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
NC_008391	Burkholderia ambifaria AMMD chromosome 2, complete sequence	0 crisprs	csa3,Cas14u_CAS-V,cas3,c2c9_V-U4,DinG,DEDDh	0	0	1
NC_008392	Burkholderia ambifaria AMMD chromosome 3, complete sequence	0 crisprs	csa3,RT,Cas14u_CAS-V	0	0	0
NC_008385	Burkholderia ambifaria AMMD plasmid unnamed1, complete sequence	0 crisprs	NA	0	0	0
NC_008390	Burkholderia ambifaria AMMD chromosome 1, complete sequence	5 crisprs	cas3,DEDDh,csa3,Cas14u_CAS-V,DinG	1	2	4

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

179356 : 187943

Escherichia_phage(33.33%)

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_011658412.1\|179356_181282_+	selenocysteine-specific translation elongation factor	A0A2K9KZ60	Tupanvirus	2.8e-17	31.7
WP_011658413.1\|181579_182596_-	dTDP-glucose 4,6-dehydratase	A0A1D7XFE8	Escherichia_phage	8.9e-79	45.2
WP_011658414.1\|182592_183477_-	dTDP-4-dehydrorhamnose reductase	NA	NA	NA	NA
WP_011658415.1\|183473_184055_-	dTDP-4-dehydrorhamnose 3,5-epimerase	I7HJC4	Enterobacteria_phage	7.1e-49	59.3
WP_011658416.1\|184051_184948_-	glucose-1-phosphate thymidylyltransferase RfbA	A0A291LA53	Escherichia_phage	1.2e-95	56.8
WP_011658417.1\|185047_186445_-	MFS transporter	NA	NA	NA	NA
WP_011658418.1\|186441_187161_-	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	1.0e-12	29.9
WP_011658419.1\|187157_187943_-	ABC transporter ATP-binding protein	R4TX06	Phaeocystis_globosa_virus	5.0e-05	23.5

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_008390

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CRISPR-Cas detection and classification

Crispr_ID: NC_008390_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_008390_1

179862-180104

Orphan

Consensus_repeat	Method
TATGCGGAAGCGCACAACAACCTCGGCAACGTGCTGCGC	PILER-CR

2 spacers

The CRISPR arrays of NC_008390_1

>merge|NC_008390|1|179862-180104|PILER-CR
TATCCGGAAGCGCACAACAACCTCGGCAACGCGCTGCGCGACGCGCGCGATCCGGCCGAGGCGATGCAGAGCTGTTCGCGCGCGATCGAATTGCGTCCCGGTTATGCGGAGGCATACAACAACCTCGGCAACGTGCTGCAGGACCTGGGCGAGCTGGATGCGGCCGCGGCGAGCTACGGCAAGGCGATCGCCTTCCATCCCGCGTATGCGGAAGCGCACAGCAACCTCGGCAACGTGCTGCGC

>NC_008390|1|1|179862-180104|PILER-CR
TATCCGGAAGCGCACAACAACCTCGGCAACGCGCTGCGC	GACGCGCGCGATCCGGCCGAGGCGATGCAGAGCTGTTCGCGCGCGATCGAATTGCGTCCCGGT
TATGCGGAGGCATACAACAACCTCGGCAACGTGCTGCAG	GACCTGGGCGAGCTGGATGCGGCCGCGGCGAGCTACGGCAAGGCGATCGCCTTCCATCCCGCG
TATGCGGAAGCGCACAGCAACCTCGGCAACGTGCTGCGC

Protein	Signature genes	Signature genes Name	Protein_function
NC_008390.1\|WP_011655677.1\|191470_192352_+\|ATPase	unknown	unknown	gnl\|CDD\|225518
NC_008390.1\|WP_006401410.1\|190256_190469_+\|30S-ribosomal-protein-S21	unknown	unknown	gnl\|CDD\|234707
NC_008390.1\|WP_011655670.1\|178334_179540_+\|methyltransferase-domain-containing-protein	unknown	unknown	gnl\|CDD\|372616
NC_008390.1\|WP_011655674.1\|186943_187240_-\|flagellar-protein-FliT	unknown	unknown	gnl\|CDD\|377507
NC_008390.1\|WP_011655661.1\|165991_167578_+\|TIGR04222-domain-containing-membrane-protein	unknown	unknown	gnl\|CDD\|275063
NC_008390.1\|WP_011655664.1\|171658_172309_-\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|379312
NC_008390.1\|WP_011655662.1\|167605_170392_-\|glycosyltransferase	unknown	unknown	gnl\|CDD\|340842
NC_008390.1\|WP_011655675.1\|187275_188703_-\|flagellar-filament-capping-protein-FliD	unknown	unknown	gnl\|CDD\|236141
NC_008390.1\|WP_011655665.1\|172319_173027_-\|WbqC-family-protein	unknown	unknown	gnl\|CDD\|378083
NC_008390.1\|WP_011655666.1\|173032_174418_-\|FAD-binding-oxidoreductase	unknown	unknown	gnl\|CDD\|223737
NC_008390.1\|WP_006751066.1\|188890_189715_-\|flagellin	unknown	unknown	gnl\|CDD\|139237
NC_008390.1\|WP_011655673.1\|184533_186798_+\|tetratricopeptide-repeat-protein	unknown	unknown	gnl\|CDD\|226428
NC_008390.1\|WP_011655676.1\|190723_191329_-\|DNA-3-methyladenine-glycosylase-I	unknown	unknown	gnl\|CDD\|377025
NC_008390.1\|WP_011655679.1\|193581_194322_-\|aquaporin-Z	unknown	unknown	gnl\|CDD\|235453
NC_008390.1\|WP_011655672.1\|182050_184537_+\|tetratricopeptide-repeat-protein	unknown	unknown	gnl\|CDD\|226428
NC_008390.1\|WP_012362821.1\|192642_193476_+\|Cof-type-HAD-IIB-family-hydrolase	unknown	unknown	gnl\|CDD\|182878
NC_008390.1\|WP_011655667.1\|174414_175200_-\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011655663.1\|170388_171597_-\|dTDP-4-amino-4,6-dideoxygalactose-transaminase	unknown	unknown	gnl\|CDD\|183283
NC_008390.1\|WP_041491065.1\|175603_177400_+\|glycosyltransferase-family-41-protein	unknown	unknown	gnl\|CDD\|226428
NC_008390.1\|WP_082089595.1\|177357_178338_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187541

Protein	Function_ID	Function_description	E-value
NC_008390.1\|WP_011655677.1\|191470_192352_+\|ATPase	gnl\|CDD\|225518	COG2971, COG2971, Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism].	3.49578e-44
NC_008390.1\|WP_006401410.1\|190256_190469_+\|30S-ribosomal-protein-S21	gnl\|CDD\|234707	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.	3.73136e-14
NC_008390.1\|WP_011655670.1\|178334_179540_+\|methyltransferase-domain-containing-protein	gnl\|CDD\|372616	pfam13489, Methyltransf_23, Methyltransferase domain. This family appears to be a methyltransferase domain.	3.11138e-13
NC_008390.1\|WP_011655674.1\|186943_187240_-\|flagellar-protein-FliT	gnl\|CDD\|377507	pfam05400, FliT, Flagellar protein FliT. This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium.	0.000529664
NC_008390.1\|WP_011655679.1\|193581_194322_-\|aquaporin-Z	gnl\|CDD\|235453	PRK05420, PRK05420, aquaporin Z; Provisional.	3.31617e-142
NC_008390.1\|WP_011655661.1\|165991_167578_+\|TIGR04222-domain-containing-membrane-protein	gnl\|CDD\|275063	TIGR04222, integral_membrane_protein, TIGR04222 domain. The majority of the proteins with a domain as described by this model have an extreme C-terminal sequence that is consists of extremely low-complexity sequence, rich in Ser or in Gly interspersed with Cys. That C-terminal region resembles ribosomal natural product precursors, although there is no evidence that C-terminal regions of these proteins undergo any modification or have any such function.	2.25322e-37
NC_008390.1\|WP_011655664.1\|171658_172309_-\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|379312	pfam13649, Methyltransf_25, Methyltransferase domain. This family appears to be a methyltransferase domain.	2.04354e-06
NC_008390.1\|WP_011655662.1\|167605_170392_-\|glycosyltransferase	gnl\|CDD\|340842	cd03814, GT4-like, glycosyltransferase family 4 proteins. This family is most closely related to the GT4 family of glycosyltransferases and includes a sequence annotated as alpha-D-mannose-alpha(1-6)phosphatidyl myo-inositol monomannoside transferase from Bacillus halodurans. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in bacteria and eukaryotes.	2.23519e-07
NC_008390.1\|WP_011655675.1\|187275_188703_-\|flagellar-filament-capping-protein-FliD	gnl\|CDD\|236141	PRK08032, fliD, flagellar capping protein; Reviewed.	8.59456e-54
NC_008390.1\|WP_011655665.1\|172319_173027_-\|WbqC-family-protein	gnl\|CDD\|378083	pfam08889, WbqC, WbqC-like protein family. This family of proteins are functionally uncharacterized. However it is found in an O-antigen gene cluster in E. coli and other bacteria suggesting a role in O-antigen production. Feng et al. suggest that wbnG may code for a glycine transferase.	6.90803e-105
NC_008390.1\|WP_011655666.1\|173032_174418_-\|FAD-binding-oxidoreductase	gnl\|CDD\|223737	COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism].	1.25218e-23
NC_008390.1\|WP_006751066.1\|188890_189715_-\|flagellin	gnl\|CDD\|139237	PRK12802, PRK12802, flagellin; Provisional.	1.85372e-86
NC_008390.1\|WP_012362821.1\|192642_193476_+\|Cof-type-HAD-IIB-family-hydrolase	gnl\|CDD\|182878	PRK10976, PRK10976, putative hydrolase; Provisional.	1.01953e-78
NC_008390.1\|WP_041491065.1\|175603_177400_+\|glycosyltransferase-family-41-protein	gnl\|CDD\|226428	COG3914, Spy, Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones].	6.56778e-112
NC_008390.1\|WP_011655673.1\|184533_186798_+\|tetratricopeptide-repeat-protein	gnl\|CDD\|226428	COG3914, Spy, Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones].	2.63777e-104
NC_008390.1\|WP_011655676.1\|190723_191329_-\|DNA-3-methyladenine-glycosylase-I	gnl\|CDD\|377025	pfam03352, Adenine_glyco, Methyladenine glycosylase. The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.	1.69707e-116
NC_008390.1\|WP_011655663.1\|170388_171597_-\|dTDP-4-amino-4,6-dideoxygalactose-transaminase	gnl\|CDD\|183283	PRK11706, PRK11706, TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional.	0
NC_008390.1\|WP_082089595.1\|177357_178338_+\|SDR-family-oxidoreductase	gnl\|CDD\|187541	cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs. UGD catalyzes the formation of UDP-xylose from UDP-glucuronate; it is an extended-SDR, and has the characteristic glycine-rich NAD-binding pattern, TGXXGXXG, and active site tetrad. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	0
NC_008390.1\|WP_011655672.1\|182050_184537_+\|tetratricopeptide-repeat-protein	gnl\|CDD\|226428	COG3914, Spy, Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones].	2.08152e-102

>NC_008390.1|WP_011655670.1|178334_179540_+|methyltransferase-domain-containing-protein
MSPDLIDAPCPVCAHTVAAPFFPGGERTLATLAWPASAEAARGLPRHALDFVQCPQCSHVWNHRFSYDAIPYQSNPNRMFNSGGIWKGHLAATRDLLLGTLPTEPTVVEIGCGEGHFVRGLAQASRGGRFAGFDPNASAGTGNGIEFHARLFEPLADMPAFRPDAIVIRHVLEHLTEPAKLVEQLAWGASRQPNACWLFAEVPCIDRVFETDRLADFFYEHVSQFTTESFRTLMARAGEIVTLAHGYDGEVVYALVRLGVPAHARTRADASLRFAARSVENRAAIAGQLTELAGSGRRVAIWGGTGKAAAFIHHFDADAARFPLVVDSDPDKVGTYVPGTGQKIEFRDALKAAPADVIIIPTQWRARDIVAEMSREGIAAAAVMIEHDGRLIDFGREPHPY
>NC_008390.1|WP_082089595.1|177357_178338_+|SDR-family-oxidoreductase
MGAPRRRRTGSRSVNGQSVLVTGGAGFLGSHLCERLVHAGYDVMCVDNFHTGSKRNIEHLIGQVNFEVIRHDVWLPLYVEADRVFNMACPASPVHYQSDPVSTVKTAVLGAINMLGLAKRCGARILQASTSEVYGDAQQHPQQESYWGNVNPNGLRACYDEGKRCAETLFFDYHRQHGVDIRVVRIFNTYGPRMRADDGRVVSNFIMQALRGEPITLYGDGSQTRSFCYVDDLVEGLLRMMNQDDDTGPINLGNPSEITIRELAECVLRLTGSKSRIEYRPLPADDPLQRRPDIGRARQRLDWQPGIALEDGLKETIAHFRKQVNA
>NC_008390.1|WP_041491065.1|175603_177400_+|glycosyltransferase-family-41-protein
MTDLTLSDSPVATIEAALAHHQADRLEEAETLYRRILDAEPRHADALHLLGLIGHQYGRYHEATELIMAAIEIKPDATYYYNLGNVMQANNRPAAAAECFRLAIELRPGYVDAYNNLGNAQRLAGHAREAVDAFCQAIALQPDHGQAYNNLGNALLDLNEIPAALEAYQHAVALRPELPEPRSNLLFAYHYSDAFDPHAYLDEAARFDALVTQRAQPYSTWQVDLGARIGRPLRVGIVSGDLKAHPVGYFIEGMLAHVKRERIELHAYPTREIEDDVTARIKPRFASWTCIAGLDDAAAAARIHDDGIDVLIDASGHTIHNRLPLFAWKPAPLQVSWPGYFASTGMRAIDYVLGDRHVMPADEAAHFVERAWHLPDSYLCFTPPAVELDGGPLPMLANGYPTFGYFGKLAKLTDHVIDVWSRVLRDVPNARLFVKAPHLDDPREQDALAARFAAHGIDAARLLFEGRSPRDEYLAAYRRVDLMLSPFPYPGGTTTAEALWMGVPVLGRRGARFLSHICESLLQAARLPEWIADDDDAYVAKAVAFARNPAELAVLRTTLRAQVLASPLCDAPRFARHFEEALHEMWVRRVDAAPGAAA
>NC_008390.1|WP_011655667.1|174414_175200_-|hypothetical-protein
MHESSIISNSNDDQLAARRELFDLMQTYPATQEEFERSLGLFVRGSLLARILATFEVYEQIVPLPGSILDLGTWRGQTAVLCENFRAILEPLNFQRRIHAFDTFTGYAGFSDGDSRDRKLFSDGTYSLAGDYADLLRNLLSLHERNNAMGHVNGKHHVWEGDCRDTLAAYEEAHPGEPVALAWFDLNVPGPTRQAFETVMKRLVPGGVVAFWQLTRGGQTPAEGIHYVRELLGKHPHRIHKAKSYPSLCYLSFPEGGGVRP
>NC_008390.1|WP_011655666.1|173032_174418_-|FAD-binding-oxidoreductase
MKIAILGNGILGLMTARAWQRAEPGIELVVVGPAQRPGSATRAAAAMLNSFTELEGDSLGTPIDRFKFELSRAATAAWPDVFAEICTPDRAVAHGFGTYVLNNAATDALDDENFAALRRFCREFEEPCEAVDPAGIPNYQPLPQFRALNAVYLKREGWANPKQFLDALQASVAAAGNVTFVSAEVERIDVAGGRVAGARLSDGTTLDADRFVLCNGANLTRVLQASLPELPVQRLFYGIGMSIELQSNENVHTHCVRTTNRGLACGVYSAPYGPDRTLVGASNYISPVPHEHGHAGSAYTLLKSAMDQINSRFSRANLVNVNVGWRPTTSDLYPLIGETSVRDLWILGGTKRDGFHLSPVLCRDLVAAMRGLPIDPRYAQLAPERPLIRNLSRDAAIAKTVRHQINAAYQHDFVPARNRMVEQLERAIRADLEALHDRLGATDWGIPPELVDMYRYGHIPV
>NC_008390.1|WP_011655665.1|172319_173027_-|WbqC-family-protein
MTAQPKRIAIVQSNYIPWKGYFDLIAATDEFILYDDAQYTRRDWRNRNQIKTPQGVQWLTVPVRVKGRYHQSIRETEIDGTEWAEQHWTRLRQNYARAPHFARYAPELEALYLHGPHDTLSALNLAMLTWVNRQLGIATRMSSSSDYTLEGDRTDKLLNLCLQAGATEYLSGPAARDYLDESRFAAAQVAVRWFDYPAYPPYAQLWGEFVHGVTVLDVLFHCGPDAHRHVVTGRH
>NC_008390.1|WP_011655664.1|171658_172309_-|class-I-SAM-dependent-methyltransferase
MHDSRHSGLLADVAAYYGARLAEHGQTARGVDWNGEDGQRLRFAQLTKIVAPAADGFSVNDLGCGYGALVDFLDEHAAGRSHAYAGNDVSPEMIDAARQRYRDRADVAFHVGDTPSSVADYGIASGIFNVHRGHGDDAWLDYIHATLDTLHATSRLGFAFNCLTSYSDPPHMRPERLYYADPCALFDRCKRRYSRHVALLHDYGLYEFTILVRKDG
>NC_008390.1|WP_011655663.1|170388_171597_-|dTDP-4-amino-4,6-dideoxygalactose-transaminase
MFAPPNLDRIPFGRPFIVGKELYYIAKAVEQGGLAGDQAFTKLCHQWLETRIGCHRALLTHSCTAALEMAAILTDVGPGDEVIMPSYTFVSTANAFALRGATPVFVDIRADTLNLDEKLVAAAITERTRAIVPVHYAGVSCDMDTIAHLADDYRLWVVEDAAQAIQSTWKGKPLGSLGHLACLSFHETKNVIAGEGGALLVNDARLVERAEIIREKGTNRSQFFRGQVDKYTWVDLGSSYLPGELIAAFLYAQFEHADVITAQRRATVKRYEDALRPLHDAGHLTLPATPLSEAGNGHLFYFLARDLGERTALLERIRAAGVFAVFHYVPLHSSPAGRHYGRCGSGMQVTDDVADRLVRLPLYHAMSDAEQDRVLQVVSDFYRSGARPAVRPASPHLEPSLS
>NC_008390.1|WP_011655662.1|167605_170392_-|glycosyltransferase
MNDSPRIFASLGHPYYVFAPPYLQTSGGVRAMHYLCHALNLLGCEAYVNTTVVHRDLRTPLLTPEVAHVHGAAGRSPVAVYPEIVDENPFNARCVARYLLAEPGRINAKPIALAPTDLVFAFGPSIVPDGWHADLLRMPLVDTRIFHCDGVDDAARSGTAVFLNRHLRRGGNLHPATADSIEISGRVAPRSAHELAELFRRVECLYLYEWSTAAFEALLCGCPVVCILNDASMPNAERWVMGGKGIAWGLDPHEIAHAKATVHEARDVYREEETTFWRQLRQFVDKTQVRADELDVRGGPNGAAAARATAPATRRMAVVCAEPAAQAQIAARFALPAREWTVDFPVGANGIDLDVLQRADVIVLHDATPSLLSGAALEQMFALGKPVVCDLDRPLDAFSLDDPHIAGSARRLAAMRDAIRRADALVVRSDAIAATYRHVNAAVHALPVDAEPARRGALYARLAEQGRRPAAAVPAPGEPPATRAQQKKRLVAYAIDPVDGASVQRRFALPFARLEDDWALVSGLADSAAIATADAVLLDRHTPGLLPLKALSAIFEFDKPVIYATDLPLAAQPTTQADSTWTGIAFTLGNAHAIIVPTPDLARQYRPWNPNVFVLPDSVDLDLFLRPVPARGDARVTIGVAGASLLPANFARVDAALRALCERHAGRIAVQFLGAQVPAGWADHPAAEFRPAPDGYRAYAQQLRALDWDVALMPLADADDGAASAIQRQEFAAAGIAVVASDRPALRITLNDGDDALLAGDAAHAWDDALERVVTQPALRRRIARTAQARVRKHDALQARLPLIREIYRMCAEGEGTAVRLPPRDAPIPGALILDAAGDAERVQAALRIVAARDERDLLSVVLTTSSGPLPEWTDRLRYLSTSAQEYAATADQLAAMPAFDWVAIIDAADMEAGASAPETAIADAAID
>NC_008390.1|WP_011655661.1|165991_167578_+|TIGR04222-domain-containing-membrane-protein
MAAIPSLPSAGDARALTDAQQALLTRLLTYSPDDPHAAQPYSRRLAEAEGWTHAHALAVIDEYKRFAFLAQAAGHPVTPSVAVDAAWHFHLQYTLEYWDVFCARVLRAPLHHMPGTGAPDEAAVYARRYQDTLDSYRRLFGCEPPASIWPRPEPRPTDAGAPHTNATNAAPSTNRPTEPPSAAIPAGRRIWRDRLPKAIVPAAAASVIATAASARDFDVLNYTGPQFLAFYLPVCIVALLLIVVLQQIEYRCRRRRAQAFSSGLTPEEAAYLMGDESRAVQVATLSLVQAGAIDLSMGGRLGARARSVNPTRGGAYADECDWLAARPEGEASFGAFRQRLARRVSNYANALRGRRGGWLWEAGEMRAARMASRAIALAVLGTGAAKLAVGLSRGRPVLLLVISMAVFAIAYRIVTRRLTGFGRGGLTVGARTALAEHQRARRDEPDSPDAVLWATALFGAGALAGTAWAAHSMALMEPPPVPPMAARGGGSSGSTSSSSDSSSNCSSSSSCSSSSCSSSSCGGCSSSS
>NC_008390.1|WP_011655672.1|182050_184537_+|tetratricopeptide-repeat-protein
MNDIQQALQEALTHHQAGRLGEAKTLYDAILHAQPGQPDAMHFLGLLACQLKQYDAGLALMERSLAERPDASYFNNLGNMLRECGRLDDAIAHYRRAVALRPDYPEAHNNLGNALRDARDPAEAMRSCSRAIELRPGYAEAYNNLGNVLQDLGELDAAAASYGKAIAFHPAYAEAHSNLGNVLRAQERHADAIVHYRRAIELNPALRVAHRGLAIALRATDDFDGALEHARAGLEPDDAEGHCMLGRSLRSMNDFDGAARLFERACEIDPGYAPAWCRLGELRCQQGEYEESLRLCRHAIELDPELADAYNFLGLAYHNLDRMAASELSHRHAIDLNPDDADAHHNLAAALFRLDKLDEAMSEYRIAQELGVDPVKIQLTLGDILWAKRDFSGAVAAFREAVEHDPHRAYARLLFNMSSSPAFAPEEWVVDAQRYGDYLARDARLLSHDREQRARQARGRPLRVGFVSGDLRQHPVGIFLESVLAHLDRTRIEPHAYVTFVVEDDVTARLKTGFASWKKLTCLNRDQAARMIHDDGIDVLVDLAGHTNWSGLPVFAHRPAPVQASWLGFFATTGCRAIDYFIGDPHTLPADEAHHFVEQPWHLPDSYLCFTPPAYDVAVGPLPMATNGGVTFGCFGKLTKISDDVIALWSRLLHALPDARLMLKAHELGASDLNRATLERFARHGIGAHQLILEGGSPRAEYFNAYNRIDIALSPFPYPGGTTTAEALWMGVPVIGMKGGRFVTHICESLLHAAGMGDWIAADEDAYLAKAIAFAGDRDALAALRATLRERTLASPLCDAARFARNLEDAFHGMWARYVAGDTDGART
>NC_008390.1|WP_011655673.1|184533_186798_+|tetratricopeptide-repeat-protein
MTGAVVERLNAAFVHHQAGRFDDARMLYEAIRRDEPDQPDATHFLGLLACQLGQFPAGLALMERAIALRADPVYLNNFGNMLRAHGRLGDAIGAYRRAIALAPDYAEAHSNLGNALRDAGDADAAMLSCAQALALRPDYAPAFNNLGNALQDKGELDAAARAYEKAIALDPGYAQARFNQGNVLRAQRRPDEAIACYREAIALQPHLHAAHHALGVLLFERDDREAAIASLTRAAESGEADCLFHLAAALERAGDLDGTVASLRRALAAAPDRADLHHHLAQTLVRQGKRREALDSCRIALSLPNPTAQMHAVMGDILCAMWHLDAGLASYDRALEIDPAFRNAHSGRMFHAAGTDRLSPMQLLERAREFGARMAAQASPRTHVPRPAAGRVLRVGFVSGDLKSHPVAVFLLSVVAALDPSRIAAVAYATQSVEDDTTAALKRHFALWRDITALDDRAAADLIVNDHIDVLVDLSGHTASNRLPLFAWKPAPVQATWLGYFATTGIAAIDYVIGDRHVLPDDEAHHFAERPWRLPDSYLCFTPPAQPLDVGPLPAEREGVVTFGCLNNANKIGDAVVALWSRVLHAVPGSRLLLKSAQLDEAALRTSLAARFAAHGIPAERLLLRGGSKRLAHIATYNDIDIVLDPFPYPGGTTSMEGLWMGAPFITRRGDRFLSHIGESILHTLGMPEWIADNDDDYVAKAAAFAQDLPHVAAVRAGLRERLLRSPLCDAPRFARHLEAAFAQMVDAAAVAAR
>NC_008390.1|WP_011655674.1|186943_187240_-|flagellar-protein-FliT
MTTDTLNQALHLTHAMQSATALRDWERVAALADARSPLLMGLSPEQTPEALDTIRRIMEIDASIAQDAQADRDQLAQQFTASRERIRAAGLYQATGML
>NC_008390.1|WP_011655675.1|187275_188703_-|flagellar-filament-capping-protein-FliD
MTTTSTSTSTTDIGSLLAQAGQSIISGATNSTLDVSSLVSALVTAKTAGQTQTLTTKQTHDNTELSAVGKLKSALSALQTAIAGLANGSTLSGLAATASGTGITASVKNGGGAVAGSYAVNVTQLATANKLSSAGITASDTIAAGSLSITLGSNAAFNVNVAAGASLSDIATSINTTAGNPGVTASVITGSDGQHLVIQSNNTGAANTVSVSGTGVNAKLTSGYSTVTKAADAQLTVDGTPVSSASNSVSGVLTGVTLNLTPAALNTTQTVTLSQDTTATTSAINAFVNAYNGYVTTAKSLSSYDPNTSTAGPLLGDAMLNTISSGLATAISGGVKTGSPSTTYSLAAIGINLQADGTLQVDSTALNTALTSNSPTVAALFNTTNGVGQTLNKLVNTYTQANGLIDQRTTALNADLKNLSNQATQLKNYSDQLTAQYNAQFTALNNLMATMANNTKYLTQLFGGTNSAGALATNK
>NC_008390.1|WP_006751066.1|188890_189715_-|flagellin
MLNINTNILSLTTQTNLSGSQSALSQAINRLSSGKRVNTAADDAAGLAISTTQTAAINALTQGVSNANNGISMIQTAAGALQSTVDNLQRIRTLAVESGDGSLDSNARANLQAEVTTRLGEIDRVATQTTFNGQTILSNAGNVTFQVGASANQTVAVNFGATVWTSTGAGLSLSGLTVSDQTSAQSAITAIDTALKNVNTFQATLGAAQNTFQAAITTTQTQATNMSAARSQITDADFATETANLSKAQVLQQAGISVLAQANSLPQQVLKLLQ
>NC_008390.1|WP_006401410.1|190256_190469_+|30S-ribosomal-protein-S21
MTTILLKENEPFEVAIRRFRRAIEKNGLIAELRERQSYEKPTAVRKRKKAAAVKRLHKRLRSQMLPKKLH
>NC_008390.1|WP_011655676.1|190723_191329_-|DNA-3-methyladenine-glycosylase-I
MSQRCNWVKTEADAHYHDTEWGVPSHDDRHLFEMLILEGAQAGLSWSTILNKRAGYREAFADFDVDAVARFTPKHIEKLLENPGIVRNRAKVQSAVTNALAVQRIRDEHGSLAHFLWSFVDHMPVQNAWQSYRDAPASTAQSDALSKALKAYGCKFVGSTICYALMQATGMVNDHEAGCPCHAKCAALGGKQQPARRRKTG
>NC_008390.1|WP_011655677.1|191470_192352_+|ATPase
MTALLFAIGIDGGGTGTRAVLADRNGRELAQGRGGPSGLGLGIERAWASIGAACADAFTRAGLAFDWAQCALGCGLAGVNNAAWLAAFRAQAPLGALAVESDAYTTVVGAHGGAPGLIVALGTGSIAAALDAAGDCRIAGGFGFPSGDEASGAWLGLRALAYAQQALDGRAPRDAFAGALLAETGAHDRDALVQWSCDANQTIYARLAPIVLAHRTHPYAAALIAQAGDEIGKMIDALDPQQALPVALCGGLADALAPAVPARHASRLRAPLDDSAHGALQLALQALRAAEAG
>NC_008390.1|WP_012362821.1|192642_193476_+|Cof-type-HAD-IIB-family-hydrolase
MYKVIATDLDGTLLNSDHQLDPYTIETVRRLDRDGLQFVIATGRHYADVAGIRDVLGIRPYLITSNGARVHAPDDTAIHAQDIDPAIVRGLVQPGVTGAHGRVIVNLFTDRGWLIDREAPHLLEFHQDSGFRYDVIDMAAHDGADIAKVLYIGEPADLAVVAEQMRVQFGDALYVTYSLPDCLEVMTANVSKGRALRAVLARLGVDTGHCIAFGDNMNDIDLLETAGHAFMMNNANPDLIAQLPHIPRIGNNFDAGVARHLRTLFSLEDTVDGVAAS
>NC_008390.1|WP_011655679.1|193581_194322_-|aquaporin-Z
MNLSQRLAAEAFGTFWLVLGGCGSAVLAAAFPGLGIGFAGVALAFGLTVLTMAFAIGHISGCHLNPAVSVGLTVAGRFPARDLAPYIVAQVVGATLGAFVLYLIATGKPGFDLVGGGFATNGFGERSPGHYSLGAAFICEVVMTGFFLFVILGATDKRAPAGFAPIAIGLCLTLIHLISIPVTNTSVNPARSTGPALFVGGEAIGQLWLFWIAPIIGAAIAGIIYPLVAGRDNAVDLLPASARTSE

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Crispr_ID: NC_008390_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_008390_2

566346-566440

Orphan

Consensus_repeat	Method
CGCGTTGCCCGCGACCGCGCCGA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_008390_2

>merge|NC_008390|2|566346-566440|CRISPRCasFinder
CGCGTTGCCCGCGACCGCGCCGACGAGGCCGCCCGCGATGGCCGTCAGGATCGACCCCTTGCCGCCGCCGATCGCGCTGCCCGCGACCGCGCCGA

>NC_008390|2|1|566346-566440|CRISPRCasFinder
CGCGTTGCCCGCGACCGCGCCGA	CGAGGCCGCCCGCGATGGCCGTCAGGATCGACCCCTTGCCGCCGCCGAT
CGCGCTGCCCGCGACCGCGCCGA

Protein	Signature genes	Signature genes Name	Protein_function
NC_008390.1\|WP_011655914.1\|560282_563282_+\|ribonucleoside-diphosphate-reductase-subunit-alpha	unknown	unknown	gnl\|CDD\|235966
NC_008390.1\|WP_011655913.1\|559226_559817_+\|1,6-anhydro-N-acetylmuramyl-L-alanine-amidase-AmpD	unknown	unknown	gnl\|CDD\|236984
NC_008390.1\|WP_011655923.1\|573852_574497_-\|UDP-N-acetylmuramate--alanine-ligase	unknown	unknown	unknown
NC_008390.1\|WP_011655916.1\|564936_565263_+\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011655912.1\|558915_559230_+\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_080294560.1\|563395_563578_+\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_006752252.1\|570650_572018_-\|acetyl-CoA-carboxylase-biotin-carboxylase-subunit	unknown	unknown	gnl\|CDD\|236307
NC_008390.1\|WP_011655920.1\|569745_570648_-\|50S-ribosomal-protein-L11-methyltransferase	unknown	unknown	gnl\|CDD\|234786
NC_008390.1\|WP_011655915.1\|563641_564853_+\|ribonucleotide-diphosphate-reductase-subunit-beta	unknown	unknown	gnl\|CDD\|235968
NC_008390.1\|WP_006756005.1\|572643_573096_-\|type-II-3-dehydroquinate-dehydratase	unknown	unknown	gnl\|CDD\|235443
NC_008390.1\|WP_011655917.1\|565291_565954_+\|histone-H1-like-DNA-binding-protein	unknown	unknown	gnl\|CDD\|237855
NC_008390.1\|WP_011655924.1\|574720_576106_+\|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl--meso-diaminopimelate-ligase	unknown	unknown	gnl\|CDD\|130153
NC_008390.1\|WP_082089588.1\|560051_560261_-\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_041491084.1\|566676_567615_-\|carbohydrate-kinase-family-protein	unknown	unknown	gnl\|CDD\|238917
NC_008390.1\|WP_006758913.1\|567708_568212_-\|thiol-peroxidase	unknown	unknown	gnl\|CDD\|179055
NC_008390.1\|WP_006752240.1\|556551_557919_-\|signal-recognition-particle-protein	unknown	unknown	gnl\|CDD\|236780
NC_008390.1\|WP_011655911.1\|558008_558902_+\|cytochrome-c-biogenesis-protein-CcsA	unknown	unknown	gnl\|CDD\|226621
NC_008390.1\|WP_011655921.1\|572103_572577_-\|acetyl-CoA-carboxylase-biotin-carboxyl-carrier-protein	unknown	unknown	gnl\|CDD\|235777
NC_008390.1\|WP_011655919.1\|568284_569700_-\|DUF3426-domain-containing-protein	unknown	unknown	gnl\|CDD\|378759
NC_008390.1\|WP_011655922.1\|573290_573845_-\|TlpA-family-protein-disulfide-reductase	unknown	unknown	gnl\|CDD\|239264

Protein	Function_ID	Function_description	E-value
NC_008390.1\|WP_011655914.1\|560282_563282_+\|ribonucleoside-diphosphate-reductase-subunit-alpha	gnl\|CDD\|235966	PRK07207, PRK07207, ribonucleoside-diphosphate reductase subunit alpha.	0
NC_008390.1\|WP_011655913.1\|559226_559817_+\|1,6-anhydro-N-acetylmuramyl-L-alanine-amidase-AmpD	gnl\|CDD\|236984	PRK11789, PRK11789, 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD.	3.50423e-122
NC_008390.1\|WP_006752240.1\|556551_557919_-\|signal-recognition-particle-protein	gnl\|CDD\|236780	PRK10867, PRK10867, signal recognition particle protein; Provisional.	0
NC_008390.1\|WP_006752252.1\|570650_572018_-\|acetyl-CoA-carboxylase-biotin-carboxylase-subunit	gnl\|CDD\|236307	PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase subunit; Validated.	0
NC_008390.1\|WP_011655917.1\|565291_565954_+\|histone-H1-like-DNA-binding-protein	gnl\|CDD\|237855	PRK14900, valS, valyl-tRNA synthetase; Provisional.	2.99048e-12
NC_008390.1\|WP_011655915.1\|563641_564853_+\|ribonucleotide-diphosphate-reductase-subunit-beta	gnl\|CDD\|235968	PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit beta; Validated.	0
NC_008390.1\|WP_006756005.1\|572643_573096_-\|type-II-3-dehydroquinate-dehydratase	gnl\|CDD\|235443	PRK05395, PRK05395, type II 3-dehydroquinate dehydratase.	7.76942e-96
NC_008390.1\|WP_011655920.1\|569745_570648_-\|50S-ribosomal-protein-L11-methyltransferase	gnl\|CDD\|234786	PRK00517, prmA, 50S ribosomal protein L11 methyltransferase.	7.20786e-122
NC_008390.1\|WP_011655924.1\|574720_576106_+\|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl--meso-diaminopimelate-ligase	gnl\|CDD\|130153	TIGR01081, mpl, UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan].	0
NC_008390.1\|WP_011655922.1\|573290_573845_-\|TlpA-family-protein-disulfide-reductase	gnl\|CDD\|239264	cd02966, TlpA_like_family, TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.	1.32631e-41
NC_008390.1\|WP_041491084.1\|566676_567615_-\|carbohydrate-kinase-family-protein	gnl\|CDD\|238917	cd01942, ribokinase_group_A, Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time.	3.02558e-98
NC_008390.1\|WP_011655921.1\|572103_572577_-\|acetyl-CoA-carboxylase-biotin-carboxyl-carrier-protein	gnl\|CDD\|235777	PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier protein.	2.47337e-85
NC_008390.1\|WP_006758913.1\|567708_568212_-\|thiol-peroxidase	gnl\|CDD\|179055	PRK00522, tpx, thiol peroxidase.	1.09654e-95
NC_008390.1\|WP_011655911.1\|558008_558902_+\|cytochrome-c-biogenesis-protein-CcsA	gnl\|CDD\|226621	COG4137, COG4137, ABC-type uncharacterized transport system, permease component [General function prediction only].	5.89301e-61
NC_008390.1\|WP_011655919.1\|568284_569700_-\|DUF3426-domain-containing-protein	gnl\|CDD\|378759	pfam11906, DUF3426, Protein of unknown function (DUF3426). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.	4.79489e-40

>NC_008390.1|WP_011655917.1|565291_565954_+|histone-H1-like-DNA-binding-protein
MATAKKKPAAKKVAAKKTVAKKAAPAKKAAAVKKVAAKKVAVKKVAAKKAAPAKKAAAKKVAAKKVATKKVAAKKVAAKKVAVKKVAAKKAAPAKKAAAKKVAAKKVATKKVAAKKAAPAKKAAAKKAAPAKKAAAKKAAPAKKAAAKKAAPAKKAAPAKKAAAPKAAAPAKKAAAPKKAVVKKAAPATTASTASVAPASGVKTALNPAAAWPFPTGSRP
>NC_008390.1|WP_011655916.1|564936_565263_+|hypothetical-protein
MQSMPGALTAQRHDRHFANPSVGWANFPPEKADGRVAVCFIKRLGVAARGAPATDLIWRARPWGHARHTVFISVSARYPRTPMNSPLRSARAEQRPREAGFDEGCSLN
>NC_008390.1|WP_011655915.1|563641_564853_+|ribonucleotide-diphosphate-reductase-subunit-beta
MLNWDDEKTAVTPASGAQQNALRTSAGMAVGLQATAPAAHQVRDIFEGDLAVPPQASAVPAAGSEARVNVADKRIINGQTDVNQLVPFKYKWAWEKYLAGCANHWMPQEINMSRDIALWKDPNGLTEDERRIVKRNLGFFVTADSLAANNIVLGTYRHITAPECRQFLLRQAFEEAIHTHAYQYIVESLGLDEGEIFNAYHEVTSIRAKDEFLIPFIHTLTDPAFKTGTLEADQKLLKSLIVFACIMEGLFFYVGFTQILALGRQNKMTGAAEQYQYILRDESMHCNFGIDLINQIKLENPHLWTAEFRAEIRELFKQAVELEYRYAEDTMPRGVLGLNASMFKSYLRFISNRRCQQIGLDPLYPNEENPFPWMSEMIDLKKERNFFETRVIEYQTGGALSWE
>NC_008390.1|WP_080294560.1|563395_563578_+|hypothetical-protein
MQAVTSDRNIPDDVAFRSAFDASSAPRDTCATRVALCMNDDALLKVLYRGRNANRKKDFS
>NC_008390.1|WP_011655914.1|560282_563282_+|ribonucleoside-diphosphate-reductase-subunit-alpha
MQTTDNATSQYESASSRPLGGTEQGAKALAPQATFADYKVIRRNGSVVSFEPSKIAIAVTKAFLAVNGGQGAASARVREQVEQLTHNVVRALVRSRPNGGTFHIEDIQDQVELALMRGGEHNVARAYVLYREKRHLERQHAGEEAAAAGGEASAGINVVDNGVTRPLDMNALRELIVSSCAGLGAAVNPEPIVAETVKNLYDGVPMSQVYDSAILAARTMIEKDPAYSQVTARILLHTIRREILGEEVLQAEMTTRYTEYFPQFLKRGVDAGLLDDKLLQFDLKRLGEALDANRDLQFGYLGLQTLYDRYFLHVEGTRIEMPQAFFMRVAMGLSLNEIDRETRAIEFYNVLSSFDFMSSTPTLFNSGTHRSQLSSCYLTTVADDLDGIYEALKENALLSKFAGGLGNDWTRVRALGSHIKGTNGKSQGVVPFLKVVNDTAVAVNQGGKRKGAVCAYLESWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVMEGADWTLFSPSTCPDLHDKFGAEFEAAYTAYEDKVARGEIKLFKKIPAQQLWRKMLGMLFETGHPWITFKDPCNVRSPQQHVGVVHSSNLCTEITLNTSDTEIAVCNLGSVNLVAHLVKQADGSYALDHDKLKRTISVAMRMLDNVIDINYYAVPKARNSNLKHRPVGMGIMGFQDCLHLLRTPYASEAAVEFADRSMEAVCYYAYYASTELAEERGRYSSYRGSLWDRGILPQDTLKLLTEARGGYVEVDTSESLDWTTLRSRIAAHGMRNSNCVAIAPTATISNIIGVSACIEPTFQNLYVKSNLSGEFTVVNEYLVRDLKERGLWDEVMVADLKYFDGMLSRIDRIPADLRAIYATAFEVDPTWLVEAASRRQKWIDQAQSLNIYMGGASGKKLDEVYKLAWLRGLKTTYYLRTMAATHVEKSTVAHGALNAVPTGGAGGSSSGGAQGAAGGFGAAGGDASSGAVNAAAALAPVEADGPVCTMRPGDAGFDECEACQ
>NC_008390.1|WP_082089588.1|560051_560261_-|hypothetical-protein
MVRREPRIKTNAARWSARAVRGERCGGDAGAVDARQPSRSCASSCVPLPRRSSLRLIATPGPPGPGAPP
>NC_008390.1|WP_011655913.1|559226_559817_+|1,6-anhydro-N-acetylmuramyl-L-alanine-amidase-AmpD
MSDAAPLSVDAHGWVREARHAPSPNFEARPAGAVPTLVVVHNISLPPGEFGGDAIESLFLNRLDCDAHPYYQSHLRGVRVSAHFLIRRDGELVQFVSCDERAWHAGSSEFFGRPRCNDFSIGIELEGADDVPFDPAQYATLGVLARTLAARYPIDAVAGHSDVAPGRKTDPGPHFDWQRFAGDAGFSAEYFPFRQH
>NC_008390.1|WP_011655912.1|558915_559230_+|hypothetical-protein
MRQILLLILLLFAGSWLARKLRQAQEQAHARTGRGDGADAPGHGGAGAARPNGGTRSLPEPMVRCAECGVHAPKGDAVAAGGEYFCSTDHARRHGARASGHDAR
>NC_008390.1|WP_011655911.1|558008_558902_+|cytochrome-c-biogenesis-protein-CcsA
MDIVLYALTAFLYGGLAVAGWRTHRQGATPLVASVPAVPVPASAASGMSAAGRALLFAALVAHGVLLHMTIFPHDAMIFGFAFALSAMFWLGAGIYWIESFFFPLDSLRLLVLPLACGASLLPLVFGGVRVLPYAAAPLFKMHFLIANIAYGLFAIAALHAVLMLMVERRLQSLRSGGRDGSTGWIASWLETLPPLLTLEKLLFRLIGAGFVLLTLTLASGILFSEQVDARAMRLDHKTVFAVLSWLMFGGLLVARKTSGWRGRGAARWVLVSFAALLLAYVGSRFVFEVLLHRSVV
>NC_008390.1|WP_006752240.1|556551_557919_-|signal-recognition-particle-protein
MLDNLTQRMARVVKTLRGEARLTEANTQEMLREVRLALLEADVALPVVREFIAKVKEKALGEEVISSLSPGQALVGVVQKELTAVIGGDYEGKAAELNLAVTPPAVILMAGLQGAGKTTTVGKLAKLLREKHKKKVLTVSCDVYRPAAIMQLKTVSEQVGADFFPSTPDQKPVDIAVAAVDWAKRHYHDVLIVDTAGRLGIDEAMMQEIAALHGTLKPAETLFVVDAMLGQDAVNTAKAFNDTLPLTGVVLTKLDGDSRGGAALSVRHITGKPIKFVGVAEKLDGLEVFHPDRMANRILGMGDILALVEEAQRGVDVQAAQKLADKVKKGGDFDLNDFRAQISQMKNMGGLSSLMDKLPAQFQQAAAGADMGQAEKSIRRMEGIISSMTPAERAKPEIIKATRKRRIAAGAGVPVQEVNRMLNQYDQMRTMMKKLKGGNMQKMMRGLKGMMPGMR
>NC_008390.1|WP_041491084.1|566676_567615_-|carbohydrate-kinase-family-protein
MTTLICGSLAYDNIMTFEGRFREHILPDQVHLLNVSFLVPTMRREFGGCAGNIAYALHMLGGDARIMATVGANDADRYLERLDSLGLSKASVRVVPEAHTAQAMITTDLDNNQITAFHPGAMMVSHLNRADEVAGVKLGIVAPDGFDGMVQHAEQFAKAGVPFVFDPGQGLPLFDGATLRRIIELATFVAVNDYEGKLVSDKTGWSEQDIASRVQALIITRGEHGSTILHKNGEEQIPVVQAERVVDPTGCGDAFRGGLLYGIENGLDWATTGRLASLMGSIKIAHQGPQTYALTRAEIDARFEAAFGYSLK
>NC_008390.1|WP_006758913.1|567708_568212_-|thiol-peroxidase
MSKVTLGGNPIDLAGTFPAVGSQAPDFKLVGKDLADLSLASFAGKRKVLNIVPSLDTPTCATSTRKFNEAASSLDNTVVVVVSGDLPFAATRFCTTEGLANVVTASTFRGGRAFANAYGVDVTSGPLNGLTARAVVVLDAQDKVIHAQLVDEIKDEPNYDAALAALK
>NC_008390.1|WP_011655919.1|568284_569700_-|DUF3426-domain-containing-protein
MLLATRCPHCETVFRLQQEQLSLHDGLVRCGHCQQVFNAAQSLVPDPARQPDPALTEAAPAGPGAAAPQSDAAPDAAPARLFATDAPVKSASDIDYKPEGWDMWAPWLDAGVDPSLQHTVQTVRAEPLVPLALPAIEAGVVRLSGTPAPIASAPAELDAAHMQAAEPDATLHETDASGTSFAAPTAEPDLREPRFVAHTPSAEPAAAEPAEPVGNARFAVPDDEHAPREPRFAFRPAQAVSEPESAPESGPDTHADERAPAPTAAASEPTAEPDIQPAAQPALPFPAALTDDDRPHFAVTRETRETGAPPRRGMLGGFFGGLVAAALAVLLVAQLAWWQRETVMIYWPVTQSWFRQACAPLGCRLTPPRAIDGLRLDATDLRQIDGPRTLELKVPLTNRYRVALAYPSLELTLLDDTNHVTVRRVLAPRDYVRPGTPIDAGLPPGSTQTMVVRLDTNGTPASNFRVQIFYP
>NC_008390.1|WP_011655920.1|569745_570648_-|50S-ribosomal-protein-L11-methyltransferase
MSYRELVVELAREHAEALSDALLELGALSVSVEDADADTPDEQPLFGEPGLVPDRTAWQRSRVIALLSPDHEPAVLLAAAVNDIGVTETPKFDVREVEEQDWVRLTQSQFEPIPIGERIWVVPSWHDAPDPDALILELDPGLAFGTGSHPTTRLCMEWLEQSVKPGQSVLDYGCGSGILAILARKCGANPVVGIDIDPQAVESARQNSERNHAEVTYGLPDACPAGEFDIVVANILSNPLKLMASMLASKVKPGGRIALSGVLARQADEVAAVYARYVDISVWREHEGWVCLAGTRRESH
>NC_008390.1|WP_006752252.1|570650_572018_-|acetyl-CoA-carboxylase-biotin-carboxylase-subunit
MFEKILIANRGEIALRIQRACRELGVKTVVVYSEADKEAKYVRLADEAVCIGPAPSNLSYLNMPALISAAEVTDAEAIHPGYGFLSENADFAERVEQSGFTFIGPRPETIRMMGDKVTAKQTMIKTGVPCVPGSEGALPDDPKEIVKIARTIGYPVIIKAAGGGGGRGMRVVHTEAALVNAVNMTREEAGRAFGNPQVYMEKFLENPRHIEIQVLSDAHKNAIWLGERDCSMQRRHQKVIEEAPAPGIPRRLIERIGDRCADACKKMGYLGAGTFEFLYENNEFYFIEMNTRVQVEHPVSEMITGVDIVQEQIRIAAGEKIALRQRDIQFRGHAIECRINAEDPFKFTPSPGRITSWHTPGGPGVRVDSHAYNGYFVPPNYDSMIGKLITYGATRDQAIRRMRIALSEMVVEGIHTNIPLHRELMIDSKFVEGGTSIHYLEHRLAQKQQVAPEEA
>NC_008390.1|WP_011655921.1|572103_572577_-|acetyl-CoA-carboxylase-biotin-carboxyl-carrier-protein
MDLRKLKTLIDLVSESGISELEVTEGEGKVRIVKNAPPVYVQQTAGFAPQVSAPAPSAALPTDGAAAPAAGAAAAPAVPQGHVVTSPMVGTFYRAPSPGADPFVQVGDTVKEGQTICIIEAMKLLNEIESDKAGVVKEILVENGQAVEYGQPLFVIG
>NC_008390.1|WP_006756005.1|572643_573096_-|type-II-3-dehydroquinate-dehydratase
MTRLLVLHGPNLNLLGTREPEVYGRVTLAQIDQALAARAQEAGAELSSFQSNHEGALVDRIQAAREEQTDFILINPAAYTHTSVAIRDAIAGVGIPFVEIHLSNVHRREAFRHHSYFSDQAEGVICGLGWKGYLYALEYALDKLQGASRG
>NC_008390.1|WP_011655922.1|573290_573845_-|TlpA-family-protein-disulfide-reductase
MMTKRMLALAVVAAAAVAGGLAAGHWFRGGSADDGVAVAAPAAQGNPVDQLWAASLTGVDGKPASLASFKGQKVVVNFWASWCGPCVEEMPELVALSHQYKQKGVRFIGIGVDSDQNVKNFLQKVKVDYPVFVSGYAGADLARNFGNTAGALPFTVVIDETGKIRETKLGQIQPAELRKTLDAL
>NC_008390.1|WP_011655923.1|573852_574497_-|UDP-N-acetylmuramate--alanine-ligase
MSRKPLVDPRRAREEIAQSAARLIAEDGLDYASAKRKAARQLFGDTRVAGEWLPDNDLIEEELREYLALFQSDTQPDELRRLRELALDWMRRLAEFNPYVTGAVLHGTANEHSDIHLQIFTDNPKDVAIYLLNQNVQYDVSETRHFAGRADVETLSFLWRPRRDVDAIGIHVALYASDDLRGAVKADARGRVARADATALRALLEASNAPSEPE
>NC_008390.1|WP_011655924.1|574720_576106_+|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl--meso-diaminopimelate-ligase
MHIHILGICGTFMGGLAVLAREAGHTVTGCDAGVYPPMSTQLEAQGITLIEGYGAEQIDLKPDLFVIGNVVTRGNPLMEAILDRGLPYVSGPQWLGEHVLAGKWVLAVAGTHGKTTTSSMLAWLLEDAGLNPGFLIGGVPLNFGVSARLTDSSFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFPDLAAIETQFHHLVRTVPGVGRLVTNGRSDALERVLARGCWSEVERFGVDGGWQALPAEDGVPVDERFAVYSQSERVGEVAWQVQGDHNRMNALAAIAAARHVGVPPAQAAESLASFRNVKRRMEVRGSIDGVTVYDDFAHHPTAIETTIAGLRARIGRQNSRILAVLEPRSNTMKLGVMKAQLPASLADADLVFGYGAPAGRDVLGWNLADALAPLGDKARAFDDLHLLVKSVVEAARPGDHVLVMSNGGFGGVHQKLLDALGSRA

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Crispr_ID: NC_008390_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_008390_3

1345726-1345798

Orphan

Consensus_repeat	Method
CGACCGCGAAGCATGGAACCAGAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_008390_3

>merge|NC_008390|3|1345726-1345798|CRISPRCasFinder
CGACCGCGAAGCATGGAACCAGAGCAAGCGCTAAAGCGCCAACTCTGGTCGACCGCGAAGCATGGGACCAGAG

>NC_008390|3|2|1345726-1345798|CRISPRCasFinder
CGACCGCGAAGCATGGAACCAGAG	CAAGCGCTAAAGCGCCAACTCTGGT
CGACCGCGAAGCATGGGACCAGAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_008390.1\|WP_011656554.1\|1343185_1345510_+\|xanthine-dehydrogenase-family-protein-molybdopterin-binding-subunit	unknown	unknown	gnl\|CDD\|224446
NC_008390.1\|WP_011656563.1\|1356033_1356816_+\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011656559.1\|1351408_1352155_+\|MipA/OmpV-family-protein	unknown	unknown	gnl\|CDD\|377682
NC_008390.1\|WP_011656548.1\|1336753_1337770_-\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|381387
NC_008390.1\|WP_011656564.1\|1356937_1357516_+\|flavin-reductase-family-protein	unknown	unknown	gnl\|CDD\|214900
NC_008390.1\|WP_041491145.1\|1352428_1352749_+\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011656545.1\|1333678_1334839_-\|D-mannonate-oxidoreductase	unknown	unknown	gnl\|CDD\|235147
NC_008390.1\|WP_011656547.1\|1335884_1336757_-\|amidohydrolase-family-protein	unknown	unknown	gnl\|CDD\|226145
NC_008390.1\|WP_011656551.1\|1339847_1341401_-\|sugar-ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224053
NC_008390.1\|WP_011656549.1\|1337836_1338784_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|380663
NC_008390.1\|WP_011656556.1\|1347910_1348891_+\|NADPH:quinone-oxidoreductase-family-protein	unknown	unknown	gnl\|CDD\|176203
NC_008390.1\|WP_041491341.1\|1341640_1342345_+\|FadR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225097
NC_008390.1\|WP_041491144.1\|1338823_1339855_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224093
NC_008390.1\|WP_011656546.1\|1334863_1335871_-\|zinc-binding-alcohol-dehydrogenase-family-protein	unknown	unknown	gnl\|CDD\|176222
NC_008390.1\|WP_011656558.1\|1350436_1351162_-\|response-regulator	unknown	unknown	gnl\|CDD\|223816
NC_008390.1\|WP_011656555.1\|1345954_1347784_+\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|173842
NC_008390.1\|WP_011656562.1\|1354477_1355638_-\|porin	unknown	unknown	gnl\|CDD\|238208
NC_008390.1\|WP_011656561.1\|1352822_1354037_-\|transglycosylase-SLT-domain-containing-protein	unknown	unknown	gnl\|CDD\|381603
NC_008390.1\|WP_006754739.1\|1342727_1343189_+\|(2Fe-2S)-binding-protein	unknown	unknown	gnl\|CDD\|224991
NC_008390.1\|WP_011656557.1\|1349065_1350436_-\|HAMP-domain-containing-protein	unknown	unknown	gnl\|CDD\|236724

Protein	Function_ID	Function_description	E-value
NC_008390.1\|WP_011656554.1\|1343185_1345510_+\|xanthine-dehydrogenase-family-protein-molybdopterin-binding-subunit	gnl\|CDD\|224446	COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion].	1.71216e-102
NC_008390.1\|WP_011656559.1\|1351408_1352155_+\|MipA/OmpV-family-protein	gnl\|CDD\|377682	pfam06629, MipA, MltA-interacting protein MipA. This family consists of several bacterial MltA-interacting protein (MipA) like sequences. As well as interacting with the membrane-bound lytic transglycosylase MltA, MipA is known to bind to PBP1B, a bifunctional murein transglycosylase/transpeptidase. MipA is considered to be a structural protein mediating the assembly of MltA to PBP1B into a complex.	1.23114e-43
NC_008390.1\|WP_011656548.1\|1336753_1337770_-\|aldo/keto-reductase	gnl\|CDD\|381387	cd19161, AKR_AKR15A1, Microbacterium luteolum pyridoxal 4-dehydrogenase (PLD) and similar proteins. Microbacterium luteolum PLD (EC1.1.1.107) is a founding member of aldo-keto reductase family 15 member A1 (AKR15A1). It catalyzes irreversible oxidation of pyridoxal.	2.32986e-156
NC_008390.1\|WP_011656564.1\|1356937_1357516_+\|flavin-reductase-family-protein	gnl\|CDD\|214900	smart00903, Flavin_Reduct, Flavin reductase like domain. This entry represents the FMN-binding domain found in NAD(P)H-flavin oxidoreductases (flavin reductases), a class of enzymes capable of producing reduced flavin for bacterial bioluminescence and other biological processes. This domain is also found in various other oxidoreductase and monooxygenase enzymes... This domain consists of a beta-barrel with Greek key topology, and is related to the ferredoxin reductase-like FAD-binding domain. The flavin reductases have a different dimerisation mode than that found in the PNP oxidase-like family, which also carries an FMN-binding domain with a similar topology.	9.96387e-29
NC_008390.1\|WP_011656545.1\|1333678_1334839_-\|D-mannonate-oxidoreductase	gnl\|CDD\|235147	PRK03643, PRK03643, tagaturonate reductase.	6.36544e-67
NC_008390.1\|WP_011656547.1\|1335884_1336757_-\|amidohydrolase-family-protein	gnl\|CDD\|226145	COG3618, COG3618, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only].	1.29867e-62
NC_008390.1\|WP_011656551.1\|1339847_1341401_-\|sugar-ABC-transporter-ATP-binding-protein	gnl\|CDD\|224053	COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism].	0
NC_008390.1\|WP_011656549.1\|1337836_1338784_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|380663	cd20008, PBP1_ABC_sugar_binding-like, monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.	6.86115e-105
NC_008390.1\|WP_011656556.1\|1347910_1348891_+\|NADPH:quinone-oxidoreductase-family-protein	gnl\|CDD\|176203	cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction.	6.09082e-158
NC_008390.1\|WP_041491341.1\|1341640_1342345_+\|FadR-family-transcriptional-regulator	gnl\|CDD\|225097	COG2186, FadR, Transcriptional regulators [Transcription].	1.11532e-54
NC_008390.1\|WP_041491144.1\|1338823_1339855_-\|ABC-transporter-permease	gnl\|CDD\|224093	COG1172, AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism].	9.05355e-90
NC_008390.1\|WP_011656546.1\|1334863_1335871_-\|zinc-binding-alcohol-dehydrogenase-family-protein	gnl\|CDD\|176222	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR 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. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.	3.23326e-177
NC_008390.1\|WP_011656558.1\|1350436_1351162_-\|response-regulator	gnl\|CDD\|223816	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].	7.39399e-78
NC_008390.1\|WP_011656555.1\|1345954_1347784_+\|acyl-CoA-dehydrogenase	gnl\|CDD\|173842	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5. Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.	1.42635e-172
NC_008390.1\|WP_011656562.1\|1354477_1355638_-\|porin	gnl\|CDD\|238208	cd00342, gram_neg_porins, Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus.	2.49474e-89
NC_008390.1\|WP_011656561.1\|1352822_1354037_-\|transglycosylase-SLT-domain-containing-protein	gnl\|CDD\|381603	cd13400, LT_IagB-like, Escherichia coli invasion protein IagB and similar proteins. Lytic transglycosylase-like protein, similar to Escherichia coli invasion protein IagB. IagB is encoded within a pathogenicity island in Salmonella enterica and has been shown to degrade polymeric peptidoglycan. IagB-like invasion proteins are implicated in the invasion of eukaryotic host cells by bacteria. Lytic transglycosylase (LT) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Members of this family resemble the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.	2.61074e-57
NC_008390.1\|WP_006754739.1\|1342727_1343189_+\|(2Fe-2S)-binding-protein	gnl\|CDD\|224991	COG2080, CoxS, Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion].	1.5165e-78
NC_008390.1\|WP_011656557.1\|1349065_1350436_-\|HAMP-domain-containing-protein	gnl\|CDD\|236724	PRK10604, PRK10604, sensor protein RstB; Provisional.	3.84699e-78

>NC_008390.1|WP_011656554.1|1343185_1345510_+|xanthine-dehydrogenase-family-protein-molybdopterin-binding-subunit
MNAPELSVHNESRRALLLGFASGGLLLAFGVPSLARAAAPVQPPVSPNPQYGGAGMPHGLRDDPHLFVAIAPDGTVTVTCIRSEMGQGVRTSVALVVADELGADWARVKVAQAVGDEPRYGNQNTDGSRSLRQSFAALRRAGAAARTMLEQAAAATWGVDVRQVKATVHEVVDTKTGRKLGFGELAAKAAALPVPDTKSVALKAPAEFRYIGKGETALIDGRDIVGGRAHYGIDTRLDGMLYAVVARPPAYGDTVASFDASAAEKLPGVVKVVQLASAPLPSGFQPLGGVAVIARDTWTAIQARARLKIDWKRGPHAGYDSAAYRKTLEAAAAQPGDVIRDDGDTAAALAGAAKRVRATYYIPHLAHATMEPPAAVARVADGRCEVWTCTQAPQTTRDEIAKALALPSERVTVNVTLLGGGFGRKSKPDYVVEAALLSKAVGAPVKLTFTREDDIAHDYFHAVSLEAFDGGLDAAGKVVAWQHRTVAPSIQSTFRAGVVHEQPGELAQGIADLPFAVPNVRIENPAAQAHTRIGWFRSVYNIPHAFGIQSFVSELAHAAGRDPKDFLLDLIGPARRFEPHITVKNVNYGEDPALYPVDTGRLRRVIETVAREAGWGRKLPKGHGLGIAAHRSFVSYTAVVCEVQVAADGAISVPRVDIAIDCGPQVNPERVRSQLEGAVVMGLGIALHGEITFKDGQPEQSNFNGFQVLRMNEAPREIRVHLVAPDDYATPLGGVGEPGLPPVAPALTNAIFAATGTRIRSLPVADQLAKQKVG
>NC_008390.1|WP_006754739.1|1342727_1343189_+|(2Fe-2S)-binding-protein
MITLTVNGGERHFDGNPDMPLLWYLRDVLGHTGTKFGCGMALCGACTVHLDGVAIRSCITPVAAAAGKKVTTIEGLSTDVNHPLQQAWQELNVAQCGYCQSGQIMQAASLLKTNPHPSDADIDDAMSGNICRCGTYTRIRAAIRLAVRRGGAA
>NC_008390.1|WP_041491341.1|1341640_1342345_+|FadR-family-transcriptional-regulator
MKQTEPKRLYQSVAAQILALIRQGGIPAGGRLPPERELATTLGVSRPSLREALIALEIGGQIEIRLGSGVYVRDPGESDSGGVPALGESPSELMQARGAIEGSVIVLATARFSAATLDRLRRTVERMKRLAVAGKSPVDADRQFHMLIAEVAGNSVLSRFVGELFDSRHDPIAAAIRGHSESPETWAAAVREHEQILKALQAGDPIAAQTAMRAHLQASEERWIGGALQHGIAP
>NC_008390.1|WP_011656551.1|1339847_1341401_-|sugar-ABC-transporter-ATP-binding-protein
MTPADLRQSPPLPPGGPTARTVLQLQGVGKRFPGVVALDGIDLDLRAGEVHAVCGENGAGKSTLMKIISGQYRADDGVVLYDGAPVQFSSATDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRALNRAAQLCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRIIKELRSEGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTSVNEIVARMVGRPLDDAYPPRRSTPTDQVLLKVRDLQRTGTFGPVSFELRKGEILGFAGLMGAGRTEVARAIFGAERPDAGSILLGDTPVEINSPREAIRHGIAYLSEDRKKDGLALAMPVAANITLANVAAISSRGFLRFADETAIAERYVRELGIRTPTVAQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETGKTNQEEILHHASGRSHA
>NC_008390.1|WP_041491144.1|1338823_1339855_-|ABC-transporter-permease
MLDITSGRTPAVDKQARQRRRDLIQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVSLQVTSIAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAGIPVPVAMLGGMLVGAACGWVNGICVTHMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFKISHIGADGFPDTIFPGIPYPVVIMVALFVAVSVLLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQLRNRKL
>NC_008390.1|WP_011656549.1|1337836_1338784_-|ABC-transporter-substrate-binding-protein
MKKLSVLAAAAILCAMFGAHAQAAGGEIAVIVKTANSNYWQNVQKGATAAMANAKGYTMTFQGPAAESAIADEVNMVENAVNRHVAGIVLAPSDPDALVPAMKKAWEAHIPVVLIDSTVSDAGKQYYQSFLSTDNAKAGELCAKAMIDRVGQTGKVAVMSYVPGAGSEVGRVGGFRKYIAAHSKLQVVGPFYSQSQMANALNQTTDVLSANPDLKGIFGANEPTAVGMGRALQQSGKGGKVVAIGFDGNQDLQGFVRDGTIQAIAVQSSYQMGYKGIETLVNVIERKPVSKQVDTGVLMVEKQNLDSPAAKNVLY
>NC_008390.1|WP_011656548.1|1336753_1337770_-|aldo/keto-reductase
MKAIATHALPRSGLVMSTLGFGCSQLGGLYKAMSTADAHALVDWAWDAGIRYFDTAPFYGYTLSERRVGQSLQARARKRYVLSTKVGRLMRPDDTVQPGDDGWAHPLPFRPHFDYTFDGIMRSYEDSQQRLGMRTIDILYVHDIGAATHGDRHAHYWEQLTRGGGFRALAELRDARAISAIGLGVNEWEVAVDAMQEADLDVVLLAGRYTLLEQEALSPLLDRCVRNDVRIVAGGVFNSGVLVGNGKFNYADAPAEVIRKVARLADVCAGFGVPLAAAALQFPLAHPAVVSCVVGARSIEQLQKNIAWLETPLPPELWTALQHDGLITAAAPVPEVCA
>NC_008390.1|WP_011656547.1|1335884_1336757_-|amidohydrolase-family-protein
MTFRIDAHQHFWQMASRDGYWPPQTLDAIYRDFGPQDLEPLLARSGVQRTVVVQSLPTQEDTRYLLDVASRTSFVAAVVGWVDLKSTDAPADIASLARDPKFRGIRPMLQDLADDDWIDDPVLEPAIDAMLAHDLAFDALVTPRHLPALLAFARRYPRLRIVIDHAAKPPIASGRSEAWHVAMSELAAHPNVHCKLSGLWTEAGPHPDLLRVEPYVRAVCDWFGASRLIWGSDWPVSRLAGHFGDYGAWLAWCEQCCDRFLGPDARARVFGGNACHFYRIDRPSGDQHAQ
>NC_008390.1|WP_011656546.1|1334863_1335871_-|zinc-binding-alcohol-dehydrogenase-family-protein
MLSIICESPGVLRHEDRAPPSRADGEILLRVQRVGICGTDMHIYSGNQPYLQYPRVMGHELSAIVAEADPGAHVVPGDAVYVMPYLSCGQCIACRQGKTNCCVNIKVLGVHRDGALTEYLSVPAQFVHKAEGVTLDQAAMIEFLAIGAHAVRRAAVSAGQRILVVGAGPIGMAAMLFAQLRGAHVTCLDTRADRLAFCQEHFAVATVQTGPTDVDELSTMTNGEFFDVVFDATGNVKAMNRGFEFIAHGGKYVLISIVPGEITFSDPEFHKREATLLGSRNATAEDFETVLDAMRAGRIPDKALNTHRMSLSDVPVEFPKLMEPGQTVVKALVEC
>NC_008390.1|WP_011656545.1|1333678_1334839_-|D-mannonate-oxidoreductase
MSEPILQFGTSRFLQAHVALFVSQALERGDAIGGIRMVQTTDNPASHARIAALAQSGSYPVKIRGREHGAIVDTVVHCRAVRAAWIADRDWAMIRHAVTHDVRVIVSNTGDAGYRLDERDSPALLALESHVPRSFPAKLLTLLHARWRARPGAGVSIFPCELVARNGDTLRTLVIGLAEQWALPAPFVTYLSQRCIWVNSLVDRIVSEPIEPVGAVAEPYALWAIERQPGMELPCTHEHIVVTDDLLSHERLKLFFLNVGHTWLADQWLVQRRSSAQTVFDAMNDTTLREGIEGVWGEEVLPVFDALGMRVRAEQYVASVRERFLNPYLNHHIADIAGNHVEKVRRRILPLIELADSLGVAPDQTRLRDTLARHGVTPSTKEANAS
>NC_008390.1|WP_011656555.1|1345954_1347784_+|acyl-CoA-dehydrogenase
MSLLMSRRDLAFLLYDWLDADALGALPRYAEHSRETFDAVLDTSERIAADLFAPHAARGDREEPRFDGERVTLIPEVEPAVRAFAAAGLIAAGQDEAFGGMRLPKLVEAASFLFFQAANIATAAYPFLTVANANLLLAHGSPAQIDAFARPELEGRFFGTMCLSEPQAGSSLSDIVTRADFECASPLGPRYRITGNKMWISGGEHELAENIVHLVLAKIPDEQGRLLPGTRGISLFIVPRYLPTDDGAARGEHNDVVLAGLNHKMGYRGTTNCLLNFGEGTRHRPQGRAGAIGYLVGEPNHGLAYMFHMMNEARIGVGAGAVALGYTGYLHALDYARNRPQGRALGPAGKDAAAPQAPIVAHPDVRRMLLAQKAYVEGGLALILYCARLVDEARAHDDAALRVEAAQLLDILTPIAKSWPSQWCLAANDLAIQVHGGYGYTRDYPVERLYRDNRLNPIHEGTHGIQALDLLGRKVGQDDGALLRTLDARIGATLQRARAADGDPHSHADALARRWARLVELTRALAALDDPQVRLANASVYLEAFGHLVVAWLWLDVTLAAHGHDSDFHDGKRAAARYFFRWELPKVDAQLDLLASVDTTTLEMRDAWF
>NC_008390.1|WP_011656556.1|1347910_1348891_+|NADPH:quinone-oxidoreductase-family-protein
MKALMCTAFGPIDRLRIDDVAIPEPAAGQVRIRVKAASLNFPDALIVQGLYQVKPALPFSPGAEFAGVIDAVGDGVSAWQPGDEVVAFTGHGGFAEQCVADVHQIAALPPGMTFEQGAALVLAYGTSLHALQQRARLQQGETLLVLGAAGGVGLAAIEIAKALGARVIAAASSADKLALCRAAGADDTIDYATEDLRRRVDELTGGRGADVVYDPVGGAYSEAALRATAWRGRFLVVGFAAGEIPKIALNLALLKERDILGVFWGDAVRRDPAEHAVNMRQLAQWFAAGKVRPAITERVPLSGAADAIARMANRQVKGKVVILPDA
>NC_008390.1|WP_011656557.1|1349065_1350436_-|HAMP-domain-containing-protein
MLRPLIRLYLIVILCGAGSIAFIQFSFDRIFYERAAQAQRDSLTTYAFVLNDYLERHPGAQRTLALRELAKHGKEGFDFVTMAEARAQLSGAPLRDLDAGKIAIGYDGKDYYMPLADGSVLHARPIQPFDLDIKIYAYLLLALAALFAVVLWISYHWRDLRRLQAAAHAFGAGRLSTRVKLSGRSNIYELSQQFNDMAERIEASIKQQREMMHGISHELKTPLARLEFGLALLAESDESGRMRERRDELRRDVRELDELVTELLTIGRLEQGASELAPMDVVVDALIDSVAGNVANDLADRGITLDVSTTGAPATHVCDPKLVARALLNLIRNSARYAARTVLLSATHDASGALVLSVDDDGPGIPAAERARVFEPFQRLDSSRDRQTGGFGLGLAIVRRVALVHGGNVRLEDSPLGGARFVISLPARTLPDFRGNAQASPACGRADLAGAASLLS
>NC_008390.1|WP_011656558.1|1350436_1351162_-|response-regulator
MYDNPLKYRVLLIEDDDRLAQLVREYLDNYEFTVTVVRRGDLAVAAVREHEPALVILDLMLPNLDGMEVCRRIRAFTNVPVLILTARADVYDQVAGLETGADDYVTKPIEPRVLVARARALLRRARPAATETRAAAPDALIFGELTISPPNRTVTWRGEPVDLKTAEFNLLLILARAAGTVLSRDDILKQLRGIEFDGLDRSVDSGISKLRRRFEDASSEPHKIKTIWGRGYLFSPSAWDE
>NC_008390.1|WP_011656559.1|1351408_1352155_+|MipA/OmpV-family-protein
MPLAGLTLAAAAHAENQYSISLGGGFAPRYPGSNQYRGIVAPGLSAKFGKGFFIDSREGAGYRLDLPHGAFVSAAVSYDPGRADENRFDLPGSDYLKGMGRIPGSVLIGVRAGVTLLDAAELSVTVDTPVTHTSRGVSGHVDLAVPVFKTAQHEIVVTGSVHAGTGRYTQTFYGVTDAQSMTSRFRPYSTSGGIDSATVSVAWNWNLSRHWSVLATGGVTRLLGRYGDSPIVQSRSNYYGMAGATYKF
>NC_008390.1|WP_041491145.1|1352428_1352749_+|hypothetical-protein
MKNTIAMLVALVASATFSGCGDMNTKHPNATVGGAARNTAPMCSADAAPDDALIGKTEAEATALLDGCLWRVLERDGKSLPGTMDYREERRDLGIRDGKVIWVRRG
>NC_008390.1|WP_011656561.1|1352822_1354037_-|transglycosylase-SLT-domain-containing-protein
MPRHTARSISHATPKIAATIALSCALHGAAWADCLDDAATFQHVSVSLLRGIAQVESGMNPNAINTNTNGTVDIGLMQINSTWLPTLAREGITRESLFDACTNAYVGAWILSQNIRQLGANWTAIGAYNAASPDKRLAYARKVYDAIRTMPDSPDTPMPILPPSFTPPQQVQAYNPFASLSVSAPPAARARTLSPAAPPPPQGGPAGPAGTYNFGWTVTGADQAKPTQVFDDGARIYVQFSDMKHMPAIFTETSSGRVLMSWELQFPYAVLTRPAQTLIFQLGPFEARAQRGAAGATTQAGAGAAAGASRSGATTAATTPAGKPHANASAKRTASADALWYLNTPSTSGSAATANTAPTTTSSASSNTPATWPTAVTSNTPPPAATPQAPAARVSTDALWYISK
>NC_008390.1|WP_011656562.1|1354477_1355638_-|porin
MKRTTLSLISLASFAAIPAAHAQSSVALYGVIDTSITYVNHAQGKDNAWMLGNSSAGNLSGSRWGVKGTEDLGGGLKALFQLENGFDPSNGRQGQGGRLFGRQAFVGLTSERYGTLTFGRQYDPLVDLVQGITADNYLGSVFATPGDVDNYDNSFRVDNAVKYTSAVYSGLQFSAMYSFGGIAGSTGAAQSYSAAVSYNNGPFSVAGGYFHATNSPASNGLRDGWTSSSDGTFDGPINSGYASAHSIGIARIAGQYVAGPFTFGLGYSNAQYRRDASSAFDSNEHYNTGQGFVNYQATDALLVGVGYSYTRSGGDTSATYHQVSAGADYSLSKRTDVYLSAAYQHASGQTGDGHGGSMAAQASIASYGYAGTSSQTMVNLGLRHRF
>NC_008390.1|WP_011656563.1|1356033_1356816_+|hypothetical-protein
MNRKIKTGAARAAITGTRRRALRSLAGAAFALGACLSASAPALAADAAAAVAAPAVTRVAMLVQLHGPNLKVDERIGQHLGERGYAVRLIDESATPDAARDADLVVISSTVSSKNVRPGWRTLDKPLVTWENDLLDDLAMTGKRHDVDFGETGKERYLWLVNAPHSISAGLPAGVADVYGKQAPMSWGRPGLGAITIATVYGQPDKAAIFAYEKGATMDYEALAPARRVMFFLANDTFANLSPAGLALFDAALDWAAGRR
>NC_008390.1|WP_011656564.1|1356937_1357516_+|flavin-reductase-family-protein
MDSHIAPVALQKAYRLLNHGPTVLVSARHDGVDNVMAAAWACALDFLPPKLTVVLDKSAKTRELVERSGRFVIQVPTAAQLQLTHAVGSHSLAERPDKLRDAGVTLFDVPGHDLPFVAGCSGWLACKLIHEPHNQQTYDLFIGEVVGAWSDTRVFRDGHWYFESADPALRSLHYIAGGNFYAIGESLHVDPG

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Crispr_ID: NC_008390_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_008390_4

1819786-1819891

Orphan

Consensus_repeat	Method
CGGGGTTCAAGGAAAGGTAAAGGAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_008390_4

>merge|NC_008390|4|1819786-1819891|CRISPRCasFinder
CGGGGTTCAAGGAAAGGTAAAGGAGTAACAGCCTGCGCGACGATGCGCGAGAACGCCCCGCCCTGCGGCAAACGCCAACGGCGGGGTTCAAGGAAAGGTAAAGCAG

>NC_008390|4|3|1819786-1819891|CRISPRCasFinder
CGGGGTTCAAGGAAAGGTAAAGGAG	TAACAGCCTGCGCGACGATGCGCGAGAACGCCCCGCCCTGCGGCAAACGCCAACGG
CGGGGTTCAAGGAAAGGTAAAGCAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_008390.1\|WP_011656934.1\|1824555_1825521_-\|bifunctional-glyoxylate/hydroxypyruvate-reductase-B	unknown	unknown	gnl\|CDD\|185307
NC_008390.1\|WP_011656921.1\|1811349_1812168_-\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|197715
NC_008390.1\|WP_011656925.1\|1816011_1816299_+\|YciI-family-protein	unknown	unknown	gnl\|CDD\|237238
NC_008390.1\|WP_011656937.1\|1827988_1828753_-\|xylose-isomerase	unknown	unknown	gnl\|CDD\|224007
NC_008390.1\|WP_006755042.1\|1818333_1819434_-\|NAD(P)H-binding-protein	unknown	unknown	gnl\|CDD\|224662
NC_008390.1\|WP_011656923.1\|1813302_1814643_+\|APC-family-permease	unknown	unknown	gnl\|CDD\|223605
NC_008390.1\|WP_011656926.1\|1816308_1817286_-\|magnesium/cobalt-transporter-CorA	unknown	unknown	gnl\|CDD\|213364
NC_008390.1\|WP_041491176.1\|1817465_1817612_+\|cytochrome-bd-I-oxidase-subunit-CydX	unknown	unknown	gnl\|CDD\|369733
NC_008390.1\|WP_011656931.1\|1821971_1822334_-\|DUF3022-domain-containing-protein	unknown	unknown	gnl\|CDD\|378603
NC_008390.1\|WP_011656922.1\|1812327_1813173_+\|carbon-nitrogen-hydrolase-family-protein	unknown	unknown	gnl\|CDD\|143600
NC_008390.1\|WP_011656932.1\|1822346_1823135_-\|YhfC-family-intramembrane-metalloprotease	unknown	unknown	gnl\|CDD\|337619
NC_008390.1\|WP_011656933.1\|1823189_1824233_-\|LacI-family-DNA-binding-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380506
NC_008390.1\|WP_011656928.1\|1819949_1820414_-\|Lrp/AsnC-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224439
NC_008390.1\|WP_011656936.1\|1826967_1827960_-\|sugar-kinase	unknown	unknown	gnl\|CDD\|238571
NC_008390.1\|WP_011656929.1\|1820768_1821311_+\|Spy/CpxP-family-protein-refolding-chaperone	unknown	unknown	gnl\|CDD\|369534
NC_008390.1\|WP_006755037.1\|1815058_1815547_-\|YbaK/EbsC-family-protein	unknown	unknown	gnl\|CDD\|239824
NC_008390.1\|WP_011656935.1\|1825526_1826807_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|340877
NC_008390.1\|WP_041491177.1\|1817608_1818226_+\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|379324
NC_008390.1\|WP_045554933.1\|1810760_1811363_-\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011656930.1\|1821439_1821871_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|290790

Protein	Function_ID	Function_description	E-value
NC_008390.1\|WP_011656934.1\|1824555_1825521_-\|bifunctional-glyoxylate/hydroxypyruvate-reductase-B	gnl\|CDD\|185307	PRK15409, PRK15409, glyoxylate/hydroxypyruvate reductase GhrB.	4.46848e-162
NC_008390.1\|WP_011656921.1\|1811349_1812168_-\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|197715	smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon.	1.08857e-13
NC_008390.1\|WP_011656925.1\|1816011_1816299_+\|YciI-family-protein	gnl\|CDD\|237238	PRK12866, PRK12866, YciI-like protein; Reviewed.	1.96121e-59
NC_008390.1\|WP_011656937.1\|1827988_1828753_-\|xylose-isomerase	gnl\|CDD\|224007	COG1082, IolE, Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism].	5.12107e-06
NC_008390.1\|WP_006755042.1\|1818333_1819434_-\|NAD(P)H-binding-protein	gnl\|CDD\|224662	COG1748, LYS9, Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism].	3.04077e-85
NC_008390.1\|WP_011656923.1\|1813302_1814643_+\|APC-family-permease	gnl\|CDD\|223605	COG0531, PotE, Amino acid transporters [Amino acid transport and metabolism].	4.91674e-40
NC_008390.1\|WP_011656926.1\|1816308_1817286_-\|magnesium/cobalt-transporter-CorA	gnl\|CDD\|213364	cd12830, MtCorA-like, Mycobacterium tuberculosis CorA-like subfamily. This bacterial subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Mg2+ transporter Mycobacterium tuberculosis CorA (which also transports Co2+). Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport.	3.48841e-142
NC_008390.1\|WP_011656931.1\|1821971_1822334_-\|DUF3022-domain-containing-protein	gnl\|CDD\|378603	pfam11226, DUF3022, Protein of unknown function (DUF3022). This family of proteins with unknown function appears to be restricted to Proteobacteria.	1.11302e-49
NC_008390.1\|WP_041491176.1\|1817465_1817612_+\|cytochrome-bd-I-oxidase-subunit-CydX	gnl\|CDD\|369733	pfam08173, YbgT_YccB, Membrane bound YbgT-like protein. This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW) which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to Proteobacteria.	8.32971e-10
NC_008390.1\|WP_011656932.1\|1822346_1823135_-\|YhfC-family-intramembrane-metalloprotease	gnl\|CDD\|337619	pfam10086, DUF2324, Putative membrane peptidase family (DUF2324). This domain, found in various hypothetical bacterial proteins, has no known function. This family appears to be related to the prenyl protease 2 family pfam02517, suggesting this family may be peptidases.	2.30229e-52
NC_008390.1\|WP_011656933.1\|1823189_1824233_-\|LacI-family-DNA-binding-transcriptional-regulator	gnl\|CDD\|380506	cd06283, PBP1_RegR_EndR_KdgR-like, ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.	2.54341e-91
NC_008390.1\|WP_011656928.1\|1819949_1820414_-\|Lrp/AsnC-family-transcriptional-regulator	gnl\|CDD\|224439	COG1522, Lrp, Transcriptional regulators [Transcription].	2.07239e-29
NC_008390.1\|WP_011656936.1\|1826967_1827960_-\|sugar-kinase	gnl\|CDD\|238571	cd01166, KdgK, 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources.	8.61309e-97
NC_008390.1\|WP_011656929.1\|1820768_1821311_+\|Spy/CpxP-family-protein-refolding-chaperone	gnl\|CDD\|369534	pfam07813, LTXXQ, LTXXQ motif family protein. This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP. This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Another member of this family, Spy, is also a periplasmic protein that may be involved in the response to stress. The homology between CpxP and Spy may indicate that these two proteins are functionally related.	7.94531e-06
NC_008390.1\|WP_006755037.1\|1815058_1815547_-\|YbaK/EbsC-family-protein	gnl\|CDD\|239824	cd04332, YbaK_like, YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX).	1.41839e-29
NC_008390.1\|WP_011656935.1\|1825526_1826807_-\|MFS-transporter	gnl\|CDD\|340877	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily. This family is composed of predominantly bacterial transporters for hexuronate (ExuT), glucarate (GudP), galactarate (GarP), and galactonate (DgoT). They mediate the uptake of these compounds into the cell. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	2.35865e-85
NC_008390.1\|WP_041491177.1\|1817608_1818226_+\|ATP-binding-protein	gnl\|CDD\|379324	pfam13671, AAA_33, AAA domain. This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.	5.00656e-20
NC_008390.1\|WP_011656922.1\|1812327_1813173_+\|carbon-nitrogen-hydrolase-family-protein	gnl\|CDD\|143600	cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases). Pseudomonas sp. MCI3434 R-amidase hydrolyzes (R,S)-piperazine-2-tert-butylcarboxamide to form (R)-piperazine-2-carboxylic acid. It does so with strict R-stereoselectively. Its preferred substrates are carboxamide compounds which have the amino or imino group connected to their beta- or gamma-carbon. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), class 13 represents proteins that at the time were difficult to place in a distinct similarity group. It has been suggested that this subgroup represents a new class. Members of the nitrilase superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Native R-amidase however appears to be a monomer.	1.71484e-111
NC_008390.1\|WP_011656930.1\|1821439_1821871_+\|hypothetical-protein	gnl\|CDD\|290790	pfam14083, PGDYG, PGDYG protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved PGDYG motif.	1.95984e-54

>NC_008390.1|WP_006755042.1|1818333_1819434_-|NAD(P)H-binding-protein
MKIAIVGAGLIGHTIAHMLRETGDYEVVAFDRDADALAKLSREGIATQRVDSADANAIREAVKGFDALVNALPYYLAVNVAAAAKAAGVHYFDLTEDVRATHAIRELADGSDRAFMPQCGLAPGFIGIAAHELVNGFSEVRDVKMRVGALPEYPTNALKYNLTWSVDGLINEYCQPCEAIRDGRKQWVQPLEGLEHFSLDGTEYEAFNTSGGLGTLCETLSGKVETLDYKSVRYPGHRELVQFLLEDLRLSSDRDTLKSIMRRAVPSTKQDVVLVFVTVTGVKDGQLVQDVFTRKIFAKDVCGMHMSAIQITTAGAMCAVLDLFREKKLPQSGFIPQEKVSLKAFLSNRFGKLYEGGTMERVHEVA
>NC_008390.1|WP_041491177.1|1817608_1818226_+|ATP-binding-protein
MTHLVFFCGHAGTGKTTLAKRLIGPLMRATGEAFCLLDKDTLYGRYSSAAMGALTSDPNDRDSPLYLKHLRDPEYQGLLDTARENLALGIGALVVGPLSREVRDRRILDRAWLGIGPEIALTVVWVHTAEDVAHQRIVARGNPNDAYKLAHWDEYRQRRFVPTGHECDGIVMFDNTAPSDADIDALLYRIVPPAPQATMVPPLPA
>NC_008390.1|WP_041491176.1|1817465_1817612_+|cytochrome-bd-I-oxidase-subunit-CydX
MWYFSWILGIGVALGFGIINVMWLEAEVFPRDDKRTDASRAGSGSRYS
>NC_008390.1|WP_011656926.1|1816308_1817286_-|magnesium/cobalt-transporter-CorA
MLINCAAYQDGRKLADIDIDAISDYVSKPECFVWVALKDPTPEEIDLMGEEFALHELALEDARKGHQRPKIEEYGDSLFAVLHTVELEEDGEFNVGELNVFVGPNYVLSIRNHTEQDFRAVRKRCEREPHLLQEGSAFVFYALMDQVVDRYFPILETLGNELEELEDRIFAKATLASSRAIIEDLYSLKRRLVMLHQHTAPLMEPLAKLTGGRIPQVCSGMQHYFRDVYDHLQRIVKTIEGRREMVVTAIQVNLGMISLAENEVTKRLGSFAALFAIPTMIAGIYGMNFANMPELHLKYGFYGCIAVMVAADLALWWRFRRAGWL
>NC_008390.1|WP_011656925.1|1816011_1816299_+|YciI-family-protein
MHYQLIYELVDDYLSRREQYRAEHLALAKAATERGELVLAGALQDPSDQAVLVFEGDSPEAAESFARADPYVQNGLVKSWRVRPWRVVVGKHAPH
>NC_008390.1|WP_006755037.1|1815058_1815547_-|YbaK/EbsC-family-protein
MPVSATLQDCLRQKSSRYEVVYHPYSHTSMETAAAAHIPGDRLAKTVLLEDDEGYVAAVLPTSHAVRLSDLWVKTGRHLVLAREMELRELFKDCDLGALPPVCMAYGMKTFLEEQLAQQPEVYFEAGDHEALIHMTQDEFLSLMETAERAHFSHKMQGMWVS
>NC_008390.1|WP_011656923.1|1813302_1814643_+|APC-family-permease
MQASSSNEPARLKRTLGLPSVLLFGLAYMAPLIVYGTYGVLAKASDDTAALAYLLALVAIAFTALSYGKLARLHPAAGSAYTYTRKTFNPHLGFMIGWATLLDYFFLPMVIWLIGAAYLNAAFPHVPTWIWIVAFIVLTSGLNIVGIDLAARFNIVLMVVQLAVVAMFVVLCVHYASAAAGAGGIAMAQPLFKPHVPFGATMAGAAIAAYSYLGFDAVSTLTEETIDPKKNMPRAILLIALIGGAIFVIAAYTMQLAHPGVEFKDTDSAAFEVAKMIGGDLFVPVFLAGLILAQFASGISAQASVGRLLYAMGRDEILPKRIFGFIHPRFKTPAINIVLAGSVGLIALKLDVATSTSFINFGAFLAFTAVNLCVIRLYLRGQSGERRIGVIGGLVFPAIGAVSDIWLLVSLEKAALVLGVAWFVLGLVYLCWITRLFRQAPPEVAI
>NC_008390.1|WP_011656922.1|1812327_1813173_+|carbon-nitrogen-hydrolase-family-protein
MQVELAQLTLVDGDVVHNTRKVIDTIEHVDSAGGTRLIVFPETTLSGFPTRDTVADVAQPLDGPALSAVRDAARQKGVAVAVGLAERDGGQFYNTTVLVDEQGDIVLRYRKTHLWASDVGVFTPGDRFETCSWNGLTVGLLICYDIEFPETARAVGALDADLLIVTNGNMDPFGPVHRRAIAARAMENQMFAVMVNRCGSGDDNLTFAGLSTLVDPFGDTVIELGRDEAVVPASVDPTRLEASREHYNYLHDARVALGLSPVEPAGGNRVVVIEPRRPRTK
>NC_008390.1|WP_011656921.1|1811349_1812168_-|helix-turn-helix-transcriptional-regulator
MDFEWRDLAFHREIGSAIDALDGPHFWARLTRVLERHVAFDNWVALCFARDAAPLVLAEQAMPDGKTDLMFQDYLAALYQLDPFYLAAFETQAPGFYTLADVAPDNFRMTEYYERYFKKNIVGDEVHFNVVIDRDHTLGFSLGKTSKYDEREMALLTLYTPWVLSLMQQRLRFETFAVKGASRPAEIDAPDPHARFGMLTGKNGRGALTTREIEVAMLSLSGFSSRAIGEKLSISFETVRAHKKHIYAKLGVGSQSELFAMFYDRGRTDERG
>NC_008390.1|WP_045554933.1|1810760_1811363_-|hypothetical-protein
MSAGDVRCARTARARRPSQASPACLPCIVERSRHVERNAECLFDSSPVCDGRVTFLRVRFDGDQCTADRGERGTVLLEPLAALLAIVVRFVRAGRRKDHDKRLAVPQQRIHVVEPALRIAVGSDRVVAYDDERKVGDIEYGERRQCGRHLSSVLGMHQVDLLRVEQHGSKRAARRPFHRFAPAPGPNGGRASHTTAITAR
>NC_008390.1|WP_011656928.1|1819949_1820414_-|Lrp/AsnC-family-transcriptional-regulator
MRPPRLDQLDDLDRQLVALLQADARASVADLARQLDVARTTVVARIARLERTNVIAGYSVRLGQDVLDASIYAYVGIILTPKFGKDVLRKLDRMPEVQLLCAVSGEYDYVAGLRADSPERLNDLLDQIGTLEGVERTTTSIILSRKIDRGTIGG
>NC_008390.1|WP_011656929.1|1820768_1821311_+|Spy/CpxP-family-protein-refolding-chaperone
MKKISLTLAMLAVAAGAFAQTPPQPQTPASTTAAAASAPSAEQRAARHEARIEQRIKYLHDQLKITSAQESQWKTFADTMRENGETMGHLYRARMENRNVSAVDDMKQYAELAQANADGAKKLADAFAPLYQSFPAEQKALADTTFRSWLHHGGEHRGSGKAKKEGKAAAAPAASAPAQP
>NC_008390.1|WP_011656930.1|1821439_1821871_+|hypothetical-protein
MLELKHIDLRTDPQARHVVKDETVTVAFAAADGELMSLEGPNRYVAGDALITGSTGDRWVVSRARFDAKYLPADPALAHGTPGAYRNRPAVVLARRMDEPFTIARSENGDTLRGVAGDWVMQYAPGDYGVVQAQRFAQVYRDA
>NC_008390.1|WP_011656931.1|1821971_1822334_-|DUF3022-domain-containing-protein
MDDYLIECQSSEFDALARVICDLFPEQTRFAESSDERGRFLSVHWLAMRFGSTPKRMTLDIRIVPPALARYLALKPMQRARSHAVLHAYTEAMLGSLEERHAAGEAVERDAELELDEDFA
>NC_008390.1|WP_011656932.1|1822346_1823135_-|YhfC-family-intramembrane-metalloprotease
MTVAPVTLAVLIAATLIIALLPFVLFRILRKPLALDRRDTIVGVAVFTLFAMIVERAFHGFVLSQTPAGGWLTQPLAFVAYSALATAVFEEVGRYLGMRILNRRYGASAGDGRGIGYGIGHAGAEAWFVGVLVWGQWSYLAWLASRGQLETQLADLPGDTVVRLHVMLATLSAQSILLLLLERCAAFVVQLALSVLVWRGVRAGRAGVLPLAIVLHALAVAPALLYQVRVLPAGSLEAVYVVLAAVLVAVLVKAGRSPRAAA
>NC_008390.1|WP_011656933.1|1823189_1824233_-|LacI-family-DNA-binding-transcriptional-regulator
MSDSQPSTQRPATISDVAREAGTGKTSVSRYLNGETHVLSADLRQRIETAIARLNYRPNQMARGLKRGRNRLLGMLAADLTNPYTIEVLQGVEAACHALGYMPLICHAANEVEMERRFLQLLTTYRVEGLIVNALGAEEDVLRPLRGAGIPAVLVDRTVEGFEADLIGLDNTDAIETALAHLVARGFDAIHFVVQPFERVSSRRLREAAFRAALGARGLPVPPTVVLDLNEPAAAAAALADLDARLDDATRRGVRAALFAANAPVALAIARHLRARFGAAWQEKAALLSIDDPEWAELIGITTIRQPTYEIGYKAVEFVHERIDGAAGDVRVAMLPGELIARASTAS
>NC_008390.1|WP_011656934.1|1824555_1825521_-|bifunctional-glyoxylate/hydroxypyruvate-reductase-B
MKPRIVAYKPLPDDVLAYLREHADVVQADGPAALADALGDAHGAIGASLKVTPQMLDRAPKLKAWSTISVGYDNFDVADLTRRGIVLAHTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWHRSIGPDLYGTDVQGKTLGIVGLGRIGGAVARRAALGFRMQVLYTNRSAHAEAETQYGARRVTLDELLAQSDFVCLQVPLSPQTHHLIGAAEFTKMKRGAILINASRGPVVDEAALIDALRAGTIRGAGLDVFEKEPLPADSPLLRMNNVVALPHIGSATHETRHAMARCAAENLVGALAGTLRRNLVNPDALAHA
>NC_008390.1|WP_011656935.1|1825526_1826807_-|MFS-transporter
MAANLAVRRWWTIMPIVFITYSLAYLDRANYGFAAAAGINQDLGISKGLSSLIGALFFLGYFFFQIPGAIYAERRSVKKLVFVSLVLWGACAALTGVVADIPSLMVIRFVLGVVEAAVMPAMLIYISNWFTKSERSRANTFLILGNPVTVLWMSIVSGYLVHEFGWRHMFIAEGVPAVIWAVCWWFLVQDKPADSPWLTAQEKRDLDAVLAAEQAAIKPVRNYGEAFRSPAVIKLCAQYFCWSIGVYGFVLWLPSIVKNGSELGMVATGWLSALPYLAATIAMLVASWASDKVGSRRGFVWPFLLIGAAAFAASYALGSSHFWISYALLVVAGAAMYAPYGPFFAIVPELLPKNVAGGAMALINSMGALGSFVGSYFVGYLNGATGSPVASYAFMSAALVAAVILTLSVKPQARDAHPLAAPLQGK
>NC_008390.1|WP_011656936.1|1826967_1827960_-|sugar-kinase
MKAALDVVTYGEAMAMFVAAEPCHLAHAAQFTKRIAGADLNVAIGLSRLGFRVGWMSRVGRDSFGTYVLDTLAREGIDASCVTVDPRYPTGFQLKSRNDDGSDPTVEYFRKGSAASHLSCDDYVADYVLGARHLHLTGVAPAISATSCELAFQLAREMRTAGKTISFDPNLRPSLWPSTDVMAKTLNALATLADWVLPGLAEGRQLTGHDTPADIAGFYLARGARGVVIKLGPEGAYFRTADGRAGTVAGERVAKVVDTVGAGDGFAVGVVSALLEGRSVEQAVARGNRIGALAIQVIGDSEGLPTRAALDQLENVSNRADRLEETVTAQ
>NC_008390.1|WP_011656937.1|1827988_1828753_-|xylose-isomerase
MADIVIVASAFGMDRVRQEGHRAFLATAAASGATGFEVRRELFASDDDATPATLAELGTALSAHGLWSVYSTPATLYTEAGALDADALRDTLLEADALGARFVKFQLGGFAGDAHAAEIVALSRGARARVVVENGQLPIGGALAQFRGLFDALAEAGTPDALGMTFDIGNWQWPGEAPLACAHALAPHVEYIHCKAVVGDGARRFAVAPAPGDPLVTGVLAALPQAVPRGIEFPFDAADLAGDAGRRVAWLAAA

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Crispr_ID: NC_008390_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_008390_5

3231808-3231879

Orphan

Consensus_repeat	Method
GGTCCCATGCTTCGCGGTCGACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_008390_5

>merge|NC_008390|5|3231808-3231879|CRISPRCasFinder
GGTCCCATGCTTCGCGGTCGACCAGAGTTAGTGCTTCAGCACTTACCCGGGTCCCATGCTTCGCGGTCGACC

>NC_008390|5|4|3231808-3231879|CRISPRCasFinder
GGTCCCATGCTTCGCGGTCGACC	AGAGTTAGTGCTTCAGCACTTACCCG
GGTCCCATGCTTCGCGGTCGACC

Protein	Signature genes	Signature genes Name	Protein_function
NC_008390.1\|WP_006754800.1\|3224039_3224576_+\|TlpA-family-protein-disulfide-reductase	unknown	unknown	gnl\|CDD\|239264
NC_008390.1\|WP_011658026.1\|3235621_3237757_-\|3-hydroxyacyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|236864
NC_008390.1\|WP_006489451.1\|3220855_3221107_+\|accessory-factor-UbiK-family-protein	unknown	unknown	gnl\|CDD\|377337
NC_008390.1\|WP_011658022.1\|3229758_3231444_-\|cation-acetate-symporter	unknown	unknown	gnl\|CDD\|236495
NC_008390.1\|WP_011658024.1\|3233235_3234381_-\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|132247
NC_008390.1\|WP_011658029.1\|3242163_3242919_-\|lipoyl(octanoyl)-transferase-LipB	unknown	unknown	gnl\|CDD\|237682
NC_008390.1\|WP_011658020.1\|3226092_3228111_-\|sensor-histidine-kinase	unknown	unknown	gnl\|CDD\|226654
NC_008390.1\|WP_011658030.1\|3243002_3243329_-\|DUF2917-domain-containing-protein	unknown	unknown	gnl\|CDD\|378568
NC_008390.1\|WP_011658025.1\|3234395_3235592_-\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|132248
NC_008390.1\|WP_011658018.1\|3223306_3223879_-\|hypothetical-protein	unknown	unknown	unknown
NC_008390.1\|WP_011658028.1\|3239018_3240899_+\|gamma-glutamyltransferase	unknown	unknown	gnl\|CDD\|223482
NC_008390.1\|WP_011658027.1\|3237985_3238948_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176114
NC_008390.1\|WP_011658017.1\|3221362_3222973_+\|YifB-family-Mg-chelatase-like-AAA-ATPase	unknown	unknown	gnl\|CDD\|223679
NC_008390.1\|WP_006753858.1\|3241178_3242171_-\|lipoyl-synthase	unknown	unknown	gnl\|CDD\|235493
NC_008390.1\|WP_011658021.1\|3228115_3229405_-\|dicarboxylate/amino-acid:cation-symporter	unknown	unknown	gnl\|CDD\|234968
NC_008390.1\|WP_011658023.1\|3231999_3233205_-\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
NC_008390.1\|WP_011658019.1\|3224657_3226013_-\|sigma-54-dependent-Fis-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225114
NC_008390.1\|WP_006398175.1\|3220160_3220499_-\|P-II-family-nitrogen-regulator	unknown	unknown	gnl\|CDD\|223424
NC_008390.1\|WP_006754805.1\|3231455_3231761_-\|DUF485-domain-containing-protein	unknown	unknown	gnl\|CDD\|377315
NC_008390.1\|WP_011658031.1\|3243431_3244418_+\|transcriptional-regulator-GcvA	unknown	unknown	gnl\|CDD\|182990

Protein	Function_ID	Function_description	E-value
NC_008390.1\|WP_006754800.1\|3224039_3224576_+\|TlpA-family-protein-disulfide-reductase	gnl\|CDD\|239264	cd02966, TlpA_like_family, TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.	4.7848e-41
NC_008390.1\|WP_011658026.1\|3235621_3237757_-\|3-hydroxyacyl-CoA-dehydrogenase	gnl\|CDD\|236864	PRK11154, fadJ, fatty acid oxidation complex subunit alpha FadJ.	9.78397e-159
NC_008390.1\|WP_006489451.1\|3220855_3221107_+\|accessory-factor-UbiK-family-protein	gnl\|CDD\|377337	pfam04380, BMFP, Membrane fusogenic activity. BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.	1.72724e-20
NC_008390.1\|WP_011658022.1\|3229758_3231444_-\|cation-acetate-symporter	gnl\|CDD\|236495	PRK09395, actP, cation/acetate symporter ActP.	0
NC_008390.1\|WP_011658024.1\|3233235_3234381_-\|acyl-CoA-dehydrogenase	gnl\|CDD\|132247	TIGR03203, pimD_small, pimeloyl-CoA dehydrogenase, small subunit. Members of this protein family are the PimD proteins of species such as Rhodopseudomonas palustris, Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.	2.68866e-100
NC_008390.1\|WP_011658029.1\|3242163_3242919_-\|lipoyl(octanoyl)-transferase-LipB	gnl\|CDD\|237682	PRK14343, PRK14343, lipoyl(octanoyl) transferase LipB.	1.03834e-158
NC_008390.1\|WP_011658020.1\|3226092_3228111_-\|sensor-histidine-kinase	gnl\|CDD\|226654	COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms].	0
NC_008390.1\|WP_011658030.1\|3243002_3243329_-\|DUF2917-domain-containing-protein	gnl\|CDD\|378568	pfam11142, DUF2917, Protein of unknown function (DUF2917). This bacterial family of proteins appears to be restricted to Proteobacteria.	2.30135e-17
NC_008390.1\|WP_011658025.1\|3234395_3235592_-\|acyl-CoA-dehydrogenase	gnl\|CDD\|132248	TIGR03204, pimC_large, pimeloyl-CoA dehydrogenase, large subunit. Members of this protein family are the PimC proteins of species such as Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.	1.16309e-157
NC_008390.1\|WP_011658031.1\|3243431_3244418_+\|transcriptional-regulator-GcvA	gnl\|CDD\|182990	PRK11139, PRK11139, DNA-binding transcriptional activator GcvA; Provisional.	4.26817e-171
NC_008390.1\|WP_011658028.1\|3239018_3240899_+\|gamma-glutamyltransferase	gnl\|CDD\|223482	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism].	0
NC_008390.1\|WP_011658027.1\|3237985_3238948_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176114	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	5.31513e-49
NC_008390.1\|WP_011658017.1\|3221362_3222973_+\|YifB-family-Mg-chelatase-like-AAA-ATPase	gnl\|CDD\|223679	COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones].	0
NC_008390.1\|WP_006753858.1\|3241178_3242171_-\|lipoyl-synthase	gnl\|CDD\|235493	PRK05481, PRK05481, lipoyl synthase; Provisional.	0
NC_008390.1\|WP_011658021.1\|3228115_3229405_-\|dicarboxylate/amino-acid:cation-symporter	gnl\|CDD\|234968	PRK01663, PRK01663, C4-dicarboxylate transporter DctA; Reviewed.	0
NC_008390.1\|WP_011658023.1\|3231999_3233205_-\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	1.81901e-147
NC_008390.1\|WP_011658019.1\|3224657_3226013_-\|sigma-54-dependent-Fis-family-transcriptional-regulator	gnl\|CDD\|225114	COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms].	0
NC_008390.1\|WP_006398175.1\|3220160_3220499_-\|P-II-family-nitrogen-regulator	gnl\|CDD\|223424	COG0347, GlnK, Nitrogen regulatory protein PII [Amino acid transport and metabolism].	3.62827e-59
NC_008390.1\|WP_006754805.1\|3231455_3231761_-\|DUF485-domain-containing-protein	gnl\|CDD\|377315	pfam04341, DUF485, Protein of unknown function, DUF485. This family includes several putative integral membrane proteins.	5.78727e-27

