CRISPRimmunity

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_017361	Helicobacter pylori SouthAfrica7, complete sequence	4 crisprs	cas14j,cas2,DEDDh	0	2	0	0
NC_017373	Helicobacter pylori SouthAfrica7 plasmid unnamed, complete sequence	0 crisprs	cas14j	0	0	0	0

1. NC_017361

CRISPR-Cas detection and classification

Crispr_ID: NC_017361_1

• CRISPR_ID: NC_017361_1
• CRISPR_location: 776949-777086
• CRISPR_type: Orphan
• Repeat_type: NA
• Spacer_info: 1 spacers

Consensus repeat of NC_017361_1

Consensus_repeat	Method
AAAACACCTAGCCATAAACACCCATTAAAATAATTGCTACTTCATCTTTAA	CRISPRCasFinder

spacers of NC_017361_1

>1.1|777000|36|NC_017361|CRISPRCasFinder
CCTTAAATCAAAAACTATTTTTTAAAGGGGTTGTTA

CRISPR arrays and Neighbor proteins around NC_017361_1

CRISPR arrays

The CRISPR arrays of NC_017361_1

>merge|NC_017361|1|776949-777086|CRISPRCasFinder
AAAACACCTAGCCATAAACACCCATTAAAATAATTGCTACTTCATCTTTAACCTTAAATCAAAAACTATTTTTTAAAGGGGTTGTTAAAAACACCTAGCCATAAACACCCATTAAAATAATTACTACTTCATCTTTAA

>NC_017361|1|1|776949-777086|CRISPRCasFinder
AAAACACCTAGCCATAAACACCCATTAAAATAATTGCTACTTCATCTTTAA	CCTTAAATCAAAAACTATTTTTTAAAGGGGTTGTTA
AAAACACCTAGCCATAAACACCCATTAAAATAATTACTACTTCATCTTTAA

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_017361.1|WP_000725317.1|766315_766582_+|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_001158794.1|778152_780213_-|cadmium-translocating-P-type-ATPase	unknown	unknown	gnl|CDD|319847
NC_017361.1|WP_001131508.1|786127_786604_-|cyclic-pyranopterin-monophosphate-synthase-MoaC	unknown	unknown	gnl|CDD|236483
NC_017361.1|WP_000739261.1|785224_786007_-|flagellar-sheath-lipoprotein-HpaA	unknown	unknown	gnl|CDD|368341
NC_017361.1|WP_001133709.1|773898_775131_+|ABC-transporter-permease	unknown	unknown	gnl|CDD|226957
NC_017361.1|WP_000912612.1|787156_787594_-|molybdenum-cofactor-biosynthesis-protein-MoaE	unknown	unknown	gnl|CDD|223391
NC_017361.1|WP_001168764.1|769598_770126_-|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_000651326.1|763686_766245_+|bifunctional-aconitate-hydratase-2/2-methylisocitrate-dehydratase	unknown	unknown	gnl|CDD|129223
NC_017361.1|WP_000643132.1|770610_771165_-|outer-membrane-lipoprotein-chaperone-LolA	unknown	unknown	gnl|CDD|178807
NC_017361.1|WP_000588083.1|771311_773909_+|preprotein-translocase-subunit-SecA	unknown	unknown	gnl|CDD|237259
NC_017361.1|WP_000540573.1|782291_782879_-|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP	unknown	unknown	gnl|CDD|178955
NC_017361.1|WP_001108226.1|775410_776910_+|outer-membrane-beta-barrel-protein-HofF	unknown	unknown	gnl|CDD|334957
NC_017361.1|WP_001185838.1|781762_782287_-|peptide-deformylase	unknown	unknown	gnl|CDD|234668
NC_017361.1|WP_001146007.1|766831_768130_+|DDE-transposase	unknown	unknown	gnl|CDD|227946
NC_017361.1|WP_001210664.1|762871_763555_-|hypothetical-protein	unknown	unknown	gnl|CDD|224344
NC_017361.1|WP_001047839.1|782898_784254_-|trigger-factor	unknown	unknown	gnl|CDD|234956
NC_017361.1|WP_000911447.1|768223_769591_+|outer-membrane-beta-barrel-protein-HofE	unknown	unknown	gnl|CDD|334957
NC_017361.1|WP_001193334.1|786614_787145_-|molybdopterin-adenylyltransferase	unknown	unknown	gnl|CDD|181837
NC_017361.1|WP_000611102.1|780236_781757_-|YifB-family-Mg-chelatase-like-AAA-ATPase	unknown	unknown	gnl|CDD|223679
NC_017361.1|WP_001080913.1|784366_785203_-|outer-membrane-protein	unknown	unknown	gnl|CDD|280099

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_017361.1|WP_000739261.1|785224_786007_-|flagellar-sheath-lipoprotein-HpaA	gnl|CDD|368341	pfam05211, NLBH, Neuraminyllactose-binding hemagglutinin precursor (NLBH). This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding hemagglutinin precursor (NLBH) or N-acetylneuraminyllactose-binding fibrillar hemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium.	4.6092e-79
NC_017361.1|WP_001158794.1|778152_780213_-|cadmium-translocating-P-type-ATPase	gnl|CDD|319847	cd07548, P-type_ATPase-Cd_Zn_Co_like, P-type heavy metal-transporting ATPase, similar to Bacillus subtilis CadA which appears to transport cadmium, zinc and cobalt but not copper out of the cell. Bacillus subtilis CadA/YvgW appears to transport cadmium, zinc and cobalt but not copper, out of the cell. Functions in metal ion resistance and cellular metal ion homeostasis. CadA/YvgW is also important for sporulation in B. subtilis, the significant specific expression of the cadA/yvgW gene during the late stage of sporulation, is controlled by forespore-specific sigma factor, sigma G, and mother cell-specific sigma factor, sigma E. This subfamily also includes Helicobacter pylori CadA an essential resistance pump with ion specificity towards Cd(2+), Zn(2+) and Co(2+), and Zn-transporting ATPase, ZiaA(N) in Synechocystis PCC 6803. Transcription of ziaA is induced by Zn under the control of the Zn responsive repressor ZiaR. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle.	0
NC_017361.1|WP_001133709.1|773898_775131_+|ABC-transporter-permease	gnl|CDD|226957	COG4591, LolE, ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane].	2.20373e-115
NC_017361.1|WP_000912612.1|787156_787594_-|molybdenum-cofactor-biosynthesis-protein-MoaE	gnl|CDD|223391	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism].	7.18115e-44
NC_017361.1|WP_000643132.1|770610_771165_-|outer-membrane-lipoprotein-chaperone-LolA	gnl|CDD|178807	PRK00031, lolA, outer membrane lipoprotein chaperone LolA.	2.53227e-51
NC_017361.1|WP_000651326.1|763686_766245_+|bifunctional-aconitate-hydratase-2/2-methylisocitrate-dehydratase	gnl|CDD|129223	TIGR00117, Aconitate_hydratase_2, aconitate hydratase 2. Aconitate hydratase (aconitase) is an enzyme of the TCA cycle. This model describes aconitase 2, AcnB, which has weak similarity to aconitase 1. It is found almost exclusively in the Proteobacteria. [Energy metabolism, TCA cycle].	0
NC_017361.1|WP_001131508.1|786127_786604_-|cyclic-pyranopterin-monophosphate-synthase-MoaC	gnl|CDD|236483	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC.	2.99557e-91
NC_017361.1|WP_000588083.1|771311_773909_+|preprotein-translocase-subunit-SecA	gnl|CDD|237259	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.	0
NC_017361.1|WP_000540573.1|782291_782879_-|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP	gnl|CDD|178955	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed.	4.25415e-144
NC_017361.1|WP_001108226.1|775410_776910_+|outer-membrane-beta-barrel-protein-HofF	gnl|CDD|334957	pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).	0
NC_017361.1|WP_001185838.1|781762_782287_-|peptide-deformylase	gnl|CDD|234668	PRK00150, def, peptide deformylase; Reviewed.	5.96258e-76
NC_017361.1|WP_001146007.1|766831_768130_+|DDE-transposase	gnl|CDD|227946	COG5659, COG5659, FOG: Transposase [DNA replication, recombination, and repair].	6.20037e-138
NC_017361.1|WP_001210664.1|762871_763555_-|hypothetical-protein	gnl|CDD|224344	COG1427, COG1427, Predicted periplasmic solute-binding protein [General function prediction only].	4.95736e-69
NC_017361.1|WP_001047839.1|782898_784254_-|trigger-factor	gnl|CDD|234956	PRK01490, tig, trigger factor; Provisional.	3.46611e-122
NC_017361.1|WP_000911447.1|768223_769591_+|outer-membrane-beta-barrel-protein-HofE	gnl|CDD|334957	pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).	0
NC_017361.1|WP_001193334.1|786614_787145_-|molybdopterin-adenylyltransferase	gnl|CDD|181837	PRK09417, mogA, molybdenum cofactor biosynthesis protein MogA; Provisional.	1.71124e-114
NC_017361.1|WP_000611102.1|780236_781757_-|YifB-family-Mg-chelatase-like-AAA-ATPase	gnl|CDD|223679	COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones].	0
NC_017361.1|WP_001080913.1|784366_785203_-|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.	8.21667e-43

Protein sequences

>NC_017361.1|WP_001108226.1|775410_776910_+|outer-membrane-beta-barrel-protein-HofF
MNYKVASAKNIATLLFLFSSQSQAFDLGKIAKIKAGAESFSKVGFNNKPINTNKGIYPTETFMTIMAYMQVDFTELLPKSATANGHHLDGSLGGWGGAVIYDSTKDFINEVTGKPYGAMAWNYVGYWGGLVGQKPWASCGLATGNLTQGQYDKMTQAEMTQLSDQEALAASTCAKTYADHTRNYVIYNAYLRYNYKDIFQIRGGRYESPADYMSGYNQGLDMTLNLGNFKFWWFSSFGRGFAYNEWLYNFYSPKTYTLKNGQTINPGVHAFYIIWNYKGFSIQPFVYFSPFNEYDPNFTITYDSNPTFTGLGFRSQTDVTVLNPFYAKRFWDTYQFGMPAGKNAHSLMIKQKFEWNEYNFGFGIYKSFGNANWMIGYHGNRLGFDFWTNTVYANTLNSLSYMMDANAFTVFAFGGGVHRKLLWGLLGRLTYGPRANEQVLSLNLGYKFTKNFSADIKFEYYNVLMHQGYKMGWNGPKLDSQPATDQDRSHIFTEIVWKL
>NC_017361.1|WP_001133709.1|773898_775131_+|ABC-transporter-permease
MPNRSLIFFLIKRYLRFDKSQPFISITALLAFFGVAVGVMVLIVAMAIMNGMSKEFEKKLFVMNYPLTLYTTSPYGISEEVVQALEKKFPNLLFSPYLQTQSLIKSAHSMNGGVVFGVDFSKERRINEVLNDALKNMDEKELTKNPFSLIIGKSLRYSLNLDLNQKADLFFTELEPTGLTLSPIMKRFVIKGGFDSGLKSYDMSYMYTNIQALSAIRRLPLGLYDGVHVYSKTPMKDIENIRNALKTINHHGIGIEGWWQQNGNFFSAMELEKRALFIVLMLIILMASLNIISSLLMVVMNRRKEIALLFSMGSSQKEIQKTFFYLGNIIGLGGVILGVVLAFVSMYLLSVFPIISLPEDVYGINTLPLDLSLIDFLLTLIGSVVIVALSSYYPSKKASAIDALSVLRNE
>NC_017361.1|WP_000588083.1|771311_773909_+|preprotein-translocase-subunit-SecA
MIKAIIGKIIGTRNDRWIKQYKKKVLAINALEPTYEKMSDIELQNAFEELKKRVRSTEKDLQEKILLEVLPESFAITREASKRILKMRHFDAQLIGGMVLNDGKIAEMKTGEGKTLVATLAVALNAMKSESVYVVTVNDYLAHRDSKEMEPLYHFLGYSVGTITASVRDDDERLEIYSKDIVYGTNNEFGFDYLRDNMKYSLEHKVQKSHAFAIVDEVDSILIDEARTPLIISGPVDRRMENYNKADEVAKSMQVEVDFTIDEKNRAILITEEGIKKAENLFGVDNLYKIENAALSHHLDQALKANYLFFIDKDYIVANNEVVIVDEFTGRLSEGRRFSEGLHQALEAKEGVSIKEESQTLADITFQNYFRMFSKLSGMTGTAQTEATEFLEIYNLEVVSIPTNLAIKRKDLNDLIYKSEKEKFDAVILKIKELHDKGQPVLVGTASIEKSETLHALLKKERIPHTVLNAKQHTKEAEIIKDAGLKGAVTIATNMAGRGVDIKLTDEIKELGGLYIIGTERHESRRIDNQLRGRSGRQGDPGVSQFYLSLEDNLLRIFGSDRIKGVMEKLGLKDGEHIESKLVTRAVENAQKKVENLHFESRKHLLEYDDVANEQRKSVYKFRDELLDVNYDIGAKIAENREYALNQIFSKLKAFDHQNLSEEELLGLKNILKEDFNTNIELENLEQADSIENFVAEKLKNDYENKMKAIDSEQRSRIERIVYLQILDNAWREHLYTMDNLKTGINLRGYNQKDPLVEYKKESYNLFLELIEDIKIEAIKTFSKIQFENEQDSSDAERYLDNFSEEREHESVTYRHEEALDEDLNMSMKAFSKTPKRNEPCPCGSGKKYKDCCAKSGPKKGLFAK
>NC_017361.1|WP_000643132.1|770610_771165_-|outer-membrane-lipoprotein-chaperone-LolA
MKAFLKIVMVLIFMSVAYAKNPSTLSKEEEVLQNLQSFSAHFKQVLKNEKPLVYHGILKAKAPNWALWVYEKPLKKEIYMNDKEVVVYEPNLFQATITPLKDKTDFFTILKRLKKQTDGSFKTTINKTTYRLVFKDGKPFSLEFKDDMNNLVTITFSQAEINPKIPNEIFVFNPKDENIDIVRQ
>NC_017361.1|WP_001168764.1|769598_770126_-|hypothetical-protein
MQKFFSRFRRWALPFYFVSALAAIDIDEVTEAQANSVKLSDQLVSLSDKLLEKAVDRGRNTDHLKDLNDLHEKIKHLRLILEPKPKDKENNPNLKDHQGSETIEIGEAIKKALGDPVFPQDALDAALQIDKQLDSFKQDSLIDVKPLKDVLAQLEAELRKAIDFQKQWLNSTKPN
>NC_017361.1|WP_000911447.1|768223_769591_+|outer-membrane-beta-barrel-protein-HofE
MLKFQKLPLLFVFILYNQSPLLAFDYKFSGVAESFSKVGFNHSKLNSKEGIFPTATFVTATIKLQVDSNLLPKNIEKHSLKIGVGGILGALAYDSTKTLIDQATHQVYGSELFFFIGRWWGYLGNAPWKDSRIESDAHTRNYVLYNSYLFYSYGDKFHLKLGRYLSNMDFMSGYTQGFEVDYKINSKIALKWFSSFGRALAAGQWIRDWYSPIVTEDGRKDVDYGIHAVQLYFSSKHVQATPFFYFSPKIYGAPGIKIHIDSNPKFKGLGLRSQTLINVIFPVYAKDLYDVYWRNSKIGEWGSSLLIHQRFDYNEFNFGFGYYQNFGNANARIGWYGNPIPFDIRSNSIYGLVFSNAVTADSVSGYVFGGGVYRGFLWGILGRYTYATRASERSINLHLGYKWNSFFSVDVNLQYYAVSMHTGYKVNDLTSPFNKAFKANTQDRSNLMVSVKFFF
>NC_017361.1|WP_001146007.1|766831_768130_+|DDE-transposase
MPYALRKRFFKRFILVVSVVSTFCAISLNAKSYLFSPLPPAHQQIIKTEPCSLECLKDLMLQNQIFSFVSQYDNNNQDESLKTYYKDILNKLNPVSIASQNPTKESYEPKIELAILLPKKVVGRYAISVMNTLLAYLNTRNNDFNIQVFDSDEESPEKLEQTYKEIEKEKFPFIIALLTKEGVENLLQNTTISTPTYVPTVNKTQLENHTEPSLSERLYFGGIDYKEQLGMLISFIGHNSPVIEYDDDGLIGERLRQITESLSIEVKHQENISYKQATSFSKNFRKHDAFFKNSTLILNTPTTKSGLILSQIGLLEYKPLKILSTQINFNPSLLLLTQPKDRKNLFIVNALQNSDETLIEYASLLESDLRHDWVNYSSAIGLEVFLNTLDPHFKKSFQESLEDNQVRYHNQIYQALGYSFEPIKNESGTKKE
>NC_017361.1|WP_000725317.1|766315_766582_+|hypothetical-protein
MKKIVVSWCVALVFLSANPEQANKVISNADLIKEIRDLKKIINAQSTEINNLKRVQEVLSGQLGSMHADMVTTRDYCISLRPYIYNWR
>NC_017361.1|WP_000651326.1|763686_766245_+|bifunctional-aconitate-hydratase-2/2-methylisocitrate-dehydratase
MKDFLEDYKKSVLERESEGIPPLPLNAKQVEAVVEILMKDPANAAFAKELLIHRVSPGVDEGAKVKAEFLAKLSQKKLECAHISALEATTLLGTMLGGYNVEPLIMGLESQDKEIAKESAKALKTTLLVYGSFDKIAAMSKTNALAKEVIESWANAEWFLNKEPLSECIEACVLKIDGETNTDDLSPASDAFTRSDIPLHAKAMLKNRIENYEQRIEAIKTKGVPVAYVGDVVGTGSSRKSATNSIMWHFGKDIPFVPNKRSGGIVIGGVIAPIFFATCEDSGALPIVADVKDLKEGDLIKIYPYKGEITLNDKVVSAFKLEPETLLDEVRASGRIPLIIGRGLTNKARKFLGLGESEAFKKPSAPKSDAKGYTLAQKIVGCACGVEGILPGTYCEPKVTTVGSQDTTGAMTRDEVKELASLKFDAPFVLQSFCHTAAYPKPSDVSLHATLPSFITQRGGVALHPGDGVIHTWLNRMGLPDTLGTGGDSHTRFPLGISFPAGSGLVAFAAVTGTMPLNMPESVLVRFKGDMNPGITLRDLVNAIPYYAIKKGLLTVEKKGKINVFNGRILEIEGLPDIKMEQAFELSDASAERSAAACVVRLNKEPMIEYLKSNIKLIDEMIASGYEDKETLKKRRDAMQAWVDKPVLLEPDSNAQYAAVIEIDVTEITEPILACPNDPDDVATLSEVLADTTGKRPHAIDEVFIGSCMTNIGHFRAFGEIVKNAPPSQARLWVVPPSKMDEQELINEGYYAIFGAAGARTEVPGCSLCMGNQARVRDNAVVFSTSTRNFDNRMGRGAKVYLGSAELGAACALLGRIPTKEEYMNLVSEKLESQKDKIYRYMNFNLMEKFKL
>NC_017361.1|WP_001210664.1|762871_763555_-|hypothetical-protein
MRFGKIDYLNMLPFDVFIKSYPTPCHFKQFLRLKKTYPSKLNQSFLFRRIDAGFISSIAGHQFALHPYSLGIVAYKEVLSVLVVNQENAFDKESASSNALSQALGLKGEVLIGNKALQFYYSNPKKDFIDLATLWYEKKRLPFVFGRLCYHQNKDFYKRLSLAFKHKKTKIPYYILKEASLKTNLKHQDILNYLKKIYYSLGKKERLGLKAFYRELLFKRIQKPKRF
>NC_017361.1|WP_001158794.1|778152_780213_-|cadmium-translocating-P-type-ATPase
MQEYHIHNLDCPDCAAKLERDLNKLDYVKKAQINFSTSKLFLDTSDFEKVKAFIKQNEPHLSLSFKEAVEKPLSFTPLISTIIVFLGAILILHLDPSPFIEKAVFVVLALVYLISGKDVILGAFRGLRKGQFFDENALMLIATIAAFCVGAYEESVSIMVFYSAGEFLQKLAIARSKKSLKALVDVAPNLAYLKKGDALVSVAPEDLQINDIVVVKVGEKVPVDGVVIKGESLLDERALSGESMPVNVKENSKVLGGSLNLKAVLEIQVEKRYKDSSIAKVVDLVQQATNEKSETEKFITKFSRYYTPSVLFIALMIAVLPPLFSMGSFDEWIYRGLVALMVSCPCALVISVPLGYFGGVGAASRKGILMKGVHVLEVLTQAKSIAFDKTGTLTKGVFKVMDIVPQNGHSKEEVLHYASCSQLLSTHPIALSIQKACEEMLKDDQHQHDIKNYEELSGMGVKAQCHADLIIAGNEKMLDQFNIAHSPSPENGTIVHVAFNQNYIGYIVISDEIKDNAIECLRDLKAQGIENFCILSGDRKSATESIAKTLGCEYHASLLPEEKTSVFKNFKERYKAPAIFVGDGINDAPTLASADVGIGMGKGSELSKQSADIVITNDSLNSLVKVLAIAKKTKSIIWQNILFALGIKAVFIVLGLMGVASLWEAVFGDVGVTLLALANSMRAMRA
>NC_017361.1|WP_000611102.1|780236_781757_-|YifB-family-Mg-chelatase-like-AAA-ATPase
MINTIFCTTMQKGVAEIVAVEATFTRALPAFVISGLANNSIQEAKQRVQSALQNNDFTFPPLKITINLSPSDLPKSGSHFDLPIALLIALQKQELSAKEWFAFGELGLDGKIKPNSNIFPMLLDIAIKRPHAKVIAPKANEELFSLIPNLQCFFVEHFKEALEILQNPEIKAHTHIKNLPFETIEIHHKEYYFSDTYALDFKEVKGQAIAKEAALIASAGFHNLLLEGSPGCGKSMIVNRMRYILPPLSLNEILEATKLRILSEQDSAYYPLRSFRNPHQSASKSSILGSSSLKEPKPGEIALAHNGMLFFDELPHFKKDILEALREPLENNKLVISRVHSKIEYETSFLFVGAQNPCLCGNLLSTTKACRCQDREITQYKNRLSEPFLDRIDLFVQMEEGSYKDAPSHSWTSKEMHQLVLLAFKQQKLRKQSVFNGKLNEEQIERFCPLNFEAQKLLEQAAERFNLSMRSINKVKKVARTIADLNACENIEKSHMLKALSFRKIS
>NC_017361.1|WP_001185838.1|781762_782287_-|peptide-deformylase
MALLEIIHYPSKILRTISKEVVSFDEKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPREDDLQHKEDCLEIINPKWIETKGSLMYREGCLSVPGFYEEVERFEKVKIEYQNRFAEVKILEASALLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKELKELQKKQKRK
>NC_017361.1|WP_000540573.1|782291_782879_-|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP
MGYIPYVIENTDRGERSYDIYSRLLKDRIVLLSGEINDSVASSIVAQLLFLEAEDPEKDIGLYINSPGGVITSGLSIYDTMNFIRPDVSTICIGQAASMGAFLLSCGAKGKRFSLPHSRIMIHQPLGGAQGQASDIEIISNEILRLKGLMNSILAQNSGQSLEQIAKDTDRDFYMSAKEAKEYGLIDKVLQKNVK
>NC_017361.1|WP_001047839.1|782898_784254_-|trigger-factor
MNLEVRKIDTANARLSAKPSIEDLEKRYDKIAQKIAQKVKIDGFRRGKVPLSLVKSRYQAQVEQDAQEEMFQEILKNALKELGIEAKDLIGSPNFTKFEKKDTHFEIEADIGLKPTIVLDKIKECVPSVGVEVPSEEKVDERLKQFAKDYAKFIDTDAQKKAQNDDKLTIDFEGFIDNAPFEGGKAQNFSLILGSKQMLEDFEKALLGMQAGEEKEFSLTFPSDYHVEHLAGKEALFKVKLHQIQAREVLEINDELAKIVLANEENATLDLLKERVKGQLFLENKARLYNEELKEKLIENLDEKILFDLPKTIIEQEMDLLFRNALYSMQAEEVKSLQENQEKAKEKRESFRNDATKSVKITFIIDALAKEEKIGVHDNEVFQTLYYEALMTGQNPENLIEQYRKNNMLAAVKMAMIEDRVLTYFLDKNLSKEQQEILEKMRPNAQKTQVS
>NC_017361.1|WP_001080913.1|784366_785203_-|outer-membrane-protein
MNRLLKRGVLAFFLSAYLRADDLVTYTVVKEEDLGYQRFLAKKCLRGKTHPPCFTKPKKPRRKLFNIDKSSHYYGTSVVQMSWLQSREKFENHSKYRDIPFAEVSLIYGYKQFFPKKERYGFRFYVSLDYAYGFFLKNKGVLGDSLRESSQIPKRYREKLQRKETFINAIFYGVGADFLYKRAFGTLILGMNFVGETWFYETKIFKKWAKDPSSIYHPYMFQVMLNVGYRYRFSRYKNWAIEFGARIPFLTNDYFETPLYTLHFKRNISVYLTSTYDF
>NC_017361.1|WP_000739261.1|785224_786007_-|flagellar-sheath-lipoprotein-HpaA
MKKNGHFKDFAWKKCLLGASVVALLVGCSPHIIETNEVALKLNYHPASAKAQALDEKILLLRPAFQYSDNIAKEYENKFKNQTAIKVEEILQNQGYKVISVDSSDKDDFSFAQKKEGYLAVAMNGEIVLRPDPKRTTQKKSEPGLLFSTGLDKMEGVLISAGFIKVTIIEPMSGESLDSFTMDLSELDIQQKFLRTTHSSHSGGLVSTMVKGTDNSNDAIKSALNKIFMDIMQEIDKKLTQKNLESYQKDAKELKNKRNR
>NC_017361.1|WP_001131508.1|786127_786604_-|cyclic-pyranopterin-monophosphate-synthase-MoaC
MPLTHLNEENQPKMVDIGDKETTERIALASGRISMNEEAYNAIVNHCVKKGPVLQTAIIAGIMGAKKTSELIPMCHSIMLNGVDIDILEEKETCSFKLYARVKTQAKTGVEMEALMSVSIGLLTIYDMVKAIDKGMVISGVMLEYKSGGKSGDYNAKK
>NC_017361.1|WP_001193334.1|786614_787145_-|molybdopterin-adenylyltransferase
MQTIHIGVLSASDRASKGVYEDLSGKAIQEVLREYLLNPLEFHYEIVADERELIEKSLIKMCDEYQCDLVVTTGGTGPALRDVTPEATEKVCQKMLPGFGELMRMTSLKYVPTAILSRQSAGIRNKSLILNLPGKPKSIRECLEAVFPAIPYCVDLILGNYMQVNEKNIQAFRPKQ
>NC_017361.1|WP_000912612.1|787156_787594_-|molybdenum-cofactor-biosynthesis-protein-MoaE
MLKIIQGALDTDKLLKAYQEEACAKNFGAFCVFVGIVREEDHIQGLSFDIHEALLKAWFEKWHHRAKDWGVTLKMAHSLGDVLIGQSSFLCVLMGKNRKNALELYEKFIEDFKRNAPIWKYDLVNNERIYAKERSHLLKGSGILA

Crispr_ID: NC_017361_2

• CRISPR_ID: NC_017361_2
• CRISPR_location: 863297-863388
• CRISPR_type: Unclear
• Repeat_type: NA
• Spacer_info: 1 spacers
• Cas_protein_info: cas2

Consensus repeat of NC_017361_2

Consensus_repeat	Method
TATTTACCCACTCTAGCCAAAAATTTCAA	CRISPRCasFinder

spacers of NC_017361_2

>2.1|863326|34|NC_017361|CRISPRCasFinder
CAAGAGAAGCTTTTAAAACTTTTCAAATTTTACC

CRISPR arrays and Neighbor proteins around NC_017361_2

CRISPR arrays

The CRISPR arrays of NC_017361_2

>merge|NC_017361|2|863297-863388|CRISPRCasFinder
TATTTACCCACTCTAGCCAAAAATTTCAACAAGAGAAGCTTTTAAAACTTTTCAAATTTTACCTATTTACACACTCTAGCCAAAAATTTCAA

>NC_017361|2|2|863297-863388|CRISPRCasFinder
TATTTACCCACTCTAGCCAAAAATTTCAA	CAAGAGAAGCTTTTAAAACTTTTCAAATTTTACC
TATTTACACACTCTAGCCAAAAATTTCAA

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_017361.1|WP_000926815.1|853400_855776_+|TonB-dependent-receptor	unknown	unknown	gnl|CDD|273808
NC_017361.1|WP_000226360.1|856373_857099_+|NYN-domain-containing-protein	unknown	unknown	gnl|CDD|224349
NC_017361.1|WP_041201138.1|876557_877088_+|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD	unknown	unknown	gnl|CDD|237892
NC_017361.1|WP_000051234.1|858491_860327_-|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein	unknown	unknown	gnl|CDD|224359
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl|CDD|225846
NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase	unknown	unknown	gnl|CDD|187632
NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease	unknown	unknown	gnl|CDD|376439
NC_017361.1|WP_000247324.1|851563_853081_-|catalase	unknown	unknown	gnl|CDD|163712
NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA	unknown	unknown	gnl|CDD|375731
NC_017361.1|WP_001134169.1|872518_872899_-|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl|CDD|224045
NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ	unknown	unknown	gnl|CDD|240528
NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase	unknown	unknown	gnl|CDD|234705
NC_017361.1|WP_000017401.1|857245_857392_-|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase	unknown	unknown	gnl|CDD|224523
NC_017361.1|WP_001221135.1|855776_856250_-|crossover-junction-endodeoxyribonuclease-RuvC	unknown	unknown	gnl|CDD|366907
NC_017361.1|WP_014534813.1|850542_851418_-|twin-arginine-translocation-signal-domain-containing-protein	unknown	unknown	unknown
NC_017361.1|WP_000635188.1|857910_858462_-|Holliday-junction-branch-migration-protein-RuvA	unknown	unknown	gnl|CDD|129193

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	2.6e-12	41.7	0.5

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_017361.1|WP_000926815.1|853400_855776_+|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].	1.17667e-43
NC_017361.1|WP_000226360.1|856373_857099_+|NYN-domain-containing-protein	gnl|CDD|224349	COG1432, COG1432, Uncharacterized conserved protein [Function unknown].	4.82371e-25
NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD	gnl|CDD|237892	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional.	0
NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA	gnl|CDD|375731	pfam18304, SabA_adhesion, SabA N-terminal extracellular adhesion domain. This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA.	1.63836e-75
NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein	gnl|CDD|224359	COG1442, RfaJ, Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].	1.71308e-95
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	gnl|CDD|225846	COG3309, VapD, Uncharacterized virulence-associated protein D [Function unknown].	1.44851e-45
NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease	gnl|CDD|376439	pfam01032, FecCD, FecCD transport family. This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system.	9.48764e-67
NC_017361.1|WP_000247324.1|851563_853081_-|catalase	gnl|CDD|163712	cd08156, catalase_clade_3, Clade 3 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 3 catalases are the most abundant subfamily and are found in all three kingdoms of life; they have a relatively small subunit size of 43 to 75 kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. Clade 3 catalases also bind NADPH as a second redox-active cofactor. They form tetramers, and in eukaryotic cells, catalases are located in peroxisomes.	0
NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein	gnl|CDD|224045	COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism].	9.75005e-100
NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ	gnl|CDD|240528	cd13123, MATE_MurJ_like, MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli MurJ (MviN) has been identified as essential for murein biosynthesis. It has been suggested that MurJ functions as the peptidoglycan lipid II flippase which is involved in translocation of lipid-anchored peptidoglycan precursors across the cytoplasmic membrane, though results obtained in Bacillus subtilis seem to indicate that its MurJ homologs are not essential for growth. Some MviN family members (e.g. in Mycobacterium tuberculosis) possess an extended C-terminal region that contains an intracellular pseudo-kinase domain and an extracellular domain resembling carbohydrate-binding proteins. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR).	1.58888e-111
NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase	gnl|CDD|234705	PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.	0
NC_017361.1|WP_001221135.1|855776_856250_-|crossover-junction-endodeoxyribonuclease-RuvC	gnl|CDD|366907	pfam02075, RuvC, Crossover junction endodeoxyribonuclease RuvC. This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo.	4.72197e-78
NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase	gnl|CDD|224523	COG1607, COG1607, Acyl-CoA hydrolase [Lipid metabolism].	2.65919e-64
NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase	gnl|CDD|187632	cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs. 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. 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.	3.77997e-90
NC_017361.1|WP_000635188.1|857910_858462_-|Holliday-junction-branch-migration-protein-RuvA	gnl|CDD|129193	TIGR00084, Holliday_junction_ATP-dependent_DNA_helicase_RuvA, Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair].	2.61732e-64

Protein sequences

>NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase
MLIYDTKLKQKVPFEPLVEKKANIYVCGPTVYDDAHLGHARSAIAFDLLRRTLELSGYEVVLVRNFTDIDDKIINKAFKENKSIQELSSIYIESYTRDLNALNVKKPSLEPKASEYLDAMVRMIETLLEKNIAYQVSNGDIYLDTSKDKDYGSLSVHNSSVEFGRIGLVQEKRLEQDFVLWKSYKGDNDVGFDSPLGKGRPGWHIECSSMVFETLALANTPYQIDIHAGGVDLLFPHHENEACQTRCTFGVEIAKYWMHNGFVNINNEKMSKSLGNSFFIKDALKNYDGEILRNYLLGVHYRSVLNFNEEDLLVSKKRLDKIYRLKQRVLGSLGNIDLNFKKEILECMQDDLNISKALSVLESMLSSMNEKLDQNPKNKALKGEILANLKFVEELLGIGFKNPTEYFQLGVNESEKQEIEKKIEERKRAKEQKDFMKADSIREELLKCKIALMDTPQGTTWEKLF
>NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ
MLKKIFLTNSLGILCSRIFGFLRDLMMANILGAGVFSDIFFVAFKLPNLFRRIFAEGSFSQSFLPSFIRSSIKGSFASLVGLIFCGVLLIWCLFIALNPLWLTKLLAYGFDEETLKLCAPIVAINFWYLLLVFITTFLGALLQYKHSFFASAYSTSLLNLCMILALFISKEKPHLEALYYLSYGVLLGGVAQILLHFYPLVRLGLFNLLSKGLLSFKTKNALKKEYRFNQVKKDLKGFFKQFFPSVLGNSSAQIASFLDTTIASFLASGSVSYLYYANRVFQLPLALFAIAISTALFPSIAIALKNNNQDLILQRLQKAWFFLVGVLLFCSIGGIMLSKEITELLFERGQFSPKDTLITSQVFSLYLLGLLPFGLTKLFSLWLYAKLEQKKAAKISLISLFLGLVASLSLMPFLGVLGLALANSLSGLFLFVLTIKAFGFQAFLGIIKPLKLWLVILFLACAEILLLLAFKSLITHLYLFYYFQGF
>NC_017361.1|WP_000051234.1|858491_860327_-|hypothetical-protein
MSLERFAPIKIERCKDIQKELKKAAAENKLQTEDLWFEILKTSIFIKNSAKDEFSEAFSGELQQLEEEEYYEKKELTLYQTHDIKIKLNAYKRFFEVKVDENLSKIEIILDECFIILDTEEHYQEMFGYIKERLAFEGVVFRHLPTMYENLKIELRNHKNKTQTKRFILYASSTFIPNIEEKPHFLLEEEYLPTHSIPLNEQEESFVKENYYIAKENQKVAWVSYPKQGREGRNLKGFYVELPKVANLPTPIGHDKNAFEEREEDNALVYYSKALQGVKMEKGRLVSKQDFIFKNGIKSIETPNLLGGVESGLVLEIQAKDELNDAIDSNLILEASAINIKGNVGKNVILVAKEINIEGQIHPESYVYANKARITNHKGVCYAKELECKYLERAKVYANSVKVEASAGSVVYAKEIALEKLKSDNKLYFSKQCLIDEVDGNGNRFIFYAFGGRENQEELKIAKQKLNALGVKSKKIIAQHQSLNHLVKNNQTIMEKLKNATEEIKRSLMQQESVKDAYSEFMFALKRLKILKAQMLELQKINNECYAKLISIENGFQHASIMTKNPFKQENIVIYHRNYPKVSNLTAMLSHNESVDVIYEDYKIKKIPKKR
>NC_017361.1|WP_000635188.1|857910_858462_-|Holliday-junction-branch-migration-protein-RuvA
MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTSALLQAGQKARLKILQVIKEDAHLLYGFLEESEKILFERLLKINGVGGRIALAILSSFSPNEFENIIATKEVKKLQQVPGIGKKLADKIMVDLIGFFIQDETKPVYNEVFLALESLGFKSAEINPILKKLKPNLGIEEAIKEALQQLRS
>NC_017361.1|WP_000017401.1|857245_857392_-|hypothetical-protein
MSGYIGFEKKAGNLREQAKFIDPSLITKDGGRLASSLNSNNPNPNTKE
>NC_017361.1|WP_000226360.1|856373_857099_+|NYN-domain-containing-protein
MVANTIILVDWENFRRDIKQTKCVNYNIALDVIVTIRAFLLDDERIIRIYFYTTPPFDFRHALWDKRNDTLQNEKSPGTEMKIFTSSDIEEILQSSEATKWEKIYSDVENFQHDLASLDQVELRLGRTKLNAIRVEFDGSYRALLEQKQVDMLMGLDIQRIAFKKIADRILIFSKDTDLIPALKLARDEGLRVDIADLSNRLSLLSHDLKYNSDKVRKLSSSEVKDKLFSIRENLTKTNWA
>NC_017361.1|WP_001221135.1|855776_856250_-|crossover-junction-endodeoxyribonuclease-RuvC
MRILGIDPGSKKCGYAIISYASNKLSLITAGFINITTTRLQEQILDLIEALDCLLDRYEVHEVAIEDIFFGYNPKSVIKLAQFRGALSLKILERIGNFSEYTPLQVKKALTGNGKAAKEQVAFMVKRLLHITSEIKPLDISDAIAVAITHAQRLKFQ
>NC_017361.1|WP_000926815.1|853400_855776_+|TonB-dependent-receptor
MLLRSYPKLRYALCFPLLTEACYSEERTLNKVTTQAKRIFTYNNEFKVTSKELDQRQSNEVKDLFRTNPDVNVGGGSVMGQKIYVRGVEDRLLRVTVDGAAQNGNIYHHQGNTVIDPGMLKSVEVTKGAANASAGPGAIAGVIKMETKGAADFIPRGKNYATSGAVSFYTNFGDRETFRAAYQSAHFDIIAYYTHQNIFYYRSGATAMKNLFHPTQADKEPGTPSEQNNALIKMNGYLSDRDTLTFSWNMTRDNATRPLRSNAIGLAYPCEAPFSPDGAQGCPNVLDSFTRYLYHSINSANNLSLQYKREAGRSFGDPRLDFTLYTSIRNAQFDPLFDPNGVYAKFPTSLASEWERENYPCVEGGYCTPSFSDVDKPSSQPRDLFLNNTGLNLKVAHVIDEATDSLFEYGFNYQNLSVFDARIPKSELYRPNQVYIDDKGQKQIACSLVDNNPNDPTLCQRGKANGNIYGGYVQANYAPHKIITFGAGVRWDAYTLYDKDWNYRYTQGFSPSAALVISPIEPLSLKITYSQVTRGVMPGDGVYMRQNDLRYAKNIKPEVGSNAEFNIDYSSQYFSGRAAAFYQALDNFISQYAQTLVVNNLSQAIRIYGYEVGGTFKYKGVSLNVGISRTWPTTRGYLMADSYELAASTGNVFIIKLDYTIPKTGINLAWLSRFVTGLDYCGFDIYLPDYGTTEKPKTPTDLAKCGSQLGLVHMHKPGYGVSNFYVNWSPKTKSRWKGLLLSAVFNNVFNKFYVDQTSPYVMSPDMPGTDAVKRAIAEPGFNARFEVAYKW
>NC_017361.1|WP_000247324.1|851563_853081_-|catalase
MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGEKGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDGIKFPDFIHTQKRDPQTNLPNHDMVWDFWSNVPESLYQVTWVMSDRGIPKSFRHMDGFGSHTFSFINAKGERFWVKFHFHTMQGVKHLTNEEAAEVRKYDPDSNQRDLFNAIARGDFPKWKLSVQIMPEEDAKKYRFHPFDVTKIWYLQDYPLMEVGEVELNRNPENYFAEVEQAAFTPANVVPGIGYSPDRMLQARLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYMQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRAEDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMKDMHAKDMHHTKKKK
>NC_017361.1|WP_014534813.1|850542_851418_-|twin-arginine-translocation-signal-domain-containing-protein
MKRRDFIKTTALGATGAVLGAQILQAEERKGSVAKYKIEAEYSIDFNSAEHTSLFIPMPSVVASNVKLQGNHASYQSMLNFGVPYLQVDFSKSAQKKQVHLSYEVASYQLKDRLFDANDFVAMGRYERDDASVANIANQLKGSTPKESVRNFYAFIKHDMPRRQKALEGKENLPKRESLPWFATISKESMFVSLCHACGIKSAEVQGLKLGQNSVVKNASRVEVYLQDSLLAFDFQSDRKEVFIPLNRHKDMQLDSALLATFGDAFALVDGRDLGNYESKLFEKRMSYTAV
>NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein
MLPPPQLSSITIPIVVAFDNNYCIPAGVSLYSMLSCAKQEKDGVKLFYQIHCLVDNLSAENAEKLKQTVAPFSAFSSIEFCDISNNDAYPFKLVSELFLRLNSFAKKRFSKMILCRLLLASIFPQYEKIIMFDVDTLFVGDISESFFIPMDKEYFGATKEDLSLVGIHSANDLFSSRLNWSRGMGVKLNRKSPIFQEVEILYQNPFNAGFMLVNLALWRECHLEEKLIDFFKARDEGLLLPEQDLFVLVCQGHILEMPCKYNVHPRMVGTKMIPKESDACMLHFYADEKPWKHFSYPYSKEWHQAAFKTSFSSLAFENLVGTIETFTKLNNHNKKDFFEFLNTKLNKKLLIQYILFKIFKKLESFCLR
>NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein
MVLEVKNLSFKYSQKLILDHLSFSVPKNSITSILAPNGSGKTTLLKCLLGLLKPLEETEIKACNKDILPLKPYEKAKLIAYIPQVEYYAFNFSVLDFVLMGKATHLNLFATPKAKHIKEATNILERLDLESLKDQGINDLSGGQRQMVLLARSLLQRTPLLLLDEPTSALDLKNQALFFDAIKDEMKKRELSVLVNIHDPNLVARHSTHVVMLKDKKLFLQASTQIAMTSHNLSTLYDTPLEAIWHDNKLVVYAL
>NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease
MLKTYHIALACVILAVVVLLFGGESLSLEEWKEVVMNVKNHFLHNEELSSLSIIILEIRLPRVILALLVGASLSGSGVVMQTIFRNPLVDPFLLGISSGAMLGVAAAIAIFESNIAILAFFGAILASLAVLAMNRVLGNSVLSLVLSGVVLSAFLGALAGAIKFFVIPQKAQAIVVWLLGSLSLSSYKDCLVAFIGLSLGFIPLFLLRWRINLLSLSDAQSLSLGINPVLLRSLCLVCVSVASALAVSVSGTIGWIGLVIPHVARLFFGANLQKLLLSSLLMGAFFLLLADVVAKTITPYDLPVGIATSVLGAPFFLWLLFKTRGV
>NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase
MGVQEKKESQKVAVITGASSGIGLECALMLLDQGYKVYALSRHATLCVALNHALCESIDIDVSDSNALKEVFLNISAKEKYCDVLINSAGYGVFGSVEDTPINEVKKQFSVNFFALCEVVQLCLPLLKNKPHSKIFNLSSIAGRMSMLFLGHYSASKHALEAYSDALRLELKPFNIQVCLIEPGPVKSNWEKTAFSVENFESEDSVYVLEVNAAKSFYSGVYQNALSAKEVAQKIVSLSMSQKIKARYLIGLKTQLLLALYQILPSSWYDSLFRLVVLGRKRDA
>NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase
MPQIQSSHSNHFDFTIDTADRTKLLMSYLVVPTTANFNNVMHGGELLNLLDKVAYVCSTRYCAKGTVTLSVDGVTFKYPIPVGNLLTFLASINYVGNTSCEVGIKVLSEDIKTREITHTNSCYFTMVAVENGKPTPMPKYEPKTEVEIRRYEGALKRKEMRTRGYLKSGKHEGA
>NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD
MYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKS
>NC_017361.1|WP_001134169.1|872518_872899_-|hypothetical-protein
MPNTTNKDYTQYSQRQLFNLMNKKEQEIEKLKRDRAYLEKKMAKELEKKDKGFTIKLEELNKILQEINKRANDCCFGHETPNIETQQAMREALNGINLTQIDSLDDFTNELKRENSKGFENVCFSV
>NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA
MKKHILSLALGSLLVSTLSAEDDGFYTSVGYQIGEAAQMVKNTKGIQQLSDNYENLNNLLTRYSTLNTLIKLSADPSAINAVRENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQKSTSSTTVFDNEPGYRSTSITCSLNGYTPGYYGPMSIENFKKLNEAYQILQTALKQGLPTLNEKNGTVSVTYSYKCAGEGNNNCDILSSNRNGGTKTETQTIDGKTVNTTISSKVVDSTASGNTSHVSYTEITNELKGVPDSAQFLLAQASTLINTINTACPFFHANNSSEANAPKFTTTTGKICGAFSEEISAIQKMITDAQELVNQTSVINSNEQSTPVGGNNGKPFNPFTDASFAEGMLKNAQAQAQMLNLAHQVGQTINPDRLTGSFKNFVTGFLATCNNLSTAGTGGTQGSPPGTVTTQTFASGCAYVGETITALNNSIAHFGAQAEQIQQAEDLAYTLANFSSQYKKLGDTYNSITTAISSIPNAQAIQNVVSKKNNPYSPQGIQENFYLNQNTYNQVQTINQELGRNPFRKVGIVSSQTNNGAMNGIGIQVGYKQFFGQKRRWGARYYGFFDYNHAFIKSSFFNSASDVWTYGFGADALYNFINDKATNFLGKNNKLSVGLFGGIALAGTSWLNSEYVNLATVNNVYNAKMNVANFQFLFNMGLRMNLARPKKKGSDHAAQHGIELGLKIPTINTNYYSFMGAELKYRRLYSVYLNYVFAY
>NC_017361.1|WP_041201138.1|876557_877088_+|hypothetical-protein
MENHFDPLIYERYLKKKETFLLFKKIGQMSAFNNLKLQLKQKALLNECVAQALGDLKQGFRYAKIEYKILKIYFTHPSFLKAFKIEEDHYTKNLKTHFLETKKTLEALNYPLDFTSIQASVKKKPYQKPVEKKENPPKKPVSINVNCEGLSDFTKKQFSKLKRACNDNTPRTPPQS
>NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD
MSVDHLISPFRDKRIILALSDAIKKLASKLTKKLVIMEVCGGHTHSIMKYGLLDLMPKNLEFVHGPGCPVCVMPRARLDEAYELATIKDSIILSLGDMMKVPGSYGSLIQAREKGLDARFLYSPMQALEIAKENPHKKVIYIAIGFETTTPMTASVLKNAKKEKLKNLFFHINHLLVPPSVSAILKDPACQINALLAPSHVSVISGAQIYSPLVDRFKLPIIVSGFEPVDILESVLMLIKQALNKEAKLEIQYKRAVSYGGNTKAQALVDACMEVRENFEWRGLGNIKHSALKLKEAFASYDAEKVFKEHLTHKITKENKACKCGEILKGIAKPLDCPLFAKTCTPQNPIGSCMVSSEGACAAYYRYKRV

Crispr_ID: NC_017361_3

• CRISPR_ID: NC_017361_3
• CRISPR_location: 876022-876104
• CRISPR_type: Unclear
• Repeat_type: NA
• Spacer_info: 1 spacers
• Cas_protein_info: cas2

Consensus repeat of NC_017361_3

Consensus_repeat	Method
TTTTTTAAGGAAACTCATTTTTTAAGG	CRISPRCasFinder

spacers of NC_017361_3

>3.1|876049|29|NC_017361|CRISPRCasFinder
AAAAATCCATTTTTTAATTTGAAACTCCA

CRISPR arrays and Neighbor proteins around NC_017361_3

CRISPR arrays

The CRISPR arrays of NC_017361_3

>merge|NC_017361|3|876022-876104|CRISPRCasFinder
TTTTTTAAGGAAACTCATTTTTTAAGGAAAAATCCATTTTTTAATTTGAAACTCCATTTTTTAAGGAAACTCCATTTTTTAAG

>NC_017361|3|3|876022-876104|CRISPRCasFinder
TTTTTTAAGGAAACTCATTTTTTAAGG	AAAAATCCATTTTTTAATTTGAAACTCCA
TTTTTTAAGGAAACTCCATTTTTTAAG

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase	unknown	unknown	gnl|CDD|235537
NC_017361.1|WP_000003589.1|878401_879130_-|hydrogenase-nickel-incorporation-protein-HypB	unknown	unknown	gnl|CDD|272891
NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD	unknown	unknown	gnl|CDD|237892
NC_017361.1|WP_000706863.1|879374_879674_-|cupin-domain-containing-protein	unknown	unknown	gnl|CDD|380358
NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein	unknown	unknown	gnl|CDD|224359
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl|CDD|225846
NC_017361.1|WP_000335461.1|878165_878402_-|HypC/HybG/HupF-family-hydrogenase-formation-chaperone	unknown	unknown	gnl|CDD|223375
NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase	unknown	unknown	gnl|CDD|187632
NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase	unknown	unknown	gnl|CDD|234680
NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease	unknown	unknown	gnl|CDD|376439
NC_017361.1|WP_041201138.1|876557_877088_+|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE	unknown	unknown	gnl|CDD|235620
NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD	unknown	unknown	gnl|CDD|235621
NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl|CDD|224045
NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ	unknown	unknown	gnl|CDD|240528
NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase	unknown	unknown	gnl|CDD|234705
NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA	unknown	unknown	gnl|CDD|375731
NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase	unknown	unknown	gnl|CDD|224523
NC_017361.1|WP_001134169.1|872518_872899_-|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_001139914.1|882629_884177_+|flagellar-hook-length-control-protein-FliK	unknown	unknown	gnl|CDD|376734

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	2.6e-12	41.7	0.5

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_017361.1|WP_000003589.1|878401_879130_-|hydrogenase-nickel-incorporation-protein-HypB	gnl|CDD|272891	TIGR00073, nickel_incorporation_protein_HypB, hydrogenase accessory protein HypB. A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs. [SS 1/05/04 I changed the role_ID and process GO from protein folding to to protein modification, since a protein folding role has not been established, but HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.] [Protein fate, Protein modification and repair].	1.32809e-108
NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD	gnl|CDD|237892	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional.	0
NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase	gnl|CDD|234680	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed.	0
NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein	gnl|CDD|224359	COG1442, RfaJ, Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].	1.71308e-95
NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD	gnl|CDD|225846	COG3309, VapD, Uncharacterized virulence-associated protein D [Function unknown].	1.44851e-45
NC_017361.1|WP_000335461.1|878165_878402_-|HypC/HybG/HupF-family-hydrogenase-formation-chaperone	gnl|CDD|223375	COG0298, HypC, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones].	1.92061e-31
NC_017361.1|WP_000706863.1|879374_879674_-|cupin-domain-containing-protein	gnl|CDD|380358	cd02230, cupin_HP0902-like, Helicobacter pylori HP0902 and related proteins, cupin domain. This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity.	1.11979e-19
NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease	gnl|CDD|376439	pfam01032, FecCD, FecCD transport family. This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system.	9.48764e-67
NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase	gnl|CDD|235537	PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.	0
NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE	gnl|CDD|235620	PRK05841, flgE, flagellar hook protein FlgE; Validated.	0
NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD	gnl|CDD|235621	PRK05842, flgD, flagellar hook assembly protein FlgD.	5.24415e-166
NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein	gnl|CDD|224045	COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism].	9.75005e-100
NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ	gnl|CDD|240528	cd13123, MATE_MurJ_like, MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli MurJ (MviN) has been identified as essential for murein biosynthesis. It has been suggested that MurJ functions as the peptidoglycan lipid II flippase which is involved in translocation of lipid-anchored peptidoglycan precursors across the cytoplasmic membrane, though results obtained in Bacillus subtilis seem to indicate that its MurJ homologs are not essential for growth. Some MviN family members (e.g. in Mycobacterium tuberculosis) possess an extended C-terminal region that contains an intracellular pseudo-kinase domain and an extracellular domain resembling carbohydrate-binding proteins. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR).	1.58888e-111
NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase	gnl|CDD|234705	PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.	0
NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA	gnl|CDD|375731	pfam18304, SabA_adhesion, SabA N-terminal extracellular adhesion domain. This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA.	1.63836e-75
NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase	gnl|CDD|224523	COG1607, COG1607, Acyl-CoA hydrolase [Lipid metabolism].	2.65919e-64
NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase	gnl|CDD|187632	cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs. 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. 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.	3.77997e-90
NC_017361.1|WP_001139914.1|882629_884177_+|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.	1.08757e-11

Protein sequences

>NC_017361.1|WP_000716245.1|873601_875827_-|Hop-family-adhesin-BabA
MKKHILSLALGSLLVSTLSAEDDGFYTSVGYQIGEAAQMVKNTKGIQQLSDNYENLNNLLTRYSTLNTLIKLSADPSAINAVRENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQKSTSSTTVFDNEPGYRSTSITCSLNGYTPGYYGPMSIENFKKLNEAYQILQTALKQGLPTLNEKNGTVSVTYSYKCAGEGNNNCDILSSNRNGGTKTETQTIDGKTVNTTISSKVVDSTASGNTSHVSYTEITNELKGVPDSAQFLLAQASTLINTINTACPFFHANNSSEANAPKFTTTTGKICGAFSEEISAIQKMITDAQELVNQTSVINSNEQSTPVGGNNGKPFNPFTDASFAEGMLKNAQAQAQMLNLAHQVGQTINPDRLTGSFKNFVTGFLATCNNLSTAGTGGTQGSPPGTVTTQTFASGCAYVGETITALNNSIAHFGAQAEQIQQAEDLAYTLANFSSQYKKLGDTYNSITTAISSIPNAQAIQNVVSKKNNPYSPQGIQENFYLNQNTYNQVQTINQELGRNPFRKVGIVSSQTNNGAMNGIGIQVGYKQFFGQKRRWGARYYGFFDYNHAFIKSSFFNSASDVWTYGFGADALYNFINDKATNFLGKNNKLSVGLFGGIALAGTSWLNSEYVNLATVNNVYNAKMNVANFQFLFNMGLRMNLARPKKKGSDHAAQHGIELGLKIPTINTNYYSFMGAELKYRRLYSVYLNYVFAY
>NC_017361.1|WP_001134169.1|872518_872899_-|hypothetical-protein
MPNTTNKDYTQYSQRQLFNLMNKKEQEIEKLKRDRAYLEKKMAKELEKKDKGFTIKLEELNKILQEINKRANDCCFGHETPNIETQQAMREALNGINLTQIDSLDDFTNELKRENSKGFENVCFSV
>NC_017361.1|WP_000271050.1|872253_872538_-|endoribonuclease-VapD
MYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKS
>NC_017361.1|WP_001135601.1|871533_872058_+|acyl-CoA-thioesterase
MPQIQSSHSNHFDFTIDTADRTKLLMSYLVVPTTANFNNVMHGGELLNLLDKVAYVCSTRYCAKGTVTLSVDGVTFKYPIPVGNLLTFLASINYVGNTSCEVGIKVLSEDIKTREITHTNSCYFTMVAVENGKPTPMPKYEPKTEVEIRRYEGALKRKEMRTRGYLKSGKHEGA
>NC_017361.1|WP_000538843.1|870539_871394_-|SDR-family-oxidoreductase
MGVQEKKESQKVAVITGASSGIGLECALMLLDQGYKVYALSRHATLCVALNHALCESIDIDVSDSNALKEVFLNISAKEKYCDVLINSAGYGVFGSVEDTPINEVKKQFSVNFFALCEVVQLCLPLLKNKPHSKIFNLSSIAGRMSMLFLGHYSASKHALEAYSDALRLELKPFNIQVCLIEPGPVKSNWEKTAFSVENFESEDSVYVLEVNAAKSFYSGVYQNALSAKEVAQKIVSLSMSQKIKARYLIGLKTQLLLALYQILPSSWYDSLFRLVVLGRKRDA
>NC_017361.1|WP_000921456.1|869566_870547_-|iron-ABC-transporter-permease
MLKTYHIALACVILAVVVLLFGGESLSLEEWKEVVMNVKNHFLHNEELSSLSIIILEIRLPRVILALLVGASLSGSGVVMQTIFRNPLVDPFLLGISSGAMLGVAAAIAIFESNIAILAFFGAILASLAVLAMNRVLGNSVLSLVLSGVVLSAFLGALAGAIKFFVIPQKAQAIVVWLLGSLSLSSYKDCLVAFIGLSLGFIPLFLLRWRINLLSLSDAQSLSLGINPVLLRSLCLVCVSVASALAVSVSGTIGWIGLVIPHVARLFFGANLQKLLLSSLLMGAFFLLLADVVAKTITPYDLPVGIATSVLGAPFFLWLLFKTRGV
>NC_017361.1|WP_000242334.1|868799_869567_-|ABC-transporter-ATP-binding-protein
MVLEVKNLSFKYSQKLILDHLSFSVPKNSITSILAPNGSGKTTLLKCLLGLLKPLEETEIKACNKDILPLKPYEKAKLIAYIPQVEYYAFNFSVLDFVLMGKATHLNLFATPKAKHIKEATNILERLDLESLKDQGINDLSGGQRQMVLLARSLLQRTPLLLLDEPTSALDLKNQALFFDAIKDEMKKRELSVLVNIHDPNLVARHSTHVVMLKDKKLFLQASTQIAMTSHNLSTLYDTPLEAIWHDNKLVVYAL
>NC_017361.1|WP_187286394.1|867620_868727_-|glycosyltransferase-family-8-protein
MLPPPQLSSITIPIVVAFDNNYCIPAGVSLYSMLSCAKQEKDGVKLFYQIHCLVDNLSAENAEKLKQTVAPFSAFSSIEFCDISNNDAYPFKLVSELFLRLNSFAKKRFSKMILCRLLLASIFPQYEKIIMFDVDTLFVGDISESFFIPMDKEYFGATKEDLSLVGIHSANDLFSSRLNWSRGMGVKLNRKSPIFQEVEILYQNPFNAGFMLVNLALWRECHLEEKLIDFFKARDEGLLLPEQDLFVLVCQGHILEMPCKYNVHPRMVGTKMIPKESDACMLHFYADEKPWKHFSYPYSKEWHQAAFKTSFSSLAFENLVGTIETFTKLNNHNKKDFFEFLNTKLNKKLLIQYILFKIFKKLESFCLR
>NC_017361.1|WP_000909807.1|861881_863279_+|cysteine--tRNA-ligase
MLIYDTKLKQKVPFEPLVEKKANIYVCGPTVYDDAHLGHARSAIAFDLLRRTLELSGYEVVLVRNFTDIDDKIINKAFKENKSIQELSSIYIESYTRDLNALNVKKPSLEPKASEYLDAMVRMIETLLEKNIAYQVSNGDIYLDTSKDKDYGSLSVHNSSVEFGRIGLVQEKRLEQDFVLWKSYKGDNDVGFDSPLGKGRPGWHIECSSMVFETLALANTPYQIDIHAGGVDLLFPHHENEACQTRCTFGVEIAKYWMHNGFVNINNEKMSKSLGNSFFIKDALKNYDGEILRNYLLGVHYRSVLNFNEEDLLVSKKRLDKIYRLKQRVLGSLGNIDLNFKKEILECMQDDLNISKALSVLESMLSSMNEKLDQNPKNKALKGEILANLKFVEELLGIGFKNPTEYFQLGVNESEKQEIEKKIEERKRAKEQKDFMKADSIREELLKCKIALMDTPQGTTWEKLF
>NC_017361.1|WP_000913464.1|860420_861881_+|murein-biosynthesis-integral-membrane-protein-MurJ
MLKKIFLTNSLGILCSRIFGFLRDLMMANILGAGVFSDIFFVAFKLPNLFRRIFAEGSFSQSFLPSFIRSSIKGSFASLVGLIFCGVLLIWCLFIALNPLWLTKLLAYGFDEETLKLCAPIVAINFWYLLLVFITTFLGALLQYKHSFFASAYSTSLLNLCMILALFISKEKPHLEALYYLSYGVLLGGVAQILLHFYPLVRLGLFNLLSKGLLSFKTKNALKKEYRFNQVKKDLKGFFKQFFPSVLGNSSAQIASFLDTTIASFLASGSVSYLYYANRVFQLPLALFAIAISTALFPSIAIALKNNNQDLILQRLQKAWFFLVGVLLFCSIGGIMLSKEITELLFERGQFSPKDTLITSQVFSLYLLGLLPFGLTKLFSLWLYAKLEQKKAAKISLISLFLGLVASLSLMPFLGVLGLALANSLSGLFLFVLTIKAFGFQAFLGIIKPLKLWLVILFLACAEILLLLAFKSLITHLYLFYYFQGF
>NC_017361.1|WP_041201138.1|876557_877088_+|hypothetical-protein
MENHFDPLIYERYLKKKETFLLFKKIGQMSAFNNLKLQLKQKALLNECVAQALGDLKQGFRYAKIEYKILKIYFTHPSFLKAFKIEEDHYTKNLKTHFLETKKTLEALNYPLDFTSIQASVKKKPYQKPVEKKENPPKKPVSINVNCEGLSDFTKKQFSKLKRACNDNTPRTPPQS
>NC_017361.1|WP_000109781.1|877038_878151_-|hydrogenase-formation-protein-HypD
MSVDHLISPFRDKRIILALSDAIKKLASKLTKKLVIMEVCGGHTHSIMKYGLLDLMPKNLEFVHGPGCPVCVMPRARLDEAYELATIKDSIILSLGDMMKVPGSYGSLIQAREKGLDARFLYSPMQALEIAKENPHKKVIYIAIGFETTTPMTASVLKNAKKEKLKNLFFHINHLLVPPSVSAILKDPACQINALLAPSHVSVISGAQIYSPLVDRFKLPIIVSGFEPVDILESVLMLIKQALNKEAKLEIQYKRAVSYGGNTKAQALVDACMEVRENFEWRGLGNIKHSALKLKEAFASYDAEKVFKEHLTHKITKENKACKCGEILKGIAKPLDCPLFAKTCTPQNPIGSCMVSSEGACAAYYRYKRV
>NC_017361.1|WP_000335461.1|878165_878402_-|HypC/HybG/HupF-family-hydrogenase-formation-chaperone
MCLAIPSKVIAINDNVALLETLGVQREASLDLMGESVKVGDYVLLHIGYVMSKIDEKEALESIELYQEMIAKMNETHE
>NC_017361.1|WP_000003589.1|878401_879130_-|hydrogenase-nickel-incorporation-protein-HypB
MSEQRKESLQNNPNLSKKDVKIVEKILSKNDIKAAEMKERYLKEGLYVLNFMSSPGSGKTTMLENLADFKDFKFCVVEGDLQTNRDADRLRKKGVSAHQITTGEACHLEASMIEGAFDLLKDEGALEKSDFLIIENVGNLVCPSSYNLGAAMNIVLLSVPEGDDKVLKYPTMFMCADAVIISKADMIEVFNFRVSQVKEDMQKLKPEAPIFLMSSKDPKSLEDFKNFLLEKKRENYQSTHSF
>NC_017361.1|WP_000706863.1|879374_879674_-|cupin-domain-containing-protein
MKIVNFLEGVHFEKLHIEALSENSSNKEIRICMPKGAIMDKHKAPGAISVQVLEGKIVFEVGNEKIEMPKGALISLEAQVSHRLDALENSVIRLSLSKK
>NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase
MEILVLNLGSSSIKFKLFDMKENKPLASGLAEKIGEEIGQLKIKSHLHHNDQELKEKLVIKDHASGLLMIRENLTKMGIIKDFNQIDAIGHRVVQGGDKFHAPVLVDEKVMQEIGKLSILAPLHNPANLAGIEFVQKAHPHIPQIAVFDTAFHATMPNYAYMYALPYELYEKYQIRRYGFHGTSHHYVAKEAAKFLNIPYEKFNAISLHLGNGSSAAAIKNGKSVDTSMGLTPLEGLIMGTRCGDIDPTVVEYIAQCANKSLEEVMKILNHESGLKGVCGDNDARNIEARKEKGDQQAELAFEMCAYRIKKYIGAYMVVLNKVDALIFTGGLGENYSALRERVCEGLEDLGIALHKPTNDNPGNGIVNLSQPNTKVQVLRIPTDEELEIAIQAKEMVEKIKVSNENS
>NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase
MQSLWIYPENTEALKIACKSLLKALKPRYQKIALFSPISGECEGLGECEGFKSLELHSAIDKQKALELVSAAQEELLFETILKRYDEIQSVHDFVIGLGYVPDFFLNTLLDLNTTLAKHLNAPIVAVAQTSLEYLKAMHSHVIKKEAPFALGLLTGETLEKPDFLSASLCKGELEASVVEKLLHTKSAITTPLAFQRSLEKKAKEQIKKVVLPESEDERILKAAHHLNAMGAVGLILLGDEETIHSQAKNLNLNLENIEIIDPNTSNHKEEFANHLYELRKSKGLNQQEAEQLVLDKTYFATMLVHLGYAHAMVSGVNHTTADTIRPALQIIKTKPGVSLVSSVFLMCLDTQVLVFGDCAIIPNPSPKELAEIATTSAQTAKQFNIAPKVALLSYATGNSAQGEMIDKIKEALTIAQKLDPQLEMDGPLQFDASIDKSVAKKKMPNSQVAGQASVFIFPDLNAGNIAYKAVQRSAKAVAIGPILQGLNKPINDLSRGALVEDIINTVLISAIQAQD
>NC_017361.1|WP_001139914.1|882629_884177_+|flagellar-hook-length-control-protein-FliK
MPSPINPIHTSANTSALKNEAKNEDTKNVPKSASKDFSKLLNQKISKEEPKDKPKNLNPSALKDTPKDTLEKTPTPHIQTPKEIAKNQQAPTLKDLLNHQENHSTTHPTAKHETQHETQHETIQKTHPTTPNETPNKNEKKPSEALSNAHQTNLLHKNPITPNHANNANATQKPTAPTDNTKPKTLKDIQTLSQKHDLNASNIQTATTPENKSPLNASDHLALKTTPQNPTTNPTLAKNDAKNTANLSSVLQSLEKKDAQNKEHTNPTNNEKKMPPLKESLQINAIKRDKTLSKKKPEKAPTKSQATATTPENTPKLALKTPLLMPLMGANPPNDNAPTPLEKEEKSKEVSENKEKTKESSHSVQNAQNTPNSDNKSIAPKETIKHFTQQLKQEIQEYKPPMSKISMDLFPKELGKVEVVIQKVGKNLKVSVISHNNSLQTFLDNQQDLKNSLNALGFEGVDLSFSQNPSKEQQAPKDQLKEQELSPLKENALKSYQENTDNEHKETSMQITLYA
>NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD
MAIDLAEVTGAKAAQERKKEQPQIANGLDKDAFMKLFLEQLKNQDPTAPMETDKIITQTAQLTQVEMQEENKKTMQEVASAMKSNKETNESLKDFQGALKDTMENLNKGMDDSLKANNALREVSTLNSVSMIGKIAETDVSGANFDGNNKLSFSLFFDEKIDASKGVPAIQILNENNELVKTISLKDYNGQKGYIHFEWDGTNEKGEKVPKGNYKIKAEYNLDSQSKQYLQTRIGRGEVESVIFDKGKPMLRMGEMILPIDSAIEFYKPEQKPLEQKFSEQKPLDQKPIEQKPIEQKPIEQKPLDQKLSDQKPIDQKPLEQKAPNQELSEQKPLEQKALDQKLSNQKPIEQKSLEQKPLEQKAPNQELSEQKQPQTPSKETA
>NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE
MNDTLLNAYSGIKTHQFGIDSLSNNIANVNTLGYRSNDPEFKTLFSSHLDALNAKSVVANDRNYGVTGSGNVLSNKDGEYMPSEGEFHMAYQGKGWFVIGPNKNGEMTINKDGFSKKQDNFLTRAGNFARDADGYLVTPEGYYVYGIDLKKIKDGTLNSTARDEDIEKLHGNTLSPLQIPQDLTYQPVLSTKVGISVNLNPKDHLKGAQEFLLNDKGEVIKERFLNQDINALANDDNEPIDAITNRKLNISVQKENGKKEDFVFTYGDAEKGENQFKTLGDLQKLLKEKTGLDLNLIKSEKDAKKPPLLLEIANPSETPITFSLSGGIADKLGLNANEMELKKGISRDSVAIKIPYYSTEVDIYDKAGDKYLLQSEYYMTNSNDPTSSPTSKRKNQTWEVKSYIVDPKNKTPINEPTWEIVGFDSATHKMKSAPMTLDFKGNKLTYSLDKSENHDSSDLTYQDSKLLEASQDGKPRGIFRDMRIEENGVISLAFSNGVVEPVARIGILAFTNDQGLRKIGGNVYEMQESTINGENRPLSGNPILGWDEEGKLKFGKIRHKYLETSNVNAGNALTNLILMQRGYSMNAKAFGAGDDMIKEAISLKK

Crispr_ID: NC_017361_4

• CRISPR_ID: NC_017361_4
• CRISPR_location: 895449-895518
• CRISPR_type: Orphan
• Repeat_type: NA
• Spacer_info: 1 spacers

Consensus repeat of NC_017361_4

Consensus_repeat	Method
ATTAAAAACTGCTACTTTAAAAA	CRISPRCasFinder

spacers of NC_017361_4

>4.1|895472|24|NC_017361|CRISPRCasFinder
ACTTAACGCTCAAGGTTTATTGAG

CRISPR arrays and Neighbor proteins around NC_017361_4

CRISPR arrays

The CRISPR arrays of NC_017361_4

>merge|NC_017361|4|895449-895518|CRISPRCasFinder
ATTAAAAACTGCTACTTTAAAAAACTTAACGCTCAAGGTTTATTGAGATTTTAAAACGCTTTATTAAAAA

>NC_017361|4|4|895449-895518|CRISPRCasFinder
ATTAAAAACTGCTACTTTAAAAA	ACTTAACGCTCAAGGTTTATTGAG
ATTTTAAAACGCTTTATTAAAAA

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_017361.1|WP_001099587.1|915416_915998_+|recombination-protein-RecR	unknown	unknown	gnl|CDD|273176
NC_017361.1|WP_001126577.1|901433_904691_-|carbamoyl-phosphate-synthase-large-subunit	unknown	unknown	gnl|CDD|235393
NC_017361.1|WP_000812497.1|893731_895333_+|Hop-family-adhesin-AlpB	unknown	unknown	gnl|CDD|280099
NC_017361.1|WP_000998400.1|898369_900811_-|TonB-dependent-receptor	unknown	unknown	gnl|CDD|224544
NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase	unknown	unknown	gnl|CDD|234680
NC_017361.1|WP_001128388.1|915094_915301_-|4-oxalocrotonate-tautomerase-family-protein	unknown	unknown	gnl|CDD|129125
NC_017361.1|WP_014534817.1|888981_891000_+|ATP-dependent-helicase	unknown	unknown	gnl|CDD|223288
NC_017361.1|WP_014534816.1|887241_887823_+|hypothetical-protein	unknown	unknown	unknown
NC_017361.1|WP_000398277.1|887832_888972_+|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl|CDD|223897
NC_017361.1|WP_001169656.1|913919_915035_+|outer-membrane-protein	unknown	unknown	gnl|CDD|280099
NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase	unknown	unknown	gnl|CDD|235537
NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE	unknown	unknown	gnl|CDD|235620
NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD	unknown	unknown	gnl|CDD|235621
NC_017361.1|WP_001248515.1|896511_898056_-|outer-membrane-beta-barrel-protein-HofG	unknown	unknown	gnl|CDD|334957
NC_017361.1|WP_001240301.1|904789_905482_-|Bax-inhibitor-1/YccA-family-protein	unknown	unknown	gnl|CDD|198414
NC_017361.1|WP_001229958.1|900997_901429_-|hypothetical-protein	unknown	unknown	gnl|CDD|376519
NC_017361.1|WP_000688670.1|905628_906627_+|type-I-glyceraldehyde-3-phosphate-dehydrogenase	unknown	unknown	gnl|CDD|273675
NC_017361.1|WP_000162906.1|892156_893710_+|Hop-family-adhesin-AlpA	unknown	unknown	gnl|CDD|280099
NC_017361.1|WP_001139914.1|882629_884177_+|flagellar-hook-length-control-protein-FliK	unknown	unknown	gnl|CDD|376734
NC_017361.1|WP_000172823.1|906706_913870_+|vacuolating-cytotoxin-domain-containing-protein	unknown	unknown	gnl|CDD|227938

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_017361.1|WP_001099587.1|915416_915998_+|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].	1.27099e-93
NC_017361.1|WP_001126577.1|901433_904691_-|carbamoyl-phosphate-synthase-large-subunit	gnl|CDD|235393	PRK05294, carB, carbamoyl-phosphate synthase large subunit.	0
NC_017361.1|WP_000812497.1|893731_895333_+|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.	1.32872e-53
NC_017361.1|WP_000998400.1|898369_900811_-|TonB-dependent-receptor	gnl|CDD|224544	COG1629, CirA, Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism].	1.17031e-35
NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase	gnl|CDD|234680	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed.	0
NC_017361.1|WP_001128388.1|915094_915301_-|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].	2.37866e-23
NC_017361.1|WP_014534817.1|888981_891000_+|ATP-dependent-helicase	gnl|CDD|223288	COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair].	3.42561e-136
NC_017361.1|WP_000398277.1|887832_888972_+|class-I-SAM-dependent-methyltransferase	gnl|CDD|223897	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair].	3.60501e-48
NC_017361.1|WP_001169656.1|913919_915035_+|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.	4.41915e-47
NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase	gnl|CDD|235537	PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.	0
NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE	gnl|CDD|235620	PRK05841, flgE, flagellar hook protein FlgE; Validated.	0
NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD	gnl|CDD|235621	PRK05842, flgD, flagellar hook assembly protein FlgD.	5.24415e-166
NC_017361.1|WP_001248515.1|896511_898056_-|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).	2.31899e-179
NC_017361.1|WP_001240301.1|904789_905482_-|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.	1.12525e-51
NC_017361.1|WP_001229958.1|900997_901429_-|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.	8.96097e-05
NC_017361.1|WP_000688670.1|905628_906627_+|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].	2.24972e-157
NC_017361.1|WP_000162906.1|892156_893710_+|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.	7.35419e-55
NC_017361.1|WP_001139914.1|882629_884177_+|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.	1.08757e-11
NC_017361.1|WP_000172823.1|906706_913870_+|vacuolating-cytotoxin-domain-containing-protein	gnl|CDD|227938	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion].	7.16464e-18

Protein sequences

>NC_017361.1|WP_000812497.1|893731_895333_+|Hop-family-adhesin-AlpB
MKQNLKPFKMIKENLMTQSQKVRFLAPLSLALSLSFNPVGAEEDGGFMTFGYELGQVVQQVKNPGKIKAEELAGLLNSNTTNNTNINIAGTGGNVAGTLGNLFMNQLGNLIDLYPTLDTSSIHQCGATNSGSSGATTAAASSTGSTSSSPCFQGNLALYNNMVSSIKTLGQQIKNNIFQGDNNTTSANLSNQLSELNTASVYLTYMNSFLNANNQAGGIFQNNTNQAYGNGVTAQQIAYILKQASITMGPSGDSGAATAFLDAALAQHLFNSANAGNDLSAKEFTGLVQNIVNDSQNALTLANNANISNSTGYQVSYGGNINQARSTQLLNNATNTLAKVTALNNELKANPWLGNFAAGNSSQVNAFNGFITKIGYKQFFGENKNVGLRYYGFFSYNGAGVGNGPTYNQVNLLTYGVGTDVLYNVFSRSFGSRSLNAGFFGGIQLAGDTYISTLRNSPQLASRPTATKFQFLFDLGLRMNFGILKKDLKSHNQHSIEIGVQIPTIYNTYYKAGGAEVKYFRPYSVYWVYGYAF
>NC_017361.1|WP_000162906.1|892156_893710_+|Hop-family-adhesin-AlpA
MTKKNRTLFLSLALCASISYAEDDGGFFTVGYQLGQVMQDVQNPGGTKRDELARELNADVTNNILNNNTGGNVAGALSNAFSQYLYSLLGAYPEKLNGNDVAANALLQGAVGNGTCAAAGTAGSSSLNTQSACTAAGYYWLPSLTDRVLSTIGSQTNYGTDTNFTNMQQQLTYLNAGNVFFNAMNNALESITKSNGSTTSGATGQNGQTYSTQAIQYLKDQQTILNNAANLLKQDELLLEAFNSAVAANIGNKEFNSAAFTGLVQGIIDQSQLVYNELTKNTISGSAVNSAGINPNQANAVNTRASQLPNALYNAQVTLDKITALNNQVRSMPYLPQFRAGNSRATNILNGFYTKIGYKQFFGKKRNIGLRYYGFFSYNGASVGFRSTQNNVGLYTYGVGTDVLYNIFSRSYQNRSVDMGFFSGIQLAGETFQSTLRDDPNVKLHGKINNTHFQFLFDFGMRMNFGKLDNKSNRHNQHTVEFGVVVPTIYNTYYKSAGTTVKYFRPYSVYWSYGYSF
>NC_017361.1|WP_014534817.1|888981_891000_+|ATP-dependent-helicase
MLETLQLNPEQLKAASALKGHNLIIASAGTGKTSTIVGRILHLLDNGIKPEEILLLTFTNKASSEMIARVAKYSKLSSKIEAGTFHAVAYRYLKEHYPNLSLKQPKELRKLLESIVDTKNAIDDDKKPYTSQHLYALYSLYTNALKQEDFSAWLSNKNPEHTPYATFYENILEEFENTKKKHNYIDYNDLLLLFKKAMLETPSPYKEVLCDEFQDTNPLQESILDAINPPSLFCVGDYDQSIYAFNGADISIISNFTQKYKNARVFTLTKNYRSSKEILDLANQVIQHNQRIYPKNLEVVKSGDFNKPTLLNYNDNIAQCQDIAKRIVMRKDFKEVAVIFRNNASADQLEAALRANNVPSKRKGSASFFESKEVALALDICTLVFNPKDIMAAIHVLSYANDIGSNTAKDIHEALMLLGNGDLKSALTHPNKEAKIYTKKKEITSMGLFEEIFALENSSRFNSVISKAFYSHPVLMHPKISLNGAKMLSDFFTLYTHAPNSPSALIKHTIESAFFQTIKTRLLKERSKNKDGSYNEFKKLQAQKRFNEKMELLSSLAKNYQDLGRFLNGTLIGSNEATQGEGVNLLSVHASKGLEFKDVYIIDLMEGRFPNHKLMNTGGGIEEERRLFYVAITRAKENLWLSYAKNELRENAKPKEHKPSVFLYEAGLLKPQ
>NC_017361.1|WP_000398277.1|887832_888972_+|class-I-SAM-dependent-methyltransferase
MEGFLHKLDVKTLGQVFTPNNIVDFMLHLRQNQGNVLEPSAGDGSFLRRLNKAVGIEIDPKICPKNALCMDFFDYPLENQFDTIIGNPPYVKHKDIAPNTKEKLNYSLFDERSNLYLFFIEKAIKHLKPKGELIFITPRDFLKSTSSVKLNEWIYKEGTITHFFELGDQKIFPNAMPNCVIFRFCKRNFSRITNDGLQFVCKKGILYFLKQSYTQKLSEVFQVKVGAVSGCDRIFKNEKHGNLEFVTSITRRTNALEKMVFVDEPNDYLLQHKESLMGRKIKKFNENNWFEWGRMHCISPKKRIYVNTKTRQKNPFFIHQCPNYDGSILALFPYNQNLDLQNLCDKLNAINWQELGFVCDGRFLFSQRSLENALLPKDF
>NC_017361.1|WP_014534816.1|887241_887823_+|hypothetical-protein
MIPTQLNEIAEFLRTNPYSLSQPLQDDRLNSSVNEEEILNTIKGHFSIQLPKAREWWDFGFEENDIFYPVNIKITTTKTADNLNCKLGIYYALYGLLSEFNNEIAWEKYFQKLHKDLCKNTNRDYYFLIINKNDPKDIFINSLKGIQTLQPNNLPFQCKWDNNREIVQRSFMESKNFILSALAESIKLRANIY
>NC_017361.1|WP_001000234.1|885372_887190_+|flagellar-hook-protein-FlgE
MNDTLLNAYSGIKTHQFGIDSLSNNIANVNTLGYRSNDPEFKTLFSSHLDALNAKSVVANDRNYGVTGSGNVLSNKDGEYMPSEGEFHMAYQGKGWFVIGPNKNGEMTINKDGFSKKQDNFLTRAGNFARDADGYLVTPEGYYVYGIDLKKIKDGTLNSTARDEDIEKLHGNTLSPLQIPQDLTYQPVLSTKVGISVNLNPKDHLKGAQEFLLNDKGEVIKERFLNQDINALANDDNEPIDAITNRKLNISVQKENGKKEDFVFTYGDAEKGENQFKTLGDLQKLLKEKTGLDLNLIKSEKDAKKPPLLLEIANPSETPITFSLSGGIADKLGLNANEMELKKGISRDSVAIKIPYYSTEVDIYDKAGDKYLLQSEYYMTNSNDPTSSPTSKRKNQTWEVKSYIVDPKNKTPINEPTWEIVGFDSATHKMKSAPMTLDFKGNKLTYSLDKSENHDSSDLTYQDSKLLEASQDGKPRGIFRDMRIEENGVISLAFSNGVVEPVARIGILAFTNDQGLRKIGGNVYEMQESTINGENRPLSGNPILGWDEEGKLKFGKIRHKYLETSNVNAGNALTNLILMQRGYSMNAKAFGAGDDMIKEAISLKK
>NC_017361.1|WP_000963240.1|884227_885376_+|flagellar-hook-assembly-protein-FlgD
MAIDLAEVTGAKAAQERKKEQPQIANGLDKDAFMKLFLEQLKNQDPTAPMETDKIITQTAQLTQVEMQEENKKTMQEVASAMKSNKETNESLKDFQGALKDTMENLNKGMDDSLKANNALREVSTLNSVSMIGKIAETDVSGANFDGNNKLSFSLFFDEKIDASKGVPAIQILNENNELVKTISLKDYNGQKGYIHFEWDGTNEKGEKVPKGNYKIKAEYNLDSQSKQYLQTRIGRGEVESVIFDKGKPMLRMGEMILPIDSAIEFYKPEQKPLEQKFSEQKPLDQKPIEQKPIEQKPIEQKPLDQKLSDQKPIDQKPLEQKAPNQELSEQKPLEQKALDQKLSNQKPIEQKSLEQKPLEQKAPNQELSEQKQPQTPSKETA
>NC_017361.1|WP_001139914.1|882629_884177_+|flagellar-hook-length-control-protein-FliK
MPSPINPIHTSANTSALKNEAKNEDTKNVPKSASKDFSKLLNQKISKEEPKDKPKNLNPSALKDTPKDTLEKTPTPHIQTPKEIAKNQQAPTLKDLLNHQENHSTTHPTAKHETQHETQHETIQKTHPTTPNETPNKNEKKPSEALSNAHQTNLLHKNPITPNHANNANATQKPTAPTDNTKPKTLKDIQTLSQKHDLNASNIQTATTPENKSPLNASDHLALKTTPQNPTTNPTLAKNDAKNTANLSSVLQSLEKKDAQNKEHTNPTNNEKKMPPLKESLQINAIKRDKTLSKKKPEKAPTKSQATATTPENTPKLALKTPLLMPLMGANPPNDNAPTPLEKEEKSKEVSENKEKTKESSHSVQNAQNTPNSDNKSIAPKETIKHFTQQLKQEIQEYKPPMSKISMDLFPKELGKVEVVIQKVGKNLKVSVISHNNSLQTFLDNQQDLKNSLNALGFEGVDLSFSQNPSKEQQAPKDQLKEQELSPLKENALKSYQENTDNEHKETSMQITLYA
>NC_017361.1|WP_001191511.1|880900_882451_-|phosphate-acetyltransferase
MQSLWIYPENTEALKIACKSLLKALKPRYQKIALFSPISGECEGLGECEGFKSLELHSAIDKQKALELVSAAQEELLFETILKRYDEIQSVHDFVIGLGYVPDFFLNTLLDLNTTLAKHLNAPIVAVAQTSLEYLKAMHSHVIKKEAPFALGLLTGETLEKPDFLSASLCKGELEASVVEKLLHTKSAITTPLAFQRSLEKKAKEQIKKVVLPESEDERILKAAHHLNAMGAVGLILLGDEETIHSQAKNLNLNLENIEIIDPNTSNHKEEFANHLYELRKSKGLNQQEAEQLVLDKTYFATMLVHLGYAHAMVSGVNHTTADTIRPALQIIKTKPGVSLVSSVFLMCLDTQVLVFGDCAIIPNPSPKELAEIATTSAQTAKQFNIAPKVALLSYATGNSAQGEMIDKIKEALTIAQKLDPQLEMDGPLQFDASIDKSVAKKKMPNSQVAGQASVFIFPDLNAGNIAYKAVQRSAKAVAIGPILQGLNKPINDLSRGALVEDIINTVLISAIQAQD
>NC_017361.1|WP_000404815.1|879660_880884_-|acetate-kinase
MEILVLNLGSSSIKFKLFDMKENKPLASGLAEKIGEEIGQLKIKSHLHHNDQELKEKLVIKDHASGLLMIRENLTKMGIIKDFNQIDAIGHRVVQGGDKFHAPVLVDEKVMQEIGKLSILAPLHNPANLAGIEFVQKAHPHIPQIAVFDTAFHATMPNYAYMYALPYELYEKYQIRRYGFHGTSHHYVAKEAAKFLNIPYEKFNAISLHLGNGSSAAAIKNGKSVDTSMGLTPLEGLIMGTRCGDIDPTVVEYIAQCANKSLEEVMKILNHESGLKGVCGDNDARNIEARKEKGDQQAELAFEMCAYRIKKYIGAYMVVLNKVDALIFTGGLGENYSALRERVCEGLEDLGIALHKPTNDNPGNGIVNLSQPNTKVQVLRIPTDEELEIAIQAKEMVEKIKVSNENS
>NC_017361.1|WP_001248515.1|896511_898056_-|outer-membrane-beta-barrel-protein-HofG
MRQEKYFLTSSLSLLSFLLCPVEAFDYRFSGRVENFSKIGFNNSQINTKKGIYPTESFIDIVTLAQVKVNLLPKGTENHRLSVSLGGAIAAIPYDKTKYDINQANGKIFGSIVENFIGGYHGYFFNKYLGPAYAGTSQSASYHARPYVVDTAFLRYDYKDVFGFKAGRYEANIDFMSGSNQGWEVYYQPYKTETQRLRFWWWSSFGRGLAFNSWIYEFFATVPYLKKGGNPSNSNDFINYGWHGITTTYSYKGLDAQFFYYFAPKTYNAPGFKLVYDTNRNFENVGFRSQSMIMTTFPLYYRGWYNPETKTYSLEDSTPHGSLLGRNGVTLNIRQVFWWDNFNWSIGFYNTFGNSDAFLGSHTMPRGNNTSYIGNEISITTRHAGMIGYDFWDNTAYDGLADAITNANTFTFYTSVGGIHKRFAWHVFGRISHANKNALGQVGRANEYSVQFNASYAFTESILLNFRITYYGARINKGYQAGYFGVPKFNNPDGDFSANYQDRSYMMTNLTLKF
>NC_017361.1|WP_000998400.1|898369_900811_-|TonB-dependent-receptor
MNDKRFRKYCSFSIFLSLLGMFEAEAKEEEKEERKTERKKDKNTQHTLGKVTTQAAKIFNYNNQTTISSKELERRQANQISDMFRRNPNINVGGGAVIAQKIYVRGIEDRLARVTVDGAAQMGASYGHQGNTIIDPGMLKSVVVTKGAAQASAGPMALIGAIKMETKSANDFIPKGKDYAISGAATFLTNFGDRETVMGAYRHNHFDVLLYYTHQNIFYYRDGDNAMKNLFDPKADNKVTASPSEQNNVMAKINGYLSERDTLTLSYNMTRDNANRPLRANFTGTFLPYSCGDFNAFPNEQNPSDCLFENDASLFKTYSVNLVHNVSLNYEREGGSRFGDPKLKINGYTSVRNVQIDPLFRPNDIATIIPFTPSLQPSQNEENKCVAQGGIYDALKQTCAITFKSLGGGSVVANKNLFIINSGFNANVIHTIDHKNDNLLEYGLNYQNLTTFDKAIPDSELIKPGDAPDACLRVMDPNDPNMNGRCQRNGATANVVGVYAQANYTLHPMVTLGAGTRYDVYTLVDKDWQLHITQGFSPSAALNVSPLENLNFRLSYAYVTRGPMPGGLVWMRQDNLRYNRNLKPEIGQNAEFNTEYSSQYFDFRAAGFVQLISNYINQFSSTLFVTNLPSQDIIYVPGYEVSGTAKYKGFSLGLSVARSWPSLKGRLIADVYELAATTGNVFIVTASYTIARTGLSITWLSRFVTDLDYCSYSPYRNGPTDIDRRPSDCPKTPGIFHVHKPGYGVSSFFITYKPTYKKLKGLSLNAVFNNVFNQQYIDQASPVMSPDEPNQDKYARGMAEPGFNARFEISYKF
>NC_017361.1|WP_001229958.1|900997_901429_-|hypothetical-protein
MALVYLAQSDTTIGLLSKDSEKLNALKKRPKNKSVLIESADFTTLKSLARAPNVFKNLIRRSAKTTFIYPNSKAVRVIKGRHGDFLKRFKTLYSTSANLTQCAYDKEIAFNLADVIVSDERGLFESASSKIFKLYKNKKVRIR
>NC_017361.1|WP_001126577.1|901433_904691_-|carbamoyl-phosphate-synthase-large-subunit
MPKRTDISNILLIGSGPIVIGQACEFDYSGTQSCKTLKSLGYRVILINSNPATVMTDPEFSHQTYIQPITPENIAAIIKKEKIDAILPTMGGQTALNVVMQMHQKGMLEGVELLGAKIEAIKKGEDRQAFKEAMLKIGMDLPKGRYAYSELEALEAINEIGFPAIIRASFTLAGGGSGVAYNIEEFQELAKNALDASPINEILIEESLLGWKEYEMEVIRDSKDNCIIVCCIENIDPMGVHTGDSITIAPSLTLTDKEYQRMRDASFAILREIGVDTGGSNVQFAIHPETLRMVVIEMNPRVSRSSALASKATGFPIAKVATMLAVGFSLDEIKNDITNTPASFEPSLDYIVVKIPRFAFEKFAGVSSTLGTSMKSIGEVMAIGGNFLEALQKALCSLENNWLGFESLSKDLETIKKEIRRPNPKRLLYIADAFRLGVCVDEVFELCQIDRWFLSQIQKLVKAEESINSSVLTDAKKLRGLKNLGFSDARIAAKIKENENLEVSPFEVELARMNLQIAPNFEEVDTCAAEFLSLTPYLYSTYAPNPLPPILKNEEKKEKKILIIGSGPNRIGQGIEFDYCCVHASFALKDLNIKSVMLNCNPETVSTDYDTSDTLYFEPIHFECVKTIIQREQVDGIIVHFGGQTPLKLAKDLAKMQAPIIGTPFKVIDIAEDREKFSLFLKELDIKQPENGMAKSVDEAYSIANVIGFPIIVRPSYVLGGQHMQILENIEELHHYLESVTHSLEISPKNPLLIDKFLEKAVELDVDAICDKKEVYIAGILQHIEEAGIHSGDSACFIPSNLSPKILDEIEQVGAKIALHLGVVGLLNIQFAVYENALYLIEVNPRASRTVPFLSKALGVPLAKVATRVMVLEDLKEALKFYDKKNIVEYSKGVYKPKIPHFVALKEAVFPFNKLYGSDLILGPEMKSTGEVMGIARSLGLAFFKAQTACFNPIKNKGLIFVSVKDKDKEEACVLMKRLVELGFELCATEGTHKALEKAGVKSLKVLKISEGRPNIMDLMMNGEISMAINTSDHKSQDDAKLIRASVLKNHVSYFTTLSAIEVLLLALEESSQEDELLALQDYLK
>NC_017361.1|WP_001240301.1|904789_905482_-|Bax-inhibitor-1/YccA-family-protein
MALYDRANSRSAYAEYSLLHESELVNFVKTTYKFFAGSLLLATVGALLGLMNFQAVVQYKWVFFIAEIAAFFGLMFSKSKPGLNLFMLFAFTSLSGVTLVPLLGMVIAKAGLGAIWQALGMTTIVFGLMSVYALKTKNDLANMGKMLFIALIVVVVCSLINLFLGSPMFQVVIAGASAVLFSLYIAYDTQNIVKGMYDSPIDAAVSLYLDFLNVFISILQIIGIFSDRNK
>NC_017361.1|WP_000688670.1|905628_906627_+|type-I-glyceraldehyde-3-phosphate-dehydrogenase
MKIFINGFGRIGRCVLRAILERSDTTPPLEVVGINDPANWEILAYLLEHDSAHGLLFKEVHYSNDRLIIGSLEIPVFSSVKDLRGVDVIIECSGKFLEPKMLENYLLLGAKKVLLSAPFIGEYDEKQYPTLVYGINHSLYQNQAIVSNASCTTNAIAPICTILDKAFNIKEGMLTTIHSYTSDQKLIDLAHPLDKRRSRAAASNIIPTSTKAALALHKVLPNLKNKMHGHSVRVPSLDVSMIDLSLFLEKKAPKESINELLIEASKGALKGVLEIDLKERVSSDFISNPHSVIVAPDLTFTLENMVKIMGWYDNEWGYSNRLVDMARFMYHY
>NC_017361.1|WP_000172823.1|906706_913870_+|vacuolating-cytotoxin-domain-containing-protein
MTLKKAKLISGFISKRSFKLDKVSRKFLPLNRILNREKSLKRHKKALKPIKKPFNKNKSFLKASVLLIGALGGLSHLRASDCKTWSWSSWTYQDNIASGANSPTHNSYCLFSSAQGSGTYYLNTLTTYSSGGASFTQKFNGGTLDIGGNIRFGEGGYLGYITGAYDAQTINFNSSHITTGNGWSGGGATLNFNATNNLTINQASFDNSHAGTQHSYMNFKGSNINVSGSSFKDDTNGGFSFSGNNNSSTISFNQTNFNQGTYKFSNSASSSFDSSNFNQGAYNFNTQSTFENSSFNQGTYDFSNNASFNNDTFNQGTYSFNASKVSFSGTNTLNSSSPFASLKGGVSFGSNAIFNLNQTLNANQTYDILTTNGAIQYGVYQSYLWDLINYKGDKAISHVEVGKNTYDVTFDINGQDETLQETFNSQSIIAQFLGDDLQQQAQKTYKEDLTNSQSALNNATNDNQIASNDTDYTKNSNPAVAKDAKDLENANQQIQQDEQALEKDLANVNQLANSTTGFNEQAFKNAQSQEQQDEQTLQNDENAFNSDQEGLQKALANAKHASPTPSPTKHTAQNTPPSKVPPTPPTQNPSAESVWGGVYWLQNKTYSNKGTYYIDPNLSGQSGQSGNTLSTYTANLLGRSFGVNANNGALIIGNDTESVNDNGLIWIGHGGFGYITGTFSAANIYLTNNFKTGEGVSGSDGGGANITFKASDNITMDGLNYNDAETVTKMIQTGASQHSYATFDAINNISATNSSFSDMTWGKFSFTAKNISFSNASFSGFTNPGGSSVISASATNSLSFTDSRLNGGAVYNLQASSLIFNNTQAVFNVLYSRGTSNFNATTQLLGNTSFTLSSQSSLNFSGNTTLQNNANITLGNKSQVTFKNSLTLNNNSNLSLDNQSVLNATGTSAFNNQANLNIYNGSQASFSSLFFNGGTLSLNASSKLNASSASFSNNTTINLDNSVLSANNTSALNANINFQGASQAHFGGNTTTDTASFNFDSASSLNFNNLTANGALNFNGYASSSSKALMNISGQFVLGNNGDIDLSNINIFDNITKSVTYNILNAQKGITGISGANGYEKILFYGMKIQNATYSNNNNVQTWSFINPLNSSQIIQESIKNGDLTIEVLNNPNSASNTIFNIAPELYNYQASKQNPTGYSYDYSSNQAGTYYLTSNIKGLFTPKGSQTPQTPGTYSPFNQPLNSLNIYNKGFSSGNLKTLLGILSQNSATLKEMIESNQLDNITNINEVLQLLDKIKITQAQKQALLDTINHLTNDINQTFSNGNLIIGATQDNVTNSTSSIWFGGDGYSSPCSLDSATCSSFRNTYLGQLLGSTSAYLGYINADFKAKSIYITGTVGSGNAFESGGSADVTFQSANNLVLNKANIEAQATDNIFNLLGQKGINEIFNQGNLANVLSQMAMEKIKQAGGLGNFIENALSPLSKELPTSLQNETLGQLIGQNNLDNLLNNSGVMNGIQNIISKKLSIFGNFVTPSIIENYLAKQSLKSMLDDKGLLNFIGGYIDASEISSILSVILKDITNPPASLQKDIGVVANDLLNEFLGQDVVKKLESQGLVDNIINNIISQGGLSGIYNQGLGSVLPPSLQNALKENNLGSLLLPRGLHDFWQKGYFNFLSNGYVFVNDSSFSNATGGSLNFVANKSIIFNGNNTIDFSKYQGALIFASNDVSNINITTLNATNGLSLNAGLNNVSVQKGEICVNLASCPTTKNSSSTSSSVTPTNESLSVRANNFTFLGTIASNGAIDLSQVKNNSVIGTLNLNENATLQANNLTITNALNNASNSTANIGGNFTLNQQATLSTNASGLNIMGNFNSYGDLVFNLNHSVSHAIINAQGTATLMANSNNPLIQFNTSSKEVGTYTLVNSSKAIYYGYNNQITGGSSLDNYLKLYTLIDINGKHMVMTNNGLTYNGQAVSIKDGGLIVGFKDSQNQYIYTSILYNKVKIAVSNDPINDLQAPTLKQYITQIQGVQSVDSIDQAGGSQAINWLNKIFETKGSPLFAPYYLESHSIKDLTTIAGDIANTLEVIANPDFKNDATNILQINTYTQQMSRLAKLSDTSTFARSDFLERLEALKNKRFADAIPNAMDVILKYSQRNKVKNNVWATGVGGASFINGGTGTLYGINVGYDRFIKGVIVGGYAAYGYSGFHGNITQSGSSNVNMGVYSRAFIKRSELTMSLNETWGYNKTFINSYDPLLSIINQSYKYNTWTTDAKINYGYDFMFKDKSVIFKPQVGLAYYYIGLSGLRGIMDDPIYNQFRANADPNKKSVLTINFALESRHYFNKNSYYFVIADVGRDLFINSMGDKMVRFIGNNTLSYRDGGRYNTFASIITGGELRLFKTFYVNAGIGARFGLDYKDINITGNIGMRYAF
>NC_017361.1|WP_001169656.1|913919_915035_+|outer-membrane-protein
MQKIVFSSFSLFSFLFSSLFSLCSAEENGAYASVGVEYSIAHAVEHNNPFLNQERIKTISNAQNQINELNQVKSQVKNMPNNFNYINNALKNHSKLTPTEMQAEQYYLQSTLKGIEKIVVLSHSAPSNPKLVQALEKMQEPTANPLAFEENLKNLELQFDHSQNNILSSLSSQITQISNSLNALDPTSYSKNISSMYGVGLSVGYKHFFTKKKNQGFRYYLFYDYGYSNFGFVGNGVTSLGKMNNHLYGLGIDYLFNFIDNEKKHSSVGFYVGFALAGSSWVGSGLGMWVSQTGFINNYLTGYQAKMHTSFFQIPLNLGIRVNVDRHNGFEMGLKIPLAVNSFYETHGKGLNTSLFFKRLVMFHVSYVYSF
>NC_017361.1|WP_001128388.1|915094_915301_-|4-oxalocrotonate-tautomerase-family-protein
MPLINIKLVPENGGPTNEQKQQLIEEVSDLMVKVLNKNKASVVVVIDEVDPNNYGLGGESVHHLRQKN
>NC_017361.1|WP_001099587.1|915416_915998_+|recombination-protein-RecR
MNTYKNSLNHFLNLVDCLEKIPNVGKKSAFKMAYHLGLENPFLALKLTHALENALENLKTCASCNALSESEICEICSDESRQNSQLCMVLHPRDVFILEDLKDFLGRYHVLNSIENVDFNALEKRLVKEKIKEIIFAFPPTLANDSLMLYIEDKLQHCRLTFTKIAQGVPTGVNFENIDSVSLSRAFNSRIKA

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_017361_3	3.1|876049|29|NC_017361|CRISPRCasFinder	876049-876077	29	MN732867	Erwinia phage Hena1, complete genome	137606-137634	6	0.793
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013461	Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S24-C21	25214-25247	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013749	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S45-C34, *** SEQUENCING IN PROGRESS ***	16930-16963	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013462	Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S33-C24	37436-37469	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013743	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S34-C32, *** SEQUENCING IN PROGRESS ***	19576-19609	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP014436	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S31-C13, *** SEQUENCING IN PROGRESS ***, 5 ordered pieces	18479-18512	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013742	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S30-C25, *** SEQUENCING IN PROGRESS ***	17320-17353	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013463	Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S42-C45	1699-1732	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013747	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S43-C36, *** SEQUENCING IN PROGRESS ***	16918-16951	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013746	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S40-C25, *** SEQUENCING IN PROGRESS ***	20494-20527	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013745	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S39-C31, *** SEQUENCING IN PROGRESS ***	20478-20511	7	0.794
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	AP013748	Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S44-C33, *** SEQUENCING IN PROGRESS ***	18885-18918	7	0.794
NC_017361_3	3.1|876049|29|NC_017361|CRISPRCasFinder	876049-876077	29	MN693957	Marine virus AFVG_250M449, complete genome	9181-9209	7	0.759
NC_017361_3	3.1|876049|29|NC_017361|CRISPRCasFinder	876049-876077	29	AP013442	Uncultured Mediterranean phage uvMED DNA, complete genome, group G17, isolate: uvMED-CGR-C22-MedDCM-OCT-S36-C18	4474-4502	7	0.759
NC_017361_3	3.1|876049|29|NC_017361|CRISPRCasFinder	876049-876077	29	NZ_CP042838	Enterococcus sp. DA9 plasmid unnamed3	331-359	8	0.724
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	MN044033	Klebsiella phage Marfa, complete genome	39139-39172	11	0.676
NC_017361_2	2.1|863326|34|NC_017361|CRISPRCasFinder	863326-863359	34	NC_031121	Bacillus phage Aurora, complete genome	12077-12110	11	0.676

1. spacer 3.1|876049|29|NC_017361|CRISPRCasFinder matches to MN732867 (Erwinia phage Hena1, complete genome) position: , mismatch: 6, identity: 0.793

aaaaatccattttttaatttgaaactcca	CRISPR spacer
gaaaatccattttggaatttgaaaaaccc	Protospacer
.************  *********  ** 

2. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013461 (Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S24-C21) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

3. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013749 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S45-C34, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

4. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013462 (Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S33-C24) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

5. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013743 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S34-C32, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

6. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP014436 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S31-C13, *** SEQUENCING IN PROGRESS ***, 5 ordered pieces) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

7. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013742 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S30-C25, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

8. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013463 (Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-C29A-MedDCM-OCT-S42-C45) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

9. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013747 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S43-C36, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

10. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013746 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S40-C25, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

11. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013745 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S39-C31, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

12. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to AP013748 (Uncultured Mediterranean phage uvMED isolate uvMED-CGF-C29A-MedDCM-OCT-S44-C33, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 7, identity: 0.794

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
caagagaagcttttaaaacatttaaaaaagtaga	Protospacer
******************* *** ***   **  

13. spacer 3.1|876049|29|NC_017361|CRISPRCasFinder matches to MN693957 (Marine virus AFVG_250M449, complete genome) position: , mismatch: 7, identity: 0.759

aaaaatccattttttaatttgaaactcca	CRISPR spacer
gaaaatccatttttttatttgattataga	Protospacer
.************** ******   *  *

14. spacer 3.1|876049|29|NC_017361|CRISPRCasFinder matches to AP013442 (Uncultured Mediterranean phage uvMED DNA, complete genome, group G17, isolate: uvMED-CGR-C22-MedDCM-OCT-S36-C18) position: , mismatch: 7, identity: 0.759

aaaaatccattttttaatttgaaactcca	CRISPR spacer
aaaaatccattttttaatatggtctgcta	Protospacer
****************** **.  . *.*

15. spacer 3.1|876049|29|NC_017361|CRISPRCasFinder matches to NZ_CP042838 (Enterococcus sp. DA9 plasmid unnamed3) position: , mismatch: 8, identity: 0.724

aaaaatccattttttaatttgaaactcca	CRISPR spacer
actaatccattttttaagttgaaaaaaac	Protospacer
*  ************** ******     

16. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to MN044033 (Klebsiella phage Marfa, complete genome) position: , mismatch: 11, identity: 0.676

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
actaagaagcttgaaaaacttttcaaatgaaaat	Protospacer
   .********  **************   * .

17. spacer 2.1|863326|34|NC_017361|CRISPRCasFinder matches to NC_031121 (Bacillus phage Aurora, complete genome) position: , mismatch: 11, identity: 0.676

caagagaagcttttaaaacttttcaaattttacc	CRISPR spacer
aattttaatcttttaaatcttttcaaatttattt	Protospacer
 *    ** ******** ************  ..