CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_012973	Helicobacter pylori B38, complete genome	4 crisprs	cas14k,DEDDh	0	2	1	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_012973_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_012973_1

718973-719067

Orphan

Consensus_repeat	Method
AAACCGAGACTAAAAACGACAAAAAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_012973_1

>merge|NC_012973|1|718973-719067|CRISPRCasFinder
AAACCGAGACTAAAAACGACAAAAAGAGCGGTAAAAAGTTTTACAAACTCCATAAAAACCATGGATTAAAAACCGAGGCTAAAAACGACAAAAAG

>NC_012973|1|1|718973-719067|CRISPRCasFinder
AAACCGAGACTAAAAACGACAAAAAG	AGCGGTAAAAAGTTTTACAAACTCCATAAAAACCATGGATTAA
AAACCGAGGCTAAAAACGACAAAAAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_012973.1\|WP_000142306.1\|731535_732663_+\|succinyldiaminopimelate-transaminase	unknown	unknown	gnl\|CDD\|180281
NC_012973.1\|WP_000499057.1\|723826_724981_-\|hydrogenase-1-small-subunit	unknown	unknown	gnl\|CDD\|273053
NC_012973.1\|WP_015828987.1\|714157_715015_-\|NAD(P)-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|224995
NC_012973.1\|WP_000981155.1\|729128_730334_-\|tetrahydrodipicolinate-N-succinyltransferase-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|225082
NC_012973.1\|WP_000943216.1\|712018_713338_-\|glutamate--tRNA-ligase	unknown	unknown	gnl\|CDD\|237094
NC_012973.1\|WP_000529532.1\|716453_717140_+\|7-cyano-7-deazaguanine-synthase-QueC	unknown	unknown	gnl\|CDD\|129461
NC_012973.1\|WP_000756719.1\|725143_725728_+\|NAD(P)H-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|225158
NC_012973.1\|WP_000373504.1\|713502_714156_-\|NAD(P)H-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|380324
NC_012973.1\|WP_000078608.1\|720860_721397_-\|hydrogenase-biosynthesis-protein-HydD	unknown	unknown	gnl\|CDD\|99873
NC_012973.1\|WP_041200516.1\|717208_718162_-\|outer-inflammatory-protein-OipA	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_000577965.1\|711728_712022_-\|YggT-family-protein	unknown	unknown	gnl\|CDD\|223833
NC_012973.1\|WP_001210382.1\|710037_711720_-\|lytic-transglycosylase-domain-containing-protein	unknown	unknown	gnl\|CDD\|381604
NC_012973.1\|WP_000038104.1\|722080_723817_-\|nickel-dependent-hydrogenase-large-subunit	unknown	unknown	gnl\|CDD\|366057
NC_012973.1\|WP_000892473.1\|730336_731416_-\|flavodoxin-dependent-(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate-synthase	unknown	unknown	gnl\|CDD\|234737
NC_012973.1\|WP_000917815.1\|728058_729117_-\|sel1-repeat-family-protein	unknown	unknown	gnl\|CDD\|223861
NC_012973.1\|WP_000896193.1\|719320_720859_-\|hydrogenase-biosynthesis-protein-HydE	unknown	unknown	unknown
NC_012973.1\|WP_000554072.1\|718313_718766_+\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_000359935.1\|721393_722068_-\|Ni/Fe-hydrogenase,-b-type-cytochrome-subunit	unknown	unknown	gnl\|CDD\|224880
NC_012973.1\|WP_000591486.1\|709219_710041_-\|UTP--glucose-1-phosphate-uridylyltransferase-GalU	unknown	unknown	gnl\|CDD\|224131
NC_012973.1\|WP_000527531.1\|708800_709208_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|236724

Protein	Function_ID	Function_description	E-value
NC_012973.1\|WP_000142306.1\|731535_732663_+\|succinyldiaminopimelate-transaminase	gnl\|CDD\|180281	PRK05839, PRK05839, succinyldiaminopimelate transaminase.	0
NC_012973.1\|WP_000499057.1\|723826_724981_-\|hydrogenase-1-small-subunit	gnl\|CDD\|273053	TIGR00391, small_subunit, hydrogenase (NiFe) small subunit (hydA). Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea. [Energy metabolism, Electron transport].	0
NC_012973.1\|WP_015828987.1\|714157_715015_-\|NAD(P)-dependent-oxidoreductase	gnl\|CDD\|224995	COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism].	1.66645e-90
NC_012973.1\|WP_000981155.1\|729128_730334_-\|tetrahydrodipicolinate-N-succinyltransferase-N-terminal-domain-containing-protein	gnl\|CDD\|225082	COG2171, DapD, Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism].	8.51296e-91
NC_012973.1\|WP_000943216.1\|712018_713338_-\|glutamate--tRNA-ligase	gnl\|CDD\|237094	PRK12410, PRK12410, glutamylglutaminyl-tRNA synthetase; Provisional.	0
NC_012973.1\|WP_000529532.1\|716453_717140_+\|7-cyano-7-deazaguanine-synthase-QueC	gnl\|CDD\|129461	TIGR00364, 7-cyano-7-deazaguanine_synthase, queuosine biosynthesis protein QueC. Members of this protein family are QueC, involved in synthesizing pre-Q0 from GTP en route to tRNA modification with queuosine. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, the gene was designated exsB, possibly because of polar effects on exsA expression in a shared polycistronic mRNA. In Arthrobacter viscosus, the homologous gene was designated ALU1 and was associated with an aluminum tolerance phenotype. [Unknown function, General].	2.02117e-110
NC_012973.1\|WP_000756719.1\|725143_725728_+\|NAD(P)H-dependent-oxidoreductase	gnl\|CDD\|225158	COG2249, MdaB, Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only].	3.05288e-53
NC_012973.1\|WP_000373504.1\|713502_714156_-\|NAD(P)H-dependent-oxidoreductase	gnl\|CDD\|380324	cd02149, NfsB-like, nitroreductase similar to Escherichia coli NfsB. NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs.	1.17223e-71
NC_012973.1\|WP_000078608.1\|720860_721397_-\|hydrogenase-biosynthesis-protein-HydD	gnl\|CDD\|99873	cd06062, H2MP_MemB-H2up, Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.	6.44098e-58
NC_012973.1\|WP_041200516.1\|717208_718162_-\|outer-inflammatory-protein-OipA	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	3.00001e-35
NC_012973.1\|WP_000577965.1\|711728_712022_-\|YggT-family-protein	gnl\|CDD\|223833	COG0762, COG0762, Predicted integral membrane protein [Function unknown].	8.06765e-07
NC_012973.1\|WP_001210382.1\|710037_711720_-\|lytic-transglycosylase-domain-containing-protein	gnl\|CDD\|381604	cd13401, Slt70-like, 70kDa soluble lytic transglycosylase (Slt70) and similar proteins. Catalytic domain of the 70kda soluble lytic transglycosylase (LT)-like proteins, which also have an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze 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. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.	3.34167e-51
NC_012973.1\|WP_000038104.1\|722080_723817_-\|nickel-dependent-hydrogenase-large-subunit	gnl\|CDD\|366057	pfam00374, NiFeSe_Hases, Nickel-dependent hydrogenase.	0
NC_012973.1\|WP_000892473.1\|730336_731416_-\|flavodoxin-dependent-(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate-synthase	gnl\|CDD\|234737	PRK00366, ispG, flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase.	0
NC_012973.1\|WP_000917815.1\|728058_729117_-\|sel1-repeat-family-protein	gnl\|CDD\|223861	COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function prediction only].	3.07629e-46
NC_012973.1\|WP_000591486.1\|709219_710041_-\|UTP--glucose-1-phosphate-uridylyltransferase-GalU	gnl\|CDD\|224131	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane].	3.81301e-162
NC_012973.1\|WP_000527531.1\|708800_709208_-\|hypothetical-protein	gnl\|CDD\|236724	PRK10604, PRK10604, sensor protein RstB; Provisional.	0.00338762
NC_012973.1\|WP_000359935.1\|721393_722068_-\|Ni/Fe-hydrogenase,-b-type-cytochrome-subunit	gnl\|CDD\|224880	COG1969, HyaC, Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion].	1.90647e-94

>NC_012973.1|WP_000554072.1|718313_718766_+|hypothetical-protein
MHQNNKTFLPNQSAHLSKIILFLNTGFLAYLLSACGANVPIEEVLVKDPKETKAQEVAREEKAIQQENATIDARTTPLINRFTNYNAYGSLNGFYNSVDNLNSPMQNGMYGGYYMPYYYMPYGFMPYGSGLMPYGPYGYGAPGYFPYVFY
>NC_012973.1|WP_041200516.1|717208_718162_-|outer-inflammatory-protein-OipA
MSNLKPKKNHEKSSLTNSLSLSFWLHAERNGFYLGLNFAEGSYIKGQGSIGKKASAENALNEAINNAKNSLFPEQNTKAIRNAQNALNEVKDSNKIANRFAGNGGSGGLFNELSLGYKYFLGKKRIIGFRHSLFFGYQLGGVGSVPGSGLIVFLPYGFNTDLLINWTNDKRASQKYVERRVKGLSIFYKDMTGRTLDANTLKKASRHVFRKSSGLVIGMELGGSTWFASNNLTPFNQVKSRTIFQLQGKFGVRWNNDEYDIDRYGDEIYLGGSSVELGVKVPAFKVNYYSDNYGDKLDYKRVVSVYLNYTYTFRRKH
>NC_012973.1|WP_000529532.1|716453_717140_+|7-cyano-7-deazaguanine-synthase-QueC
MGQEICVIGFSGGQDSTTLAVWAKKRFKKVCLVGFDYAQKHSVELECAQKIASLLQLPYEIISLDFLENITRSALFKNSNDLIGHSHAQNKDLPNSFVPNRNAIFITLLHSYAQKLGASNIALGVSQADFSGYPDCKEDFIKSIEHALNLGSNTAIKIVTPLMFLSKAQEFQMAKDLGVLDLVIKETHTCYQGERKILHAYGYGCDKCPACQLRKKGFEEFQAKALFQ
>NC_012973.1|WP_015828987.1|714157_715015_-|NAD(P)-dependent-oxidoreductase
MKIGWIGLGAMGTPMATRLCDAGLKVSVYNRTESKAAPLKEKGVAVYTNPIDLAAKVDLIFIMLSDKTAIDAVLVPEFWEQMSKKIVVNMSTIAPLESLDLEKTAQKHQATYLEAPVSGSVGAAKAGALLILAAGEKEVVAQLKPVLVHLGSQTFYLGKIGQGAGAKLSINSLLAQMGVAYSEALLLAKHLGVDAELFLQIIGQSGMNSPLFQAKKGMWLQDSYPVAFSLKLMLKDIRLAKNEAGEAIQLPFLSKVQELYSQAEKSGLGALDMAAVYHYLKKGEH
>NC_012973.1|WP_000373504.1|713502_714156_-|NAD(P)H-dependent-oxidoreductase
MDREQVIALQHQRFAAKKYDPNRRISQKDWEALVEVGRLAPSSIGLEPWKMLLLKNERMKEDLKPMAWGALFGLEGASHFVIYLARKGVTYDSDYVKKVIHEVKKRDYDTNSRFAQIIKNFQENDMKLNSERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLEEKGYLNTAEFGVSVMACFGYRNQEITPKTRWKTEVIYEVIE
>NC_012973.1|WP_000943216.1|712018_713338_-|glutamate--tRNA-ligase
MLRFAPSPTGDMHIGNLRAAIFNYIVAKQQHKPFLIRIEDTDKERNIEGKDQEILEILKLMGISWDKLVYQSHNIDYHREMAEKLLKENKAFYCYASAEFLEREKEKAKNEKRPFRYLDEWAALEKDKNHAPVVRLKAPNHAVSFNDAIKKEVKFEPYELDSFVLLRKDKSPTYNFACACDDLLYEISLIIRGEDHVSNTPKQILIQEALGSNDPIVYAHLPIILDEVSGKKMSKRDEASSVKWLLNQGFLPVAIVNYLITIGNKVPKEVFSLDEAIEWFSLENLSSSPAHFNLKYLKHLNHEHLKLLDDEKLLELTSIKDKNLLGLLRLFIEECGTLLELKEKISLFLEPKDIVKTYENEDFKERCLALFNALKSMDFQAYKDFESFKKEAMRSSQLKGKDFFKPLRILLTGNSHGIELPLIFPYIQSHHQEVLRLKA
>NC_012973.1|WP_000577965.1|711728_712022_-|YggT-family-protein
MIFSTLLNAIAVILSSLITIYMWIVIIYSLISFVQPNPSNPIMQILARLCEPVFYFLRSRFKLVFNGLDFAPLVVVIVLKFLDLTLIQWLFALAKNL
>NC_012973.1|WP_001210382.1|710037_711720_-|lytic-transglycosylase-domain-containing-protein
MRFFILFFMGALGVSFSQTEFNLKDLEKKPAGIVRDYYLWRYISDKKTTLENAKKAYELTQNKNNALQKAMQEKGSDNAEKNPDVKLPEDIYCKQTALESMLEETDTFQASCIAIALKSKIRDFDKIPLQTLKPLQIKIKEAYPVLYEELEILQSKHVSASLFKANAQVFSALFNHLSYEKKLQIFEKHIPIKELNRLLDEDYPAFNRLIYQVILDPKLDHFKDALTKTNATHSNAQTFFILGINEILRKKPSKALKYFERSEAVVKDDDFSKDRAIFWQYLVSKKKKTLERLSQSPALNLYSLYASRKLQTTPSYRIISHIQNLSQEDPPFNTHDPFSWQIFKEKTLSLKDEGAFNAMLKSLYYEKSTPELTYLLSQRNKDKIYYYLSPYEGIIEWQNIDEKAMAYAIARQESFLLPAVISRSFALGLMQIMPFNVGPFAKRLGMDNIDLNDMFNPNIALKFGNYYLNHLKKEFNHPLFVAYAYNAGPGFLRRWLESSKRFKEKNHFEPWLSMELMPYSETRLYGFRVMLNYLIYQEIFGNFIPIDAFLEQTLNSKDKP
>NC_012973.1|WP_000591486.1|709219_710041_-|UTP--glucose-1-phosphate-uridylyltransferase-GalU
MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPSQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKRL
>NC_012973.1|WP_000527531.1|708800_709208_-|hypothetical-protein
MGNLTYYAYMYLILFVCLLPVLLVGLAWRFFRPPLKQDIPNKSLSLENLNEQIKNLKSAPALEKLKSNFNERFKICPKDKETLWLETIQNLVASEFFELEDAINFGQELENANPSHAQKIANATGLALKNKKEKG
>NC_012973.1|WP_000896193.1|719320_720859_-|hydrogenase-biosynthesis-protein-HydE
MAFVFLFKCVNEKTSLNFTPLLEQMVLHLQARFYSVYKDNTTSFYLQASAEITLEFAQKLSEILPFSLDFSFLSLKEITEPLDENLFQTTSLSKPLFMNAKEHQDFLDKNASLYADALGFVKNTAFKGNIIHSPKELIDCLTQLKGMLKTQDFIPIFTSRGALSLSLKNPSPSVIFSDLSSVLSCTKLPLEDAKYLASLEKPSIKASLKSVFKDTFKNDEIIAQLPYDPILNLLCHILQDEGIEFVFMHESRSCEALLHYEALFKTPKRLITPTKKFVLENNLSTLPFKDELEFLSTTPNSIVLYFSFKHPTRLLLHANGSLKTLLSVSFDFNQIFNLLKQDEKASRMLQNYATKFPDFYARIVELSKYNLGGANLLDFFRILGFVLGYSEDFCTQSVISLARECLRPKGPRIDYKILKDDSLKMALNFSKIMHSAMSFRLAGVENEILSLGILDSLAEFLGNFIWDNAQNFSVQEVTIAGDFFGEKVFLDLFVQYFPKTLALKTHAFLDYE
>NC_012973.1|WP_000078608.1|720860_721397_-|hydrogenase-biosynthesis-protein-HydD
MSQKILILGIGNILFGDEGIGVHLAHYLKKNFSFFPSVDIVDGGTMAQQLIPLITSYEKVLILDCVSAKGVEIGSVYAFDFKDAPKEITWAGSAHEVEMLHTLRLTEFLGDLPKTFIVGLVPFVIGNKTTFKLSSKILNALETALKAIETQLNAWGVKMQRTDHIALECIAELSYKGF
>NC_012973.1|WP_000359935.1|721393_722068_-|Ni/Fe-hydrogenase,-b-type-cytochrome-subunit
MDKMNKVVLHKEYSGFVRFFHWVRALSIFTLIATGFYIAYPFLQPNSSFYKGVYLLQAYVRSFHVMFGFLLISALIFRTYLFFTKESLMERRSFGQLLSPKAWIDQMKAYFLISGKPHTKGAYNPIQLVAYSTLIVLIVLMSLSGIVLYYNVYHAGLGAFLGSTFKWFEALCGGLANVRFIHHLATWGFILFVPVHVYMVFFHSIRYDSSGADSMINGYGYTKE
>NC_012973.1|WP_000038104.1|722080_723817_-|nickel-dependent-hydrogenase-large-subunit
MSKKIVVDPITRIEGHLRIEVIVDDDNVITDAFSSSTLFRGLETIIKGRDPRDAGFIAQRICGVCTYSHYKAGITAVENALGITPPLNAQLVRSLMNMALLFHDHVVHFYTLHGLDWCDIMSALKADPVQAAKLSFKYSPYPINTGAGELKAVQKRLNDFAKSGSLGPFSNGYYGHKTYRLSPEQNLIVLSHYLKLLEIQREAAKMTAIFGAKQPHPQSLTVGGVTSVMDILDPTRLAEWKSKFEVVANFINHAYYPDLVMAGEMFANEQSVIKGCGLRNFIAYEEVLLGKDKYLLSSGVVLDGDISKLHPIDESLIKEEVTHSWYQYEDTKEVQLHPYDGQTNPHYTGLKDGESVGIENKIIPAKVLDTKNKYSWIKSPRYDSKPMEVGPLSSVVVGLAAKNPYVTEVATKFLKDTKLPLEALFSTLGRTAARCIEAKTIADNGLLAFDALVENLKSDQSTCAPYHIDKNQEYKGRYIGQVPRGMLSHWVRIKNGVVENYQAVVPSTWNAGPRDSQNQRGAYEMSLIGTKIADLTQPLEIIRTIHSFDPCIACSVHVMDFKGQSLNEFKVEPNFAKF
>NC_012973.1|WP_000499057.1|723826_724981_-|hydrogenase-1-small-subunit
MFYDEKKTYQKIEERLEIVSSFNAHNEHKNLQDEFKGAGISRRDLLKWAGMMSATLALPASFAPLTLKAVEVANRLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAIEKHKNNYILMVEGGIPQGTEYFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGVQAAYPNPSNAQPLHKIIDKPVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWAYGNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSWPIGAGHGCIGCSEPNFWDTMSPFEEPLANRSIKTAFDGLGADKVADKVGTTLLSATAIGIVAHALLSKAIKNKE
>NC_012973.1|WP_000756719.1|725143_725728_+|NAD(P)H-dependent-oxidoreductase
MKKVLIINGAKAFGSSGGKLNETLTHHAKKTLESLGLEVDTTIVDKGYEHAQEVEKVFSADATIWQMPGWWMGEPWIVKKYIDEVFSVGHGKLYASDGRSSQNPTRNYGKGGLMQGKKYMLSLTWNAPIEAFNDPSEFFEGVGVDVVYLHLHKAFQFLGLSALPTFICNDVVKNPQVEQYLNSLTTHLRQAFGK
>NC_012973.1|WP_000917815.1|728058_729117_-|sel1-repeat-family-protein
MLKQSLLLLVFLILQLSGAEENNQAPKNTPPELNPANAKGAPNPNTQITPKNDNSNLLDKLGSPENAQTELSAGIDLAKKGDYQGAFKLFSQSCDNGNAAGCFAVGAMYANGVGIQTNRLKAARYYEMGCSGGDATACANLAQMYENKKNADSNDKENALQLYAVACQGGDMFACNNLGWMFANGSGVPKDYYKAISYYKFSCENGNDMGCYNLGLMSNVNNIYGIDKAQLSQVDLNYLACNAGDMMGCANLGWIYANGDLGAPLNNHYAAKYFQMACDGGILGSCNNLGVLYQKGLGVPQDDQRALDLFSYACDNGFESSCRNYGNFKEHLLRVNPNYGRLFMPYNSYEIP
>NC_012973.1|WP_000981155.1|729128_730334_-|tetrahydrodipicolinate-N-succinyltransferase-N-terminal-domain-containing-protein
MMNKFKNFVSNYQQSDHYREPLGFGIARVDIAPISKKILCATYPVLNWKEENLGSYAVFCNSLSKDKILKESASERVVEIDESFVLKALDFYTPFLNEAYSNKMAHKNIQVVLELLKALEENRLKNNNGESLYRLVILYEDKPCESVESAYMKLLALSLGKAPLRSLNLEGIFNQLSNAAWSGNKPYELEWLRTNEVALKMRGHFPSIDFIDKFPRYLMQLIPEFDNIRLLDSSKTRFGAYLGTGGYTQMPGASYVNFNAGAMGVCMNEGRISSSVVVGEGTDIGGGASVLGVLSGGNNNPISIGKNCLLGANSVTGISLGDGCIVDAGVAILAGSVIEIEENEFKKLLEVNSALEKHANNLYKGKELSGKNGVHFRSNSQNGKLIAFRSVKKIELNQNLH
>NC_012973.1|WP_000892473.1|730336_731416_-|flavodoxin-dependent-(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate-synthase
MLENRVKTKQIFIGGVAIGGDAPISTQSMTFSKTADIESTKNQIDRLKLAGADLVRVAVSNEKDALALKELKKVSPLPLIADIHFHYKFALIAAQSVDAIRINPGNIGSKDKIKAVVDACKEKNIPIRIGVNAGSLEKQFDQKYGPTPKGMVESALYNAKLLEDLDFTNFKISLKASDVMRTIEAYRMLRPLVIYPFHLGVTEAGNLFSSSIKSAMALGGLLMEGIGDTMRVSITGELENEIKVARAILRHSGRLKEGINWISCPTCGRIEANLVDMASKVEKRLSHIKTPLDISVMGCVVNALGEAKHADMAIAFGNRSGLIIKEGKVIHKLAEKDLFETFVIEVENLAKEREKSLKD
>NC_012973.1|WP_000142306.1|731535_732663_+|succinyldiaminopimelate-transaminase
MTFEPYPFERLRALFKEITPKKKGLDLGIGEPQFETPKFIQDALKQHAHSLNIYPKSTFEESLRAAQRGFFKRRFKIELKENELISTLGSREVLFNFPSFVLFDYQNPTIAYPNPFYQIYEGAAKFIKAKSLLMPLTKENDFTPSLNEKELQEVDLVILNSPNNPTGRTLSVEELIGWVKLALKHDFILINDECYSEIYENTPPPSLLEACMLVGNEAFKNVLVIHSLSKRSSAPGLRSGFIAGDSSLLEKYKAFRTYLGYTSANAIQKASEIAWLDDTHAEFFRNIYANNLKLARKIFKNTLIYPYSFYVYLPVKKGENFAKMLYQNEGITTLPALYLGRNRIGADCVRLALVYDTPLLENPLEIIETYRENHA

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Crispr_ID: NC_012973_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_012973_2

891090-891209

Orphan

Consensus_repeat	Method
AATATTGAGATTATCCCCCAAGAACGGCTTTAAT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_012973_2

>merge|NC_012973|2|891090-891209|CRISPRCasFinder
AATATTGAGATTATCCCCCAAGAACGGCTTTAATAATAAAGGTGATCAAACGCTAAAGATATTTAGGATTTCTGTGGTTTAAAAACAATATTGAGATTATCCCCCAAGAACGGCTTTAAT

>NC_012973|2|2|891090-891209|CRISPRCasFinder
AATATTGAGATTATCCCCCAAGAACGGCTTTAAT	AATAAAGGTGATCAAACGCTAAAGATATTTAGGATTTCTGTGGTTTAAAAAC
AATATTGAGATTATCCCCCAAGAACGGCTTTAAT

Protein	Signature genes	Signature genes Name	Protein_function
NC_012973.1\|WP_001126549.1\|896631_899889_-\|carbamoyl-phosphate-synthase-large-subunit	unknown	unknown	gnl\|CDD\|235393
NC_012973.1\|WP_000874625.1\|901904_909479_+\|vacuolating-cytotoxin-domain-containing-protein	unknown	unknown	gnl\|CDD\|227938
NC_012973.1\|WP_001099633.1\|911055_911637_+\|recombination-protein-RecR	unknown	unknown	gnl\|CDD\|273176
NC_012973.1\|WP_000998205.1\|893570_896012_-\|TonB-dependent-receptor	unknown	unknown	gnl\|CDD\|273808
NC_012973.1\|WP_001139988.1\|878918_880457_+\|flagellar-hook-length-control-protein-FliK	unknown	unknown	gnl\|CDD\|376734
NC_012973.1\|WP_001115888.1\|910692_910899_-\|4-oxalocrotonate-tautomerase-family-protein	unknown	unknown	gnl\|CDD\|129125
NC_012973.1\|WP_001240216.1\|899986_900679_-\|Bax-inhibitor-1/YccA-family-protein	unknown	unknown	gnl\|CDD\|198414
NC_012973.1\|WP_001248521.1\|891700_893245_-\|outer-membrane-beta-barrel-protein-HofG	unknown	unknown	gnl\|CDD\|334957
NC_012973.1\|WP_000688668.1\|900825_901824_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|273675
NC_012973.1\|WP_000427105.1\|883884_885036_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|223897
NC_012973.1\|WP_000894533.1\|885039_887067_+\|ATP-dependent-helicase	unknown	unknown	gnl\|CDD\|223288
NC_012973.1\|WP_000963327.1\|880507_881428_+\|flagellar-hook-assembly-protein-FlgD	unknown	unknown	gnl\|CDD\|235621
NC_012973.1\|WP_001161792.1\|876981_878538_-\|phosphate-acetyltransferase	unknown	unknown	gnl\|CDD\|235537
NC_012973.1\|WP_079996176.1\|876062_876965_-\|acetate/propionate-family-kinase	unknown	unknown	gnl\|CDD\|234680
NC_012973.1\|WP_001169510.1\|909530_910625_+\|Hop-family-outer-membrane-protein-HopJ/HopK	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_000592400.1\|887653_889207_+\|Hop-family-adhesin-AlpA	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_015828999.1\|883293_883875_+\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_001230017.1\|896195_896627_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|376519
NC_012973.1\|WP_000812511.1\|889228_890827_+\|Hop-family-adhesin-AlpB	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_001000236.1\|881424_883242_+\|flagellar-hook-protein-FlgE	unknown	unknown	gnl\|CDD\|235620

Protein	Function_ID	Function_description	E-value
NC_012973.1\|WP_001126549.1\|896631_899889_-\|carbamoyl-phosphate-synthase-large-subunit	gnl\|CDD\|235393	PRK05294, carB, carbamoyl-phosphate synthase large subunit.	0
NC_012973.1\|WP_000874625.1\|901904_909479_+\|vacuolating-cytotoxin-domain-containing-protein	gnl\|CDD\|227938	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion].	3.40852e-20
NC_012973.1\|WP_001115888.1\|910692_910899_-\|4-oxalocrotonate-tautomerase-family-protein	gnl\|CDD\|129125	TIGR00013, Probable_tautomerase_K2, 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function. [Energy metabolism, Other].	4.5194e-26
NC_012973.1\|WP_001099633.1\|911055_911637_+\|recombination-protein-RecR	gnl\|CDD\|273176	TIGR00615, Recombination_protein_RecR, recombination protein RecR. All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair].	6.9426e-98
NC_012973.1\|WP_000998205.1\|893570_896012_-\|TonB-dependent-receptor	gnl\|CDD\|273808	TIGR01786, hemoglobin-haptoglobin-binding_protein, TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein. This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model (TIGR01776). Accessions which score above trusted to this model while not scoring above trusted to the more specific models are most likely to be hemoglobin transporters. Nearly all of the species containing trusted hits to this model have access to hemoglobin, transferrin or lactoferrin or related proteins in their biological niche. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins].	8.64531e-46
NC_012973.1\|WP_001230017.1\|896195_896627_-\|hypothetical-protein	gnl\|CDD\|376519	pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.	0.00042225
NC_012973.1\|WP_001248521.1\|891700_893245_-\|outer-membrane-beta-barrel-protein-HofG	gnl\|CDD\|334957	pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).	2.1498e-178
NC_012973.1\|WP_000688668.1\|900825_901824_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	gnl\|CDD\|273675	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I. This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively. Two Pfam models cover the two functional domains of this protein; pfam00044 represents the N-terminal NAD(P)-binding domain and pfam02800 represents the C-terminal catalytic domain. An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine. This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria. This enzyme is described by TIGR001532. These sequences generally score between trusted and noise to this GAPDH model due to the close evolutionary relationship. There exists the possiblity that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to posess a limited E4PD activity as well as a robust GAPDH activity). There are a great number of sequences in the databases which score between trusted and noise to this model, nearly all of them due to fragmentary sequences. It seems that study of this gene has been carried out in many species utilizing PCR probes which exclude the extreme ends of the consenses used to define this model. The noise level is set relative not to E4PD, but the next closest outliers, the class II GAPDH's (found in archaea, TIGR01546) and aspartate semialdehyde dehydrogenase (ASADH, TIGR01296) both of which have highest-scoring hits around -225 to the prior model. [Energy metabolism, Glycolysis/gluconeogenesis].	2.91967e-162
NC_012973.1\|WP_000427105.1\|883884_885036_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|223897	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair].	3.902e-51
NC_012973.1\|WP_000894533.1\|885039_887067_+\|ATP-dependent-helicase	gnl\|CDD\|223288	COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair].	6.44724e-135
NC_012973.1\|WP_000963327.1\|880507_881428_+\|flagellar-hook-assembly-protein-FlgD	gnl\|CDD\|235621	PRK05842, flgD, flagellar hook assembly protein FlgD.	2.40058e-175
NC_012973.1\|WP_001161792.1\|876981_878538_-\|phosphate-acetyltransferase	gnl\|CDD\|235537	PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.	0
NC_012973.1\|WP_079996176.1\|876062_876965_-\|acetate/propionate-family-kinase	gnl\|CDD\|234680	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed.	4.71042e-177
NC_012973.1\|WP_001169510.1\|909530_910625_+\|Hop-family-outer-membrane-protein-HopJ/HopK	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	4.56839e-48
NC_012973.1\|WP_000592400.1\|887653_889207_+\|Hop-family-adhesin-AlpA	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.79597e-54
NC_012973.1\|WP_001240216.1\|899986_900679_-\|Bax-inhibitor-1/YccA-family-protein	gnl\|CDD\|198414	cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor (BI)-1/YccA-like proteins. This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, BI-1 like proteins play a role in pathogen resistance. A characterized prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.	1.17402e-52
NC_012973.1\|WP_001000236.1\|881424_883242_+\|flagellar-hook-protein-FlgE	gnl\|CDD\|235620	PRK05841, flgE, flagellar hook protein FlgE; Validated.	0
NC_012973.1\|WP_000812511.1\|889228_890827_+\|Hop-family-adhesin-AlpB	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.31684e-53
NC_012973.1\|WP_001139988.1\|878918_880457_+\|flagellar-hook-length-control-protein-FliK	gnl\|CDD\|376734	pfam02120, Flg_hook, Flagellar hook-length control protein FliK. This is the C terminal domain of FliK. FliK controls the length of the flagellar hook by directly measuring the hook length as a molecular ruler. This family also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems.	1.39753e-12

>NC_012973.1|WP_000812511.1|889228_890827_+|Hop-family-adhesin-AlpB
MKQNLKPFKMIKENLMTQSQKVRFLAPLSLALSLSFNPVGAEEDGGFMTFGYELGQVVQQVKNPGKIKAEELAGLLNSNTTNNTNINIAGTGGNVAGTLGNLFMNQLGNLIDLYPTLNTSNIHQCGANNTSSSSNAAAAAATSSSSTSPCFQGNLALYNEMVGSIKTLSQNISKNIFQSNNNTTSQNLSNQLSELNTASVYLTYMNSFLNANNQAGGIFQNNTNQAYGNGVTAQQIAYILKQASITMGPSGDSGAAAAFLDAALAQHVFNSANAGNDLSAKEFTSLVQNIVNNSQNALTLANNANISNSTGYQVSYGGNIDQARSTQLLNNTTNTLAKVTALNNELKANPWLGNFAAGNSSQVNAFNGFITKIGYKQFFGENKNVGLRYYGFFSYNGAGVGNGPTYNQVNLLTYGVGTDVLYNVFSRSFGSRSLNAGFFGGIQLAGDTYISTLRNSPQLASRPTATKFQFLFDLGLRMNFGILKKDLKSHNQHSIEIGVQIPTIYNTYYKAGGAEVKYFRPYSVYWVYGYAF
>NC_012973.1|WP_000592400.1|887653_889207_+|Hop-family-adhesin-AlpA
MIKKNRTLFLSLALCASISYAEDDGGFFTVGYQLGQVMQDVQNPGGAKADELARELNADVTNNILNNNTGGNVAGALSNAFSQYLYSLLGAYPTKLNSNDVSANALLSGAVGSGTCAAAGTAGGTSLNTQSACTAAGYYWLPSLTDRILSTIGSQTNYGTNTNFPNMQQQLTYLNAGNVFFNAMNKALEKNGTTTASGTNGATGSDGQTYSQQAIQYLQGQQNILNNAANLLKQDELLLEAFNSAVAANIGNKEFNSAAFTGLVQGIIDQSQAVYNELTKNTISGSAVNNAGINSNQANAVQGRASQLPNALYNAQVTLDKINALNNQVRSMPYLPQFRAGNSRATNILNGFYTKIGYKQFFGKKRNIGLRYYGFFSYNGASVGFRSTQNNVGLYTYGVGTDVLYNIFSRSYQNRSVDMGFFSGIQLAGETFQSTLRDDPNVKLHGKINNTHFQFLFDFGMRMNFGKLDGKSNRHNQHTVEFGVVVPTIYNTYYKSAGTTVKYFRPYSVYWSYGYSF
>NC_012973.1|WP_000894533.1|885039_887067_+|ATP-dependent-helicase
MLETLQLNPEQLKAAKALKGYNLVIASAGTGKTSTIVGRILYLLDNGIKPEEILLLTFTNKASNEMIARVAKYFKSSSKIEAGTFHAVAYRYLKEHYPNLSLKQPKELRKLLESIVDTKNAIDDDKKPYTSQHLYALYSLYTNALKQEDFSAWLSNKNPEHAPYAALYENILEEFENTKKKHNYIDYNDLLLLFKKAMLERPSPYKEVLCDEFQDTNPLQESILDAINPPSLFCVGDYDQSIYAFNGADISIISNFTQKYKNAQVFTLTKNYRSSKEILDLANQVIQRNERIYPKNLEVVKSGKFNKPTLLNYNDNIAQCQDIAKRIVMRKNFKEVAVIFRNNASADQLEAALRSHNVPSKRKGSASFFESKEVALALDICALLFNPKDIMAAIHILSYISDIGSNTAKDIHEALMLLGNGDLKLALTHPSKEAKIYTKKKEITSMGLFEEIFALENSSRFNSVIDKAFHSHPVLMHSKISLNGAKMLSDFFILYTKAPTHSPSALIKHILESAFFQTFKTRLLKERSKNKDGSYNEFKKLQAQKRFNEKMDLLSSLAKNYQNLGRFLNGTLIGSSEATQGCGVNLLSVHASKGLEFKDVYIIDLMEGRFPNHKLMNTGGGIEEERRLFYVAITRAKENLWLSYAKNELRENAKPKEHKPSVFLYEAGLLKPDSK
>NC_012973.1|WP_000427105.1|883884_885036_+|class-I-SAM-dependent-methyltransferase
MENFLNKWDIKTLGQVFTPKNIVDFMLTLKHNQGSVLEPSAGDGSFLKRLKKAVGIEIDPKICPKNALCMDFFDYPLENQFDTIIGNPPYVKHKDIAPSTKEKLHYSLFDERSNLYLFFIEKAIKHLKPQGELIFITPRDFLKSTSSVKLNEWIYKEGTITHFFELGDQKIFPNAMPNCVIFRFCKGDFSRIANDGLQFVCKKGILYFLNQSYTQKLSEVFKVKVGAVSGCDKIFKNEKHGNLEFVTSITKRTNVLEKMVFVNKPNDYLLQHKDSLMQRKIKKFNESNWFEWGRMHHISPKKRIYVNTKTRQKNPFFIHQCPNYDGSILALFPYNQNLDLQNLCDKLNAINWQELGFVCDGRFLFSQRSLENALLPKDFLNLG
>NC_012973.1|WP_015828999.1|883293_883875_+|hypothetical-protein
MIPTQLNEIAEFLRTNPYHLSQPLQDRRLNSSVNEEEILNTIKDYFPIQLPKAREWWDFSFEENKIFYPVNIKTTTTKTADNLNGKLGIYYALCGLLPEFNNEIAWEKYFQKLHKDLGKNTNRDYYFLIINKNDPKDIFINSLKGIQTLQPNNLPFQCKWDNNRKIVQRSFIESKNSILSALAESVKLRANIY
>NC_012973.1|WP_001000236.1|881424_883242_+|flagellar-hook-protein-FlgE
MNDTLLNAYSGIKTHQFGIDSLSNNIANVNTLGYRSNDPEFKTLFSSHLDALNAKSVVANDRNYGVTGSGNVLSNKDGEYMPSEGEFHMAYQGKGWFVIGPNKNGEMTINKDGFSKKQDNFLTRAGNFARDADGYLVTPEGYYVYGIDLKKIKDGTLNSTARDEDIEKLHGNTLSPLQIPQDLTYQPVLSTKVGISVNLNPKDHLKGVQDFFLNDKGEIIKERFLNQDINALANDDNEPIDAITNRKLNISIQKEDGKKEDFIFTYGDAEKGENQFKTLGDLQKLLKEKTGLDLNLIKSEKDAKSPPLLLEIANPSQTPITFSLSGGIADKLGLNANGMELKKGISRDSVAIKIPYYSTEVDIYDKAGDKYLLQSEYYMTNSNDPTSSPTSKRKNQTWEVKSYIVDPKNKTPINDPTWEIVGFDSATHKMKSAPMTLDFKGNKLTYSLDKSENHDSSDLPYQDSKLLEASQDGKPRGIFRDMRIEENGVISLAFSNGVVEPVARIGILAFTNDQGLRKIGGNLYEMQEGTINGENRPLSGNPILGWDEEGKLKFGKIRHKYLETSNVNAGNALTNLILMQRGYSMNARAFGAGDDMIKEAISLKK
>NC_012973.1|WP_000963327.1|880507_881428_+|flagellar-hook-assembly-protein-FlgD
MAIDLAEVTGAKAAQERKKEQPTIANGLDKNAFMKLFLEQLKNQDPTAPMETDKIITQTAQLTQVEMQEENKKTMQEVASAMKSNKETNESLKDFQGALKDTMENLNKGMDDSLKANNALREVTALNSVSMIGKIAETDVSGANFDGNNKLSFSLFFDEKIDASKGVPAIQILNENNELVKTIPLKDYSGQKGYINFEWDGTNEKGEKVPKGNYKIKAEYNLDSQSKQYLQTRIGRGEVESVIFDKGKPMLRMGEMILPIDSAIEFYKPDQKPIEQKPLEQKPLEQKLSDQKPIDQKPQTPPKETA
>NC_012973.1|WP_001139988.1|878918_880457_+|flagellar-hook-length-control-protein-FliK
MPSPVNPIHTNANALNSGAKNEDTKNAPKSASKDFSKILNQKISKDKTTPKEDPNALKATPKDAKEDAKALEKAPTPHHQHAQNPAKDQQAPTLKDWLNHKKTTASHEAQHEKNHETNPKTPNETLNKNEKKPNGVTSNAHQTNLPNKNPITPTNHANNAIKNPTAPTHNAKESKTLKDIQTLSQKHDLNASNIQAATTPENKTPLNASDQLALKTTQTPTNHTLAKNDAKNTANLSSVLQSLEKKESHNKEHANPQNNEKKTPPLKEALQMNAIKRDKTLSKKKPEKTQTKTQTTAPSIALENAPKIPLKTPPLMPLIGANPPNDNPPTLLEKEETTKEVSDNKEKAKETSSSAQSAQNTQASDKTSDNKSIAPKETIKHFTQQLKQEIQEYKPPMSKISMDLFPKELGKVEITIQKMGKNLKVSVISHNNSLQTFLDNQQDLKNSLNALGFEGVDLSFSQDSSKEQEKEPFKEPFKEQELTPLKENALKSYQENTDHENKETSMQITLYA
>NC_012973.1|WP_001161792.1|876981_878538_-|phosphate-acetyltransferase
MQGLWIYPEDTEVLGVACKILLKALKPRYQKIALFSPINGGCEGFWECESLNSLEFHSAIDKQKALELASTAQEELLFETILKRYDELQTTHDFVISLGYVPKFFLNALLDLNTILAKHLNAPMVAVAQTSLDHLKAMHSHILKKEAPFAVGLFAGEMLEKPDFLSASLCKQQCELEADLIESVLQTKSKIITPLAFQMSLEKKAKKQIKKVVLPESEDERILKAAHRLNAMGAVGLILLGDKEIINSQAKNLNLNLENAEIIDPNTSHYREEFAKSLYELRKSKGLSEQEAKQLVLDKTYFATMPVHSGYAHAMVSGVNHTTAETIRPALQVIKTKPGVSLVSSVFLMCLDTQVLVFGDCAIIPNPSPKELAEIATTSAQSAKQFNIAPKVAMLSYATGNSAQGEMIDKINEALTIAQRLDPQLEIDGPLQFDASIDKSVAKKKMPNSQVAGQASVFIFPDLNAGNIAYKAVQRSAKAVAIGPILQGLNKPINDLSRGALVEDIINTVLISAIQAQD
>NC_012973.1|WP_079996176.1|876062_876965_-|acetate/propionate-family-kinase
MEILVLNLGSSSIKFKLFDMKENKPLASGLAEKIGEEIGQLKIKSHLHHNDQELKEKLVVKDHASGLLMIRENLTKMGIIKDFNQIDAIGHRVVQGGDKFHAPVLVDEKVMQEIGNLSILAPLHNPANLAGIEFVQKAHPHIPQIAVFDTAFHASMPSYAYMYALPYELYEKYQIRRYGFHGTSHHYVAKEAAKFLNTAYEEFNAISLHLGNGSSAAAIQKGKSVDTSMGLTPLEGLIMGTRCGDIDPTVVEYTVQCANKSLEEVMKMLNHESGLKGICGDNEKHRSQKRKRRPTSQTRF
>NC_012973.1|WP_001248521.1|891700_893245_-|outer-membrane-beta-barrel-protein-HofG
MRQEKYFLTSSLSLLSFLLCPVEAFDYRFSGRVENFSKIGFNNSQINTKKGIYPTESFIDIVTLAQVKVNLLPKGTENHRLSVSLGGAIAAIPYDKTKYYINQANGKVFGSIVENFIGGYHGYFFNKYLGPAYAGTSQSASYHARPYVVDTAFLRYDYKDVFGFKAGRYEANIDFMSGSNQGWEVYYQPYKTETQRLRFWWWSSFGRGLAFNSWIYEFFATVPYLKKGGNPNNSNDFINYGWHGITTTYSYKGLDAQFFYYFAPKTYNAPGFKLVYDTNRNFENVGFRSQSMIMTTFPLYYRGWYNPETNTYSLEDSTPHGSLLGRNGVTLNIRQVFWWDNFNWSIGFYNTFGNSDAFLGSHTMPRGNNTSYIGSEISITTRHAGMIGYDFWDNTAYDGLADAITNANTFTFYTSVGGIHKRFAWHVFGRVSHANKNALGQVGRANEYSLQFNASYAFTESVLLNFRITYYGARINKGYQAGYFGAPKFNNPDGDFSANYQDRSYMMTNLTLKF
>NC_012973.1|WP_000998205.1|893570_896012_-|TonB-dependent-receptor
MNDKHFRKYCSFSIFLSLLGMFELEAKEEEKEERKTERKKDKEKNAQHTLGKVTTQAAKIFNYNNQTTISSKELERRQANQISDMFRRNPNINVGGGAVIAQKIYVRGIEDRLARVTVDGAAQMGASYGHQGNTIIDPGMLKSVVVTKGAAQASAGPMALIGAIKMETKSASDFIPKGKDYAISGAATFLTNFGDRETIMGAYRNHHFDMLLYYTHQNIFYYRDGDNAMKNLFDPKAENKVTGSPSEQNNVMAKINGYLSERDTLTLSYNMTRDNANRPLRANFTGTFLPYSCGDFNAFPNEQNPDDCLFENDASLFKTYSVNLVHNVSLNYEREGGSRFGDPKLKINGYTSIRNVQIDPLFRPSDIATSIPFTPNPKLSEENECVTQGGIYDATKQTCSITFKSLGGGSVVANKNLFIINSGFNANVIHTIDHKNDNLLEYGLNYQNLTTFDKAIPNSELVKPGDAPDACLRVRGPDDPNMNGRCQRNGATANVVGVYAQANYTLHPMITLGAGTRYDVYTLVDKDWQLHITQGFSPSAALNVSPLENLNFRLSYAYVTRGPMPGGLVWMRQDNLRYNRNLKPEIGQNVEFNTEYSSQYFDFRAAGFVQLISNYINQFSSTLFVTNLPAQDIIYVPGYEVSGTAKYKGFSLGLSVARSWPSLKGRLIADVYELAATTGNVFILTASYKIPRTGLSITWLSRFVTDLSYCSYSPYRNGPTDIDRRPSNCPKTPGIFHVHKPGYGVSSFFITYKPAYKKLKGLSLNAVFNNVFNQQYINQASPVMSPDEPNQDKYARGMAEPGFNARFEISYKF
>NC_012973.1|WP_001230017.1|896195_896627_-|hypothetical-protein
MALVYLVQSDTTIGLLSKDSEKLNALKKRPKNQSVLIESTDFSTLKSLVRAPNAFKSLIRRSAKTTFIYPNSKAVRVIRGRHGDFLKRFKTLYSTSANLTQCAYDKEIASNLADVIVSDERGLFESASSKIFRLYKNKKVRIR
>NC_012973.1|WP_001126549.1|896631_899889_-|carbamoyl-phosphate-synthase-large-subunit
MPKRTDISNILLIGSGPIVIGQACEFDYSGTQSCKTLKSLGYRVILINSNPATVMTDPEFSHQTYIQPITPENIAAIIKKEKIDAILPTMGGQTALNAVMQMHQKGMLEGVELLGAKIEAIKKGEDRQAFKEAMLKIGMDLPKGRYAYSELEALEAINEIGFPAIIRASFTLAGGGSGVAYNIEEFQELAKNALDASPINEILIEESLLGWKEYEMEVIRDSKDNCIIVCCIENIDPMGVHTGDSITIAPSLTLTDKEYQRMRDASFAILREIGVDTGGSNVQFAIHPETLRMVVIEMNPRVSRSSALASKATGFPIAKVATMLAVGFSLDEIQNDITNTPASFEPSLDYIVVKIPRFAFEKFAGVSSTLGTSMKSIGEVMAIGGNFLEALQKALCSLENNWLGFESLSKDLEAIKKEIRRPNPKRLLYIADAFRLGVSVDEVFELCQIDRWFLSQIQKLVKAEEGINSSVLTDAKKLRGLKNLGFSDARIAAKIKENENLEVSPFEVELARSNLQIVPNFEEVDTCAAEFLSLTPYLYSTYAPNPLPPIENKQEKQEKKILIIGSGPNRIGQGIEFDYCCVHASFALKDLNIKSVMLNCNPETVSTDYDTSDTLYFEPIHFECVKSIIQRERVDGIIVHFGGQTPLKLAKDLAKMQAPIIGTPFKVIDIAEDREKFSLFLKELDIKQPKNGMAKSVDEAYSIANVIGFPIIVRPSYVLGGQHMQILENIEELRHYLESVTHSLEISPKNPLLIDKFLEKAVELDVDVICDKKEVYIAGILQHIEEAGIHSGDSACFIPSTLSPEILDEIERVSAKIALHLGVVGLLNIQFAVYENSLYLIEVNPRASRTVPFLSKALGVPLAKVATRVMVLEDLKEALKFYDKKNIVEYSKGVYKPKMPHFVALKEAVFPFNKLYGSDLILGPEMKSTGEVMGIARSLGLAFFKAQTACFNPIKNKGLIFVSIKDKDKEEACVLMKRLVQLGFELCATEGTHKALEKAGVKSLKVLKISEGRPNIMDLMMNGEISMAINTSDHKSQDDAKLIRASVLKNHVSYFTTLSAIEVLLLALEESSQKDELLALQDYLK
>NC_012973.1|WP_001240216.1|899986_900679_-|Bax-inhibitor-1/YccA-family-protein
MALYDRADSHNAYAENSLLHESELVSFVKTTYKFFAGSLLLATIGALLGLMNFQAVVQYKWVFFIAEIAAFFGLMFSKSKPGLNLFMLFAFTSLSGVTLVPLLGMVIAKAGLGAIWQALGMTTIVFGLMSVYALKTKNDLANMGKMLFIALIVVVVCSLINLFLGSPMFQVVIAGASAILFSLYIAYDTQNIVKGMYDSPIDAAVSLYLDFLNVFISILQIIGIFSDRDK
>NC_012973.1|WP_000688668.1|900825_901824_+|type-I-glyceraldehyde-3-phosphate-dehydrogenase
MKIFINGFGRIGRCVLRAILERSDTSPHLEVIGINDPANWEILAYLLEHDSVHGLLPKEVRYSNYKLIIGSLEIPVFNSIKDLKGVDVIIECSGKFLEPKTLENYLLLGAKKVLLSAPFMGEYDEKQYPTLVYGVNHFLYQNQAIVSNASCTTNAIAPICAILDKAFKIKEGMLTTIHSYTSDQKLIDLAHPLDKRRSRAAASNIIPTTTKAALALHKVLPNLKNKMHGHSVRVPSLDVSMIDLSLFLEKKAPKDPINDLLIEASKRVLKGVLEIDLKERVSSDFISNPHSVIIAPDLTFTLENMVKIMGWYDNEWGYSNRLVDMAQFMYHY
>NC_012973.1|WP_000874625.1|901904_909479_+|vacuolating-cytotoxin-domain-containing-protein
MAFKKARLISRFISKGSFKLNKISKKIFTLNQILKREKPLKRHKKALKPIKKLSDRNKSFLKASVLLIGALGGLSHLRANECRYWSWPSWSYQDNIESGPNSPTHNSYCLFSSTQGSGTYYLNTLTTYSAGGASFTQKFNGGTLNVGGNIRFGGTGINGGDVGYITGTYDAANIYLTSHLTTGNSYADGGGATLNFNATNNLTINQASFDNNDAGTQKSYMNFKGSNIKVSGSSFKDDTDGGFSFSGNNNNSTISFNQTNFNQGTYHFSNSASSSFDNSSFNQGSYHFNSAQSTFENSNFNQGTYNFNDNTSFNNDTFNQGTYSFNTSKVSFSGINTLNSSSPFASLKGSVSFNSGAVFNLNQTLNNNQTYDILTTNGAIQYGVYQSYLWDLINYKGDKAISHVGVGNNTYDVTFNINGQDETLQETFNKQSIITQFLGDDLQQQAQQTYQEDLTHSQNALNNVTSDNTIANNDTSYTQSKNTTVAKDAQGLENTNQKIQQDEQALEKDLAQIKQLANSPTGFSEQAFNQAQKQEQQDEQTLQNDENAFNTKQEGLKQAIQQAQAQQQKQEQQQAQQTYQEDLTHSQNALNNVTSDNTIANNDTSYTQSKNTTVAKDAQGLENTNQKIQQDEQALEKDLAQIKQLANSPTGFSEQAFNQAQKQEQQDEQTLQNDEKTFNAEQEGLKQAIANAKPASPTPSPTPTPTKHTVQNTPPSQVPPTPTQNPPAESVWSGVYWLQNKTYSNKGIYYIDPNLSGQSGQSGNTLSTYTANLFGRSFGVNIQNGTLIIGNNTESVNDNGLIWIGHGGFGYITGTFSAANIYLTNNFKTGEGVSNSDGGGANITFKASDNITMDGLNYNDAETVTKMIQTGASQHSYATFDALNNISVTNSSFSDMTWGKFSFSAKNISFSNASFSGFTNPGGSSTISANASNSLSFVNSRLNGGAIYNLWANSLIFNNTQAVFNVLYSRGTSNFNATTQLLGNTNFTLSSQSLLNFNGDTTLQDNANITLGNKSQAAFKNSLTLDNDSNLSLDNQSVLNANGASAFNNQASLNIYNGSQAAFSSLFFNGGTLSLNASSKLNASSASFSNNTTINLDDSVLSASNTSSLNANINFQGASQADFGGNTTIDTASFNFDSTSSLSFNNLTANGALNFNGYAPSLTKALMSVSGQFVLGNNGDINLSDINIFDNITKSVTYNILNAQKGITGISGANGYEKILFYGMKIQNATYSDNNNIQTWSFINPLNSSQIIQESIKNGDLTIEVLNNPNSASNTIFNIAPELYNYQASKQNPTGYSYDYSDNQAGTYYLTSNIKGLFTPKGSQTPQAPGTYSPFNQPLNSLNIYNKGFSSENLKTLLGILSQNSATLKEMIESNQLDNITNINEVLQLLDKIKITPAQKQALLETINHLTDNINQTFSNGNLIIGATQDNVTNSTSSIWFGGNGYSSPCMLDSATCSSFRNTYLGQLLGSTSPYLGYINADFKAKSIYITGTLGSGNAFESGGSADVTFQSANNLVLNKANIEAQATDNIFNLLGQEGIDKIFNQGNLANVLSQVAMEKIKQAGGLGNFVENALSPLSKELPASLQSETLGQLIGQNNLDDLLNNSGVMNAIQNIISKKLSIFGNFVTPSIIENYLAKQSLKSMLDDKGLLNFIGGYIDASELSSILSVILKDITNPPASLQKDIGVVANDLLKEFLGQDVVKKLESQGLVSNIINNIISQGGLSDVYNQGLGSVLPPSLQNALKENDLGALLSPRGLHDFWQKGYFNFLSNGYVFVNNSSFSNATGGSLNFVANKSIIFNGDNTIDFSKYQGVLIFASNGVSNINITTLNATNGLSLNAGLNNVSVQKGEICVNLANCPTTKNNSSTNSSVTPTNESLSVRANNFTFLGAITSNGAIDLSQVTNNSVIGTLNLNENATLQANNLTITNAFNNASNSTANINGNFTLNQQATLSTNASGLNVMGNFNSYGDLVFNLSHSVSHAIINAQGNATIMANDNNPLIQFNTSSKEVGTYTLIDSAKAIYYGYNDQITGGSSLDNYLKLYTLIDINGKHMVMTGNGLTYNGQAVNIKDGGLVVGFKDSQNQYIYTSILYNKVKIAVSNDPINNLQAPTLKQYIAQIQGVQSVDSIDQVGGNQAINWLNKIFETKGSPLFAPYYLESHSTKDLTTIAGDIANTLEVIANPDFKNDATNILQINTYTQQMSRLAKLSDTSTFASADFHERLEALKNKRFADAIPNAMDVILKYSQRNRVKNNVWATGVGGASFINGGTGTLYGINVGYDRFIKGVIVGGYAAYGYSGFHGNITQSGSSNVNIGVYSRAFIKRSELTMSLNETWGYNKTFINSYDPLLSIINQSYRYDTWTTDAKINYGYDFMFKDKSVIFKPQVGLAYYYIGLSGLRGIMDDPIYNQFRANADPNKKSVLTINFALESRHYFNKNSYYFVIADVGRDLFINSMGDKMVRFIGNNTLSYRDGGRYNTFASIITGGEIRLFKTFYVNAGIGARFGLDYKDINITGNIGMRYAF
>NC_012973.1|WP_001169510.1|909530_910625_+|Hop-family-outer-membrane-protein-HopJ/HopK
MQKILFPLPLLFLSYCIAEENGAYASVGFEYSISHAVEHNNPFLNQERIQIISNAQNQIYKLNQVKNEITSMPNTFNYINNALKNNSKLTPTEMQAEQYYLQSTLQNIEKIVMLSGGVASNPKLAQALEKMQEPITNPLELAENLRNLELQFAQSQNRMLSSLSSQIAQISNSLNVLDPSSYSKNISSMYGVSLSVGYKHFFTKKKNQGLRYYLFYDYGYTNFGFVGNGFDGLGKMNNHLYGLGIDYLYNFIDNAQKHSSVGFYVGFALAGSSWVGSGLGMWVSQTDFINNYLTGYQAKMHTSFFQIPLNFGVRVNVNRHNGFEMGLKIPLAVNSFYETHGKGLNTSLFFKRLVVFNVSYVYSF
>NC_012973.1|WP_001115888.1|910692_910899_-|4-oxalocrotonate-tautomerase-family-protein
MPFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASVVVIIDEVDSNNYGLGGESVHHLRQKN
>NC_012973.1|WP_001099633.1|911055_911637_+|recombination-protein-RecR
MNTYKNSLNHFLNLVDCLEKIPNVGKKSAFKMAYHLGLENPYLALKITHALENALENLKTCVSCNALSESEVCEICSDESRQNSQLCMVLHPRDVFILEDLKDFLGRYYVLNSIEEVDFNALEKRLIEENIKEIIFAFPPTLANDSLMLYIEDKLQHFHLTFTKIAQGVPTGVNFENIDSVSLSRAFNSRIKA

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Crispr_ID: NC_012973_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_012973_3

902685-902880

Orphan

I-B

Consensus_repeat	Method
TTCAATCAAGGGACTTATCACTTTA	CRISPRCasFinder

3 spacers

The CRISPR arrays of NC_012973_3

>merge|NC_012973|3|902685-902880|CRISPRCasFinder
TTCAATCAAGGGACTTATCACTTTAGTAACAGCGCAAGTTCAAGCTTTGATAATAGTAGTTTCAATCAAGGGAGTTATCACTTTAATAGCGCCCAATCCACTTTTGAAAACAGCAATTTCAATCAAGGCACTTATAATTTTAATGACAATACTAGCTTTAATAACGACACCTTCAATCAAGGCACTTATAGCTTTA

>NC_012973|3|3|902685-902880|CRISPRCasFinder
TTCAATCAAGGGACTTATCACTTTA	GTAACAGCGCAAGTTCAAGCTTTGATAATAGTAGT
TTCAATCAAGGGAGTTATCACTTTA	ATAGCGCCCAATCCACTTTTGAAAACAGCAAT
TTCAATCAAGGCACTTATAATTTTA	ATGACAATACTAGCTTTAATAACGACACC
TTCAATCAAGGCACTTATAGCTTTA

Protein	Signature genes	Signature genes Name	Protein_function
NC_012973.1\|WP_001126549.1\|896631_899889_-\|carbamoyl-phosphate-synthase-large-subunit	unknown	unknown	gnl\|CDD\|235393
NC_012973.1\|WP_001115888.1\|910692_910899_-\|4-oxalocrotonate-tautomerase-family-protein	unknown	unknown	gnl\|CDD\|129125
NC_012973.1\|WP_000426984.1\|913698_914241_+\|GTP-cyclohydrolase-I-FolE	unknown	unknown	gnl\|CDD\|129173
NC_012973.1\|WP_000998205.1\|893570_896012_-\|TonB-dependent-receptor	unknown	unknown	gnl\|CDD\|273808
NC_012973.1\|WP_001052421.1\|911633_912779_+\|tRNA-pseudouridine(13)-synthase-TruD	unknown	unknown	gnl\|CDD\|272903
NC_012973.1\|WP_001169510.1\|909530_910625_+\|Hop-family-outer-membrane-protein-HopJ/HopK	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_000236828.1\|916625_917228_+\|6-pyruvoyl-tetrahydropterin-synthase-family-protein	unknown	unknown	gnl\|CDD\|223792
NC_012973.1\|WP_000427105.1\|883884_885036_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|223897
NC_012973.1\|WP_000894533.1\|885039_887067_+\|ATP-dependent-helicase	unknown	unknown	gnl\|CDD\|223288
NC_012973.1\|WP_000070345.1\|914256_915168_+\|polyprenyl-synthetase-family-protein	unknown	unknown	gnl\|CDD\|223220
NC_012973.1\|WP_001248521.1\|891700_893245_-\|outer-membrane-beta-barrel-protein-HofG	unknown	unknown	gnl\|CDD\|334957
NC_012973.1\|WP_000688668.1\|900825_901824_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|273675
NC_012973.1\|WP_162465584.1\|912747_913698_+\|zinc-metalloprotease-HtpX	unknown	unknown	gnl\|CDD\|235081
NC_012973.1\|WP_000592400.1\|887653_889207_+\|Hop-family-adhesin-AlpA	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_001240216.1\|899986_900679_-\|Bax-inhibitor-1/YccA-family-protein	unknown	unknown	gnl\|CDD\|198414
NC_012973.1\|WP_000726631.1\|915964_916624_+\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_000722449.1\|915164_915968_+\|5'/3'-nucleotidase-SurE	unknown	unknown	gnl\|CDD\|234732
NC_012973.1\|WP_001099633.1\|911055_911637_+\|recombination-protein-RecR	unknown	unknown	gnl\|CDD\|273176
NC_012973.1\|WP_000812511.1\|889228_890827_+\|Hop-family-adhesin-AlpB	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_001230017.1\|896195_896627_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|376519

Protein	Function_ID	Function_description	E-value
NC_012973.1\|WP_001126549.1\|896631_899889_-\|carbamoyl-phosphate-synthase-large-subunit	gnl\|CDD\|235393	PRK05294, carB, carbamoyl-phosphate synthase large subunit.	0
NC_012973.1\|WP_001115888.1\|910692_910899_-\|4-oxalocrotonate-tautomerase-family-protein	gnl\|CDD\|129125	TIGR00013, Probable_tautomerase_K2, 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function. [Energy metabolism, Other].	4.5194e-26
NC_012973.1\|WP_000426984.1\|913698_914241_+\|GTP-cyclohydrolase-I-FolE	gnl\|CDD\|129173	TIGR00063, GTP_cyclohydrolase_1, GTP cyclohydrolase I. alternate names: Punch (Drosophila),GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid].	1.51291e-106
NC_012973.1\|WP_000998205.1\|893570_896012_-\|TonB-dependent-receptor	gnl\|CDD\|273808	TIGR01786, hemoglobin-haptoglobin-binding_protein, TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein. This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model (TIGR01776). Accessions which score above trusted to this model while not scoring above trusted to the more specific models are most likely to be hemoglobin transporters. Nearly all of the species containing trusted hits to this model have access to hemoglobin, transferrin or lactoferrin or related proteins in their biological niche. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins].	8.64531e-46
NC_012973.1\|WP_001052421.1\|911633_912779_+\|tRNA-pseudouridine(13)-synthase-TruD	gnl\|CDD\|272903	TIGR00094, tRNA_pseudouridine_synthase_D, tRNA pseudouridine synthase, TruD family. an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification].	2.05206e-139
NC_012973.1\|WP_001169510.1\|909530_910625_+\|Hop-family-outer-membrane-protein-HopJ/HopK	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	4.56839e-48
NC_012973.1\|WP_000236828.1\|916625_917228_+\|6-pyruvoyl-tetrahydropterin-synthase-family-protein	gnl\|CDD\|223792	COG0720, COG0720, 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism].	1.06233e-20
NC_012973.1\|WP_000427105.1\|883884_885036_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|223897	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair].	3.902e-51
NC_012973.1\|WP_000894533.1\|885039_887067_+\|ATP-dependent-helicase	gnl\|CDD\|223288	COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair].	6.44724e-135
NC_012973.1\|WP_000070345.1\|914256_915168_+\|polyprenyl-synthetase-family-protein	gnl\|CDD\|223220	COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism].	7.04085e-76
NC_012973.1\|WP_001248521.1\|891700_893245_-\|outer-membrane-beta-barrel-protein-HofG	gnl\|CDD\|334957	pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).	2.1498e-178
NC_012973.1\|WP_000688668.1\|900825_901824_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	gnl\|CDD\|273675	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I. This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively. Two Pfam models cover the two functional domains of this protein; pfam00044 represents the N-terminal NAD(P)-binding domain and pfam02800 represents the C-terminal catalytic domain. An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine. This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria. This enzyme is described by TIGR001532. These sequences generally score between trusted and noise to this GAPDH model due to the close evolutionary relationship. There exists the possiblity that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to posess a limited E4PD activity as well as a robust GAPDH activity). There are a great number of sequences in the databases which score between trusted and noise to this model, nearly all of them due to fragmentary sequences. It seems that study of this gene has been carried out in many species utilizing PCR probes which exclude the extreme ends of the consenses used to define this model. The noise level is set relative not to E4PD, but the next closest outliers, the class II GAPDH's (found in archaea, TIGR01546) and aspartate semialdehyde dehydrogenase (ASADH, TIGR01296) both of which have highest-scoring hits around -225 to the prior model. [Energy metabolism, Glycolysis/gluconeogenesis].	2.91967e-162
NC_012973.1\|WP_162465584.1\|912747_913698_+\|zinc-metalloprotease-HtpX	gnl\|CDD\|235081	PRK02870, PRK02870, heat shock protein HtpX; Provisional.	0
NC_012973.1\|WP_000592400.1\|887653_889207_+\|Hop-family-adhesin-AlpA	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.79597e-54
NC_012973.1\|WP_001240216.1\|899986_900679_-\|Bax-inhibitor-1/YccA-family-protein	gnl\|CDD\|198414	cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor (BI)-1/YccA-like proteins. This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, BI-1 like proteins play a role in pathogen resistance. A characterized prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.	1.17402e-52
NC_012973.1\|WP_000722449.1\|915164_915968_+\|5'/3'-nucleotidase-SurE	gnl\|CDD\|234732	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional.	2.31407e-125
NC_012973.1\|WP_001099633.1\|911055_911637_+\|recombination-protein-RecR	gnl\|CDD\|273176	TIGR00615, Recombination_protein_RecR, recombination protein RecR. All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair].	6.9426e-98
NC_012973.1\|WP_000812511.1\|889228_890827_+\|Hop-family-adhesin-AlpB	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.31684e-53
NC_012973.1\|WP_001230017.1\|896195_896627_-\|hypothetical-protein	gnl\|CDD\|376519	pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.	0.00042225

>NC_012973.1|WP_000688668.1|900825_901824_+|type-I-glyceraldehyde-3-phosphate-dehydrogenase
MKIFINGFGRIGRCVLRAILERSDTSPHLEVIGINDPANWEILAYLLEHDSVHGLLPKEVRYSNYKLIIGSLEIPVFNSIKDLKGVDVIIECSGKFLEPKTLENYLLLGAKKVLLSAPFMGEYDEKQYPTLVYGVNHFLYQNQAIVSNASCTTNAIAPICAILDKAFKIKEGMLTTIHSYTSDQKLIDLAHPLDKRRSRAAASNIIPTTTKAALALHKVLPNLKNKMHGHSVRVPSLDVSMIDLSLFLEKKAPKDPINDLLIEASKRVLKGVLEIDLKERVSSDFISNPHSVIIAPDLTFTLENMVKIMGWYDNEWGYSNRLVDMAQFMYHY
>NC_012973.1|WP_001240216.1|899986_900679_-|Bax-inhibitor-1/YccA-family-protein
MALYDRADSHNAYAENSLLHESELVSFVKTTYKFFAGSLLLATIGALLGLMNFQAVVQYKWVFFIAEIAAFFGLMFSKSKPGLNLFMLFAFTSLSGVTLVPLLGMVIAKAGLGAIWQALGMTTIVFGLMSVYALKTKNDLANMGKMLFIALIVVVVCSLINLFLGSPMFQVVIAGASAILFSLYIAYDTQNIVKGMYDSPIDAAVSLYLDFLNVFISILQIIGIFSDRDK
>NC_012973.1|WP_001126549.1|896631_899889_-|carbamoyl-phosphate-synthase-large-subunit
MPKRTDISNILLIGSGPIVIGQACEFDYSGTQSCKTLKSLGYRVILINSNPATVMTDPEFSHQTYIQPITPENIAAIIKKEKIDAILPTMGGQTALNAVMQMHQKGMLEGVELLGAKIEAIKKGEDRQAFKEAMLKIGMDLPKGRYAYSELEALEAINEIGFPAIIRASFTLAGGGSGVAYNIEEFQELAKNALDASPINEILIEESLLGWKEYEMEVIRDSKDNCIIVCCIENIDPMGVHTGDSITIAPSLTLTDKEYQRMRDASFAILREIGVDTGGSNVQFAIHPETLRMVVIEMNPRVSRSSALASKATGFPIAKVATMLAVGFSLDEIQNDITNTPASFEPSLDYIVVKIPRFAFEKFAGVSSTLGTSMKSIGEVMAIGGNFLEALQKALCSLENNWLGFESLSKDLEAIKKEIRRPNPKRLLYIADAFRLGVSVDEVFELCQIDRWFLSQIQKLVKAEEGINSSVLTDAKKLRGLKNLGFSDARIAAKIKENENLEVSPFEVELARSNLQIVPNFEEVDTCAAEFLSLTPYLYSTYAPNPLPPIENKQEKQEKKILIIGSGPNRIGQGIEFDYCCVHASFALKDLNIKSVMLNCNPETVSTDYDTSDTLYFEPIHFECVKSIIQRERVDGIIVHFGGQTPLKLAKDLAKMQAPIIGTPFKVIDIAEDREKFSLFLKELDIKQPKNGMAKSVDEAYSIANVIGFPIIVRPSYVLGGQHMQILENIEELRHYLESVTHSLEISPKNPLLIDKFLEKAVELDVDVICDKKEVYIAGILQHIEEAGIHSGDSACFIPSTLSPEILDEIERVSAKIALHLGVVGLLNIQFAVYENSLYLIEVNPRASRTVPFLSKALGVPLAKVATRVMVLEDLKEALKFYDKKNIVEYSKGVYKPKMPHFVALKEAVFPFNKLYGSDLILGPEMKSTGEVMGIARSLGLAFFKAQTACFNPIKNKGLIFVSIKDKDKEEACVLMKRLVQLGFELCATEGTHKALEKAGVKSLKVLKISEGRPNIMDLMMNGEISMAINTSDHKSQDDAKLIRASVLKNHVSYFTTLSAIEVLLLALEESSQKDELLALQDYLK
>NC_012973.1|WP_001230017.1|896195_896627_-|hypothetical-protein
MALVYLVQSDTTIGLLSKDSEKLNALKKRPKNQSVLIESTDFSTLKSLVRAPNAFKSLIRRSAKTTFIYPNSKAVRVIRGRHGDFLKRFKTLYSTSANLTQCAYDKEIASNLADVIVSDERGLFESASSKIFRLYKNKKVRIR
>NC_012973.1|WP_000998205.1|893570_896012_-|TonB-dependent-receptor
MNDKHFRKYCSFSIFLSLLGMFELEAKEEEKEERKTERKKDKEKNAQHTLGKVTTQAAKIFNYNNQTTISSKELERRQANQISDMFRRNPNINVGGGAVIAQKIYVRGIEDRLARVTVDGAAQMGASYGHQGNTIIDPGMLKSVVVTKGAAQASAGPMALIGAIKMETKSASDFIPKGKDYAISGAATFLTNFGDRETIMGAYRNHHFDMLLYYTHQNIFYYRDGDNAMKNLFDPKAENKVTGSPSEQNNVMAKINGYLSERDTLTLSYNMTRDNANRPLRANFTGTFLPYSCGDFNAFPNEQNPDDCLFENDASLFKTYSVNLVHNVSLNYEREGGSRFGDPKLKINGYTSIRNVQIDPLFRPSDIATSIPFTPNPKLSEENECVTQGGIYDATKQTCSITFKSLGGGSVVANKNLFIINSGFNANVIHTIDHKNDNLLEYGLNYQNLTTFDKAIPNSELVKPGDAPDACLRVRGPDDPNMNGRCQRNGATANVVGVYAQANYTLHPMITLGAGTRYDVYTLVDKDWQLHITQGFSPSAALNVSPLENLNFRLSYAYVTRGPMPGGLVWMRQDNLRYNRNLKPEIGQNVEFNTEYSSQYFDFRAAGFVQLISNYINQFSSTLFVTNLPAQDIIYVPGYEVSGTAKYKGFSLGLSVARSWPSLKGRLIADVYELAATTGNVFILTASYKIPRTGLSITWLSRFVTDLSYCSYSPYRNGPTDIDRRPSNCPKTPGIFHVHKPGYGVSSFFITYKPAYKKLKGLSLNAVFNNVFNQQYINQASPVMSPDEPNQDKYARGMAEPGFNARFEISYKF
>NC_012973.1|WP_001248521.1|891700_893245_-|outer-membrane-beta-barrel-protein-HofG
MRQEKYFLTSSLSLLSFLLCPVEAFDYRFSGRVENFSKIGFNNSQINTKKGIYPTESFIDIVTLAQVKVNLLPKGTENHRLSVSLGGAIAAIPYDKTKYYINQANGKVFGSIVENFIGGYHGYFFNKYLGPAYAGTSQSASYHARPYVVDTAFLRYDYKDVFGFKAGRYEANIDFMSGSNQGWEVYYQPYKTETQRLRFWWWSSFGRGLAFNSWIYEFFATVPYLKKGGNPNNSNDFINYGWHGITTTYSYKGLDAQFFYYFAPKTYNAPGFKLVYDTNRNFENVGFRSQSMIMTTFPLYYRGWYNPETNTYSLEDSTPHGSLLGRNGVTLNIRQVFWWDNFNWSIGFYNTFGNSDAFLGSHTMPRGNNTSYIGSEISITTRHAGMIGYDFWDNTAYDGLADAITNANTFTFYTSVGGIHKRFAWHVFGRVSHANKNALGQVGRANEYSLQFNASYAFTESVLLNFRITYYGARINKGYQAGYFGAPKFNNPDGDFSANYQDRSYMMTNLTLKF
>NC_012973.1|WP_000812511.1|889228_890827_+|Hop-family-adhesin-AlpB
MKQNLKPFKMIKENLMTQSQKVRFLAPLSLALSLSFNPVGAEEDGGFMTFGYELGQVVQQVKNPGKIKAEELAGLLNSNTTNNTNINIAGTGGNVAGTLGNLFMNQLGNLIDLYPTLNTSNIHQCGANNTSSSSNAAAAAATSSSSTSPCFQGNLALYNEMVGSIKTLSQNISKNIFQSNNNTTSQNLSNQLSELNTASVYLTYMNSFLNANNQAGGIFQNNTNQAYGNGVTAQQIAYILKQASITMGPSGDSGAAAAFLDAALAQHVFNSANAGNDLSAKEFTSLVQNIVNNSQNALTLANNANISNSTGYQVSYGGNIDQARSTQLLNNTTNTLAKVTALNNELKANPWLGNFAAGNSSQVNAFNGFITKIGYKQFFGENKNVGLRYYGFFSYNGAGVGNGPTYNQVNLLTYGVGTDVLYNVFSRSFGSRSLNAGFFGGIQLAGDTYISTLRNSPQLASRPTATKFQFLFDLGLRMNFGILKKDLKSHNQHSIEIGVQIPTIYNTYYKAGGAEVKYFRPYSVYWVYGYAF
>NC_012973.1|WP_000592400.1|887653_889207_+|Hop-family-adhesin-AlpA
MIKKNRTLFLSLALCASISYAEDDGGFFTVGYQLGQVMQDVQNPGGAKADELARELNADVTNNILNNNTGGNVAGALSNAFSQYLYSLLGAYPTKLNSNDVSANALLSGAVGSGTCAAAGTAGGTSLNTQSACTAAGYYWLPSLTDRILSTIGSQTNYGTNTNFPNMQQQLTYLNAGNVFFNAMNKALEKNGTTTASGTNGATGSDGQTYSQQAIQYLQGQQNILNNAANLLKQDELLLEAFNSAVAANIGNKEFNSAAFTGLVQGIIDQSQAVYNELTKNTISGSAVNNAGINSNQANAVQGRASQLPNALYNAQVTLDKINALNNQVRSMPYLPQFRAGNSRATNILNGFYTKIGYKQFFGKKRNIGLRYYGFFSYNGASVGFRSTQNNVGLYTYGVGTDVLYNIFSRSYQNRSVDMGFFSGIQLAGETFQSTLRDDPNVKLHGKINNTHFQFLFDFGMRMNFGKLDGKSNRHNQHTVEFGVVVPTIYNTYYKSAGTTVKYFRPYSVYWSYGYSF
>NC_012973.1|WP_000894533.1|885039_887067_+|ATP-dependent-helicase
MLETLQLNPEQLKAAKALKGYNLVIASAGTGKTSTIVGRILYLLDNGIKPEEILLLTFTNKASNEMIARVAKYFKSSSKIEAGTFHAVAYRYLKEHYPNLSLKQPKELRKLLESIVDTKNAIDDDKKPYTSQHLYALYSLYTNALKQEDFSAWLSNKNPEHAPYAALYENILEEFENTKKKHNYIDYNDLLLLFKKAMLERPSPYKEVLCDEFQDTNPLQESILDAINPPSLFCVGDYDQSIYAFNGADISIISNFTQKYKNAQVFTLTKNYRSSKEILDLANQVIQRNERIYPKNLEVVKSGKFNKPTLLNYNDNIAQCQDIAKRIVMRKNFKEVAVIFRNNASADQLEAALRSHNVPSKRKGSASFFESKEVALALDICALLFNPKDIMAAIHILSYISDIGSNTAKDIHEALMLLGNGDLKLALTHPSKEAKIYTKKKEITSMGLFEEIFALENSSRFNSVIDKAFHSHPVLMHSKISLNGAKMLSDFFILYTKAPTHSPSALIKHILESAFFQTFKTRLLKERSKNKDGSYNEFKKLQAQKRFNEKMDLLSSLAKNYQNLGRFLNGTLIGSSEATQGCGVNLLSVHASKGLEFKDVYIIDLMEGRFPNHKLMNTGGGIEEERRLFYVAITRAKENLWLSYAKNELRENAKPKEHKPSVFLYEAGLLKPDSK
>NC_012973.1|WP_000427105.1|883884_885036_+|class-I-SAM-dependent-methyltransferase
MENFLNKWDIKTLGQVFTPKNIVDFMLTLKHNQGSVLEPSAGDGSFLKRLKKAVGIEIDPKICPKNALCMDFFDYPLENQFDTIIGNPPYVKHKDIAPSTKEKLHYSLFDERSNLYLFFIEKAIKHLKPQGELIFITPRDFLKSTSSVKLNEWIYKEGTITHFFELGDQKIFPNAMPNCVIFRFCKGDFSRIANDGLQFVCKKGILYFLNQSYTQKLSEVFKVKVGAVSGCDKIFKNEKHGNLEFVTSITKRTNVLEKMVFVNKPNDYLLQHKDSLMQRKIKKFNESNWFEWGRMHHISPKKRIYVNTKTRQKNPFFIHQCPNYDGSILALFPYNQNLDLQNLCDKLNAINWQELGFVCDGRFLFSQRSLENALLPKDFLNLG
>NC_012973.1|WP_001169510.1|909530_910625_+|Hop-family-outer-membrane-protein-HopJ/HopK
MQKILFPLPLLFLSYCIAEENGAYASVGFEYSISHAVEHNNPFLNQERIQIISNAQNQIYKLNQVKNEITSMPNTFNYINNALKNNSKLTPTEMQAEQYYLQSTLQNIEKIVMLSGGVASNPKLAQALEKMQEPITNPLELAENLRNLELQFAQSQNRMLSSLSSQIAQISNSLNVLDPSSYSKNISSMYGVSLSVGYKHFFTKKKNQGLRYYLFYDYGYTNFGFVGNGFDGLGKMNNHLYGLGIDYLYNFIDNAQKHSSVGFYVGFALAGSSWVGSGLGMWVSQTDFINNYLTGYQAKMHTSFFQIPLNFGVRVNVNRHNGFEMGLKIPLAVNSFYETHGKGLNTSLFFKRLVVFNVSYVYSF
>NC_012973.1|WP_001115888.1|910692_910899_-|4-oxalocrotonate-tautomerase-family-protein
MPFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASVVVIIDEVDSNNYGLGGESVHHLRQKN
>NC_012973.1|WP_001099633.1|911055_911637_+|recombination-protein-RecR
MNTYKNSLNHFLNLVDCLEKIPNVGKKSAFKMAYHLGLENPYLALKITHALENALENLKTCVSCNALSESEVCEICSDESRQNSQLCMVLHPRDVFILEDLKDFLGRYYVLNSIEEVDFNALEKRLIEENIKEIIFAFPPTLANDSLMLYIEDKLQHFHLTFTKIAQGVPTGVNFENIDSVSLSRAFNSRIKA
>NC_012973.1|WP_001052421.1|911633_912779_+|tRNA-pseudouridine(13)-synthase-TruD
MNLNFMPLLHAYNHASIDFHFNSSARDFCVHEVPLYEFSNTGEHAVIQVRKSGLSTLEMLQVFSQILGVKIAELGYAGLKDKNALTTQFISLPKKYAPLLEKNTHNLQERNLKILSLNYHHNKIKLGHLKGNRFFMRFKKMTPLNAQKTKQVLEQIAQFGMPNYFGSQRFGKFNDNHKEGLKILQNKTKFAHQKLNAFLISSYQSYLFNSLLSKRLEISKIISDFSVKENLEFFKQKNLSVDSNTLKSLKNQAHPFKILEGDVMCHYPYGKFFDALELEKEGKRFLKKEVAPTGLLDGKKALYAKNLSLEIEKEFQHNLLSSHTKTLGSRRFFWVFAENVISQYVKEKAQFELGFYLPKGSYASALLKEIKHEKGENDDEF
>NC_012973.1|WP_162465584.1|912747_913698_+|zinc-metalloprotease-HtpX
MRKEKMMTNFEKIIAQNRIKTNAVLTTYCTIFAFIGLLVDAIRINANDLGIALFKLITFQIFPTITIIMFLAAFVIIVVCIQNFSSIMLSGDGYKLIDTSKVLSSKENQIHRLLLELLEEAKLHFEPKLYIINAPYMNAFASGWDESNSLIALTSALIERLDRDELKAVIAHELSHIRHNDIRLTMCVGILSNIMLLVANFSVYFFMGNRKNSGANLARMILLLLQIVLPFLTLILQMYLSRTREYMADSGAAFLMHDNKPMIRALQKISNDYANNDYKGIDQNSTRSAAYLFNAEMFSTHPSVKNRIQSLRKRVI
>NC_012973.1|WP_000426984.1|913698_914241_+|GTP-cyclohydrolase-I-FolE
MENFFNQFFENIGEDKNREGLKETPKRVQELWKFLYKGYKEDPRVALKSAYFQGVCDEMIVAQNIEFYSTCEHHLLPFLGNISVGYIPKEKIVGISAIAKLIEIYSKRLQIQERLTTQIAETFDEIIEPRGVIVVCEAKHLCMSMQGVQKQNAIIKTSVLRGLFKKDPKTRAEFMQLLKS
>NC_012973.1|WP_000070345.1|914256_915168_+|polyprenyl-synthetase-family-protein
MSNPNLSFYYNECERFESFLNHHHLHLESFHPYLEKAFFEMVLNGGKRFRPKLFLAVLCALVGQKDYSNQQTEYFKIALSIECLHTYSLIHDDLPCMDNAALRRNHPTLHAKYDETTAVLIGDALNTYSFELLSNSLLESHIIVELVKILSANGGIKGMILGQALDCYFENTPLNLEQLTFLHEHKTAKLISTSLMMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEKESGKTTHLDSAKNSFVNLLGLKKASDYAQTLKTEVLNDLNLLKPAYPLLQENLNALLNTLFKGKT
>NC_012973.1|WP_000722449.1|915164_915968_+|5'/3'-nucleotidase-SurE
MKKILLTNDDGYHAKGIKALEQALEEMAEIYVVAPKHEKSACSQCITITAPLRAEKIKGKEGRHYRIDDGTPSDCVYLAINELFKHVCFDLVISGINLGSNMGEDTIYSGTVAGAIEGTIQGVPSIAISQILSNKNKNTPLSFDLAQKIIQDLVQNIFTKGYPLKGRKLLNVNVPNCSLQEYKGERITPKGYRLYKKEVHKRTDPKNESYFWLGLHPLEWQKRENENRLSDFDAIASNHASITPLNLDLTSYDDLKSLESWHEGILK
>NC_012973.1|WP_000726631.1|915964_916624_+|hypothetical-protein
MKKKHRLAFLGLIVGVFFFFNACQHRLHMGYYSEVTGDYLFNYNSTIVVAYDRSDAMTSYYINVIVYELQKLGFYNVFTQAEFPLDKAKNVIYARIVRNISAVPFYQYNYQLIDQVNKPCYFLGGQFYCSQTPTDYYAINGFSEQILMSANSHFILDWYDVVLQKRVLYVDGSVSGRTCGYQMLYRDLIKSTIKRIDFNRPERYYYNLRLPLYQPCYRE
>NC_012973.1|WP_000236828.1|916625_917228_+|6-pyruvoyl-tetrahydropterin-synthase-family-protein
MVIRRLYKFCASHVVRNCSSLKCAQNIHGHNYEVEVFIETNRLDSANMALDFGLMQQEMQVFIESFDHAHHFWDKESLEFQRFIENHCVRYVKCSFNLSAESYALMFLYYLTRILQKSVFSNDEGELKISSVRVHETKNGYAESFLKDLENPHFKSLVHNHCVSFSQGIQNLWHDKDFFNKIISDEKQCFFHAKPLHQIP

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Crispr_ID: NC_012973_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_012973_4

1072128-1072213

Orphan

Consensus_repeat	Method
CATGCGAGAAGTAGTGGTTCAAGAAC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_012973_4

>merge|NC_012973|4|1072128-1072213|CRISPRCasFinder
CATGCGAGAAGTAGTGGTTCAAGAACGCTTCAAGGGAGTTTTCTTTGATCTCTGCATGGGCATGCGAGAAGTAGTGGTTCAAGAAC

>NC_012973|4|4|1072128-1072213|CRISPRCasFinder
CATGCGAGAAGTAGTGGTTCAAGAAC	GCTTCAAGGGAGTTTTCTTTGATCTCTGCATGGG
CATGCGAGAAGTAGTGGTTCAAGAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_012973.1\|WP_000816961.1\|1080349_1081183_+\|outer-membrane-protein	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_001265794.1\|1070902_1071949_+\|NAD(P)-dependent-alcohol-dehydrogenase	unknown	unknown	gnl\|CDD\|176186
NC_012973.1\|WP_000892732.1\|1064294_1065167_-\|Sel1-like-repeat-protein-HcpC	unknown	unknown	gnl\|CDD\|223861
NC_012973.1\|WP_000883549.1\|1067773_1069051_+\|glucose-6-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|223441
NC_012973.1\|WP_000542251.1\|1069061_1069745_+\|6-phosphogluconolactonase	unknown	unknown	gnl\|CDD\|273494
NC_012973.1\|WP_000124332.1\|1076666_1077890_+\|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha	unknown	unknown	gnl\|CDD\|181999
NC_012973.1\|WP_000940224.1\|1063335_1064088_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187604
NC_012973.1\|WP_001124083.1\|1065880_1067707_-\|phosphogluconate-dehydratase	unknown	unknown	gnl\|CDD\|130264
NC_012973.1\|WP_000893829.1\|1078956_1080279_+\|adenylosuccinate-lyase	unknown	unknown	gnl\|CDD\|181437
NC_012973.1\|WP_000238137.1\|1077902_1078847_+\|pyruvate-ferredoxin-oxidoreductase-subunit-beta	unknown	unknown	gnl\|CDD\|239471
NC_012973.1\|WP_001153025.1\|1065241_1065862_-\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	unknown	unknown	gnl\|CDD\|273490
NC_012973.1\|WP_001196114.1\|1060033_1061068_-\|UDP-glucose-4-epimerase-GalE	unknown	unknown	gnl\|CDD\|273487
NC_012973.1\|WP_001127925.1\|1081193_1083170_-\|excinuclease-ABC-subunit-B	unknown	unknown	gnl\|CDD\|235395
NC_012973.1\|WP_000611616.1\|1083210_1083861_-\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_000714286.1\|1061782_1063318_+\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_000576599.1\|1073434_1074742_+\|hypothetical-protein	unknown	unknown	unknown
NC_012973.1\|WP_000486466.1\|1075688_1076249_+\|pyruvate-flavodoxin-oxidoreductase-subunit-gamma	unknown	unknown	gnl\|CDD\|180284
NC_012973.1\|WP_015829014.1\|1074748_1075411_-\|outer-membrane-protein	unknown	unknown	gnl\|CDD\|280099
NC_012973.1\|WP_000656174.1\|1076264_1076657_+\|4Fe-4S-binding-protein	unknown	unknown	gnl\|CDD\|236596
NC_012973.1\|WP_001126938.1\|1069731_1070742_+\|glucokinase	unknown	unknown	gnl\|CDD\|129832

Protein	Function_ID	Function_description	E-value
NC_012973.1\|WP_000816961.1\|1080349_1081183_+\|outer-membrane-protein	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.52741e-34
NC_012973.1\|WP_001265794.1\|1070902_1071949_+\|NAD(P)-dependent-alcohol-dehydrogenase	gnl\|CDD\|176186	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. 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 contains a host of 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.	1.57843e-160
NC_012973.1\|WP_000892732.1\|1064294_1065167_-\|Sel1-like-repeat-protein-HcpC	gnl\|CDD\|223861	COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function prediction only].	9.48591e-48
NC_012973.1\|WP_000883549.1\|1067773_1069051_+\|glucose-6-phosphate-dehydrogenase	gnl\|CDD\|223441	COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism].	0
NC_012973.1\|WP_000542251.1\|1069061_1069745_+\|6-phosphogluconolactonase	gnl\|CDD\|273494	TIGR01198, 6-phosphogluconolactonase_6PGL., 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with [Energy metabolism, Pentose phosphate pathway].	4.60062e-93
NC_012973.1\|WP_000124332.1\|1076666_1077890_+\|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha	gnl\|CDD\|181999	PRK09622, porA, 2-oxoacid:ferredoxin oxidoreductase subunit alpha.	0
NC_012973.1\|WP_000940224.1\|1063335_1064088_+\|SDR-family-oxidoreductase	gnl\|CDD\|187604	cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.	2.24764e-145
NC_012973.1\|WP_001124083.1\|1065880_1067707_-\|phosphogluconate-dehydratase	gnl\|CDD\|130264	TIGR01196, Phosphogluconate_dehydratase, 6-phosphogluconate dehydratase. A close homolog, designated MocB (mannityl opine catabolism), is found in a mannopine catabolism region of a plasmid of Agrobacterium tumefaciens. However, it is not essential for mannopine catabolism, branches within the cluster of 6-phosphogluconate dehydratases (with a short branch length) in a tree rooted by the presence of other dehydyatases. It may represent an authentic 6-phosphogluconate dehydratase, redundant with the chromosomal copy shown to exist in plasmid-cured strains. This model includes mocB above the trusted cutoff, although the designation is somewhat tenuous. [Energy metabolism, Entner-Doudoroff].	0
NC_012973.1\|WP_000893829.1\|1078956_1080279_+\|adenylosuccinate-lyase	gnl\|CDD\|181437	PRK08470, PRK08470, adenylosuccinate lyase; Provisional.	0
NC_012973.1\|WP_000238137.1\|1077902_1078847_+\|pyruvate-ferredoxin-oxidoreductase-subunit-beta	gnl\|CDD\|239471	cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity.	2.00638e-135
NC_012973.1\|WP_001153025.1\|1065241_1065862_-\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	gnl\|CDD\|273490	TIGR01182, KHG/KDPG_aldolase_., Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida [Amino acid biosynthesis, Glutamate family, Energy metabolism, Entner-Doudoroff].	9.03136e-111
NC_012973.1\|WP_001196114.1\|1060033_1061068_-\|UDP-glucose-4-epimerase-GalE	gnl\|CDD\|273487	TIGR01179, UDP-glucose_4-epimerase, UDP-glucose-4-epimerase GalE. Alternate name: UDPgalactose 4-epimerase This enzyme interconverts UDP-glucose and UDP-galactose. A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded from this model and described by a separate model. [Energy metabolism, Sugars].	0
NC_012973.1\|WP_001127925.1\|1081193_1083170_-\|excinuclease-ABC-subunit-B	gnl\|CDD\|235395	PRK05298, PRK05298, excinuclease ABC subunit UvrB.	0
NC_012973.1\|WP_000486466.1\|1075688_1076249_+\|pyruvate-flavodoxin-oxidoreductase-subunit-gamma	gnl\|CDD\|180284	PRK05844, PRK05844, pyruvate flavodoxin oxidoreductase subunit gamma; Validated.	3.48516e-128
NC_012973.1\|WP_015829014.1\|1074748_1075411_-\|outer-membrane-protein	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	6.09953e-36
NC_012973.1\|WP_000656174.1\|1076264_1076657_+\|4Fe-4S-binding-protein	gnl\|CDD\|236596	PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta; Reviewed.	5.72644e-84
NC_012973.1\|WP_001126938.1\|1069731_1070742_+\|glucokinase	gnl\|CDD\|129832	TIGR00749, Glucokinase_Glucose_kinase., glucokinase, proteobacterial type. This model represents glucokinase of E. coli and close homologs, mostly from other proteobacteria, presumed to have equivalent function. This glucokinase is more closely related to a number of uncharacterized paralogs than to the glucokinase glcK (fromerly yqgR) of Bacillus subtilis and its closest homologs, so the two sets are represented by separate models. [Energy metabolism, Glycolysis/gluconeogenesis].	0

>NC_012973.1|WP_001265794.1|1070902_1071949_+|NAD(P)-dependent-alcohol-dehydrogenase
MRVPSKGFAIFSKDGHFKPHDFSRHAVGPKDVLIDILYAGICHSDIHSAYSEWREGIYPMVPGHEIAGVIKEVGKEVKKFKVGDVVGVGCFVNSCKACKPCKEHQEQFCAKVVFTYDCLDSFHGNEPHMGGYSNNIVVDENYVISVDKNAPLEKVAPLLCAGITTYSPLKFSKVTKGTKVGVAGFGGLGGMAVKYAVAMGAEVSVFARNEHKKQDALSMGVKHFYTDPKQCKEELDFIISTIPTHYDLKDYLKLLTYSGELALVGLPPVEVAPALNVFEFIHLGNRKVYGSLIGGIKETQEMMDFSIKHNIYPEVDLILGKDIDTAYHNLTHGKAKFRYVIDMKKSFD
>NC_012973.1|WP_001126938.1|1069731_1070742_+|glucokinase
MPKTETYPRLLADIGGTNARFGLEVTPRQIECIEVLRCEDFESLSDAVRFYLSKCKESLKLHPIYGSFAVATPIMGDFVQMTNNHWTFSIETTRQCLTLKKLLVINDFVAQAYAISAMQENDLAQIGGIKCEINAPKAILGPGTGLGVSTLIQNSDGSLKVLPGEGGHVSFAPFDDLEILVWQYARSKFNHVSAERFLSGSGLVLIYEALSKRKGLEKVAKLSKAELTPQIISERALNGDYPICRLTLDTFCSMLGTLAADVALTLGARGGVYLCGGIIPRFIDYFKTSPFRARFETKGRMGAFLASIPVHVVLKKTPGLDGAGIALENYLLHDKI
>NC_012973.1|WP_000542251.1|1069061_1069745_+|6-phosphogluconolactonase
MGYQLFEFESLKDCHKALTERFKEFFNTALKKHHQVSIAFSGGRSPIGLLQKLSVLDLKWHECLISLVDERIIDTSHDDSNTKLLHDYLLQNNALKASFTPLLPEKISSDTNALFNFANQHFKQPHLAILGMGTDGHTASLFPETSAFLNEEKENIVLTKPANAPYERLSMSVHALENCEKLFLSISGVEKREVLEKALKENAPYSLPIARILHSKKVTTEVFYAKN
>NC_012973.1|WP_000883549.1|1067773_1069051_+|glucose-6-phosphate-dehydrogenase
MLDFDLVLFGATGDLAMRKLFVSLYEIYSHYGFKKDSRIIASGRKELSNEEFLALLCEKTQLHSREKGEEFLAHISYLHVRLDNPKDFEELSKIATKNKPLIFYFSISPSFFATTAQHLAKNALNHTNTRLILEKPLGHDLKTCQEIFQSISAFFKEEQIFRIDHYLGKKGVQNILELRLNNPILNILWDQISAVEICVYETLGVEERGEFYDKIGALRDMVQNHLLQVLSLIATDLPNDLKDLRKEKIKVLKTLQPPKDFKKQVIRAQYQGYRDENKVHKESQTETFVAIKAFLDTPKFKGVPFYLKHAKKMPHNQASVKIHFNAVNTLEFFLSQDKITLTLKDHQNPLILETHNKQEFLQPYAKLLYDAIQNNHNNFAHQLELEASWVFIDTLIEGFMNNATPLYSYESHHLNESEFLKPLYQ
>NC_012973.1|WP_001124083.1|1065880_1067707_-|phosphogluconate-dehydratase
MPKHSLEQIKEKITERSKKTRELYLENIFNPKNQPKIESLGCANIAHVTASMPEHLKMPLGSHKRKHFAIITAYNDMLSAHQPFKNYPDWIKKELQEHNAYASVASGVPAMCDGITQGYDGMELSLFSRDVIALSTAVGLSHNVFDGAFFLGVCDKIVPGLLIGALSFGNLASVFVPSGPMVSGIENYKKAKARQDFAMGKINREELLKVEMQSYHDVGTCTFYGTANSNQMMMEFMGLHVANSSFINPNNPLRKVLVEESAKRLASGKVLPLAKLIDEKSILNALIGLMATGGSTNHTLHLIAIARSCGVILNWDDFDAVSNLIPLLAKVYPNGSADVNAFEACGGLAFVIKELLKEGLLFEDVHTIMDTETQKGMQNYTKTPFLENDQLVYKDAINHSLNTDILRPVSEPFAANGGLKILKGNLGRAVVKISAIKDEHRKVKARAIVFKTQSEFLERFKNKELERDFVAVLPFQGPKSNGMPELHKLTTNLGALQDMGYKVALVTDGRMSGASGKVPSAIHLSPEGALNGAIIKIKDGDWIELDAPNNALNVLEKDFEKRDINPLFLETLENLEKPTFGLGRELFTSLRLNVNTAEEGGMSFGIKV
>NC_012973.1|WP_001153025.1|1065241_1065862_-|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase
MQDKTIEVLQISPIVPVVVIENIKDAVPLAQSLIEGGIPIIEVTLRSSCALEAIELIAKNVPKMRVGAGTILNLTQLEQAQNRGAEFLISPGLTPSLLEHAKKKGMPLIPGVSSSSEVMQALELGYNALKFFPAEYCGGVKLLNAFNGPFKGVKFCPTGGISADNMRSYLNLENVLCVGGSWLTPKDLIQNKEWDKITEICKRALA
>NC_012973.1|WP_000892732.1|1064294_1065167_-|Sel1-like-repeat-protein-HcpC
MLENVKKSFFRVLCLGALCLGGLMAEQDPKELVGLGAKSYKERDFTQAKKYFEKACDLKENSGCFNLGVLYYQGHGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFAKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGDGVVKNFKEALARYSKACEMQNGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAKGACDILKQLKIKV
>NC_012973.1|WP_000940224.1|1063335_1064088_+|SDR-family-oxidoreductase
MAHILVSGATSGFGLEIAKAFLQKNHVVFGTGRRKENLQKLQLTYPKHFIPLCFDLQKKLETKRALEAIFSMTDRIDALINNAGLALGLNKAYECELDDWEIMIDTNIKGLLHLTRLILPSMIEHNHGTIINLGSIAGTYPYPGGNVYGASKAFVKQFSLNLRADLAGTNIRVSNVEPGLCGETEFSMVRFKGDKIKAQSVYENTLYLKPQDIANIVLWIYEQPLHVNINRIEIMPTSQTFAPLPTHKNP
>NC_012973.1|WP_000714286.1|1061782_1063318_+|hypothetical-protein
MKKFLYTLLALLLIGLLTTYLILFTEWGNKIIASYIEKKINPNERYLSVKTFKLRFNSLDFKAQANDDSTLILKGDFSLLKQSVNLNYHIDIKNLYSFKEWIPYPLRGAIVTSGNIKGHRKALVIQGVSNAAQSHTTYNALLDDFKLSHLSLNAQDANLEDLLYLLNRPAYANAKVSLQADFNSLKPLEGHLILTANNALINNALINQIFHLNLKDTLIFNLSHSSDFKENKAISDTTLTSPLINFTALKSEYLFSVLKLNAPYTLEIPNLAKLYNITNHPLKGSLTLKGAIEQSPKLLKVSGHSNLLDGALDFTLLNKDLKARFSNISTLKALDLFHYPKFFQSIADANLDYDLSTKQGTLKARLKNARFLKNAFSDFLYSISKFDITKEIYNDANLVSQINQQRLLSDLSLKSPKTQLKIHNGLLDLNTKQMDMLMDAEILKFVFKMKLQGNMHQPKFSLILNEKAIQQNLQQGLKEILKNDTLKKGLDHLFKDDKLKEKLEKGLKGLF
>NC_012973.1|WP_001196114.1|1060033_1061068_-|UDP-glucose-4-epimerase-GalE
MALLFTGACGYIGSHTARAFLEKTKENIIIVDDLSTGFLEHLKALEHYYPNRVVFIQANLNETHKLDAFLNKQQLKDPIEAVLHFGAKISVEESTHLPLEYYTNNTLNTLELVKLCLKHAIKRFIFSSTAVVYGESSSSLNEESPLNPINPYGASKMMSERILLDTSKIADFKCVILRYFNVAGACMHNDYTTPYTLGQRTLNATHLIKIACECAVGKRKKMGIFGTNYPTRDGTCIRDYIHVDDLANAHLASYQTLLEKNKSEIYNVGYNQGHSVKEVIEKVKEISNNDFLVEILDKRQGDPASLIANNTKILQNTPFKPLYDNLDTIIKSALDWEEHLLRFQ
>NC_012973.1|WP_000576599.1|1073434_1074742_+|hypothetical-protein
MIFLKKSLYALLISSFSIPPLIKAASFVYDLKFMSFNFNLVAPNNNPYWNSLTKMQARLMPQIGVQLDKRQALMFGAWFIQNLHTHYSYFPYSWGVTMYYQYIGKNLRFFLGIVPRSYQIGHYPLSAFKKLFWFIDPTFRGGAFQFKPAYDPNRWWNGWFEGVVDWYGGRNWNNQPKKKNYDFDQFLYFVSSEFQFLKGYLGLGGQLVIFHNASHHSMGDNYPYGGNSYLKPGDVTPQWPNGYPYFSQKNNPQGGEIGKYSNPTILDRVYYHAYLKADFKNLMPYMDNIFMTFGTQSSQTHYCVRYASECKNARFYNSFGGEFYAQAQYKGFGIFNRYYFSNKPQMHFYATYGQSLYTGLPWYRAPNFDMIGLYYVYKNKWISVRADAFFNFLGGGDGYHLYGKGGKWITTYQQFLTLTIDTRELIDFVKSKTSK
>NC_012973.1|WP_015829014.1|1074748_1075411_-|outer-membrane-protein
MDKTMVKILMGMALLSSLQAAEAELDEKSKKPKFADRNTFYLGVGYQLSAINTSFSTESIDKSYFMTGNGFGVVLGGKFVAKTQAVEHVGFRYGLFYDQTFSSHKSYISTYGLEFSGLWDAFNSPKMFLGLEFGLGIAGATYMPGGAMHGIIAQNLGKENSLFQLLVKVGFRFGFFHNEITFGLKFPFIPNKRTEIVDGLSATTLWHRLPVAYFNYIYNF
>NC_012973.1|WP_000486466.1|1075688_1076249_+|pyruvate-flavodoxin-oxidoreductase-subunit-gamma
MFQIRWHARAGQGAITGAKGLADVISKTGKEVQAFASYGSAKRGAAMMAYNRVDDEPILNHERFMQPDYVLVIDPGLVFIENIFANEKEDTTYIITSYLNKEELFEKKPELKTRKVFLVDCLKISMETLKRPIPNTPMLGALMKVSGMLEIEAFKEAFKKVLGKKLTQEVIDANMLAIQRAYEEVQ
>NC_012973.1|WP_000656174.1|1076264_1076657_+|4Fe-4S-binding-protein
MKDWNEFEMGAVLFPFEKNAQSEMEKHNDERHYTEQSYFTTSVAHWRVAKPVHNNNICINCFNCWVYCPDAAILSREGKLKGVDYSHCKGCGVCVDVCPTNPKSLWMFEEQIEPATALTQWPQKQEKKKS
>NC_012973.1|WP_000124332.1|1076666_1077890_+|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha
MARSIELQEIEVWDGNTASSNALRQAQIDVIAAYPITPSTPIVQNYGSFKDNGYIDGEFVLVESEHAAMSACVGAAAAGGRVSTATSSQGLALMVEVLYQASGMRLPIVLNLVNRALAAPLNIHGDHSDMYLSRDSGWISLCTCNPQEAYDFTLMAFRIAEHQKVRVPTIVNQDGFLCSHTVQNVRPLSDAVAYQFVGEYQTKHSLLDFDKPVSYGAQAEEEWHYEHKAQLHHAIMSASSVIEEVFNDFAKLTGRQYHLTKTFQLEDAEIAIFALGTTYESAIVAAKEMRKKGIKAGVATIHSLRPFPYERLGQDLKNLKALAILDKSSPAGAMGAMFNEVTSAVYQTQGTKHPVVSNYIYGLGERDMTIAHLCEIFEEINEDALKGTLTHPTQQFVGLRGPKMSFF
>NC_012973.1|WP_000238137.1|1077902_1078847_+|pyruvate-ferredoxin-oxidoreductase-subunit-beta
MVKEVKTLKGFSQSAEKFQGSHLLCPGCGHGIIVREVLNAVDGPIVLGNSTGCLEVCSAVYPHTSWDVPWIHIGFENGSTAISGVEAMYKALTNKGRYQGQKPKFVAFGGDGASYDIGLQFISGCMERGHDMTYICLDNENYANTGGQRSGSTPLGASTSTTPSGSVSFGKKEKKKDIVNIMASHGVPYVAQLSPNKWKDMNKKIKTALDTEGPCFINALSPCTTEWKFESNKTIELADMAVDSLMFPLFEIFNGRELKITYRPRNIIPVRDYLGAQKRFKHLFKKENEHIIEELQKDVNERWEYLQRREEAKV
>NC_012973.1|WP_000893829.1|1078956_1080279_+|adenylosuccinate-lyase
MLERYANEEMKALWNEQTKFETYLEVEKAVVRAWNKLGQIQDSDCEKICAKAAFNLERIKEIEKTTKHDLIAFTTCVAESLGEESRFFHYGITSSDCIDTAMALLMTKSLKLIQKGVKNLYETLKNRALEHKDTLMVGRSHGVFGEPITFGLVLALFADEIKRHLKALDLTMEFISVGAISGAMGNFAHAPLELEELACEFLGLKTANISNQVIQRDRYARLACDLALLASSCEKIAVNIRHLQRSEVYEVEESFSTGQKGSSAMPHKRNPILSENITGLCRVIRSFTTPMLENVALWHERDMSHSSVERFALPDLFITSDFMLSRLNGVIENLVVYPKNMLKNLALSGGLVFSQRVLLELPKKGLSREESYSIVQENAMKIWEVLQQGAFKNADENLFLNALLNDERLKKYLSEDEIKACFDYSYYTKNVGAIFKRVFG
>NC_012973.1|WP_000816961.1|1080349_1081183_+|outer-membrane-protein
MKRALYLILGLSYALHADSFKDVLTKGDYTFFNKKVVSPIKRYADRSAFYLGLGYQLGSIQHNYSNLNLSQQFNKSQIIFSDGLSPVFKNSYVSNGLGVQVGYKWVGKHEEMKWFGFRWGLFYDLSASLYGQKESQSVIISTYGTYMDLLLNAYNGDKFFAGFNLGIAFAGVYDKLSDALLYQALLLDTFGGKVDPNGFQFLVDLGVRLGNKRNQFGFGIKIPTYYFNHYYSMNNISNNSEDVLKVLRFLEYGINSLLYQVDFRRNYSVYFNYTYSF
>NC_012973.1|WP_001127925.1|1081193_1083170_-|excinuclease-ABC-subunit-B
MPLFDLKSPYPPAGDQPQTIEALTKSLKNNNHYQTLVGVTGSGKTYTMANIIAQTNKPTLIMSHNKTLCAQLYSEFKAFFPHNRVEYFISHFDYYQPESYIPRRDLFIEKDSSINDDLERLRLSATTSLLGYDDVIVIASVSANYGLGNPEEYLKVMEKIKVGEKRAYKSFLLKLVEMGYSRNEVVFDRGSFRATGECVDIFPAYNDAEFIRIEFFGDEIERIAVFDALERNEIKRLDSVMLYAASQFAVGSERLNLAIKSIEDELALRLKFFKEQDKMLEYNRLKQRTEHDLEMISATGVCKGIENYARHFTGKAPNETPFCLFDYLGIFEREFLVIVDESHVSLPQFGGMYAGDMSRKSVLVEYGFRLPSALDNRPLKFDEFIHKNCQFLFVSATPNKLELELSKKNVAEQIIRPTGLLDPKFEVRDSDKQVQDLFDEIKLVVARDERVLITTLTKKMAEELCKYYAEWGLKVRYMHSEIDAIERNHIIRSLRLKEFDILIGINLLREGLDLPEVSLVAIMDADKEGFLRSETSLIQTMGRAARNANGKVLLYAKKITQSMQKAFEITSYRRAKQEEFNKIHNITPKTVTRALEEELKLRDDEIRIAKALKKDKMPKSEREKIIKELDKKMRECTKNLDFEEAMRLRDEIAQLRTL
>NC_012973.1|WP_000611616.1|1083210_1083861_-|hypothetical-protein
MINYPNLPNSALEITEQPEVKEITNELLKQLQNALNSNSLFTEQVELSLKGIVRILEVLLSLDFFKNANEIDSSLRNSIEWLNNAGESLKNKMKEYEGFFSEFNTSMKSNEQEVTSILNANAENIKSEIKKLENQLIETTTRLLTSYQIFLNQARENATTQINTNQTQAINNINEAKTTANNEINANKTASLETLKQEKKPIIIKTLIFLRLNKAC

You can click texts colored in the table to view more detailed information

Click the colored protein region to show detailed information

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_012973_3	3.3\|902827\|29\|NC_012973\|CRISPRCasFinder	902827-902855	29	NZ_CP045351	Vibrio sp. THAF100 plasmid pTHAF100_a, complete sequence	1090166-1090194	6	0.793
NC_012973_3	3.3\|902827\|29\|NC_012973\|CRISPRCasFinder	902827-902855	29	KJ101592	Enterobacter phage PG7, complete genome	168930-168958	7	0.759
NC_012973_3	3.3\|902827\|29\|NC_012973\|CRISPRCasFinder	902827-902855	29	GU323318	Enterobacteria phage CC31, complete genome	161397-161425	7	0.759
NC_012973_3	3.3\|902827\|29\|NC_012973\|CRISPRCasFinder	902827-902855	29	LT614807	Cronobacter phage Pet-CM3-4 genome assembly, chromosome: I	167672-167700	7	0.759
NC_012973_3	3.2\|902770\|32\|NC_012973\|CRISPRCasFinder	902770-902801	32	U88974	Streptococcus thermophilus temperate bacteriophage O1205, complete genome	23169-23200	8	0.75
NC_012973_3	3.2\|902770\|32\|NC_012973\|CRISPRCasFinder	902770-902801	32	NC_004303	Streptococcus phage O1205, complete genome	23169-23200	8	0.75
NC_012973_3	3.2\|902770\|32\|NC_012973\|CRISPRCasFinder	902770-902801	32	MK448589	Streptococcus satellite phage Javan632, complete genome	4591-4622	8	0.75
NC_012973_3	3.2\|902770\|32\|NC_012973\|CRISPRCasFinder	902770-902801	32	NZ_CP022523	Pseudoalteromonas sp. NC201 plasmid pNC201, complete sequence	752261-752292	9	0.719

1. spacer 3.3|902827|29|NC_012973|CRISPRCasFinder matches to NZ_CP045351 (Vibrio sp. THAF100 plasmid pTHAF100_a, complete sequence) position: , mismatch: 6, identity: 0.793

atgacaatactagctttaataacgacacc	CRISPR spacer
gtaagaatattagctttagtaacgacacg	Protospacer
.*.* ****.********.*********

2. spacer 3.3|902827|29|NC_012973|CRISPRCasFinder matches to KJ101592 (Enterobacter phage PG7, complete genome) position: , mismatch: 7, identity: 0.759

atgacaatactagctttaataacgacacc	CRISPR spacer
atgacaatactaccttcaataacttcttt	Protospacer
************ ***.******  * ..

3. spacer 3.3|902827|29|NC_012973|CRISPRCasFinder matches to GU323318 (Enterobacteria phage CC31, complete genome) position: , mismatch: 7, identity: 0.759

atgacaatactagctttaataacgacacc	CRISPR spacer
atgacaatactaccttcaataacttcttt	Protospacer
************ ***.******  * ..

4. spacer 3.3|902827|29|NC_012973|CRISPRCasFinder matches to LT614807 (Cronobacter phage Pet-CM3-4 genome assembly, chromosome: I) position: , mismatch: 7, identity: 0.759

atgacaatactagctttaataacgacacc	CRISPR spacer
atgacaatactaccttcaataacttcttt	Protospacer
************ ***.******  * ..

5. spacer 3.2|902770|32|NC_012973|CRISPRCasFinder matches to U88974 (Streptococcus thermophilus temperate bacteriophage O1205, complete genome) position: , mismatch: 8, identity: 0.75

atagcgcccaatccacttttgaaaacagcaat	CRISPR spacer
ttagcgcccaaaacacttttgaaaactgatcc	Protospacer
 **********  ************* *   .

6. spacer 3.2|902770|32|NC_012973|CRISPRCasFinder matches to NC_004303 (Streptococcus phage O1205, complete genome) position: , mismatch: 8, identity: 0.75

atagcgcccaatccacttttgaaaacagcaat	CRISPR spacer
ttagcgcccaaaacacttttgaaaactgatcc	Protospacer
 **********  ************* *   .

7. spacer 3.2|902770|32|NC_012973|CRISPRCasFinder matches to MK448589 (Streptococcus satellite phage Javan632, complete genome) position: , mismatch: 8, identity: 0.75

----atagcgcccaatccacttttgaaaacagcaat	CRISPR spacer
aaccgta----ccaatcgccttttgaaaacagcaag	Protospacer
    .**    ******  ****************

8. spacer 3.2|902770|32|NC_012973|CRISPRCasFinder matches to NZ_CP022523 (Pseudoalteromonas sp. NC201 plasmid pNC201, complete sequence) position: , mismatch: 9, identity: 0.719

----atagcgcccaatccacttttgaaaacagcaat	CRISPR spacer
gatcaagg----caatctccttttgaaaacagcaac	Protospacer
    * .*    *****. ****************.

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1513748 : 1522879

Helicobacter_phage(66.67%)

integrase,transposase

attL 1513482:1513500|attR 1520931:1520949

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
1513482:1513500	attL	NA	NA	NA	NA
WP_001249876.1\|1513748_1514027_+	hypothetical protein	A0A1S5RFL3	Helicobacter_phage	2.4e-26	80.4
WP_000553147.1\|1514026_1515151_+\|integrase	site-specific integrase	A0A1S5RH79	Helicobacter_phage	7.3e-191	94.4
WP_000434472.1\|1515362_1515683_+	hypothetical protein	A0A1S5RHA0	Helicobacter_phage	9.3e-43	81.1
WP_000634088.1\|1515669_1515810_+	hypothetical protein	A0A1S5RFE1	Helicobacter_phage	3.1e-11	86.7
WP_001106758.1\|1515810_1516740_+	helix-turn-helix domain-containing protein	A0A1S5RFB4	Helicobacter_phage	2.5e-160	93.2
WP_079996194.1\|1517055_1517241_+	hypothetical protein	A0A1S5RFM5	Helicobacter_phage	2.4e-19	89.5
WP_000176316.1\|1517856_1519086_-\|transposase	IS200/IS605 family element transposase accessory protein TnpB	G3MB42	Bacillus_virus	3.1e-70	39.8
WP_000836802.1\|1519072_1519705_-\|transposase	IS607 family transposase	A0A1V0SJI5	Klosneuvirus	2.1e-38	45.5
WP_001114660.1\|1519701_1519896_-	type II toxin-antitoxin system HicA family toxin	NA	NA	NA	NA
WP_000906663.1\|1519888_1520107_-	type II toxin-antitoxin system HicB family antitoxin	NA	NA	NA	NA
WP_000943868.1\|1520999_1521977_+	Sel1-like repeat protein HcpG	NA	NA	NA	NA
1520931:1520949	attR	NA	NA	NA	NA
WP_015829049.1\|1522015_1522879_-	3'-5' exonuclease	A0A0A7RWA3	Clostridium_phage	1.1e-13	31.8

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_012973

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CRISPR-Cas detection and classification

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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