>NC_008390.1|WP_006754805.1|3231455_3231761_-|DUF485-domain-containing-protein
MELSVIESVTACRDYQQLVRARRRFSFTLTALMIATYYGFILLVALAPHVLAAPLYRGATTTVGIVAGVAIILVAIGLTAWYVLRANRAFDRRVAAILQRS
>NC_008390.1|WP_011658022.1|3229758_3231444_-|cation-acetate-symporter
MRLTSSALGALAVLVSSTAHATSVAGPMPDKVELNPVAIAMFFAFVFATLALTRWAARRTRSTRDFYTAGGGITGLQNGLAIAGDYMSAASFLGLSGMVFMFGFDGLIYSIGFLVGWPFVMFLIAEPLRNLGKFTFVDVVAYRFAQRPIRLLTSANALTIVVLYLVVQMVGAGKLIQLLFGLSYGTAELIVGVLMVVYVFFGGMTATTWVQVIKAVLLLCGATLLVLLALGEFGFSVDEMFRRAVAVHPGALSIMGPGKLIRDPANALSLGIALMFGTAGFPHILMRFFTVPNAKEARKSVLYATGFIGYFYLLTFVIGFSAIVLLAQHPEFFRLGANGTFNLTHDLLGGSNMVAVKLAQAVGGNWFYGFIAAVTFATILAVVAGLTLAGATTISHDLYAQMWARGKPDERLEMRISRAATIGLSAIAIALSILFEHVNVAFMVGLVAAVAASANFPVLAMSIFWRGMTTRGAVLGGGLGLASAVALTVLSKSVWVDVLHHAHAPVFLDNPALVSVPLAFFGIVVGSLADRGERARRERDAFAQQEFYAQTGVLASRAVQH
>NC_008390.1|WP_011658021.1|3228115_3229405_-|dicarboxylate/amino-acid:cation-symporter
MKKKPFYKVLYVQVIFAIIVGVILGHFYPALATDMKPLGDGFIKLIKMVIGPIIFCTVVTGIAGMEDMKKVGRVGGKALLYFEVVSTFALLLGLAATHILRPGVGFNIDPATLDGKAVASYAAKAHGQSTVDFLLHIIPNTMVDAFAQGEILQILLIALLFGSVLAHLGERGKVVTDFIDGLTRVLFGIVHIVTKLAPIGAFGAMAFTIGKYGVGSLVPLLKLIGTFYLTSIVFVLVVLGTIARVTGFSIIRFVSYIKEELLIVLGTSSSEAALPQLMEKLEKAGCSRSVVGLVVPTGYSFNLDGTNIYMTMAVLFIAQATNIELTWMQQLTLLAVAMLTSKGASGVTGAGFITLAATLAVVPTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLRQALTGGGEVKTTEAAGV
>NC_008390.1|WP_011658020.1|3226092_3228111_-|sensor-histidine-kinase
MSEQAAVPPAAAAPRGGRGGQGGDAEPYDTIGDPHRQEVTSVKRRLLILVVLAVALAAACALTWTITWRRGVAELQRNAAVRVDRTTNALKSTLDRYESLPYLLGSHPYVQDLLAEPKRADFTGRANRYLEDLNEHAHATVTYVVGADGLCVAASNWRAPDSFVGIEYRFRPYFIDAMNGRVGRFFGIGTISRDPGYYISQPVWRDGKIAGVVVVKLNLEWFQGADASEPLVVADDHGVVFLSSVPAWKYHTLHPLTGPVAASIYETRQYAQQPVTPLPLRVEQVLGADAEIVRLGPGLRAPRFLASKRRIGEPDWLLVTLAPIAPIDADARNATIVTGFGFVSVALLAFYWRMRRARVREMIRGRALLQQAYAELNRRVEERTADLSEANEQLQKEVGDRIRAEQELRAAHDELIQASKLAALGQMAAGITHELNQPLAALRSFSDNTRVLLDRGEQAAARENLEAIAALTERMGKITNQLKLFVGRAKPRNEQALVVRALRSVLSLLGERLRGVALTLTLQDATVSPAQDAPLDLARDYPDLVARCEDLRLEQVLINLLGNALDAVAGVAAPAIEVTIAVSVATLAVEVRDNGPGIAPDLLPRLFEPFFTTKEMGRGLGLGLAISSSIASDAGGALTARNAPSGGALFVLTLRRTRTHHPDSLSEPAGSR
>NC_008390.1|WP_011658019.1|3224657_3226013_-|sigma-54-dependent-Fis-family-transcriptional-regulator
MANRLQVIYIEDDALVRRASVQSLQLAGFDVVGFESAEAADKAIVAETAGVIVSDIRLPGASGLDLLAQCRERVPDVPVILVTGHGDISMAVQAMRDGAYDFIEKPFAAERLIETVRRALERRELVLENHALRRELAGQNIVAPRIIGRSPAIEQVRKLIANVAPTDASVLINGDTGAGKELIARSLHELSPRRDKPFIAVNCGALPEPMFESEMFGYEPGAFTGAAKRRVGKLEYASGGTLFLDEIESMPLALQVKLLRVLQDGVLERLGSNQPIRVNCRVVAAAKGDMSELVAAGTFRRDLLYRLNVVTIALPPLAERREDIVPLFEHFMLDAAVRYGRPAPVLTDRQRASLMQRDWPGNVRELRNAADRFVLGVADMPQDAGASGDDAESDQTLKERIEQFERAVIAQALNQTGGAVAATADRLHVGKATLYEKMKRYGLSAKGETER
>NC_008390.1|WP_006754800.1|3224039_3224576_+|TlpA-family-protein-disulfide-reductase
MNTTPPAQRRTGPARYIVAAVVVAAIAVAGFFAFNGKSSVPDATFTLLSGQKVSTAGDLKGKVYLVNFWATSCATCMQEMPQMVETYNRFKGQGLEFVAVAMNYDPPMYVANYAQTRQLPFKVALDDGSVAKQFGNVQLTPTTFVVDKNGKILKRYVGAPQFAELDALLKKALDGNAA
>NC_008390.1|WP_011658018.1|3223306_3223879_-|hypothetical-protein
MPKEVIDSLRPLFRPLRHFAALACVSAALTACSPSYDWRTLHNDAGYTIDLPAKPTVEDHPIAVGGASMPMRMQAAHVDGAVFAVGTLTLPDDRDDTRRAALEFLRAGLSRNLEGAPRTASVPVPLAAGGAVNGLELRVAGAASGGDHAQKTIVARLVARGRHAYQAVVIADGPLAQEQLDQFFGSFKLD
>NC_008390.1|WP_011658017.1|3221362_3222973_+|YifB-family-Mg-chelatase-like-AAA-ATPase
MSLAVVRSRAPAAGRAPDVTVEVHLANGLPSFSIVGLPDLEVRESRERVRAALQNCGFEFPVRRITVNLAPADLPKESGRFDLPIALGILAANGQIPADALAGREFAGELSLTGALRPMRGAFAMACGAARDWRAGETGSSVGSGARPDAMSDPAAGPPAASRPPELYLPLDSAAEAALVPGVTVFGAPDLPALCAHLAGAPDARLAPVAAPCLDGEPAPAAPDLADVIGQRGARRALEVAAAGGHHMLMIGPPGAGKSMLAARLPGLLPPLTDDEALTSAALLSASRLGFSPAQWRRRPFRSPHHSSSAAALVGGRNPPQPGEITLAHLGVLFLDELPEFDRHVLEMLREPLEVGRITISRAAQQADFPAACQLIAAMNPCPCGWHGDPSGRCRCSPDVASRYLRKLSGPLLDRIDIQIDLPALSPAELAARATAHGESSATVAARVAQARALQFERQGKTNHMLSGRETDDLCRPTDDGERLLREAGERFGWSARAYFRVLKVARTIADLAGDPLPTAAQIAEAIRYRRALTAL
>NC_008390.1|WP_006489451.1|3220855_3221107_+|accessory-factor-UbiK-family-protein
MKQPSDVFNDLQSRVSDLLKNSPAKDVERNVKAMLSQGFSKLDLVTREEFDTQAQVLARTRVRLEELEKRVAELEQKLAAPQA
>NC_008390.1|WP_006398175.1|3220160_3220499_-|P-II-family-nitrogen-regulator
MKLITAIIKPFKLDETREALSALGVSGITVTEVKGFGRQKGHTELYRGAEYVVDFLPKMKIEAAVSDDLVDQAVEAIERAARTGKIGDGKIFVTPIEQVIRIRTGETGADAL
>NC_008390.1|WP_011658023.1|3231999_3233205_-|CoA-transferase
MTNDPRALPLAGVKVLDFSRVLAGPWSAMVLADFGADVIKIEHPARGDDTRDWGLRIGDTETTYFNSVNRSKRSICVDLQTEAGRRIARELAAQADVLIHNFKAGGAEKLGLGYDALAELNPRLVHCAISGYDRSGPEAARPGYDLVVQGEAGLMALNGEADQPPLKFGVAAVDLFTGMYSAQAILAALYERHATGRGRRIEMALFDCGLMITAYYGLDALLMGEDPPRYGNAHPSIVPYGVFDAADGPLVITVGNNTQFARFCDAIERPDLAADERYRTNLGRSANRAELLPEIRRELARRPRATLLAALSGAGIPCGEVLGLHDALTSERATRAGLVTRQPHPVAGGVDVLAPPYRFDGARLPVRGAPPVLGADTDDVLGGWLGLSTDELARLRADRIV
>NC_008390.1|WP_011658024.1|3233235_3234381_-|acyl-CoA-dehydrogenase
MDFQHTEDRRMLADTLNRFIAEQYAFPVRDRIAQSADGFDRTMWQRFAELGAVGALFAEADGGFGGAGFDIAVVFECLGRGLVVEPFLGALLAGRALSLAGGAAHRERLAALIDGSASAAFAHDEPGSHYELTTVRTRAERVGDGWVLTGAKGVVDQAAQAAFFVVSARVSGHDDDAAGIGLFVVPADAPGVSLRDYRKIDGGRAAEVRFERVALPADAALGAPNAHDGEAGAALLERVLGYGLLALSAEALGAMDIAKEYTLDYLRTRKQFGMPIGSFQALQHRMADLLLEVEQARSAVINAAAQLEAPRAVRERALAAAKYSIGRIGTLVAEESIQLHGGIGMTWELPLSHYAKRLVMIDHQLGDEDHHLARYIALSKQ
>NC_008390.1|WP_011658025.1|3234395_3235592_-|acyl-CoA-dehydrogenase
MDLNFTPEEEAFRADVQRFLAAELPARTARKVKGGLHLTRDDMREWHAILNARGWLASHWPREFGGPGWSVAQKFLFDNECALAGAPRIVPFGVNMLGPVLIKYGSEAQQRHWLPRILDGTDWWCQGYSEPGAGSDLASVKTSAVRHGDHYVVNGQKTWTTLGHYANMIFCLVRTATDVRKQEGISFLLIDMNTPGVEVRPIITFDGEHEVNEVFFTDVRVPVENLVGEENRGWTCAKYLLTYERTNIAGIGFSTAALERLRAVAAKVTKNGRPLADDPFFAARVARVEIELENMRTTNLRVLAAVAGGGVPGAESSMLKIRGTQIRQEITALMRRAMGPYAQPFVDDALDADYDGEPIGPEEAASAAQQYFNNRKLSIFGGSNEIQKNIIAKMMLGL
>NC_008390.1|WP_011658026.1|3235621_3237757_-|3-hydroxyacyl-CoA-dehydrogenase
MHSTASPEPSRAGTVTRERRDKVLVVTIDHPPVNALSADVRRGLSDALDAAQTDDAIRAVLIVGAGRNFIAGADIREFGKPPVPPSLPDVCEQIESSAKPVVVALHGATLGGGLEVALAAHYRLAVPGAKLGLPEVTLGLLPGAGGTQRAPRLIGAKAALDLMLTGRHASADEALALGLIDRLAHSDDTLAEGLAYAQELVSLGAPARRTRDARGLADRVSAQAAIDAARADLPKKSRGLFSPAKIVDAVEAALTQSFDAGMKLERSLFLQCIDSPQRAGLVHAFFAEREAAKAPEARRASARPVERIGVVGGGTMGAGIAVAALDAGLPVTMIERDEAALARGRAHVEKVYDGLVAKGRMTPAAHAARLARFKGSTSYDALAQADVVIEAVFEDMAVKQAVFAELARVCKPGAVLATNTSYLDIDELAASIDRPADVIGLHFFSPANVMKLLEIVVPARVSAEVVATAFALAKQLKKTPVRAGVCDGFIGNRILAVYRTAADYLMEDGASPYQIDRAVREFGFPMGPFQVVDLAGGDIGWATRKRRAATRDPRARYVEISDRLCERGWFGQKTARGYYLYPDGARVGTPDPEVEAIVADERAKKGITPRAFSDDEILRRYLAAMINEGANVVHEKIALRPLDVDAVFLHGYGFPRYRGGPMHYADTVGLANVLADIRAFANEDPLFWKPSPLIVELVERGADFASLNHID
>NC_008390.1|WP_011658027.1|3237985_3238948_+|LysR-family-transcriptional-regulator
MDLNALTLLVEILDAGNLSKAAQRLKVSRANVSYRLNQLERSIGQQLVRRTTRRIEPTEIGLKLYEHGRRIRNELLAAQESVTTLGQDLQGRVRLSVPSGYGQMVMSDWLLAFKRLHPGIVLDVVFENRVEDLMRDEIDIAVRVMPEPPQNLVARDMGAVRYVACASAAFAAAHGMPASLGALAAAPVVTATVMGRQLRIAAYLGDERHEVLLEPTLISENFLFLRQAILAGIGVGIVPDYVVQEDMRRGMVVTSLDAYRLSIFGTHMYMLYMPNRHHTRATATFIEFILEQAGKTGRGGPGAMRQGFLSDDNPPPARRQ
>NC_008390.1|WP_011658028.1|3239018_3240899_+|gamma-glutamyltransferase
MFDRIRPHSRPWTLAAAVAFALVAFGAGCTSPSAPSGAVVPVAAASGAAVPLPGVHSPELSSGWTDKPGWTSQHAMIAAANPLATQAGYDMLKAGGTAIDAAIATQMVLALVEPQSSGIGGGAFMLYFDGHATQAYDGRETAPAAATERLFYGPTGQPMRFYEGVVGGRSVGTPGVLRMLDAAHRAHGKLPWRRLFQPAIRLAEHGFTISPRLAMLIANDKYLMNDPAARAYFYNDDGTPKAAGTVLKNPALATVLRQVADRGANAFYTGAIARDIVAKVRKHPTNPGLLSLQDLARYKAKVRAPLCTDYRRSVVCGMPPPSSGGLAIAQMLGILETMPDWQQIGAQKPVRNEVGYEPTPFAAHLFSEAGRLAFADRARYVADPDFAPLPGGSWASLTDKAYLAQRARLIGDNSMGVAQAGTPQGAALALADDRSPELPSTSDIAIVDRYGQALSMTTSVEDAFGSRLMVRGFMLNNQLTDFSFVSSENGRPVANRVQPGKRPRSAMSPELVFDQKTKQVTMIVGSAGGPAIINHVAKTLIGVLDWGMTMQQAIALPNVGSTNGPTQLERGRVSDALVDGLKGRGHDVQVVELNSGLQGIQRLNLQGQTVWFGGADPRREGVAMGD
>NC_008390.1|WP_006753858.1|3241178_3242171_-|lipoyl-synthase
MTDVTASPAPADSAATAAYDPTAKQKAQAKTARIPIKVIPIEKLKKPEWIRVKAATGSSRFNEIKTILREHNLHTVCEEASCPNIGECFGKGTATFMIMGDKCTRRCPFCDVGHGRPDPLDADEPKNLARTIAALKLKYVVITSVDRDDLRDGGAGHFVECIREVREQSPETRIEILTPDFRGRLDRAISILNAAPPDVMNHNLETVPRLYKEARPGSDYAHSLKLLKDFKALHPDVATKSGLMVGLGETEEEILQVMRDLRAHDVDMLTIGQYLQPSEHHLPVRAYVHPDTFKMYEEEAYKMGFTHAAVGAMVRSSYHADLQAHGAGVV
>NC_008390.1|WP_011658029.1|3242163_3242919_-|lipoyl(octanoyl)-transferase-LipB
MSVSPVSIVSTPVAVSESPAGSPVQPAVPVTVRWRGSEAYQTSFDAMRAFTDTRTADTGDEIWVVEHPPVYTLGQAGDPAHLLVADSGVPLVKVDRGGQITYHGPGQIVVYLLLDLRRRKLMVRTLVTKIEEAVIETLAAYNLASVRKAGAPGIYVASGVHEGAKIAALGLKIRNGCSYHGLSLNVKMDLRPFLAINPCGYAGLETVDMASLEVAADWNDVAHTLVGRLIANLDGESAAADKPQALEHSND
>NC_008390.1|WP_011658030.1|3243002_3243329_-|DUF2917-domain-containing-protein
MQEISSSITFEIPAGETVPMKVQRSTRLTVQCGPVWATRSNDVEDYFLVDGETLRLRRGERLWLSAESGQGAHVAFSVSRPAAEVARGVLARVRDRVNALVHDGWRTV
>NC_008390.1|WP_011658031.1|3243431_3244418_+|transcriptional-regulator-GcvA
MDLRQLPALNAIRAFEAAARHENFSRAADELFVTHGAVSHQVRALEEELGVQLFARNGKRLCLTGAGMRYAQQVRTALMMLADATREVRASDRDRRLVVSMLSSFAARFVTPRIGTFIERHPEIDVELQSTNNLTDFARDDVDLAIRFGFGNYPGLHVEPLFDEVFFPACAPTLNGGKLPQTPADLVHYNLLRSDDELWRPWFDAAGLDTLTEPKRGILYQDSSNLLLAAIEGQGIALVRRSLAVHDLLDGRLVRLFDIDGASPWHYFFVCPPPLLNAPRVQAFRAWMFEEVAQFKLLCDELDARRAAGKTPAECAQEGGWKGLRAQP

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_008390_1	1.2\|180003\|63\|NC_008390\|PILER-CR	180003-180065	63	NC_008390.1	182501-182563	5	0.921

1. spacer 1.2|180003|63|NC_008390|PILER-CR matches to position: 182501-182563, mismatch: 5, identity: 0.921

gacctgggcgagctggatgcggccgcggcgagctacggcaaggcgatcgccttccatccc	CRISPR spacer
gacctgggcgaactggatgcggccgcggcaagctacggcaaggcgatcgccttccatccc	Protospacer
***********.*****************.******************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049158	Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence	1079643-1079667	1	0.96
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049318	Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence	1084323-1084347	1	0.96
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049157	Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence	601866-601890	2	0.92
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049317	Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence	1040805-1040829	2	0.92
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049158	Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence	1412247-1412271	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049158	Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence	1258699-1258723	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049318	Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence	1416915-1416939	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049318	Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence	1263368-1263392	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP012748	Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence	445488-445512	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP012748	Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence	445537-445561	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP012748	Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence	445586-445610	3	0.88
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049158	Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence	1028033-1028057	4	0.84
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049318	Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence	1032713-1032737	4	0.84
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049157	Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence	601904-601928	4	0.84
NC_008390_3	3.1\|1345750\|25\|NC_008390\|CRISPRCasFinder	1345750-1345774	25	NZ_CP049317	Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence	1040767-1040791	4	0.84
NC_008390_5	5.1\|3231831\|26\|NC_008390\|CRISPRCasFinder	3231831-3231856	26	NZ_CP017563	Paraburkholderia sprentiae WSM5005 plasmid pl1WSM5005, complete sequence	646888-646913	4	0.846
NC_008390_5	5.1\|3231831\|26\|NC_008390\|CRISPRCasFinder	3231831-3231856	26	NZ_CP014688	Acetobacter persici strain TMW2.1084 plasmid pAC1084_1, complete sequence	141665-141690	4	0.846
NC_008390_5	5.1\|3231831\|26\|NC_008390\|CRISPRCasFinder	3231831-3231856	26	NZ_CP049317	Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence	1915500-1915525	7	0.731
NC_008390_5	5.1\|3231831\|26\|NC_008390\|CRISPRCasFinder	3231831-3231856	26	NZ_CP049157	Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence	1719554-1719579	7	0.731

1. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049158 (Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence) position: , mismatch: 1, identity: 0.96

caagcgctaaagcgccaactctggt	CRISPR spacer
caagcgctgaagcgccaactctggt	Protospacer
********.****************

2. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049318 (Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence) position: , mismatch: 1, identity: 0.96

caagcgctaaagcgccaactctggt	CRISPR spacer
caagcgctgaagcgccaactctggt	Protospacer
********.****************

3. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049157 (Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence) position: , mismatch: 2, identity: 0.92

caagcgctaaagcgccaactctggt	CRISPR spacer
aaggcgctaaagcgccaactctggt	Protospacer
 *.**********************

4. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049317 (Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence) position: , mismatch: 2, identity: 0.92

caagcgctaaagcgccaactctggt	CRISPR spacer
aaggcgctaaagcgccaactctggt	Protospacer
 *.**********************

5. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049158 (Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
aagccgctaaagcgccaactctggt	Protospacer
 *. *********************

6. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049158 (Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgccaactccgat	Protospacer
.********************.*.*

7. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049318 (Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
aagccgctaaagcgccaactctggt	Protospacer
 *. *********************

8. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049318 (Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgccaactccgat	Protospacer
.********************.*.*

9. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP012748 (Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgctaactctcgt	Protospacer
.**************.****** **

10. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP012748 (Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgctaactctcgt	Protospacer
.**************.****** **

11. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP012748 (Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence) position: , mismatch: 3, identity: 0.88

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgctaactctcgt	Protospacer
.**************.****** **

12. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049158 (Caballeronia sp. SBC1 plasmid pSBC1_2, complete sequence) position: , mismatch: 4, identity: 0.84

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgccaactccgcc	Protospacer
.********************.* .

13. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049318 (Caballeronia sp. SBC2 plasmid pSBC2-2, complete sequence) position: , mismatch: 4, identity: 0.84

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctaaagcgccaactccgcc	Protospacer
.********************.* .

14. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049157 (Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence) position: , mismatch: 4, identity: 0.84

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctgaagcgccaactcaggc	Protospacer
.*******.************ **.

15. spacer 3.1|1345750|25|NC_008390|CRISPRCasFinder matches to NZ_CP049317 (Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence) position: , mismatch: 4, identity: 0.84

caagcgctaaagcgccaactctggt	CRISPR spacer
taagcgctgaagcgccaactcaggc	Protospacer
.*******.************ **.

16. spacer 5.1|3231831|26|NC_008390|CRISPRCasFinder matches to NZ_CP017563 (Paraburkholderia sprentiae WSM5005 plasmid pl1WSM5005, complete sequence) position: , mismatch: 4, identity: 0.846

agagttagtgcttcagcacttacccg	CRISPR spacer
ggagttagcgcttcagcacttactct	Protospacer
.*******.**************.*

17. spacer 5.1|3231831|26|NC_008390|CRISPRCasFinder matches to NZ_CP014688 (Acetobacter persici strain TMW2.1084 plasmid pAC1084_1, complete sequence) position: , mismatch: 4, identity: 0.846

agagttagtgcttcagcacttacccg	CRISPR spacer
agagttagttcttcagcgcttacatg	Protospacer
********* *******.***** .*

18. spacer 5.1|3231831|26|NC_008390|CRISPRCasFinder matches to NZ_CP049317 (Caballeronia sp. SBC2 plasmid pSBC2-1, complete sequence) position: , mismatch: 7, identity: 0.731

agagttagtgcttcagcacttacccg	CRISPR spacer
gccgttagtgcttcagcacttatgga	Protospacer
.  *******************.  .

19. spacer 5.1|3231831|26|NC_008390|CRISPRCasFinder matches to NZ_CP049157 (Caballeronia sp. SBC1 plasmid pSBC1_1, complete sequence) position: , mismatch: 7, identity: 0.731

agagttagtgcttcagcacttacccg	CRISPR spacer
gccgttagtgcttcagcacttatgga	Protospacer
.  *******************.  .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

726163 : 735248

Hokovirus(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_011656038.1\|726163_728116_+	molecular chaperone DnaK	A0A1V0SH73	Hokovirus	2.7e-148	49.4
WP_011656039.1\|728369_729506_+	molecular chaperone DnaJ	A0A1V0SBY2	Catovirus	2.2e-22	26.9
WP_011656040.1\|729510_731430_+	aminodeoxychorismate synthase component I	S4VT78	Pandoravirus	3.1e-56	36.6
WP_011656041.1\|731581_732397_-	3-methyl-2-oxobutanoate hydroxymethyltransferase	A0A0N7HVJ8	Ostreococcus_lucimarinus_virus	3.9e-37	33.3
WP_011656042.1\|732439_733126_-	deoxynucleoside kinase	A0A0M3UL55	Enterococcus_phage	9.4e-08	29.5
WP_011656043.1\|733122_733665_-	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	NA	NA	NA	NA
WP_041491091.1\|733700_735248_-	polynucleotide adenylyltransferase PcnB	H7BUW3	unidentified_phage	5.2e-22	30.3

DBSCAN-SWA_2

833079 : 843509

Enterobacteria_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_011656130.1\|833079_834141_+	dTDP-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	1.9e-87	47.6
WP_011656131.1\|834152_835046_+	glucose-1-phosphate thymidylyltransferase RfbA	I7I009	Enterobacteria_phage	3.7e-97	59.2
WP_011656132.1\|835030_835582_+	dTDP-4-dehydrorhamnose 3,5-epimerase	I7HJC4	Enterobacteria_phage	6.1e-50	53.6
WP_082089582.1\|835500_836475_+	dTDP-4-dehydrorhamnose reductase	A0A291LA50	Escherichia_phage	4.3e-22	32.7
WP_011656134.1\|836692_838138_+	mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase	A0A1V0SH58	Hokovirus	2.9e-51	27.8
WP_011656135.1\|838207_838456_+	hypothetical protein	NA	NA	NA	NA
WP_011656136.1\|838455_839784_+	methyltransferase domain-containing protein	NA	NA	NA	NA
WP_011656137.1\|839783_843509_+	glycosyltransferase	Q684B1	Sulfolobus_virus	1.6e-05	39.5

DBSCAN-SWA_3

2024036 : 2105205

uncultured_Caudovirales_phage(26.19%)

integrase,holin,capsid,plate,portal,head,protease,tail,terminase

attL 2023829:2023878|attR 2070243:2070292

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
2023829:2023878	attL	NA	NA	NA	NA
WP_011657092.1\|2024036_2025281_+\|integrase	tyrosine-type recombinase/integrase	Q7M297	Enterobacteria_phage	2.0e-72	40.0
WP_011657093.1\|2025494_2027015_+	hypothetical protein	NA	NA	NA	NA
WP_011657094.1\|2027011_2028304_+	hypothetical protein	NA	NA	NA	NA
WP_127456332.1\|2028300_2029467_+	adenine methyltransferase	NA	NA	NA	NA
WP_011657096.1\|2029610_2030315_-	DUF159 family protein	A0A1S5NTJ1	Burkholderia_phage	2.4e-107	75.1
WP_011657097.1\|2030368_2030860_+	hypothetical protein	C7BGE3	Burkholderia_phage	1.3e-67	72.8
WP_011657098.1\|2031058_2031466_+	PAAR domain-containing protein	A4JX23	Burkholderia_virus	6.8e-14	46.2
WP_011657099.1\|2031470_2031974_+	DUF4123 domain-containing protein	A4PE24	Ralstonia_virus	5.4e-21	41.7
WP_041491364.1\|2032321_2032909_+	hypothetical protein	NA	NA	NA	NA
WP_011657102.1\|2032914_2033649_+	hypothetical protein	A4PE26	Ralstonia_virus	4.1e-33	40.1
WP_011657103.1\|2033688_2034477_-	DNA adenine methylase	Q8W6S4	Burkholderia_virus	4.7e-144	90.5
WP_082089628.1\|2034646_2035141_-	DUF2514 family protein	C7BGD9	Burkholderia_phage	4.1e-21	40.4
WP_041491193.1\|2035137_2035632_-	glycoside hydrolase family 104 protein	Q6J1Q5	Burkholderia_virus	1.7e-75	87.2
WP_011657106.1\|2035634_2035919_-\|holin	holin	C7BGD7	Burkholderia_phage	2.3e-40	94.7
WP_011657107.1\|2035997_2037047_-	phage late control protein	A0A2H4JBF6	uncultured_Caudovirales_phage	6.1e-83	47.3
WP_011657108.1\|2037056_2037263_-\|tail	phage tail protein	A0A2H4J9Z9	uncultured_Caudovirales_phage	1.2e-14	58.2
WP_011657109.1\|2037237_2038116_-\|tail	phage tail protein	A0A2H4J875	uncultured_Caudovirales_phage	3.6e-36	37.5
WP_011657110.1\|2038127_2040572_-\|tail	tail length determination protein	A0A2H4JG00	uncultured_Caudovirales_phage	2.1e-57	34.1
WP_011657111.1\|2040652_2040955_-\|tail	phage tail assembly protein	K4I007	Acidithiobacillus_phage	3.3e-05	40.0
WP_011657112.1\|2041052_2041556_-\|tail	phage major tail tube protein	Q7M2A5	Pseudomonas_phage	1.7e-43	54.3
WP_011657113.1\|2041566_2042736_-\|tail	phage tail sheath family protein	A0A2H4J869	uncultured_Caudovirales_phage	1.6e-156	71.6
WP_011657114.1\|2042815_2043577_-\|tail	tail assembly chaperone	E5E3Q6	Burkholderia_phage	4.2e-57	55.2
WP_011657115.1\|2043590_2045798_-\|tail	tail fiber protein	A4JWY0	Burkholderia_virus	9.3e-65	36.1
WP_011657116.1\|2045785_2046364_-\|tail	phage tail protein I	Q6QI98	Burkholderia_phage	3.0e-31	44.7
WP_011657117.1\|2046353_2047250_-\|plate	baseplate J protein	S4TNY7	Salmonella_phage	3.9e-46	40.4
WP_041491366.1\|2047246_2047564_-\|plate	phage baseplate protein	A0A2H4JA09	uncultured_Caudovirales_phage	1.5e-21	48.5
WP_011657119.1\|2047581_2047782_-	hypothetical protein	NA	NA	NA	NA
WP_127456331.1\|2047872_2048709_+	hypothetical protein	NA	NA	NA	NA
WP_011657121.1\|2048692_2049373_-\|plate	phage baseplate assembly protein V	A0A1B2LRU5	Wolbachia_phage	1.3e-17	29.8
WP_011657122.1\|2049376_2049901_-	hypothetical protein	A0A1B2LRU9	Wolbachia_phage	1.1e-24	38.8
WP_011657123.1\|2049890_2050421_-\|tail	phage tail protein	A0A2H4JBV1	uncultured_Caudovirales_phage	2.4e-11	29.9
WP_011657124.1\|2050423_2050714_-	hypothetical protein	NA	NA	NA	NA
WP_011657125.1\|2050715_2051711_-\|capsid	major capsid protein	A0A2H4J890	uncultured_Caudovirales_phage	1.7e-114	60.0
WP_011657126.1\|2051795_2052140_-\|head	head decoration protein	NA	NA	NA	NA
WP_011657127.1\|2052170_2053256_-\|protease	Clp protease ClpP	A0A2H4JDI2	uncultured_Caudovirales_phage	5.4e-50	39.2
WP_011657128.1\|2053257_2054745_-\|portal	phage portal protein	A0A2H4JFL5	uncultured_Caudovirales_phage	2.0e-135	51.9
WP_011657129.1\|2054741_2054948_-	hypothetical protein	NA	NA	NA	NA
WP_041491195.1\|2054957_2057072_-\|terminase	phage terminase large subunit family protein	A0A2D1GMT1	Marinobacter_phage	4.6e-178	53.1
WP_041491196.1\|2057570_2057765_-	hypothetical protein	NA	NA	NA	NA
WP_041491197.1\|2058081_2058336_+	hypothetical protein	NA	NA	NA	NA
WP_041491198.1\|2058580_2059354_-	hypothetical protein	NA	NA	NA	NA
WP_011657133.1\|2059576_2062084_-	virulence protein E	A0A2D1GN57	Marinobacter_phage	1.2e-95	40.4
WP_166488179.1\|2062159_2062333_-	hypothetical protein	NA	NA	NA	NA
WP_011657134.1\|2062345_2062729_-	hypothetical protein	NA	NA	NA	NA
WP_085963129.1\|2062715_2063258_-	hypothetical protein	C7BGG0	Burkholderia_phage	1.1e-30	48.8
WP_011657136.1\|2063646_2064078_+	transcriptional regulator	A0A0P0J076	Acinetobacter_phage	4.5e-16	64.4
WP_041491200.1\|2064534_2064753_+	hypothetical protein	NA	NA	NA	NA
WP_011657137.1\|2064802_2065165_+	hypothetical protein	NA	NA	NA	NA
WP_011657138.1\|2065164_2066763_+	hypothetical protein	NA	NA	NA	NA
WP_082089626.1\|2067189_2067393_+	AlpA family phage regulatory protein	A0A2H4J8C8	uncultured_Caudovirales_phage	2.9e-05	38.9
WP_127456330.1\|2067785_2068346_-	hypothetical protein	NA	NA	NA	NA
WP_011657139.1\|2068348_2069863_-	hypothetical protein	NA	NA	NA	NA
WP_011657141.1\|2070855_2071785_+	hypothetical protein	NA	NA	NA	NA
2070243:2070292	attR	NA	NA	NA	NA
WP_011657142.1\|2072229_2072760_-	isochorismatase family protein	NA	NA	NA	NA
WP_011657143.1\|2073522_2075664_+	hypothetical protein	NA	NA	NA	NA
WP_011657144.1\|2075809_2077210_-	GGDEF domain-containing protein	A0A127AWB9	Bacillus_phage	4.9e-19	32.0
WP_011657145.1\|2077507_2078686_-	acetyl-CoA C-acyltransferase	NA	NA	NA	NA
WP_011657146.1\|2078735_2079368_-	bifunctional nicotinamidase/pyrazinamidase	A0A2K9L2K0	Tupanvirus	1.8e-21	37.1
WP_011657147.1\|2079413_2081498_-	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA
WP_011657148.1\|2081680_2083324_-	fatty-acid--CoA ligase	A0A2H4PQU7	Staphylococcus_phage	1.2e-21	24.5
WP_011657149.1\|2083487_2085056_+	YdiU family protein	A0A075BSJ0	Microcystis_phage	1.6e-55	31.7
WP_011657150.1\|2085094_2085526_+	peptide-methionine (R)-S-oxide reductase MsrB	NA	NA	NA	NA
WP_006753406.1\|2085650_2086181_+	septation protein A	NA	NA	NA	NA
WP_011657151.1\|2086182_2086491_+	BolA family transcriptional regulator	NA	NA	NA	NA
WP_011657152.1\|2086509_2087292_+	peptidyl-prolyl cis-trans isomerase	NA	NA	NA	NA
WP_011657153.1\|2087525_2088068_-	N-acetyltransferase	A9YX37	Burkholderia_phage	1.2e-05	70.0
WP_011657154.1\|2088067_2092132_-	phosphoribosylformylglycinamidine synthase	A9YX36	Burkholderia_phage	1.3e-221	91.6
WP_011657155.1\|2092483_2093788_+	FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_011657156.1\|2093841_2095386_+	NAD(P)H-hydrate dehydratase	NA	NA	NA	NA
WP_012364074.1\|2095497_2097120_+	glucose-6-phosphate isomerase	NA	NA	NA	NA
WP_011657158.1\|2097195_2097897_-	ATP-binding cassette domain-containing protein	G9BWD6	Planktothrix_phage	5.1e-33	37.9
WP_011657159.1\|2097895_2098573_+	arylesterase	NA	NA	NA	NA
WP_011657160.1\|2098663_2100598_-	peptidyl-prolyl cis-trans isomerase	NA	NA	NA	NA
WP_011657161.1\|2101312_2103736_-	endopeptidase La	A0A0R6PGP8	Moraxella_phage	1.7e-224	53.2
WP_006754177.1\|2103933_2105205_-\|protease	ATP-dependent Clp protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	2.1e-133	58.5

DBSCAN-SWA_4

2662039 : 2671168

Burkholderia_phage(28.57%)

integrase

attL 2669770:2669785|attR 2677824:2677839

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_127456315.1\|2662039_2663221_+	hypothetical protein	Q6J1Q8	Burkholderia_virus	3.5e-26	50.6
WP_011657591.1\|2663266_2664343_+\|integrase	site-specific integrase	NA	NA	NA	NA
WP_011657592.1\|2664751_2665318_+	hypothetical protein	A0A2H4JCL4	uncultured_Caudovirales_phage	7.8e-08	29.5
WP_011657593.1\|2665554_2665815_+	hypothetical protein	I6NSR8	Burkholderia_phage	1.0e-23	63.9
WP_011657594.1\|2665973_2666234_+	hypothetical protein	I6NSR8	Burkholderia_phage	4.3e-22	59.0
WP_158380531.1\|2666508_2667381_+	STAS domain-containing protein	NA	NA	NA	NA
WP_081085431.1\|2667374_2667665_+	STAS-like domain-containing protein	J7KJ12	Streptococcus_phage	3.2e-10	43.9
WP_082089617.1\|2667727_2668006_-	hypothetical protein	D2IZW1	Enterococcus_phage	1.6e-06	36.4
WP_011657596.1\|2668313_2668868_+	hypothetical protein	NA	NA	NA	NA
WP_011657597.1\|2669121_2669646_+	hypothetical protein	NA	NA	NA	NA
2669770:2669785	attL	NA	NA	NA	NA
WP_011657598.1\|2669953_2671168_+\|integrase	integrase arm-type DNA-binding domain-containing protein	Q7M297	Enterobacteria_phage	5.2e-86	41.1
WP_011657598.1\|2669953_2671168_+\|integrase	integrase arm-type DNA-binding domain-containing protein	Q7M297	Enterobacteria_phage	5.2e-86	41.1
2677824:2677839	attR	NA	NA	NA	NA

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_008391

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_008390

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection