRQTASSLIATAALLREESRGGHYRIDAPEPKAEWAGKVIGISKNGVQLTTRKTKIKETI
>NZ_CP025135.1|WP_101189742.1|811942_812797_+|carboxylating-nicotinate-nucleotide-diphosphorylase
MNRLKAEQALTQFLLEDIGDRDVSSVLFDRTDTGEAIVRMKQSGVVAGLDCYEWGYRLLDQSVEVELLKRDGDRVETGEAIVKISGPIASLLAGERVLLNLIQRMSGVATLTAKCVEALDSDHTRIVDTRKTIPGLRMFEKYAVRAGGGFNHRNGLYDAVMLKDNHIAAAGSITEAVKKVRDSLGHMTMIEVEVETQQQLMEAIDARPDTIMFDNQTPETIRRWVQLVPETIRTEASGGIDLEKLSDYRDTGVDVISIGALTHSVSNLDISMNLSISPKEAVIS
>NZ_CP025135.1|WP_101189743.1|812793_813888_+|quinolinate-synthase-NadA
MTSLLEELQMADAMPTSYLTASTDELHERAKRARATLGKRLYILGHHYQKDEVIHYADVTGDSLQLSQIAGRQTADYILFCGVHFMAETADILTEPHQAVILPDMRAGCSMADMANIDQTERAWAELQTLFGDTIIPLTYVNSTAAIKAFVGRNGGATVTSSNAQEMVEWALSQKQRMLFLPDQHLGRNTAVKLGIPLEQMAVWDPIKQKLELDCAIEDVQVILWKGHCSVHMNFLPKHVDNLREKEPDRNILVHPECTYEVVSASDFAGSTKYIIDMIEASEPGSKWAIGTEMNLVNRLIKDFPDRDIVSLNPFMCPCLTMNRIDLPHFTWILEELVEGRVLNRIQVDEQTASEAKLALAKML
>NZ_CP025135.1|WP_101189744.1|815539_816724_+|iron-containing-alcohol-dehydrogenase
MSSKITFMPISHTGWGALEQLAGEAERLNASNILIVTDPFLDELGMTKKIVEPLEAKGWKTSIYTEVVPEPPLEVGERLVTYTKEHKFDLVIGLGGGSALDLAKLAGVLATHEGKVADYLNLTGERELVDKGIPKILIPTTSGTGSEVTNIAVLSLESTKDVVTHDYLLPDVAIVDPALTVSLPPKVTAATGIDALTHAVEAYVSKNANPVTDGLALQAIRLISGSIRRAVEDGENKEARTNMSYGSYLAGLAFFNAGVAGVHALAYPLGGQFHISHGESNAVLLPYVMGYIRPSCEKRMKDIVEAMGVNVTQMDEQQASYECVEELKKLVADVNIPVSLKGFDIGEGALDSLADDGIKQTRILARSPMPLEREDIYAIYHAAYSGEVAEKKTV
>NZ_CP025135.1|WP_101189745.1|816800_817829_-|NADP-dependent-oxidoreductase
MTPNTYKEIHLANRPEGTPTDKDFNFIEKEIPSIGKDEVLLRTLYLSVDPYMRGRMKDVKSYVEPFKLNEAITGGILAEVVESNSDKFQQGDVVNGTLNWAEYNVANAQSVQKVDPSLAPITTRLGILGLTGLTAYFGLLDIGKPQQGETVVVSGAAGAVGSVVGQIAKLKGAHVVGIAGSQEKIDYLINELGFDAAVNYKSDSFKEDFKKAIPNGVDVYFDNVGGEVSDAVIFEINRNARIVLCGTISSYNNPEADLGPRIQWKFITTSSMMKGFTLGDYAHDFKTGAQALAGWLQEGKLKYEETITEGFEKTPEAFLGLFEGSNLGKQLVKVADPEFAKL
>NZ_CP025135.1|WP_101189746.1|817983_819111_+|NADH-dependent-flavin-oxidoreductase
MNPQYKPLFEEITLPNGVVLSDRLGVAPMTTYSGNPDGTVSDAELAYYQRRAGLGSLFVSACIAVSENGIAFPNQFVAFKDDVMPRLKQLATEMKSQGSKAILQMQHGGRQGQPDLIEAGETVAPSAIAESADKPKPRALTGEEITAIIRDFGETTRRAIEAGFDGVEIHGANTYLIQQFVSATYNQREDEWGGSLENRLKFGLAVLDEVKQVAAKHADDSFIIGYRLSPEENNADSVGYTIKETQQLVERLIEGGIHYIHVSLMEFKKAPRGMEEGDSIVQILSKQINGRVPFVVVGGVTRPGHAVAALEEGADIVVMGRQALVDPEWTEKVKQGNEADINETIPQELVGKLDIPETMWNAITSYGMVKVDAKV
>NZ_CP025135.1|WP_101189747.1|819227_819872_+|DUF1643-domain-containing-protein
MSLIPAEDLKHIFSVEAKFYHTEIEEETFLMRREARIRRNGAFTTRTDAVIVMINPSNCAQAGKTVNSPREAEWIPTKPNPTQYQLMNLMERQAWDLITLINLSDICEGNIMNFKSIENKFNEAGIPHSLFQEQNTQQREELLGTSVHLIFAWGSSTVAKRLAAQFGLFQNGCAEKPYDYAKAWVAGENGFPRHPKPATMADRVVWLERMESLL
>NZ_CP025135.1|WP_101189748.1|820833_821187_+|helix-turn-helix-transcriptional-regulator
MAKLAENLKALRVQNKLSMQVVADHLIITRATYSNFETGKGEPNLKLLVKMADLYNVSLDELSGRQFTPNGVVIDQVRMKTEMNREINAMVKQIANEFIQSKEADIVKRIQKKFSLA

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Crispr_ID: NZ_CP025135_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP025135_2

2418022-2418214

Orphan

Consensus_repeat	Method
CAAATTGTGTCGTGCACAGGGAC	CRISPRCasFinder

3 spacers

The CRISPR arrays of NZ_CP025135_2

>merge|NZ_CP025135|2|2418022-2418214|CRISPRCasFinder
CAAATTGTGTCGTGCACAGGGACGAACCAAGAGCGAAATCCTGCTGCGGCGCGAATCGCACACGCCAAATTGTGTGGTGCACAGGGACAGCTCCCAAACGCCCGGCGAATTGTGTCGCGCACAGGGACAAACAACTACCAAAACCCAGCCACGACGCGATTTCTACGCCCCGAATTGTGCCGTACACAGGGAC

>NZ_CP025135|2|2|2418022-2418214|CRISPRCasFinder
CAAATTGTGTCGTGCACAGGGAC	GAACCAAGAGCGAAATCCTGCTGCGGCGCGAATCGCACACGC
CAAATTGTGTGGTGCACAGGGAC	AGCTCCCAAACGCCCGG
CGAATTGTGTCGCGCACAGGGAC	AAACAACTACCAAAACCCAGCCACGACGCGATTTCTACGCCC
CGAATTGTGCCGTACACAGGGAC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP025135.1\|WP_101190995.1\|2418351_2418621_+\|phosphocarrier-protein-HPr	unknown	unknown	gnl\|CDD\|237503
NZ_CP025135.1\|WP_101191004.1\|2423308_2424727_-\|sodium:alanine-symporter-family-protein	unknown	unknown	gnl\|CDD\|224040
NZ_CP025135.1\|WP_101190989.1\|2410927_2411569_-\|3-hexulose-6-phosphate-synthase	unknown	unknown	gnl\|CDD\|132172
NZ_CP025135.1\|WP_101190983.1\|2408405_2408738_-\|winged-helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|334619
NZ_CP025135.1\|WP_101190991.1\|2411909_2413115_-\|mannitol-1-phosphate-5-dehydrogenase	unknown	unknown	gnl\|CDD\|235031
NZ_CP025135.1\|WP_157824163.1\|2426215_2426440_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190997.1\|2418617_2420324_+\|phosphoenolpyruvate--protein-phosphotransferase	unknown	unknown	gnl\|CDD\|224006
NZ_CP025135.1\|WP_101192198.1\|2409608_2410238_-\|cyclase-family-protein	unknown	unknown	gnl\|CDD\|224790
NZ_CP025135.1\|WP_101190985.1\|2408796_2409621_-\|HAD-family-phosphatase	unknown	unknown	gnl\|CDD\|319818
NZ_CP025135.1\|WP_145990606.1\|2405918_2408177_-\|S8-family-serine-peptidase	unknown	unknown	gnl\|CDD\|173810
NZ_CP025135.1\|WP_101191009.1\|2426502_2426685_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190979.1\|2405129_2405570_-\|CopY/TcrY-family-copper-transport-repressor	unknown	unknown	gnl\|CDD\|131745
NZ_CP025135.1\|WP_101191001.1\|2421111_2421702_+\|PIN-domain-containing-protein	unknown	unknown	gnl\|CDD\|379205
NZ_CP025135.1\|WP_101190999.1\|2420474_2421128_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|133390
NZ_CP025135.1\|WP_157824162.1\|2421853_2422024_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190993.1\|2413121_2415197_-\|BglG-family-transcription-antiterminator	unknown	unknown	gnl\|CDD\|226234
NZ_CP025135.1\|WP_145990608.1\|2425109_2425625_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|180687
NZ_CP025135.1\|WP_145990607.1\|2422161_2422611_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190977.1\|2402317_2402590_-\|glutaredoxin-family-protein	unknown	unknown	gnl\|CDD\|239274
NZ_CP025135.1\|WP_101190987.1\|2410371_2410908_-\|6-phospho-3-hexuloisomerase	unknown	unknown	gnl\|CDD\|240138

Protein	Function_ID	Function_description	E-value
NZ_CP025135.1\|WP_101190995.1\|2418351_2418621_+\|phosphocarrier-protein-HPr	gnl\|CDD\|237503	PRK13780, PRK13780, phosphocarrier protein HPr; Provisional.	5.30839e-35
NZ_CP025135.1\|WP_101191004.1\|2423308_2424727_-\|sodium:alanine-symporter-family-protein	gnl\|CDD\|224040	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism].	1.13345e-176
NZ_CP025135.1\|WP_101190989.1\|2410927_2411569_-\|3-hexulose-6-phosphate-synthase	gnl\|CDD\|132172	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of this protein family are 3-hexulose-6-phosphate synthase (HPS), or the HPS domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase.	9.70721e-82
NZ_CP025135.1\|WP_101190983.1\|2408405_2408738_-\|winged-helix-turn-helix-transcriptional-regulator	gnl\|CDD\|334619	pfam01638, HxlR, HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.	2.96386e-45
NZ_CP025135.1\|WP_101190991.1\|2411909_2413115_-\|mannitol-1-phosphate-5-dehydrogenase	gnl\|CDD\|235031	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional.	0
NZ_CP025135.1\|WP_101190997.1\|2418617_2420324_+\|phosphoenolpyruvate--protein-phosphotransferase	gnl\|CDD\|224006	COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism].	0
NZ_CP025135.1\|WP_101192198.1\|2409608_2410238_-\|cyclase-family-protein	gnl\|CDD\|224790	COG1878, COG1878, Kynurenine formamidase [Amino acid transport and metabolism].	2.93302e-49
NZ_CP025135.1\|WP_101190985.1\|2408796_2409621_-\|HAD-family-phosphatase	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.	4.07406e-76
NZ_CP025135.1\|WP_145990606.1\|2405918_2408177_-\|S8-family-serine-peptidase	gnl\|CDD\|173810	cd07484, Peptidases_S8_Thermitase_like, Peptidase S8 family domain in Thermitase-like proteins. Thermitase is a non-specific, trypsin-related serine protease with a very high specific activity. It contains a subtilisin like domain. The tertiary structure of thermitase is similar to that of subtilisin BPN'. It contains a Asp/His/Ser catalytic triad. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53 the it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values.	3.39556e-82
NZ_CP025135.1\|WP_101190979.1\|2405129_2405570_-\|CopY/TcrY-family-copper-transport-repressor	gnl\|CDD\|131745	TIGR02698, Uncharacterized_16.5_kDa_protein_in_ptsI_3'region, copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI. [Transport and binding proteins, Cations and iron carrying compounds, Regulatory functions, DNA interactions].	4.11599e-49
NZ_CP025135.1\|WP_101191001.1\|2421111_2421702_+\|PIN-domain-containing-protein	gnl\|CDD\|379205	pfam13470, PIN_3, PIN domain. Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).	1.61241e-07
NZ_CP025135.1\|WP_101190999.1\|2420474_2421128_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|133390	cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.	2.25096e-07
NZ_CP025135.1\|WP_101190993.1\|2413121_2415197_-\|BglG-family-transcription-antiterminator	gnl\|CDD\|226234	COG3711, BglG, Transcriptional antiterminator [Transcription].	1.8015e-43
NZ_CP025135.1\|WP_145990608.1\|2425109_2425625_-\|hypothetical-protein	gnl\|CDD\|180687	PRK06770, PRK06770, hypothetical protein; Provisional.	2.73102e-29
NZ_CP025135.1\|WP_101190977.1\|2402317_2402590_-\|glutaredoxin-family-protein	gnl\|CDD\|239274	cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, could be a mechanism for regulating the oxidation state of the protein.	2.59959e-16
NZ_CP025135.1\|WP_101190987.1\|2410371_2410908_-\|6-phospho-3-hexuloisomerase	gnl\|CDD\|240138	cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.	6.20198e-77

>NZ_CP025135.1|WP_101190993.1|2413121_2415197_-|BglG-family-transcription-antiterminator
MFVTVREKSIIELVTRMSAKHTVNSLATYLDVSARTIQRDLKSVDKLLEGFGLTMKRNAADALFIDGNNEKIYRLMQKLAASSAPEATPEEKKLRLLVILMEEGAFFKKQVLSNQLGISTTTLTSYLDELGNWLRKFSVTLSRQRGVGVEVDGAEAHKRHALAAYFLIHFYEELIESLYYLQQGKTQDDKVLGYFNPDYLSAANKLVGERISDEQIRLADSDYTGLVVHLALALQRTEKGFLLDAQPADSESNGEYHVIEAICDDLHERLGVELTERDVEFLVVVLKGSKIQASNVLYYDSVLLGKLVKNMIRDVSGQLGVDLTKDFSLYQGLLAHMEPLIFRLKQKLESFNPLTDEIKKKYPMLFLAVKQTLETEFDDLEFSADEVAFIVLHFGSALLMNEERVQIDAVVVCPTGIGTSKMLASRIQKELPEIDTVKILSIHDFEAANFQDYDLVISTIRLPVTDVDYLMVSPLLNEQDISHIENYLQHNIQKVTRNKQYLPAEALSEAGRTHRPNLRRLLLDIKQVQTGMEAILEHFGVVNMRGTDYWRVLEAVLDGMESDGLLDAASTLRQLKDRETKGGLGIPGTNMALFHCRDESVGQLLFQVVHLDTPSTVKGMDGRDVQMTNLLLMLTPVELSEREQEIMSLISSSLIESEAAMMIFSSSNEGVIRGKLEQLFYEYLQNNLMKE
>NZ_CP025135.1|WP_101190991.1|2411909_2413115_-|mannitol-1-phosphate-5-dehydrogenase
MKQAIHFGAGNIGRGFIGALFSESGYHVSFVDVAEQVIDGLNEQGQYRVNMAQETEESVLVENVSGINNMKDEEAVIAKIQQATYLTTAIGPNILPRIAPLIAKGIEARVKGSLASGPDLVPASDLDVATDMSAGSEKLYIIACENQIGATDILKGHILSHLSDEAKADLAGKVYFFNSAVDRIVPIQEGHSLDVLVEPYYEWVVETTEDIPHVSGMTIVDDLAPFIERKLFTVNTGHAVIAYYGYLASKTTIDETLADPEIEREVRETLKETGAYLVKQYGLDEQEHLAYIDKNIERFKNAYLNDGVTRVGRAPIRKLGPEDRLVRPAVQAQKAGLSYSHLAKAIAAALLFDYAEDEEAVKIQEMIAQGGPERVLTEVSGLEADSELAKEVVRQYGALKK
>NZ_CP025135.1|WP_101190989.1|2410927_2411569_-|3-hexulose-6-phosphate-synthase
MKLQLALDLVNIPQAIELIKEVEGSIDIVELGTPVINKEGLKAVREVKAAFPHLEVLADVKIMDAAAYEVGNAAAAGADIVTILAQAEDSSIKGAVEEAKKLGKKILVDMIAVKDIETRAAELDVLGADYICVHTGYDLQAEGKDSFADLRTIKSVVKNAKTAIAGGIKLETLPEVIRAQPDLIIVGGGITSKDDKKSEAAKIKALMNESVTV
>NZ_CP025135.1|WP_101190987.1|2410371_2410908_-|6-phospho-3-hexuloisomerase
MKEISAELSHTLGQVSDAEASRLVTAMGQADKIFVAGGGRSGFMAKAFVMRMVHMGLNAYVVGETVTPSLQENDLFIVGSGSGETGSLLAMTEKAKTIGATVAAVTTNPESSIGKLADLHITIPAQAKAEGASGKSIQPMGSLFEQSLLVVYDALVLTYMEQQGITADAMFGTHANLE
>NZ_CP025135.1|WP_101192198.1|2409608_2410238_-|cyclase-family-protein
MKIHDVTGAIFEGMAVYKDAAEKQPKFNQETDGYVTETRLELDVHTGTHIDAPLHMLPGGETFESIPLERLVGECKVVDLTKVTGGISRADLEGFELDKGDFVLLKTQNSFDDYFNFDFVYLAQDGADYLAEIGVRGIGTDALGIERSQEGHPTHKTLFNNNIIIIEGLRLRDVVQGGYYMVAAPLKLIGTDASTARVLLFEGASLCIK
>NZ_CP025135.1|WP_101190985.1|2408796_2409621_-|HAD-family-phosphatase
MYKMIAIDLDGTLLNDDLAVTADTMAAIRESMEHGVVVTIATGRMYPSAQRIALELGLDAPMITYQGAMIKSATSGEVLRERVVPFEIAQKCIHLAAQKQMHIQVYQDDVLYSAVDNEQVKAYSKEVGVGYKVEPDLLGLAKNGFMKLLFIDEPEALAPVQEELQAVLGDEACIEKSKLRYLEVTHPEANKGSALSFLADELGIDRSQVIGIGDNHNDTELVKAAGFGIAMGNAVDELKELADYTSLSNNEEGVLHVLNKFILEPRAAVVDSAQ
>NZ_CP025135.1|WP_101190983.1|2408405_2408738_-|winged-helix-turn-helix-transcriptional-regulator
MPNLGEKTFNCEKELTLSIIGGKWKMLVLWHLGKSGTKRFGELKKLMPGITQRMLVNQLRELEDHLIVHREVYPVVPPKVEYSLTEQGESLMPILDSMYDWGKGYMERNL
>NZ_CP025135.1|WP_145990606.1|2405918_2408177_-|S8-family-serine-peptidase
MNTSKKFGITVLTGAAVFHAAGLASADEAEQTDRVIVTLEAGTSSQALTGETVDALNINTANEVVTVEVPKGQSVEDYIEQLGMAPGVANVEADHLLQTTAAPNDPYYSFQYHHEMIGSERAWARTMGTTDVLVAVLDNGFDLDHPDLNGQIVSSYATATSMSEDDHGTHVAGIIGAAHNNRTYGAGVAPDAGLLAIDVFEGERAYSSDVIEGIYYAADAGADVINMSLGNYFYNESYQTAIDYAHERGVLVIASSGNDYTDNTHYPSGYENVMAVGSTDRADRFSGFSNYGADQDITAPGTGIWSTIAGGSFSSMSGTSMASPVVAGIAALVKANEPDLSNEEIAQRLYDTSVDLGAAGKDPYFGHGRIDAEAALMIFDIEQPAVSDVYDSSVEITGTLNQAVEDAVITVDNEDGEIARQEDYTGAGKFSLAIPKQAAGRVLTLTVRDRYGNQSEALEIVVKETQPEELPGRISGIDRYQTAIAISQTGWESADTVVIATAGNFPDALAGGPLAYLEDAPILLTRSGELHSETALEIERLGAEKAIILGGSGAVSDAVEAELKTMNLATERIGGETRYETATLIAEKMGSRRAVVANGLNFPDVLSVSPYAAKNGIPILLTRSDALPKETASALERYTSSLVIGGTGVVSEDVFGHLPNPERFGGKTRYDTGLEVATRLPLGDSRAFIATGLNFPDALTGSVLAAKNDAPILLVRPDNIPSATEQQLPTYRGFSIFGGTGVVSEDVKGMLR
>NZ_CP025135.1|WP_101190979.1|2405129_2405570_-|CopY/TcrY-family-copper-transport-repressor
MAIEEKVEMTASEREIMRVVWTLGEATSKDIVDVLEAKKEWKPATAKTFIGRLVKKGFLLAEPEGNKYIYSAAISEEDSVKTAAHRLFDQICHKQAGKTIADMLAEAPLSHQDVELIQQVLDEKKKHAVDEVACNCVPGQCKCSTH
>NZ_CP025135.1|WP_101190977.1|2402317_2402590_-|glutaredoxin-family-protein
MDNKTELVLYTRPTCSDCQDAKAYLAEQGIPYEHKDVGADPSLEEDMKNISGAKIVPVFAFYKKGLFGKKLTHHFIGFERNRQEIVDLLL
>NZ_CP025135.1|WP_101190995.1|2418351_2418621_+|phosphocarrier-protein-HPr
MVEKTFTITDPAGMHARPASALVGSLSKFQSDITMEFKDKKVNLKSILGVMSLGVPSGSQVQIAADGADEAEAMETIERVLQEQGISNA
>NZ_CP025135.1|WP_101190997.1|2418617_2420324_+|phosphoenolpyruvate--protein-phosphotransferase
MSRLSGIAASNGIAIAKAFRLEHPDLTVDKKNVADPQAEIERFGSAVDESIAELEVIKKRTAEQISEKEADIFGAHLLVLQDPELIGPITDKIKTDSVNAEFALHETSTMFVDMFEAMDNEYMKERAADVRDVTKRVLAHLLGVKIQNPSLITDEVVIIAEDLTPSDTVQLNPQYIKGFITDIGGRTSHSAILARTLEIPAVVGAKSAMSSIQNGTIVIIDGLEGEILLDPDEATLAEYKEKQTAFADQKAEWAKLKNEATLTKDGVAVELGANIGTPKDLTGVLENGGEAIGLYRTEFLYMGRDNFPTEQEQFDAYSAVLKGMEGKPTVVRTLDIGGDKELSYLKLPKELNPFLGLRAIRLCLEMPDMFRTQLRALLRASVHGNLKIMFPMIATLDEFREAKALLLEEKAKLESEGVEVSDSIEVGIMVEIPSTAVMADTFAKEVDFFSIGTNDLIQYTMAADRMNESVSYLYQPYNPAILRLVKTVIDASHKEGKWTGMCGEMAGDEIAIPILLGLGLDEFSMSASSILKARSQLSRLSKADMEGHTEHILGLATSQEVEDYVKNL
>NZ_CP025135.1|WP_101190999.1|2420474_2421128_+|helix-turn-helix-domain-containing-protein
MISTIDQEQENLWASVETLSTINTEQAEAVLKTTVERSLRQMGFTTPAISSLALKITDPQTVIELHQIERKIKHQLKNKNREMAYELLIDYLSKLSEMTDKDPAVIQKKLIASLMANSAKSPLRASLVNRPASHQKTGNSFYSPSEAAEKIGLSDQTIRRMCEKGKFAGAFKTDGGHWRIPKANFITTDEQDKRAKAFFDRIDTKNEEAGNVDEFDL
>NZ_CP025135.1|WP_101191001.1|2421111_2421702_+|PIN-domain-containing-protein
MNSIYDSPVRPKVFIDTTILCGALRTDGINRKILQAARFPHLFQPVFSKVCLFEFVRSAAEGLGKGKNRVAYSSDEIEEFFQAFLNPIFEYYEGLPVNSILGRYSVETIIREHLPIGDVLIELSGCDRDTAQTIAEKQEMSEPLSKFDQDDFHVWVTALRENCNFILTSNHRRFPAEIGEIKRIHPIRFYEELLNT
>NZ_CP025135.1|WP_157824162.1|2421853_2422024_-|hypothetical-protein
MTAIVKEEMTMEIPNKTYLQTYKEHIDGYKQYKLEKLAPQWHVPVDRKALKVESGL
>NZ_CP025135.1|WP_145990607.1|2422161_2422611_-|hypothetical-protein
MDRSIKSSGGMVEMMDIQQVASPDNKTAEMMAAQAVEKSRSCPIGSAPEIEGRRVPQLYIGLPMDRGVSVRLYRDEQEGLNEATILLSVEQLPSFTRALIEHPILLPTSYSQRSSVEDEQHALRIASKEDFPDFVERLTDALHALPQKK
>NZ_CP025135.1|WP_101191004.1|2423308_2424727_-|sodium:alanine-symporter-family-protein
MEQFLQGVADFSAWLWGIPLITLLLVSGLYMTFKLGFFQFRYFGYIVGQTFGSIFRRPKGEGTVTPFQALTSALSSTIGAANIVGVPAAIMFGGPGAIFWMWVIALIGMALKFAESVLAVEYREKNAKGEFVGGPMYYMTKGLNMKWLGIWFSFALMIELIPSIMVQGNSIANTVQATFNVPVLWTGIATAVLVSIVVFGGIKRIGKVTEIFVPFMALMYVGGAVVILLMNVKAVPEFFMLIFSNAFSPAPVVGGFAGAAIVEIIRWGFARGLYSNEAGLGTAPIAHAAATTDHPVRQGFWAVIGVVVDTLIVCTATAFVILSSGVWTEEGAMENSSALTSLAFEEYFGDFGAILVTIALIFFVLSTILVVVFYGAKQAEFLFGLKAAYGMQVVYIFAVILGAVGAAEVIWGFLDIMLAAILIPNVIAILLLSNKVKELKNEFFTSDEYYRKDRKVKKRAKRQKAVREGYES
>NZ_CP025135.1|WP_145990608.1|2425109_2425625_-|hypothetical-protein
MKTVLRTIIILLVGLGILAGAGYWAYKSLTTSDEQQISQAAEEADDKLQQGEDTEAPKANEQVETVGLSEGEFQIHLHQMTHQKIEATEKRGAIEMTPERIDEMLKILQANEGAYEEYEFYEQSLTAWEEGNFSNAVNVHNTIWEWHNGTVGRATGLLSEEQEAAYVEDNF
>NZ_CP025135.1|WP_157824163.1|2426215_2426440_-|hypothetical-protein
MDGDEFEFSILGGNIAGHYFAIAVKAHIVAILENHNAKEILVRELIFDGPVSDGAIIAIEAFDGEFFVFEQLTG
>NZ_CP025135.1|WP_101191009.1|2426502_2426685_+|hypothetical-protein
MITEDFSGPINYYLPPGYYYPSLLYPLLYPWITSIVGLALILFNFPYGAMKKRSAAKNAQ

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Crispr_ID: NZ_CP025135_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP025135_3

2421757-2421844

Orphan

Consensus_repeat	Method
GAATTGTGTCGCGCACAGGGACA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP025135_3

>merge|NZ_CP025135|3|2421757-2421844|CRISPRCasFinder
GAATTGTGTCGCGCACAGGGACACTCAAACACCAGAATCCCACTGCGACGCGAATCTTCCCCCGCGAATTGTGTCGTGCACAGGGACA

>NZ_CP025135|3|3|2421757-2421844|CRISPRCasFinder
GAATTGTGTCGCGCACAGGGACA	CTCAAACACCAGAATCCCACTGCGACGCGAATCTTCCCCCGC
GAATTGTGTCGTGCACAGGGACA

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP025135.1\|WP_101190995.1\|2418351_2418621_+\|phosphocarrier-protein-HPr	unknown	unknown	gnl\|CDD\|237503
NZ_CP025135.1\|WP_101191004.1\|2423308_2424727_-\|sodium:alanine-symporter-family-protein	unknown	unknown	gnl\|CDD\|224040
NZ_CP025135.1\|WP_101190989.1\|2410927_2411569_-\|3-hexulose-6-phosphate-synthase	unknown	unknown	gnl\|CDD\|132172
NZ_CP025135.1\|WP_101190993.1\|2413121_2415197_-\|BglG-family-transcription-antiterminator	unknown	unknown	gnl\|CDD\|226234
NZ_CP025135.1\|WP_101190991.1\|2411909_2413115_-\|mannitol-1-phosphate-5-dehydrogenase	unknown	unknown	gnl\|CDD\|235031
NZ_CP025135.1\|WP_157824163.1\|2426215_2426440_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190997.1\|2418617_2420324_+\|phosphoenolpyruvate--protein-phosphotransferase	unknown	unknown	gnl\|CDD\|224006
NZ_CP025135.1\|WP_101191011.1\|2426720_2427194_+\|VanZ-family-protein	unknown	unknown	gnl\|CDD\|377417
NZ_CP025135.1\|WP_101190985.1\|2408796_2409621_-\|HAD-family-phosphatase	unknown	unknown	gnl\|CDD\|319818
NZ_CP025135.1\|WP_101191017.1\|2429460_2429934_-\|ParB-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|366971
NZ_CP025135.1\|WP_101191009.1\|2426502_2426685_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101191013.1\|2427397_2428015_-\|HAD-family-hydrolase	unknown	unknown	gnl\|CDD\|223620
NZ_CP025135.1\|WP_145990608.1\|2425109_2425625_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|180687
NZ_CP025135.1\|WP_101191001.1\|2421111_2421702_+\|PIN-domain-containing-protein	unknown	unknown	gnl\|CDD\|379205
NZ_CP025135.1\|WP_101190999.1\|2420474_2421128_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|133390
NZ_CP025135.1\|WP_157824162.1\|2421853_2422024_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101192198.1\|2409608_2410238_-\|cyclase-family-protein	unknown	unknown	gnl\|CDD\|224790
NZ_CP025135.1\|WP_101191015.1\|2428194_2428779_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|368849
NZ_CP025135.1\|WP_145990607.1\|2422161_2422611_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101190987.1\|2410371_2410908_-\|6-phospho-3-hexuloisomerase	unknown	unknown	gnl\|CDD\|240138

Protein	Function_ID	Function_description	E-value
NZ_CP025135.1\|WP_101190995.1\|2418351_2418621_+\|phosphocarrier-protein-HPr	gnl\|CDD\|237503	PRK13780, PRK13780, phosphocarrier protein HPr; Provisional.	5.30839e-35
NZ_CP025135.1\|WP_101191004.1\|2423308_2424727_-\|sodium:alanine-symporter-family-protein	gnl\|CDD\|224040	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism].	1.13345e-176
NZ_CP025135.1\|WP_101190989.1\|2410927_2411569_-\|3-hexulose-6-phosphate-synthase	gnl\|CDD\|132172	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of this protein family are 3-hexulose-6-phosphate synthase (HPS), or the HPS domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase.	9.70721e-82
NZ_CP025135.1\|WP_101190993.1\|2413121_2415197_-\|BglG-family-transcription-antiterminator	gnl\|CDD\|226234	COG3711, BglG, Transcriptional antiterminator [Transcription].	1.8015e-43
NZ_CP025135.1\|WP_101190991.1\|2411909_2413115_-\|mannitol-1-phosphate-5-dehydrogenase	gnl\|CDD\|235031	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional.	0
NZ_CP025135.1\|WP_101190997.1\|2418617_2420324_+\|phosphoenolpyruvate--protein-phosphotransferase	gnl\|CDD\|224006	COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism].	0
NZ_CP025135.1\|WP_101191011.1\|2426720_2427194_+\|VanZ-family-protein	gnl\|CDD\|377417	pfam04892, VanZ, VanZ like family. This family contains several examples of the VanZ protein, but also contains examples of phosphotransbutyrylases.	0.00182743
NZ_CP025135.1\|WP_101190985.1\|2408796_2409621_-\|HAD-family-phosphatase	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.	4.07406e-76
NZ_CP025135.1\|WP_101191017.1\|2429460_2429934_-\|ParB-N-terminal-domain-containing-protein	gnl\|CDD\|366971	pfam02195, ParBc, ParB-like nuclease domain.	0.000324977
NZ_CP025135.1\|WP_101191013.1\|2427397_2428015_-\|HAD-family-hydrolase	gnl\|CDD\|223620	COG0546, Gph, Predicted phosphatases [General function prediction only].	1.09974e-31
NZ_CP025135.1\|WP_101191001.1\|2421111_2421702_+\|PIN-domain-containing-protein	gnl\|CDD\|379205	pfam13470, PIN_3, PIN domain. Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).	1.61241e-07
NZ_CP025135.1\|WP_101190999.1\|2420474_2421128_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|133390	cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.	2.25096e-07
NZ_CP025135.1\|WP_101192198.1\|2409608_2410238_-\|cyclase-family-protein	gnl\|CDD\|224790	COG1878, COG1878, Kynurenine formamidase [Amino acid transport and metabolism].	2.93302e-49
NZ_CP025135.1\|WP_101191015.1\|2428194_2428779_-\|hypothetical-protein	gnl\|CDD\|368849	pfam06338, ComK, ComK protein. This family consists of several bacterial ComK proteins. The ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level.	4.62537e-32
NZ_CP025135.1\|WP_145990608.1\|2425109_2425625_-\|hypothetical-protein	gnl\|CDD\|180687	PRK06770, PRK06770, hypothetical protein; Provisional.	2.73102e-29
NZ_CP025135.1\|WP_101190987.1\|2410371_2410908_-\|6-phospho-3-hexuloisomerase	gnl\|CDD\|240138	cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.	6.20198e-77

>NZ_CP025135.1|WP_101191001.1|2421111_2421702_+|PIN-domain-containing-protein
MNSIYDSPVRPKVFIDTTILCGALRTDGINRKILQAARFPHLFQPVFSKVCLFEFVRSAAEGLGKGKNRVAYSSDEIEEFFQAFLNPIFEYYEGLPVNSILGRYSVETIIREHLPIGDVLIELSGCDRDTAQTIAEKQEMSEPLSKFDQDDFHVWVTALRENCNFILTSNHRRFPAEIGEIKRIHPIRFYEELLNT
>NZ_CP025135.1|WP_101190999.1|2420474_2421128_+|helix-turn-helix-domain-containing-protein
MISTIDQEQENLWASVETLSTINTEQAEAVLKTTVERSLRQMGFTTPAISSLALKITDPQTVIELHQIERKIKHQLKNKNREMAYELLIDYLSKLSEMTDKDPAVIQKKLIASLMANSAKSPLRASLVNRPASHQKTGNSFYSPSEAAEKIGLSDQTIRRMCEKGKFAGAFKTDGGHWRIPKANFITTDEQDKRAKAFFDRIDTKNEEAGNVDEFDL
>NZ_CP025135.1|WP_101190997.1|2418617_2420324_+|phosphoenolpyruvate--protein-phosphotransferase
MSRLSGIAASNGIAIAKAFRLEHPDLTVDKKNVADPQAEIERFGSAVDESIAELEVIKKRTAEQISEKEADIFGAHLLVLQDPELIGPITDKIKTDSVNAEFALHETSTMFVDMFEAMDNEYMKERAADVRDVTKRVLAHLLGVKIQNPSLITDEVVIIAEDLTPSDTVQLNPQYIKGFITDIGGRTSHSAILARTLEIPAVVGAKSAMSSIQNGTIVIIDGLEGEILLDPDEATLAEYKEKQTAFADQKAEWAKLKNEATLTKDGVAVELGANIGTPKDLTGVLENGGEAIGLYRTEFLYMGRDNFPTEQEQFDAYSAVLKGMEGKPTVVRTLDIGGDKELSYLKLPKELNPFLGLRAIRLCLEMPDMFRTQLRALLRASVHGNLKIMFPMIATLDEFREAKALLLEEKAKLESEGVEVSDSIEVGIMVEIPSTAVMADTFAKEVDFFSIGTNDLIQYTMAADRMNESVSYLYQPYNPAILRLVKTVIDASHKEGKWTGMCGEMAGDEIAIPILLGLGLDEFSMSASSILKARSQLSRLSKADMEGHTEHILGLATSQEVEDYVKNL
>NZ_CP025135.1|WP_101190995.1|2418351_2418621_+|phosphocarrier-protein-HPr
MVEKTFTITDPAGMHARPASALVGSLSKFQSDITMEFKDKKVNLKSILGVMSLGVPSGSQVQIAADGADEAEAMETIERVLQEQGISNA
>NZ_CP025135.1|WP_101190993.1|2413121_2415197_-|BglG-family-transcription-antiterminator
MFVTVREKSIIELVTRMSAKHTVNSLATYLDVSARTIQRDLKSVDKLLEGFGLTMKRNAADALFIDGNNEKIYRLMQKLAASSAPEATPEEKKLRLLVILMEEGAFFKKQVLSNQLGISTTTLTSYLDELGNWLRKFSVTLSRQRGVGVEVDGAEAHKRHALAAYFLIHFYEELIESLYYLQQGKTQDDKVLGYFNPDYLSAANKLVGERISDEQIRLADSDYTGLVVHLALALQRTEKGFLLDAQPADSESNGEYHVIEAICDDLHERLGVELTERDVEFLVVVLKGSKIQASNVLYYDSVLLGKLVKNMIRDVSGQLGVDLTKDFSLYQGLLAHMEPLIFRLKQKLESFNPLTDEIKKKYPMLFLAVKQTLETEFDDLEFSADEVAFIVLHFGSALLMNEERVQIDAVVVCPTGIGTSKMLASRIQKELPEIDTVKILSIHDFEAANFQDYDLVISTIRLPVTDVDYLMVSPLLNEQDISHIENYLQHNIQKVTRNKQYLPAEALSEAGRTHRPNLRRLLLDIKQVQTGMEAILEHFGVVNMRGTDYWRVLEAVLDGMESDGLLDAASTLRQLKDRETKGGLGIPGTNMALFHCRDESVGQLLFQVVHLDTPSTVKGMDGRDVQMTNLLLMLTPVELSEREQEIMSLISSSLIESEAAMMIFSSSNEGVIRGKLEQLFYEYLQNNLMKE
>NZ_CP025135.1|WP_101190991.1|2411909_2413115_-|mannitol-1-phosphate-5-dehydrogenase
MKQAIHFGAGNIGRGFIGALFSESGYHVSFVDVAEQVIDGLNEQGQYRVNMAQETEESVLVENVSGINNMKDEEAVIAKIQQATYLTTAIGPNILPRIAPLIAKGIEARVKGSLASGPDLVPASDLDVATDMSAGSEKLYIIACENQIGATDILKGHILSHLSDEAKADLAGKVYFFNSAVDRIVPIQEGHSLDVLVEPYYEWVVETTEDIPHVSGMTIVDDLAPFIERKLFTVNTGHAVIAYYGYLASKTTIDETLADPEIEREVRETLKETGAYLVKQYGLDEQEHLAYIDKNIERFKNAYLNDGVTRVGRAPIRKLGPEDRLVRPAVQAQKAGLSYSHLAKAIAAALLFDYAEDEEAVKIQEMIAQGGPERVLTEVSGLEADSELAKEVVRQYGALKK
>NZ_CP025135.1|WP_101190989.1|2410927_2411569_-|3-hexulose-6-phosphate-synthase
MKLQLALDLVNIPQAIELIKEVEGSIDIVELGTPVINKEGLKAVREVKAAFPHLEVLADVKIMDAAAYEVGNAAAAGADIVTILAQAEDSSIKGAVEEAKKLGKKILVDMIAVKDIETRAAELDVLGADYICVHTGYDLQAEGKDSFADLRTIKSVVKNAKTAIAGGIKLETLPEVIRAQPDLIIVGGGITSKDDKKSEAAKIKALMNESVTV
>NZ_CP025135.1|WP_101190987.1|2410371_2410908_-|6-phospho-3-hexuloisomerase
MKEISAELSHTLGQVSDAEASRLVTAMGQADKIFVAGGGRSGFMAKAFVMRMVHMGLNAYVVGETVTPSLQENDLFIVGSGSGETGSLLAMTEKAKTIGATVAAVTTNPESSIGKLADLHITIPAQAKAEGASGKSIQPMGSLFEQSLLVVYDALVLTYMEQQGITADAMFGTHANLE
>NZ_CP025135.1|WP_101192198.1|2409608_2410238_-|cyclase-family-protein
MKIHDVTGAIFEGMAVYKDAAEKQPKFNQETDGYVTETRLELDVHTGTHIDAPLHMLPGGETFESIPLERLVGECKVVDLTKVTGGISRADLEGFELDKGDFVLLKTQNSFDDYFNFDFVYLAQDGADYLAEIGVRGIGTDALGIERSQEGHPTHKTLFNNNIIIIEGLRLRDVVQGGYYMVAAPLKLIGTDASTARVLLFEGASLCIK
>NZ_CP025135.1|WP_101190985.1|2408796_2409621_-|HAD-family-phosphatase
MYKMIAIDLDGTLLNDDLAVTADTMAAIRESMEHGVVVTIATGRMYPSAQRIALELGLDAPMITYQGAMIKSATSGEVLRERVVPFEIAQKCIHLAAQKQMHIQVYQDDVLYSAVDNEQVKAYSKEVGVGYKVEPDLLGLAKNGFMKLLFIDEPEALAPVQEELQAVLGDEACIEKSKLRYLEVTHPEANKGSALSFLADELGIDRSQVIGIGDNHNDTELVKAAGFGIAMGNAVDELKELADYTSLSNNEEGVLHVLNKFILEPRAAVVDSAQ
>NZ_CP025135.1|WP_157824162.1|2421853_2422024_-|hypothetical-protein
MTAIVKEEMTMEIPNKTYLQTYKEHIDGYKQYKLEKLAPQWHVPVDRKALKVESGL
>NZ_CP025135.1|WP_145990607.1|2422161_2422611_-|hypothetical-protein
MDRSIKSSGGMVEMMDIQQVASPDNKTAEMMAAQAVEKSRSCPIGSAPEIEGRRVPQLYIGLPMDRGVSVRLYRDEQEGLNEATILLSVEQLPSFTRALIEHPILLPTSYSQRSSVEDEQHALRIASKEDFPDFVERLTDALHALPQKK
>NZ_CP025135.1|WP_101191004.1|2423308_2424727_-|sodium:alanine-symporter-family-protein
MEQFLQGVADFSAWLWGIPLITLLLVSGLYMTFKLGFFQFRYFGYIVGQTFGSIFRRPKGEGTVTPFQALTSALSSTIGAANIVGVPAAIMFGGPGAIFWMWVIALIGMALKFAESVLAVEYREKNAKGEFVGGPMYYMTKGLNMKWLGIWFSFALMIELIPSIMVQGNSIANTVQATFNVPVLWTGIATAVLVSIVVFGGIKRIGKVTEIFVPFMALMYVGGAVVILLMNVKAVPEFFMLIFSNAFSPAPVVGGFAGAAIVEIIRWGFARGLYSNEAGLGTAPIAHAAATTDHPVRQGFWAVIGVVVDTLIVCTATAFVILSSGVWTEEGAMENSSALTSLAFEEYFGDFGAILVTIALIFFVLSTILVVVFYGAKQAEFLFGLKAAYGMQVVYIFAVILGAVGAAEVIWGFLDIMLAAILIPNVIAILLLSNKVKELKNEFFTSDEYYRKDRKVKKRAKRQKAVREGYES
>NZ_CP025135.1|WP_145990608.1|2425109_2425625_-|hypothetical-protein
MKTVLRTIIILLVGLGILAGAGYWAYKSLTTSDEQQISQAAEEADDKLQQGEDTEAPKANEQVETVGLSEGEFQIHLHQMTHQKIEATEKRGAIEMTPERIDEMLKILQANEGAYEEYEFYEQSLTAWEEGNFSNAVNVHNTIWEWHNGTVGRATGLLSEEQEAAYVEDNF
>NZ_CP025135.1|WP_157824163.1|2426215_2426440_-|hypothetical-protein
MDGDEFEFSILGGNIAGHYFAIAVKAHIVAILENHNAKEILVRELIFDGPVSDGAIIAIEAFDGEFFVFEQLTG
>NZ_CP025135.1|WP_101191009.1|2426502_2426685_+|hypothetical-protein
MITEDFSGPINYYLPPGYYYPSLLYPLLYPWITSIVGLALILFNFPYGAMKKRSAAKNAQ
>NZ_CP025135.1|WP_101191011.1|2426720_2427194_+|VanZ-family-protein
MKAKYIPVLLWALCILIATNNYNFTALLANDIDFNIRLFPNLSDLFITSDIHLDSKLYVFQKTGHALSFGILYLLMNQAVKERHVAFVLCSLFAFFTEFLQLFFERSGRLVDVLIDIAGVYAAYRLSIYVKAHGGIVPAFSHATQTISNVLKDDKTH
>NZ_CP025135.1|WP_101191013.1|2427397_2428015_-|HAD-family-hydrolase
MDSIIFDLDGTLWNPLDVSVAVWNRVLADNGVDEMLSKDDLRGIMGLQADQVGEKLFPHLSKEQCEKLTEESSQLECEYLRKQGGQLYESVERVLERLSQKYNLYIVSNCQEGYIESFYEYHGLDSHFVDFENPGRTGLSKGENIQLIMERNDVAKAVYVGDTKGDHEAAKMAGLPFVYAAYGFGDVDEYDYKLEEFEELLALFG
>NZ_CP025135.1|WP_101191015.1|2428194_2428779_-|hypothetical-protein
MRKRKNFKLEMNMEKEIGQETVLILPDYDENGCLNSVIYHTDGMIKVESKPFDLIDTNLRFRGSSMRGAVEGSAAILGKLNKNPIIIDRDKGVILLPSKSALLDGCVWLSLQHIMECISIDGCTTKVNLSNGSSIILDGSKKSIQRRMEKAYELQFKIPEAQKRFFESGRVIPETTYHLVKQAGQVNYEHKALE
>NZ_CP025135.1|WP_101191017.1|2429460_2429934_-|ParB-N-terminal-domain-containing-protein
MRKLKANRNFTPCVPVVDDETFGGFPFTWNITHVQTWIDNNLDQVDLSVVQIAPPSKGTDSDSLDEAWILEADLTKPVIIVWMRPEFFKLIDGNHRVAKARRMGVAELPAYYLTEQQHRQFFAREQADMMYVKYWNEKLEQVEKGWGQWAVVGQMKV

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Crispr_ID: NZ_CP025135_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP025135_4

3018673-3018777

Orphan

Consensus_repeat	Method
TCAGCCGCAGCTTTTCGTTCTTCT	CRISPRCasFinder

1 spacers

csa3

The CRISPR arrays of NZ_CP025135_4

>merge|NZ_CP025135|4|3018673-3018777|CRISPRCasFinder
TCAGCCGCAGCTTTTCGTTCTTCTTCAGCTTGTCTCGCGGCAGCTGCTTCTTCAGCTGCTTGTTGTTCAGCCGCCGCCTGTTCAGCCGCAGCTTTTCGTTCTGCT

>NZ_CP025135|4|4|3018673-3018777|CRISPRCasFinder
TCAGCCGCAGCTTTTCGTTCTTCT	TCAGCTTGTCTCGCGGCAGCTGCTTCTTCAGCTGCTTGTTGTTCAGCCGCCGCCTGT
TCAGCCGCAGCTTTTCGTTCTGCT

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP025135.1\|WP_101191818.1\|3024763_3024892_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|315923
NZ_CP025135.1\|WP_101191812.1\|3014805_3015492_-\|DsbA-family-protein	unknown	unknown	gnl\|CDD\|372611
NZ_CP025135.1\|WP_101191822.1\|3035175_3036342_-\|ThiF-family-adenylyltransferase	unknown	unknown	gnl\|CDD\|235717
NZ_CP025135.1\|WP_101191823.1\|3036690_3037011_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|238045
NZ_CP025135.1\|WP_101191813.1\|3015520_3016615_-\|copper-resistance-protein-CopD	unknown	unknown	gnl\|CDD\|224195
NZ_CP025135.1\|WP_101191814.1\|3016611_3017178_-\|copper-resistance-protein-CopC	unknown	unknown	gnl\|CDD\|377255
NZ_CP025135.1\|WP_101191805.1\|3004231_3004714_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101191817.1\|3019978_3021466_-\|alpha-amylase	unknown	unknown	gnl\|CDD\|200478
NZ_CP025135.1\|WP_101191808.1\|3011316_3012975_-\|cytochrome-C-biogenesis-protein	unknown	unknown	gnl\|CDD\|224252
NZ_CP025135.1\|WP_101191810.1\|3013553_3014261_-\|cytochrome-C-biogenesis-protein-CcdA	unknown	unknown	gnl\|CDD\|280792
NZ_CP025135.1\|WP_101192234.1\|3022193_3023624_-\|SH3-domain-containing-protein	unknown	unknown	gnl\|CDD\|119407
NZ_CP025135.1\|WP_101192235.1\|3028571_3029183_+\|CadD-family-cadmium-resistance-transporter	unknown	unknown	gnl\|CDD\|129861
NZ_CP025135.1\|WP_101191811.1\|3014365_3014806_-\|disulfide-bond-formation-protein-B	unknown	unknown	gnl\|CDD\|179540
NZ_CP025135.1\|WP_157824201.1\|3023972_3024236_+\|metalloregulator-ArsR/SmtB-family-transcription-factor	csa3	COG0640_csa3_CAS-I-A	gnl\|CDD\|238042
NZ_CP025135.1\|WP_101191821.1\|3034802_3035186_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_157824179.1\|3006434_3006830_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP025135.1\|WP_101191819.1\|3025173_3027087_+\|heavy-metal-translocating-P-type-ATPase	unknown	unknown	gnl\|CDD\|319849
NZ_CP025135.1\|WP_101191809.1\|3012988_3013525_-\|thiol-disulfide-oxidoreductase-ResA	unknown	unknown	gnl\|CDD\|179545
NZ_CP025135.1\|WP_101191820.1\|3027275_3028124_-\|cation-transporter	unknown	unknown	gnl\|CDD\|224151
NZ_CP025135.1\|WP_101191806.1\|3005253_3006186_+\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_CP025135.1\|WP_101191818.1\|3024763_3024892_+\|hypothetical-protein	gnl\|CDD\|315923	pfam13358, DDE_3, DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.	1.79916e-08
NZ_CP025135.1\|WP_101191812.1\|3014805_3015492_-\|DsbA-family-protein	gnl\|CDD\|372611	pfam13462, Thioredoxin_4, Thioredoxin.	8.84775e-44
NZ_CP025135.1\|WP_101191817.1\|3019978_3021466_-\|alpha-amylase	gnl\|CDD\|200478	cd11339, AmyAc_bac_CMD_like_2, Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.	1.35094e-34
NZ_CP025135.1\|WP_101191823.1\|3036690_3037011_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|238045	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.	3.08936e-15
NZ_CP025135.1\|WP_101191813.1\|3015520_3016615_-\|copper-resistance-protein-CopD	gnl\|CDD\|224195	COG1276, PcoD, Putative copper export protein [Inorganic ion transport and metabolism].	7.09764e-19
NZ_CP025135.1\|WP_157824201.1\|3023972_3024236_+\|metalloregulator-ArsR/SmtB-family-transcription-factor	gnl\|CDD\|238042	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.	6.90126e-19
NZ_CP025135.1\|WP_101191820.1\|3027275_3028124_-\|cation-transporter	gnl\|CDD\|224151	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].	1.29965e-77
NZ_CP025135.1\|WP_101191814.1\|3016611_3017178_-\|copper-resistance-protein-CopC	gnl\|CDD\|377255	pfam04234, CopC, CopC domain. CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm.	1.146e-20
NZ_CP025135.1\|WP_101191808.1\|3011316_3012975_-\|cytochrome-C-biogenesis-protein	gnl\|CDD\|224252	COG1333, ResB, ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones].	2.14436e-114
NZ_CP025135.1\|WP_101191810.1\|3013553_3014261_-\|cytochrome-C-biogenesis-protein-CcdA	gnl\|CDD\|280792	pfam02683, DsbD, Cytochrome C biogenesis protein transmembrane region. This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange proteins. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family.	3.11771e-42
NZ_CP025135.1\|WP_101192234.1\|3022193_3023624_-\|SH3-domain-containing-protein	gnl\|CDD\|119407	cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.	2.10238e-52
NZ_CP025135.1\|WP_101192235.1\|3028571_3029183_+\|CadD-family-cadmium-resistance-transporter	gnl\|CDD\|129861	TIGR00779, quaternary_amine_transporter, cadmium resistance transporter (or sequestration) family protein. These proteins are members of the Cadmium Resistance (CadD) Family (TC 2.A.77). To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes several closely related Staphylococcal proteins reported to function in cadmium resistance. Members are predicted to span the membrane five times; the mechanism of resistance is believed to be export but has also been suggested to be binding and sequestration in the membrane. Closely related but outside the scope of this model is another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export. Still more distant are other members of the broader LysE family (see Vrljic. et al, ). [Transport and binding proteins, Amino acids, peptides and amines].	1.46589e-70
NZ_CP025135.1\|WP_101191811.1\|3014365_3014806_-\|disulfide-bond-formation-protein-B	gnl\|CDD\|179540	PRK03113, PRK03113, putative disulfide oxidoreductase; Provisional.	7.70184e-57
NZ_CP025135.1\|WP_101191822.1\|3035175_3036342_-\|ThiF-family-adenylyltransferase	gnl\|CDD\|235717	PRK06153, PRK06153, hypothetical protein; Provisional.	3.32571e-162
NZ_CP025135.1\|WP_101191819.1\|3025173_3027087_+\|heavy-metal-translocating-P-type-ATPase	gnl\|CDD\|319849	cd07551, P-type_ATPase_HM_ZosA_PfeT-like, P-type heavy metal-transporting ATPase, similar to Bacillus subtilis ZosA/PfeT which transports copper, and perhaps zinc under oxidative stress, and perhaps ferrous iron. Bacillus subtilis ZosA/PfeT (previously known as YkvW) transports copper, it may also transport zinc under oxidative stress and may also be involved in ferrous iron efflux. ZosA/PfeT is expressed under the regulation of the peroxide-sensing repressor PerR. It is involved in competence development. Disruption of the zosA/pfeT gene results in low transformability. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle.	0
NZ_CP025135.1\|WP_101191809.1\|3012988_3013525_-\|thiol-disulfide-oxidoreductase-ResA	gnl\|CDD\|179545	PRK03147, PRK03147, thiol-disulfide oxidoreductase ResA.	1.62617e-92

>NZ_CP025135.1|WP_101191814.1|3016611_3017178_-|copper-resistance-protein-CopC
MKKVVLFLLFFLSLTSSAVFAHTALESANPAEGDVVTEELQEMVLEFNTDLEQGSSFTVEDERGQEVPIGVEIGGQSMTGTLGAAIANGTYTVNWKIIGADGHPIEGTYAFTLKVSEDLISSGITEEATPSTEDELADQGETEEPLNENLAAPQETTNAPYVMVIVLMILAVIAVGTLMWVSNKRGNK
>NZ_CP025135.1|WP_101191813.1|3015520_3016615_-|copper-resistance-protein-CopD
MIWIYVTETLLYLCFSLLIGTLVIQLVPSHLKPHLKINKRVLQVAILGIAFLSAAPVIRLILFLYEDIGLLVTTQNVIGEFEVGQAWTVTVFISVFFYLFVSLVPVFKRKAFIGIALVFSFILLLAVGWASHAASLTDWSGFVVHTLHFTAVAVWVGLLLVVSWFSTTAQNWLSFLKWYTPVALSCLAIVVGSGIFIMTLAVDVTEYQDAWMMPYGQAILLKHLLVLPVLLFAWINGVWMRRKLQRGEDINPVPWSRAESVVLLLIFAATAVLGQQEPPHSIEAYLKGSGASDLFRYFYSGQIDPAMHLQVDFTLLGSLFFGVAVIFGFLVLYCFKQKAPSFVSLLMSLFSVLALYVGLMMSIS
>NZ_CP025135.1|WP_101191812.1|3014805_3015492_-|DsbA-family-protein
MNNNQKKAKPSGLKFAVLLTSLAVVILVAIVVLTNQQEAPAVETAQIDLSGQPILGEEEAPVTVVEFGDFKCPSCKAWGETVYPQLVQDYVDTGEAKFSYINVLFHGEESTLASLAAESVYQQSPEVYWDFHKALFAAQPEVNHDGAWITPEKVLEVTAVYPSIDQTKLKEDMEKQATMDAVEVDTALVEEAGVAQTPTIVINGQTLEDPFDYEAIKELIEQELMGEE
>NZ_CP025135.1|WP_101191811.1|3014365_3014806_-|disulfide-bond-formation-protein-B
MEKERIQSSQNAILLYGAWFVALIATLGSLYFSEIKGFIPCELCWYQRIAMYPLVLILGIATFRNDAKVFIYVLPLSLLGGSISILHYLEQKVPGFGGIKPCVSGVPCSSEYINWFGFVTIPFLALIAFILISVAMVVLVVKNKKD
>NZ_CP025135.1|WP_101191810.1|3013553_3014261_-|cytochrome-C-biogenesis-protein-CcdA
MAEVSLLLAFGAGLLSFLSPCSLPLYPAFLSYITGVSVNDLKTEKGVMRRNALIHTILFLIGFSIIFLALGLSTSFIGSFFLENQALLRQLGAILMVFFGLVLTGILKFDFLLSDKKVHFQKRPSGYAGSVLIGIGFAAGWTPCTGPILAGVIALGVADPDRGLLYMLFYVLGFAIPFLLMSLFIEKMSFLKKKSALFMSIGGALMILMGVLLYFDMMTEIIAFLSQFTGGFTGF
>NZ_CP025135.1|WP_101191809.1|3012988_3013525_-|thiol-disulfide-oxidoreductase-ResA
MTVKKKKRSYVRAAILLVMAGAIVFTIYNSFAGEKSELLQVGDEAPDFALVDLEGKEHQLSDYQGQGVFVNFWGTWCKPCEKEFPLMEKQYQVYKDQGVQILAVNIAQSDYEVRQFAEQRDLTFPIVIDKTKSVMEAYNIRPLPTTLLVNPEGKITKIITGEMSEEDIASYMEEIKPE
>NZ_CP025135.1|WP_101191808.1|3011316_3012975_-|cytochrome-C-biogenesis-protein
MENVQCQCGHTNPPGTKLCESCGRSLTEKDQNSKLVDMRYEGTARRSQTYNKSIIDKIWNFFSSVKVGVSIIVVLLVAAAIGTILPQQAFVPASTEATIQAYYADTYGSVGRVYHALGFHDLYSSYWFIALVGMLAISLVIASLDRFVPLYKSLKNQRVLRHPSFMDKQRIYGSGPGAEDALEKAETKLKELKYTVRTEKNGLLAEKGRFSRWGPYVNHIGLIIFLFGVMLRMMPGFYVDETLWLREGETRAIPEVPGYYLENKNFKLETYTGEGEDAKFGEAIDRVGTVVKNYQTDIVLYQEPEDSLPGATDNLEVVQEYPIRVNQPLKFDGYAVYQMDYKLNELKAMTFALTNKETEESLGELTIDLINPDALYELETGSTVELLGYYPDFSGFEDGEPQTATPLPNNPGFLVELTTPETPEGETSFITIQNTVEPLGENQYKLTFQNADTRNVSGLTVRKDSTLPILGLGGLIFMIGVAQGMYFNHRRFWIQQKADGTILLAGHTNKNWFGLKKDLDRVVDSAKLPAYTDQQDEIDKKEKAEKEGESSS
>NZ_CP025135.1|WP_157824179.1|3006434_3006830_-|hypothetical-protein
MDLEISAADFMNIGILKSIIKRTYKIYIQAISLMLGDKKSALGFYQNTVDAKGVLITAEEREEKEIQLFEASIKNIHTKWTLDNVKIADSEKLRNKLKYMEEGDTVKVRFIPGTKNEITYEYSLQDYKTEG
>NZ_CP025135.1|WP_101191806.1|3005253_3006186_+|hypothetical-protein
MDLNLLIATVITATAALIAIIGGFLISRVITLSSEQSGIRRRLREIMLDIKTKEQLLDEVEENLLEEDREDFINEYYSELIFDKVPLEVIIDNLEGSYRERSMNDLEPVINEIIQINKDLKTMFEGSGIKYSTELPKDFGDFANIRSEDLEGRRSWYELLYDEYQYRLPKKPKTDPFGFSSIYDIDVPPSLFSNSMSTQAAAQAYQQKSRDRDTYRNELSSLKQQGSEQKKILEDYGKPHGMWGGLMVLIYASIVGIAYPVTLLPYPLQTYNDEATRILILLLFLSQLLALFIYLGISMYSLTKDEKAPE
>NZ_CP025135.1|WP_101191805.1|3004231_3004714_-|hypothetical-protein
MKSIRVTKYNPKNRDAKGLYTLVDEWTSISDVGKTYHGQIFTMEQYLETEEKYIRAVEVLMQKTRVNHLKLLDLENHSHETALNLSEGKTIPIILIKDLVKMILREEVWARLVAKNQFEIHFGWDYYMYFVGESLTDDIIEELRKIDDLYVEDVQSPHLD
>NZ_CP025135.1|WP_101191817.1|3019978_3021466_-|alpha-amylase
MKAKWFLAIITGILLVSLVTPAAAKEKNSLQDEIIYDLLVDRYFNKVIQNDYEVDSRDITAFNGGDFKGLASEMQYIKDMGFTMVSIGPVFATDTYDGKEVIDYQQFERHFGTEEEFQEAIDKIHELDMKVIIDIPTQRVSKEHVWNKENPEWFSENEDGTMALDTTNPEAQRKLIDWFSEFVEEYEIDGIRLQTADQLDEDFISQFSETMKSIRDVYIISDLEMGPQSGLDAVVKPGIEEDLRSSYKNFDPLSTTSPDFEETAEGQLTRVDSLLSNRFTSDIVAVRGFPPTRWNLLMFQLLTMPGIPIVQYGSEIAMNGSAPPESHSILNMGVDEELIDHITSLTSLRNQSEALRTGETEVLHEKDGWLVYKRSNKEESWIIAINNSSSTKSLTIPAEVIGDDKEMRGLFENDVVRQNDDGDYQITLDRELGEAFNVIERKGFNKAYIAALILLYTLFISFLVLAWRRGRKRNLAKANKSKNSDVEEFPKPNHG
>NZ_CP025135.1|WP_101192234.1|3022193_3023624_-|SH3-domain-containing-protein
MLLMILLVSIYTPKSYANTNLTFVDVANHRAQAEISYLVTRGFVHGVTATTFVPNRQVTRGEAAAMLGRALGLSGVKRNTKFSDVRVGNFASGYVDELVRKGIISGYPDGSFQPYKVLSRGEMALLINRSFNLGGISISTSVDNLMRKGIAQGFPDGSFRTDETIIRADFAIFLVRSLNENFRVKPEGVSFSKTMYVNTGADALNMRSGPSTSDKVISSLKHGTTVNVASSKNGWSHVQVNGVIGYVSTNYLVALKPTVPAPVSTSLGTSDLKVIIDPGHGGTDPGSVANGFQEKMITLNVGKHMKNYFDQTPIATTMTRSTDVFIELSDRAKAAAKNDGDVFVSIHTNKFNGEVNGQETFYYAKTTATNPNVQESRALSIYLQARMQEAWKLTNRQVKVGNLAVLRENTVPASLTEIGFIDNSKDLQFIKSELERQRMGKALFLGTLDYFYHYEKRTDVLPYYKKAGASLSKKLH
>NZ_CP025135.1|WP_157824201.1|3023972_3024236_+|metalloregulator-ArsR/SmtB-family-transcription-factor
MDFEKKEVSVTSSRLDEETLFVVSQTFKALSDPTRIRILNLLCSGEYSVNDLAEKLNFGQSTVSHQLRFLKQLRLVKYRRAGTTLYY
>NZ_CP025135.1|WP_101191818.1|3024763_3024892_+|hypothetical-protein
MILDNARIHHAKLIQPFLEENRCRPQMVFLPPCSPILNIMLM
>NZ_CP025135.1|WP_101191819.1|3025173_3027087_+|heavy-metal-translocating-P-type-ATPase
METVKEQQSHETHNHDHDHGKMPIILYFIGLALALIALFLNGEYTITKNILFSIATISAGYHVILLEGIGETVENTKAKNKFTPNSHILMGLAALGASLIGNFWEGTLLILIFSGAHFLEDYAEGRSKREITKLLKLNPTTARLIISDGNTKIVDVNELKVGDRLQVLNGDQVPIDGVILSGNTSIDESSINGESIPKEKSKGDVVFGSTINGTGTFTMEVSKENKDTVFSKILQLVNQNQNNQTKAASIIQKFEPKYVTVVLMAIPLFIILTPMILDWTWSQSTYRGLVLLVAASPCALAAATVSVTLSATSNLAKRGVLSKGSSYLSQLAGIQAIAFDKTGTLTKGKPEVTNYYFTNSVNEENIIDIVVALEKESNHPLADAILRKFEQKNKLAIEVENQIGRGLTGDYKGKNYRIGKPTSFDGVSDEYIHLNSEWASEGKTVVYVAEDEEVIGLIGLMDIPSEHAKETIEYFKKLGIHTTLITGDSEMTGKAVAEQLGLDEVIANVMPEDKSNIIDQQKENYGITAMVGDGVNDAPALVKADVGIAMGDGTDVAVDVSDLVLMKNDLSKLVKAHQISLKMNRVIWQNIIFSMTVVAFLIIVTLLGLTDIAISVIIHEGSTLVVILNGLRLLRSR
>NZ_CP025135.1|WP_101191820.1|3027275_3028124_-|cation-transporter
MAKAHKSTKNIKLAFMINLLFSIGELIGGFLINSVAIMSDAIHDLGDAIALGISWFLQNFSNKEGDEKFSFGYKRFSLLGALINAAVLIAGSIYIFTQAIPLLFNPEHSNAQGMIWFAIVGVLLNGYAAFKLHKGKSVNEGVLSWHMLEDVLGWVAVLIVGIVLLFKDIHILDPILSLAIALFILVNVVRNLTKTMKILLEGVPEGIDIEEIQAKIEKIPGVLSVGDLNIWSIDGEENALNLHLSVEGDNLADSAAIKEKVRKATSDLRIVHSAIELEWKDR
>NZ_CP025135.1|WP_101192235.1|3028571_3029183_+|CadD-family-cadmium-resistance-transporter
MITTIFSAVAAYVATSIDYVIILLILFSQTMKKGQLKSIVIGQYLGTAILVGVSLLAAYGLALVPEHWVGLLGLIPIYLGIKVWLKEEENDEEDILSRLSSGKSNRLFVTVTVITLAAGGDNIGVYIPYFSTLNLSETVVMLVVFAVMVAVLCYLSYRLASVKAVSETIEKWERWIVPVVFIGLGIMILVENGTFRFLWSLMN
>NZ_CP025135.1|WP_101191821.1|3034802_3035186_-|hypothetical-protein
MKHRFVEYIPSQMESDVLYISIEFDVAKHLCPCGCKSVIVTSLSPARWKLIYDGETVSLRPSVGNWTLNCKSHYFITNDKVEWAGAINQQQVDAVLESDHSAIKKHVEGHQKPLSIFEKLKKWLGLK
>NZ_CP025135.1|WP_101191822.1|3035175_3036342_-|ThiF-family-adenylyltransferase
MSTQLIDLNEDLKKLKDDGYSTSIVESNLVVAGIPYVNAEKKILFGAIFCPLTISGESIGAPQDHTVYFAGEYPCNQLGQPSSSFVNSATTNKLNSEILGNYYLSSKPVTGSYADFYTKMTKYIELLSDPAKSIDPGISAQYSSEYTFNESSVFKYADTHTARANLTNASQKLRNQKIAIVGLGGTGSYLLDFVSKTPVKQISIFDGDDILNHNAFRMPGAMTLNELRERPSKSSFFKEKYEALRNEIVAYDQYLNEANVDLLGGHDFVFLAIDKAEAKRTIISYLMTQGIPFIDLGMGVTLVNDSVRGTVRRTLVTPENQTYLNKIAMSEAADQDIYAQNIQISELNALNAVQAVITWKKMNGFYATEDTFFNSTFIIDEEEFGHEA
>NZ_CP025135.1|WP_101191823.1|3036690_3037011_+|helix-turn-helix-transcriptional-regulator
MKNRLIRKRKELNITQTELAKRAGLTAPSISQYESGLRNPPYEAILKLANALSVSADYLISGSEASNDNSIDPIQSVLLKITQSLSTSQKKMSFFCSLLVRARKTF

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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

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

2307053 : 2318038

Streptococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_101190822.1\|2307053_2308913_-	polysaccharide biosynthesis protein	A0A2P1ELS8	Moumouvirus	1.1e-26	28.5
WP_101190824.1\|2308949_2309648_-	CpsD/CapB family tyrosine-protein kinase	A0A1X9I5D6	Streptococcus_phage	1.3e-28	35.4
WP_101190826.1\|2309583_2310372_-	chain-length determining protein	A0A1X9I5E1	Streptococcus_phage	2.8e-16	31.9
WP_101190828.1\|2310414_2310837_-	hypothetical protein	NA	NA	NA	NA
WP_101190830.1\|2311061_2311754_-	response regulator transcription factor	NA	NA	NA	NA
WP_101190832.1\|2311775_2315033_-	response regulator	A0A1V0SGX0	Hokovirus	2.7e-28	29.1
WP_101190834.1\|2315338_2317009_-	diguanylate cyclase	A0A2D0WBV8	Bordetella_phage	1.3e-07	36.8
WP_101190836.1\|2317279_2318038_+	NRDE family protein	A0A1V0S7Z6	Shearwaterpox_virus	1.3e-34	37.0

DBSCAN-SWA_2

3222897 : 3230932

Bacillus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_101191985.1\|3222897_3223644_+	ABC transporter ATP-binding protein	G3M9Y6	Bacillus_virus	3.3e-22	30.8
WP_101191986.1\|3223699_3225445_-	aminodeoxychorismate synthase component I	A0A0B5J984	Pandoravirus	1.9e-52	31.4
WP_101191987.1\|3225419_3226043_-	aminodeoxychorismate/anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	5.8e-49	50.8
WP_101191988.1\|3226338_3226737_-	DUF1259 domain-containing protein	NA	NA	NA	NA
WP_101191989.1\|3226981_3227161_-	hypothetical protein	NA	NA	NA	NA
WP_101192251.1\|3227235_3227643_-	hypothetical protein	A7KUZ7	Bacillus_phage	7.8e-18	41.9
WP_101191990.1\|3227701_3228748_-	ribonucleotide-diphosphate reductase subunit beta	A7KUZ8	Bacillus_phage	2.5e-105	56.3
WP_101191991.1\|3228754_3230932_-	ribonucleoside-diphosphate reductase subunit alpha	A7KUZ9	Bacillus_phage	2.1e-263	60.8

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. NZ_CP025123

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CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NZ_CP025125

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

3. NZ_CP025135

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection