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_002928	Bordetella parapertussis 12822, complete genome	7 crisprs	RT,csa3,DEDDh,cas3,DinG	1	0	1	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_002928_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_1

822409-822565

Orphan

Consensus_repeat	Method
GGCATCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA	PILER-CR

2 spacers

The CRISPR arrays of NC_002928_1

>merge|NC_002928|1|822409-822565|PILER-CR
GGCGTCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTACGCCATCCGGGGTGCCTGTCCCCGCAGGGGGACTGGCACCGGCAAGATTTCACGGCATCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA

>NC_002928|1|1|822409-822565|PILER-CR
GGCGTCTGCCCGTGCGTGTGCCTGTCCCCGCTGGGACAGGCACATTGCCGTA	CGCCATCCGG
GGTGCCTGTCCCCGCAGGGGGACTGGCACCGGCAAGATTTCACGGCATCTGC	CCGTGCGTGTGCCTGTCCCCGCTG
GGACAGGCACATTGCCGTA

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_003808385.1\|810157_810580_-\|VOC-family-protein	unknown	unknown	gnl\|CDD\|319943
NC_002928.3\|WP_003808382.1\|809586_810150_+\|dCTP-deaminase	unknown	unknown	gnl\|CDD\|234753
NC_002928.3\|WP_010927672.1\|814597_815830_+\|NAD(P)/FAD-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|367519
NC_002928.3\|WP_003808423.1\|828848_830297_-\|YdgA-family-protein	unknown	unknown	gnl\|CDD\|377603
NC_002928.3\|WP_003808413.1\|823607_824819_+\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
NC_002928.3\|WP_003808419.1\|825812_826646_+\|enoyl-CoA-hydratase/isomerase-family-protein	unknown	unknown	gnl\|CDD\|119339
NC_002928.3\|WP_010927679.1\|833653_834553_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224094
NC_002928.3\|WP_010927673.1\|817857_818958_+\|glycine-cleavage-system-aminomethyltransferase-GcvT	unknown	unknown	gnl\|CDD\|234742
NC_002928.3\|WP_003808415.1\|824847_825816_+\|tripartite-tricarboxylate-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270234
NC_002928.3\|WP_003808411.1\|822797_823538_-\|FadR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|225097
NC_002928.3\|WP_010927670.1\|810607_811027_-\|VOC-family-protein	unknown	unknown	gnl\|CDD\|380093
NC_002928.3\|WP_010927671.1\|812278_814549_+\|arginine/lysine/ornithine-decarboxylase	unknown	unknown	gnl\|CDD\|224893
NC_002928.3\|WP_010929676.1\|819039_819414_+\|glycine-cleavage-system-protein-GcvH	unknown	unknown	gnl\|CDD\|234918
NC_002928.3\|WP_010927677.1\|830472_831948_-\|M81-family-metallopeptidase	unknown	unknown	gnl\|CDD\|377823
NC_002928.3\|WP_010927674.1\|819473_822338_+\|aminomethyl-transferring-glycine-dehydrogenase	unknown	unknown	gnl\|CDD\|235432
NC_002928.3\|WP_010927680.1\|834555_835497_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223674
NC_002928.3\|WP_033446726.1\|815932_816568_+\|superoxide-dismutase	unknown	unknown	gnl\|CDD\|223678
NC_002928.3\|WP_003808390.1\|811055_811574_-\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|372596
NC_002928.3\|WP_010927678.1\|831991_833650_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224048
NC_002928.3\|WP_010927676.1\|826696_828721_-\|DUF945-family-protein	unknown	unknown	gnl\|CDD\|377603

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_003808385.1\|810157_810580_-\|VOC-family-protein	gnl\|CDD\|319943	cd08355, TioX_like, Micromonospora sp. TioX and similar proteins. Micromonospora sp. TioX is encoded by a gene of the thiocoraline biosynthetic gene cluster. Thiocoraline is a thiodepsipeptide with potent antitumor activity. TioX may be involved in thiocoraline resistance or secretion. TioX belongs to vicinal oxygen chelate (VOC) superfamily that is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.	7.44146e-58
NC_002928.3\|WP_003808382.1\|809586_810150_+\|dCTP-deaminase	gnl\|CDD\|234753	PRK00416, dcd, deoxycytidine triphosphate deaminase; Reviewed.	2.45509e-113
NC_002928.3\|WP_010927672.1\|814597_815830_+\|NAD(P)/FAD-dependent-oxidoreductase	gnl\|CDD\|367519	pfam03486, HI0933_like, HI0933-like protein.	6.72401e-171
NC_002928.3\|WP_003808423.1\|828848_830297_-\|YdgA-family-protein	gnl\|CDD\|377603	pfam06097, DUF945, Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function.	1.75279e-118
NC_002928.3\|WP_003808413.1\|823607_824819_+\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	7.1626e-149
NC_002928.3\|WP_003808419.1\|825812_826646_+\|enoyl-CoA-hydratase/isomerase-family-protein	gnl\|CDD\|119339	cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.	4.25427e-71
NC_002928.3\|WP_010927679.1\|833653_834553_-\|ABC-transporter-permease	gnl\|CDD\|224094	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	6.84311e-84
NC_002928.3\|WP_010927673.1\|817857_818958_+\|glycine-cleavage-system-aminomethyltransferase-GcvT	gnl\|CDD\|234742	PRK00389, gcvT, glycine cleavage system aminomethyltransferase GcvT.	0
NC_002928.3\|WP_003808415.1\|824847_825816_+\|tripartite-tricarboxylate-transporter-substrate-binding-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	5.45752e-112
NC_002928.3\|WP_003808411.1\|822797_823538_-\|FadR-family-transcriptional-regulator	gnl\|CDD\|225097	COG2186, FadR, Transcriptional regulators [Transcription].	1.4512e-42
NC_002928.3\|WP_010927670.1\|810607_811027_-\|VOC-family-protein	gnl\|CDD\|380093	pfam18029, Glyoxalase_6, Glyoxalase-like domain. This entry comprises a diverse set of domains related to the Glyoxalase domain. The exact specificity of these proteins is uncertain.	3.08152e-15
NC_002928.3\|WP_010927671.1\|812278_814549_+\|arginine/lysine/ornithine-decarboxylase	gnl\|CDD\|224893	COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism].	0
NC_002928.3\|WP_010929676.1\|819039_819414_+\|glycine-cleavage-system-protein-GcvH	gnl\|CDD\|234918	PRK01202, PRK01202, glycine cleavage system protein GcvH.	1.40219e-66
NC_002928.3\|WP_010927677.1\|830472_831948_-\|M81-family-metallopeptidase	gnl\|CDD\|377823	pfam07364, DUF1485, Metallopeptidase family M81. This is a family of proteobacterial metallo-peptidases.	8.85912e-105
NC_002928.3\|WP_010927674.1\|819473_822338_+\|aminomethyl-transferring-glycine-dehydrogenase	gnl\|CDD\|235432	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase.	0
NC_002928.3\|WP_010927680.1\|834555_835497_-\|ABC-transporter-permease	gnl\|CDD\|223674	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	5.91448e-121
NC_002928.3\|WP_033446726.1\|815932_816568_+\|superoxide-dismutase	gnl\|CDD\|223678	COG0605, SodA, Superoxide dismutase [Inorganic ion transport and metabolism].	6.82185e-105
NC_002928.3\|WP_003808390.1\|811055_811574_-\|GNAT-family-N-acetyltransferase	gnl\|CDD\|372596	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain.	1.09696e-12
NC_002928.3\|WP_010927678.1\|831991_833650_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224048	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].	0
NC_002928.3\|WP_010927676.1\|826696_828721_-\|DUF945-family-protein	gnl\|CDD\|377603	pfam06097, DUF945, Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function.	3.89582e-106

>NC_002928.3|WP_010927674.1|819473_822338_+|aminomethyl-transferring-glycine-dehydrogenase
MSRAPDTHSDFIPRHIGPSDEDQATMLAAIGAASLDALIDEVVPPRIRSRAPLALPAARSETDVLQDLKRMAARNQIYRNYIGQGYYGTHTPNVVLRNVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVADLTGLDISNASLLDEGTAAAEAMTLARRGSRSSSPVFFVSQHCHPQTLEVVRTRAEGLGIELVIGDESRGLPECFGVLLQYPHSLGGVADYRELAQAAHAQGAVVACVTDLLALALIEPPGQWGADIAVGSAQRFGVPFGFGGPHAGFMACRDAYKRNMPGRLVGVSKDAQGNPALRLALQTREQHIRREKATSNICTAQVLLAVMAGLYAVWHGPRGVRRIAERVQSLTGALRAALAGLGVKVANDTWFDTLLLETGVATPAILAAADCARTNLRQVDGARLAVSLDETVTLADLQALVNVFAAGLGKDEVALPAPQASLDGIPAAVRRQGPILSHPVFSSVQSETDMLRYLRKLADKDLALDRTMIPLGSCTMKLNATAEMIPITWPEFALIHPFAPASQTPGYRELIDGLSAQLCEITGYDGISLQPNSGAQGEYAGLLAIRAYHQANGQPQRNVCLIPASAHGTNPASAQLAGMDVVVVASDANGNVDLADLRARIAQVGERLAALMITYPSTHGVFEEAVTEICDAVHEAGGQVYLDGANMNAMVGVAQPGKFGSDVSHLNLHKTFCIPHGGGGPGVGPVAVRAHLAPYLPGVLDAQGRLDPEAKVGPVSAAPYGSAGILPIPYVYIALMGAEGLRRATEVAILNANYIAARLRDHYPVLYAGRNGRVAHECILDVRPLKETSGISAEDIAKRLMDYGFHAPTMSFPVAGTLMVEPTESEGLAELERFIEAMIAIRAEIAQIESGERDRDDNVLRNAPHTAQMLLAEEWHHDYPRQQAAYPVASLRENKYWPPVARVDNAYGDRNLVCACLPVEAYA
>NC_002928.3|WP_010929676.1|819039_819414_+|glycine-cleavage-system-protein-GcvH
MSLPTDRKYTESHEWVQAEGDVFVVGITDNAQEQLGDLVFVGDVKVGATLKAGETAGVVESVKAASDIYAPVDGEIVAFNDELEANPSLINESAYTAWIFKIKPANAADLDKLLDAAGYQAVAG
>NC_002928.3|WP_010927673.1|817857_818958_+|glycine-cleavage-system-aminomethyltransferase-GcvT
MSAPLKRTPLAEEHLAAGARMVDFGGWDMPLAYGSQLEEHHAVRQDAGMFDVSHMLNVDVGGADATAFLRRLVANDVARLATPGRALYSCMLNPQGGIIDDLIIYYFAPDQWRVVVNAGTADKDIAWMQRVAAADGFDVAIAPRRDLAMVAVQGPNARAKVWAARPAWQAASEPLAPFSAAAVEAGTLVARTGYTGEDGFEIVLPADAVVQLWRDLLAQGVRPCGLGARDTLRLEAGMNLYGQDMDELVHPDQAGLSWTVALKDEARRFVGRDAIEQFAVPRAFVGLKLQERGVMRAHMPVRCAQGMGELTSGTMSPTLGVSVGFARVPVGVQPGDAVEVEIRGKWVPALVCKLPFVRHGKAVEHS
>NC_002928.3|WP_033446726.1|815932_816568_+|superoxide-dismutase
MPYVLPALSYAYDALEPHIDARTMEIHHTRHHQTYVNGLNAALEGAGLDSEEPVEQLLRRIPALPPGIHGAVRNHGGGHANHSLFWTVMSPSGGGRPDGRLAADIQAQLGGHDAFQAAFTQAALGRFGSGWAWLTVTPAGRLRVDSSANQDSPLMEGNTPILGLDVWEHAYYLQYQNRRPEYIEAFYRVVDWAEVARRYEIALAELGREAA
>NC_002928.3|WP_010927672.1|814597_815830_+|NAD(P)/FAD-dependent-oxidoreductase
MSSREYPVSMFDVAVIGAGAAGMMCAAVAGQRGLRVVLIDHAAKLAEKIRISGGGRCNFTNLGAGPANFLSDNPHFCRSALAGYTPQDFLGLLRRHRVHWHEKHRGQLFCDDSSETIIEVLRAECGQGGVAWRMPCRVDEIARREGGGFTLRTSTGAIDARAVVVATGGMAIPQLGATDYALKVARQFGLKVVEPRPALVPLTFDPAQWQPFAALSGVALEVTLSTGQGKGRAAFLEDLLFTHRGLSGPAILQISSYWKPGEAIVLDLAPGRDLAAELIGAKPGNRQQLHTVLAGLWPRRLADTWLDVAGRAVGADLAAARLADVPDRTLRALAALIHDWRLVPSGTAGYKKAEVMRGGVDTRALDQKSMQARGVPGLYFIGEAVDVTGWLGGYNFQWAWASGYACGNAL
>NC_002928.3|WP_010927671.1|812278_814549_+|arginine/lysine/ornithine-decarboxylase
MKFRFPIFIIDEDYRSENASGLGIRALASAIEAEGVEVIGVTSYGDLSSFAQQQSRASAFILSIDDEEFDVDSPEDVAGAIKNLRTFIGELRFRNADIPIYLYGETRTSEHIPNDILRELHGFIHMFEDTPEFVARHIIREARSYVDGLLPPFFRELVKYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAESELNAARIFHADHCFFVTNGTSTSNKVVWHANVAAGDVVVVDRNCHKSILHAITMTGAIPVFLRPTRNHLGIIGPIPLDEFDPENIRRKIEANPFAREALNKKPRILTLTQSTYDGVIYNVEMIKEKLGTYVDTLHFDEAWLPHAAFHEYYRDMHAIGPDRPRSQDAMVFATHSTHKLLAGISQASQIIVQESESRKLDRNLFNEAYLMHTSTSPQYAIIASCDVAAAMMEPPGGTALVEESIREAMDFRRAMRKVASEFGKDDWWFKVWGPNRLAPEGIGHRDDWVLESGDHWHGFGDLAPGFNMLDPIKATIITPGLDMSGSFGESGIPAALVSKYLAEHGVVVEKTGLYSFFILFTIGITKGRWNTLLTALQQFKDDYDRNQPLWRILPEFCRGHRRYERMGLRDLCQQIHEAYRERDVARLTTEMYLSDMVPALKPSDAFARMAHREVERVEIDQLEGRVTGVLLTPYPPGIPLLIPGERFNRTIVQYLQFAREFNERFPGFETYIHGLADEEGPDGAKRYYVDCLKDAGEQ
>NC_002928.3|WP_003808390.1|811055_811574_-|GNAT-family-N-acetyltransferase
MNLSTIRPLTPEDAAEFQRVRLAALREAPEAFGSSYEEESVDTIAQWRARLAPREGYVLLGAFVDGALAGVGGVARGHTMKQRHKAEIWGIYVVPAQRRGGLARQLTEALLARAARMTGVRHVLLSVGADNGAAHALYASLGFAEYGREPDAMLVGGRLLANILMIRPLAAR
>NC_002928.3|WP_010927670.1|810607_811027_-|VOC-family-protein
MQAQVLINIDVPDAARAALFYERAFGLRPQRRLGPQAIEMAGAAVPFYLLEKATGSQAATGTSQGRDYARHWTPVHLDFVVDDCDRAVATAVAAGAMLEDPPHSHAWGRIAHLSDPYGNGVCILQFLGEGYDALAAAAP
>NC_002928.3|WP_003808385.1|810157_810580_-|VOC-family-protein
MPAPATVASPVVTCLRYRNASAAIEWLVHAFGFEAQRIVPGPADTIVHAQLTLGSGMIMLASVTDTPFSRYMKQPDEVGGVETQSVYLVVADPDQAYRDAQAAGAEILIDIADADYGGRGFSCRDPEGHIWSVGSYDPWQ
>NC_002928.3|WP_003808382.1|809586_810150_+|dCTP-deaminase
MSIKSDRWIRRAAEAGMIEPFEPGQVRTAGGNRIVSYGTSSYGYDVRCADEFKIFTNINSTIVDPKQFDEKSFVDFKGDVCIIPPNSFALARTVEYFRIPRSVLTICLGKSTYARCGIIVNVTPLEPEWEGHVTLEFSNTTPLPAKIYAGEGCAQMLFLESDEVCETSYRDRGGKYQGQRGVTLPRT
>NC_002928.3|WP_003808411.1|822797_823538_-|FadR-family-transcriptional-regulator
MKTVETNPNPLGPIKAVRSRDLLADALREQILSGARPSGVALPSERELTEETGLSRAAVRDALRVLESEGLIETRQGRYGGSVVKLPANDALARPVALFARARGISLQEMIEARVAIEPTIAELAALRRTPEDLQALIQATDLLQEALPRVEQFLDLNVRWYFALADACHNDLLRAFIVSIAGLILAATSREGQTPEPTRRLILQSHRRVVDAVIAGDAPAARRRMERHVAGYQEHYERLGLTPSA
>NC_002928.3|WP_003808413.1|823607_824819_+|CoA-transferase
MAAVSSSVPPTPLGGVRVLDLSKVLAGPLCTQYMADMGADVIKVEAAGQGDDTRGWPPFQDGQAAVFLSCNRNKRSIALDLKSAHGRAVVQRLAAWADVVVHSFGPGVAQKLGVDWEALSEINPRLVYCAISGFGPVGSLSHGKGFDVVLQAFCGMISITGETEGGAVRSPFSPVDQATGLHALIGILAALRQRDASGRGVTVDASLFDTALGFMGYFMQGYWARGTEPARAGAGHESLCPYQDFATADKPIILGIANDALWRAFCTLAGRPELVSDPRFATNAQRVANRAQTLAATRELLAARTRGEWLPALEQAGIPCSPIHTLAEVDAHPHTRESGMVFDYPETGADTGPLKGVAQPVRFDGMRLTTPKRPPSLNQDWASVLADAGYSDPEVRDLLQQMA
>NC_002928.3|WP_003808415.1|824847_825816_+|tripartite-tricarboxylate-transporter-substrate-binding-protein
MMNVLIRRALCAAIASLAAAAAHAAYPEQPVRIVVAFAPGSGTDNVARYYATRLSEELKQPFVVENKPGANGSIAATQVARTQPDGYTLFLGSNSTLSAAPFLFKKLPYEPLKDFTAVARLSDIPSMLVVGADSPIRDFDQFIGKARAEPGRVTWANANTAHLAAGMALTKQAQLDMISVPYKSSPQALTDVIGGQVTAMVVDTSAGTAFVQQGKVRALAVTTARPVAAMPGVPSMSERFPGIDVYSWLGIVGPAGMPDEVVSVVNQAILKINASEDTVRFLRENAGAEPPPSSSPAEFTQFMHAQLEVWRKLLRDANVEPM
>NC_002928.3|WP_003808419.1|825812_826646_+|enoyl-CoA-hydratase/isomerase-family-protein
MSQQESRMSAPACVSEFVRYDVDAGVARITLDRPDRRNAIDVPMRAALLAAVQAATADPAVRAVVLTGAGGHFCSGGDVSTMRGASMSAEQGRDRMAPIGACARALLEMPKPVIAAVDGIAFGGGFGLCLCADLVLATPAARFCLSFMRIGLVPDFAAAFTLPRLVGLQRARQLIYTAAEIDGRQALEYGLVSELVDAGRLAPRAAEVATAMAGMPATAFALTKQALLRSSSSELAAMVEMEMTSQGVAFNTGYHQQAVERLLEKKPPLYSFPAPTA
>NC_002928.3|WP_010927676.1|826696_828721_-|DUF945-family-protein
MKKSIGITAGVIVVLAGGWLGGTWYTGKRIETETQQRLGVLNEKLAAVVPGYTLRVDQLKYERGFFTTQARYGLSLSQDIKEESGTVTPLPLGSTEFDARFEHGPFPRSALASGQFLPQMAFVHAELARTELVKPLFELTKNAAPLWSDTIVSYSGNASTRSGLAPIDFTEDDVTLSFSGATLTSTFQRATRSGTARLDAEYVRFTADGDQDTQMSATGWSVDMRSHQGKHGFTLGESTMAIKRIAMIDKRESLDISLDDLSYRALATEDGDYIDIEAAYKTGPLTVNKIPFGSGELNVKVSRLDGQALKALSDGYNQLLRGYFATGETDEGLKDEQLTMLIENGGRLLAGGPSLSLGPVAWRTEKGESSLMSSIVLVKPATTSGELTPREYLEEAVKAIDVKMVVSKPMVRDLAIHYETSQGKTPEEAAKEADETIDAFAGMAEILNIGRNDGDKLVGTFTYAAGVAKLNGRDVPVNELFDNLYDSASASLDDDEHNHEDDAAMSAEAASEAVEAAAEAAAAEAAQEAADAAAWATEGDSLRSVNAGLLTSILAEGGYDSTTEEGASGPVIVIDANGLPLRDLRAELYCIDDDECMDVSMKASFGKRKTSLKALNAWNQKYRWTRAYLDDDNQAVLRMDLSAEGGVGRENLSIMVNTFMQMVGNFEDEVYAAR
>NC_002928.3|WP_003808423.1|828848_830297_-|YdgA-family-protein
MKKSVAVTTGVIIVAVGGWLAGTWYTGQRIETESQTRLNEINAQLAAAFPEFPVRINQLKLERGFFTSQARYGVEVGKSEETGKPEATVEVDARIEHGPFAPGALARGKLMPQLAFVHAEVANTEDLKKVFEVTKGATPLWSDTVVAYNGDSTSTGGLAAIDYSGDEGKFAFSGATFDGSYQRATQAAIGSLKADSLALDASADDDGGPLLFTLDGLAVTVDSRMGKSGLSIGDSALSVKRLEVKQPEGDAHLTVADMAYAARIGEQDEFINGEISYGAGEITYNGIALGNGRAVFKAERLNAAAIKVVADEYNKAIKLQAEGKDPVPDNAEMRKLLMAQADTLLAGKPVLTLDPVQWKTAQGESVFNARVALSKPASSDLMAVDYFSQAIESIDASATLSKPMIKALMVGYLQSQEGMDAQQAAAAADQQVSSLAGMAEMMNLGKNEGDNIVSKFHYAAGTVDLNGRKMPADQLLGSILGG
>NC_002928.3|WP_010927677.1|830472_831948_-|M81-family-metallopeptidase
MRWLLAMIKHETNTVSPVPTPLERFFRGSPEILAGERAIRAYENTDSGLGGYIEVARREGAEIVVPVAAESWPSAPTDRATYERLCGLVLDEARRGGFDAILLDLHGAMVAEGVEDAEGDLLRRLRDIAPAIPVGVTLDMHANIYDDIVRHATVISGFHTYPHVDIRAAGLRAANAIARTLRGEIKPVMSWANKPMLPHIMRQGTHAEPNKSLQARCKALESEGVIAASVFVGFPHADIREAGLSAVVCTDANLAQAEQYRDELLETAWRGRADWVFHAEPLAPTIARAKAIENGPVVLLDHYDNTGSGGTMDTTAVLAEILDQGLENVAFYAICDPQAAQQAAAAGVGATVTLPLGGKVAMPALRQASPPLHLTARVKLLFDGVYLNRGPMYRGVRNDTGLTVVLDTGKVEIVVVSRHQEPFDINCLLSAGIDPLQKRYVALKSRVHWRAGFADMATHVIECTGVGVTTSDYGQVEFRHVRRPVYPLDAI
>NC_002928.3|WP_010927678.1|831991_833650_-|ABC-transporter-ATP-binding-protein
MPYAPYPPAGDTSAAVLAIRNLSVSVCGAGNRVVRNLSLDVHAGETVCVVGESGSGKSVTSLAVMGLLPEGILEVSGGSARVLGEDIVTASARRRRELRATRMAMVFQEPMTALNPVHRVGSQVDEVLRLHRRMPRAQRRAKVLEMFRSVHLPDVERIYDAYPHQLSGGQRQRIVIAMALILEPKLLIADEPTTALDVTTQKQILALIRELQDRHQTAVLFITHDFGVVAEIADRIVVMNRSDLTEAGTRDEILARPSQNYTRRLVSSVPSLVPTQREAPGGEPVLRITGLGRTYAERRSLFGATRTVVAASEVDLTLRRGEILGIVGESGSGKSTVARCIVRLIEPSAGRMLLGETDIARLSGAGLRPLRRKVQIVFQDPYRSLNPRRAVGESIIEGLLNFGMPRAQALVRAARTLGVVGLGPDVMRRYPHQFSGGQRQRLCIARALVMDPEVLVADEAVSALDVSVQAQVLELIEQVRERTGVSVLFITHDLRVAAQVCDTIAVMQHGKVVETGAAQTVLTRPGHAYTRALIDAAPGRGWDFRNFRPLPA
>NC_002928.3|WP_010927679.1|833653_834553_-|ABC-transporter-permease
MPTHSDAVADGALPENEPPQAGAWRRVRREFSGAPVLAALAVLALVVGAALLAPWLGTVDPTAIDPGARLKPPFGDYLFGTDAFGRDIWSRVVYGARVSLVAGLGAALVSVTLGLVIGVIAGWFRTLDGLIMRTMDAVMAIPGILLAIALVSVTGASLATVLVAITIPEIPRVVRLVRGQILSVRGEPYVEAALALGTPLPLLLWRHLVPSTVAPLTVQGTYVFASAMLTEAILSFLGAGIPPEIASWGNIMSEGRMYFRMLPGLILFPGLFLSLTVLSVNILGDALRDALDPKMTRRT
>NC_002928.3|WP_010927680.1|834555_835497_-|ABC-transporter-permease
MLAFIARRLLATIPVLIMVAVVVFAILRASPGDPAIIMAGDAATPERIAQIRHVMGLDQPLVKQFFIWTGRLVRGDMGTSLMSGVPVTQLIGQRLEPSLSLAVITLAFTLAVAIPLGILAAWRRGRLLGRAVMGFSVLGFSVPVFVTGYVLIWAFAIKLGWFNVQGYTPLAQGFWPYLHRLVLPSLALSTVYVALIARITRTSIIEVMGEDFIRTARAKGLGETGVLLGHALRNAAVPIATVIGVGVALLISGVVVTESVFNIPGLGRLVVEAVMARDYPVIQGLTLFFAFVYVFINLVVDCAYTVFDPRIRY

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Crispr_ID: NC_002928_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_2

1052357-1052443

Orphan

Consensus_repeat	Method
CGTGGTGCCTGTCCCCGCGGGGAC	CRISPRCasFinder

1 spacers

csa3

The CRISPR arrays of NC_002928_2

>merge|NC_002928|2|1052357-1052443|CRISPRCasFinder
CGTGGTGCCTGTCCCCGCGGGGACGGATACCGTCTTAGGAGCGGGGAGGGTGGTGCGGGGGAACGTGGTGCCTGTCCCCGCGGGGAC

>NC_002928|2|1|1052357-1052443|CRISPRCasFinder
CGTGGTGCCTGTCCCCGCGGGGAC	GGATACCGTCTTAGGAGCGGGGAGGGTGGTGCGGGGGAA
CGTGGTGCCTGTCCCCGCGGGGAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_010927776.1\|1042827_1044804_-\|EAL-domain-containing-protein	unknown	unknown	gnl\|CDD\|379843
NC_002928.3\|WP_003809056.1\|1056749_1056965_-\|hypothetical-protein	unknown	unknown	unknown
NC_002928.3\|WP_041937359.1\|1037461_1039957_+\|copper-translocating-P-type-ATPase	unknown	unknown	gnl\|CDD\|319783
NC_002928.3\|WP_003809022.1\|1034287_1034722_-\|PaaI-family-thioesterase	unknown	unknown	gnl\|CDD\|239527
NC_002928.3\|WP_003809067.1\|1061885_1062851_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270234
NC_002928.3\|WP_003809064.1\|1060564_1061845_+\|arsenic-transporter	unknown	unknown	gnl\|CDD\|185342
NC_002928.3\|WP_003809025.1\|1035780_1036707_-\|VOC-family-protein	unknown	unknown	gnl\|CDD\|379203
NC_002928.3\|WP_010927775.1\|1040005_1040698_+\|HD-domain-containing-protein	unknown	unknown	gnl\|CDD\|182251
NC_002928.3\|WP_010927780.1\|1056975_1058445_-\|TolC-family-outer-membrane-protein	unknown	unknown	gnl\|CDD\|273829
NC_002928.3\|WP_003809026.1\|1036993_1037362_+\|DUF861-domain-containing-protein	unknown	unknown	gnl\|CDD\|225981
NC_002928.3\|WP_010927782.1\|1060241_1060568_+\|helix-turn-helix-transcriptional-regulator	csa3	COG0640_csa3_CAS-I-A	gnl\|CDD\|223713
NC_002928.3\|WP_003809070.1\|1062894_1064031_-\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
NC_002928.3\|WP_003809053.1\|1053152_1054595_-\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|130902
NC_002928.3\|WP_003809041.1\|1042152_1042779_+\|hydrolase	unknown	unknown	gnl\|CDD\|238494
NC_002928.3\|WP_010927779.1\|1054597_1056772_-\|type-I-secretion-system-permease/ATPase	unknown	unknown	gnl\|CDD\|274550
NC_002928.3\|WP_010927773.1\|1032376_1033165_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213260
NC_002928.3\|WP_003809046.1\|1044819_1045503_-\|transglutaminase-like-cysteine-peptidase	unknown	unknown	gnl\|CDD\|226198
NC_002928.3\|WP_010927778.1\|1052465_1053131_-\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|225107
NC_002928.3\|WP_010927777.1\|1045583_1052231_-\|retention-module-containing-protein	unknown	unknown	gnl\|CDD\|333740
NC_002928.3\|WP_076879797.1\|1058796_1060089_-\|TIGR03862-family-flavoprotein	unknown	unknown	gnl\|CDD\|274820

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_010927776.1\|1042827_1044804_-\|EAL-domain-containing-protein	gnl\|CDD\|379843	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain. This domain is the N-terminal periplasmic domain of the LapD and MoxY receptor proteins.	3.66319e-38
NC_002928.3\|WP_010927782.1\|1060241_1060568_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|223713	COG0640, ArsR, Predicted transcriptional regulators [Transcription].	2.26872e-12
NC_002928.3\|WP_041937359.1\|1037461_1039957_+\|copper-translocating-P-type-ATPase	gnl\|CDD\|319783	cd02094, P-type_ATPase_Cu-like, P-type heavy metal-transporting ATPase, similar to human copper-transporting ATPases, ATP7A and ATP7B. The mammalian copper-transporting P-type ATPases, ATP7A and ATP7B are key molecules required for the regulation and maintenance of copper homeostasis. Menkes and Wilson diseases are caused by mutation in ATP7A and ATP7B respectively. This subfamily includes other copper-transporting ATPases such as: Bacillus subtilis CopA , Archeaoglobus fulgidus CopA, and Saccharomyces cerevisiae Ccc2p. 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_002928.3\|WP_003809022.1\|1034287_1034722_-\|PaaI-family-thioesterase	gnl\|CDD\|239527	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not been determined. Sequence similarity between PaaI, E. coli medium chain acyl-CoA thioesterase II, and human thioesterase III suggests they all belong to the same thioesterase superfamily. The conserved fold present in these thioesterases is referred to as an asymmetric hot dog fold, similar to those of 4-hydroxybenzoyl-CoA thioesterase (4HBT) and the beta-hydroxydecanoyl-ACP dehydratases (FabA/FabZ).	3.80366e-22
NC_002928.3\|WP_003809067.1\|1061885_1062851_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	2.10162e-113
NC_002928.3\|WP_003809064.1\|1060564_1061845_+\|arsenic-transporter	gnl\|CDD\|185342	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB.	0
NC_002928.3\|WP_003809025.1\|1035780_1036707_-\|VOC-family-protein	gnl\|CDD\|379203	pfam13468, Glyoxalase_3, Glyoxalase-like domain. This domain is related to the Glyoxalase domain pfam00903.	1.55135e-31
NC_002928.3\|WP_010927775.1\|1040005_1040698_+\|HD-domain-containing-protein	gnl\|CDD\|182251	PRK10119, PRK10119, putative hydrolase; Provisional.	2.80135e-80
NC_002928.3\|WP_010927780.1\|1056975_1058445_-\|TolC-family-outer-membrane-protein	gnl\|CDD\|273829	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family. Members of this model are outer membrane proteins from the TolC subfamily within the RND (Resistance-Nodulation-cell Division) efflux systems. These proteins, unlike the NodT subfamily, appear not to be lipoproteins. All are believed to participate in type I protein secretion, an ABC transporter system for protein secretion without cleavage of a signal sequence, although they may, like TolC, participate also in the efflux of smaller molecules as well. This family includes the well-documented examples TolC (E. coli), PrtF (Erwinia), and AprF (Pseudomonas aeruginosa). [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Porins].	1.98618e-74
NC_002928.3\|WP_003809026.1\|1036993_1037362_+\|DUF861-domain-containing-protein	gnl\|CDD\|225981	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only].	1.25112e-24
NC_002928.3\|WP_003809070.1\|1062894_1064031_-\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	8.85561e-148
NC_002928.3\|WP_003809053.1\|1053152_1054595_-\|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit	gnl\|CDD\|130902	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking].	3.83731e-118
NC_002928.3\|WP_003809041.1\|1042152_1042779_+\|hydrolase	gnl\|CDD\|238494	cd01012, YcaC_related, YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.	1.08247e-67
NC_002928.3\|WP_010927779.1\|1054597_1056772_-\|type-I-secretion-system-permease/ATPase	gnl\|CDD\|274550	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis].	0
NC_002928.3\|WP_010927773.1\|1032376_1033165_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213260	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters. NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.	2.27641e-113
NC_002928.3\|WP_003809046.1\|1044819_1045503_-\|transglutaminase-like-cysteine-peptidase	gnl\|CDD\|226198	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General function prediction only].	8.27062e-29
NC_002928.3\|WP_010927778.1\|1052465_1053131_-\|response-regulator-transcription-factor	gnl\|CDD\|225107	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription].	2.19301e-24
NC_002928.3\|WP_010927777.1\|1045583_1052231_-\|retention-module-containing-protein	gnl\|CDD\|333740	NF012211, tand_rpt_95, tandem-95 repeat protein. This 95-amino acid repeat occurs in tandem in proteins that may be several thousand amino acids long.	1.20527e-16
NC_002928.3\|WP_076879797.1\|1058796_1060089_-\|TIGR03862-family-flavoprotein	gnl\|CDD\|274820	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family. This model describes a sharply distinctive clade of proteins within the larger family of flavoproteins described by pfam03486 and TIGRFAMs model TIGR00275. The function is unknown.	1.21991e-156

>NC_002928.3|WP_010927777.1|1045583_1052231_-|retention-module-containing-protein
MANSSPAVVTAVTGRAWIRNSDGSLTELHEGSKVPQGSDIVTASGSTVALQVDGGMPLVIGEGREVAVTPDLNGGGGDASEAAVALPTTTDSERLLAALQDGRDPFDELDPTAAVIGGSGDSAGSSFVRLAKILESTTPMDLAYPNPGRGEDGVRTFLGGATAGADDEAAPAPANQAPNALDDLGQTRQGQTLRGNLMLNDSDPDGDPLAVVSVNGRPMTSGGLTLPGSGGGTFTVQPDGSYTFVPGNEHQSLGEGQTTTTTITYTITDPSGATSTATLTVTVTGTNDAPTLTPGVTLDDQANDDGEAITPVDISGQFEDIDNGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGNNGVYTVTITATDSGGKSVSQTFEWDVTNPAPTAVADTGATDEDTTLTVTDPAQGVLRNDTDPDNDDLHVSAVNGQPANVGAAIAGDNGGTFTLNADGTYTFNPGPDFQNLAKDATAETSITYTVSDGEGGTSSATLTITVAGGNDAPILTPGVTLDDQANDDGEAITPVDISGQFTDPDTGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGANNDGVYTVEITATDANGASVSQTFEWDVNNPAPTAVADTGTTDEDTTLTVTDPAQGVLKNDTDPDNDDLHVSAVNGQPGNVGAAIAGDNGGTFTLNADGTYTFNPGPDFQNLAKDATAETSITYTVSDGEGGTSSATLTVTVTGTNDAPTLTPNVTLDDQANNDGEAITPVDISGQFEDVDNGDTLTFTADGLPPGLTLDPATGIISGTLDNSASQGGANNDGVYTVEITATDANGASVSQTFEWDVNNPAPTAVADTGTTDEDTTLTVTDPAQGVLRNDTDPDNDDLHVSAVNGQPANVGVAIAGDNGGTFTLNADGTYSFNPGNAFQHLAQGDSVETSISYTVSDGEGGTSTTTLTVTVTGVNDTGAISVNLGADDGKVYEAGLDNAADDSETTGGTITVSASDGISSVTIGGQTFTVAQLSGDLSSLPAINTTEGTLTITGYTPSADGKSADITFSYTLNEAQTHSQPGNDTITDNIGVTVTGNGDSETSSSFNITIVDDVPTFQTVTDTVLANEAGQTQTGTLEFESGADGVGSLNITGITGLPNDWTTSAMNNASVNIFSPDGTHVFTVTLNTDGTYTVDQLATRPGTTESVNMGSQITNSPQASYDFGIASVTVLHSNQQVQFNGKGSNVPNVSHEFGIGNTWFEGGESFQMTFESPMLNFNFGIATVNNPGSVKVTLFDGVNTLTLTVPVNAGDTSLSITQDQIQAAAAAAVPPISFGEFSTATLEGVGGLKVSLTTLSYTNSVPADDMDFTVHVTGTDGDGDPAQTEFDVTSGAEAAVVDAFNRVMEDSGDTVGGSVMLSTALAVVSVSVNGTDVTNATAGNPVTFHTGKGTLIVTGYDPQSGALSYTYTEKGQAHNHGNGKNSVHDDFTVTVTDSDGQERSGDLVIQILDSVPTAHADLDNVTEGVTQNVSAADGVLANDTSADGWHHAGAIVGVAAGDTGAISHGKVGQAIDGLYGKLTLNANGSYSYKANASGQGALPGDGQDVFTYTVRDADGDLTSTTLTINIDQFVAGSNDNNTITGGAGNDVMLGDQGGIKQNVTAGTSYNIALVLDLSDSMNDKWGSGSNKPTRLQTAKDALKALLENQLAVHDGEINVSLITFNGSSSALKKSITGLTPENVDEMVDILMGLKASSATPYGAAFDRTTQWFEGQPTVDSEGKPYKNLTFFLTDGEPSTEWSYNRDNEFAELAAISDVHGIGIGSGVSTSTLNKYDNTGGYYTGGQETHVNFSGNSNANNVNTWDKDGTGTVTKNDNAMRITDTTADGQAFKVTMNPDHRMNVTSAGGASFSFALSMGNKNPADKFEWVLMKWDGTQWNEVERGTDASTRTGIHGPGQYGFQFIVNDNSGGGQFYATVDTIRSYTSGRTGNSQTVLDPSDLESALIGGSQSTELAPVGNDKLYGGDGNDILFGDAINTDNLPWGVAGNPAKPADLPNGSGLEALKDFLFLKNGVQPTDADLHKYISENHALFDVDGDTRGGNDELHGGAGSDELHGGEGKDLLIGGQGDDILYGGDGSDTFKWELNDQGVVGAPARDTIKDFSNADIADGGDVLDLGELLQGENSGNLTQFLKFSSDGQDTVIQVNTQGHVNTQGADQTIVLENIDLTAGGTKDDAAIIQDLLSRHKLQVDQ
>NC_002928.3|WP_003809046.1|1044819_1045503_-|transglutaminase-like-cysteine-peptidase
MPLSTRPRKAPRLALAALLSLACGWGGVHALDVDTGKLQSLAASRYGARGARAVDDWLQLLRNDTSASEANQLARVNAFWNQRVLSGEDTHIWGRADYWATPLETLGKGAGDCEDYVIGKYFSLISLGVPTEKLRFIYVRARIGGPYSNQQIAHMVLGYYPTPNAVPLVLDSLISTIMPANERRDLTPVFSFNADGVYVDGKQASPVDRLSRWRDLLLRMEREGLRP
>NC_002928.3|WP_010927776.1|1042827_1044804_-|EAL-domain-containing-protein
MSILRRLLLSLTLAIGIILLGTLVLSINAARGYLSDQLQVQSTDAAVSLALSLSQPANNDPVTQELLVSALFDGGHFSLVRLADPQGAVMVERGAQPAASVPAWFQALAPLANRAASHAVSDGWRQIGEVTLVANDAYAWETLWASSLRMAALIMGAGVLWALFAFALVRWIEKRLLFQVSEQVRAIDSRASGEQAFARVAEFSGIVDALAQTRERVRATAEEQSSHIESLEVELNQDPVTGLANRKYFINEFRRALDEKPADSPALPAPLSSAGGHVLVFRQRDLTALNRHMPRQFIDQWLQSVCQRISALVTAQGLAQSLVARLNGSDFAVLLPHCAAPQAQVIADLVRAELRTLRIPVGEGGLCRWAMALADYAPGTQFNGVLARLDFGLTRAESAGDDHAVLVGPDNADPFSAAGQSAWMDALVTALDQQRFSLAFEPLHAVDGRLVRMEAMLMLHNDDAREPIPAMLFIPAAVRLNLSAECDLQAVRLALDWLAAQPGELAVRLSLPSLGKRSFLRQLELMLADRRAQVGRLYLEVDAHGLVDREGDVIALERIAAHFGAHVGLRRLAQQFGAMSRLHSLPLAYVKLGGGFVGGMSQSPGSRQLAGSVIDTARALNIDVYAEDVPDAATRDILASMGVEVMRGPGVTPPPAQE
>NC_002928.3|WP_003809041.1|1042152_1042779_+|hydrolase
MGKRYAKLDKNNVAVLMVDHQVGLLSLVRDIDPDKFKNNVLAVADLATYFKLPTILTTSFEDGPNGPLVQELKDQFPEAPYIARPGQINAWDNEDFVKAVKATGKKQLLIAGVVTEVCVAFPALSAIEEGYEVFVVTDASGTFNEVTRHSAWSRMEQAGAQLMTWFGVACELHRDWRNDIEGLGALFSSHIPDYRNLIAAYTTVKGGK
>NC_002928.3|WP_010927775.1|1040005_1040698_+|HD-domain-containing-protein
MTNPGDGAAGAVDCATLDHWRPRLAAIAAAAGQDDAAHDLGHLRRVWGAARAMLQAHPEADALVVLAASYLHDLVNLPKNHPERHLASRQAAAAARERLARAGFPAARLDAVAHAIEAHSFSAGIAPRTIEARIVQDADRLDALGPVGLARMFHVGGSLGRALAHPSDPLAAQRALDDSRYTLDHIEAKLARLPHGMQTEAGRRLGEQRLAWLRDFRAAFAAQWGGGQLR
>NC_002928.3|WP_041937359.1|1037461_1039957_+|copper-translocating-P-type-ATPase
MNASSLAGAPSTGAISLPIEGMTCASCVGRVERALKAVPGVSDAVVNLATERADVRFAGAPDVGAAVQAVEQAGYAVAASTMELAVSGMTCASCVGRVERALKAVPGVRAASVNLATERAHVEIAGAVAPQALVQAVAAAGYEARPLDPGGAAADAAARRQAAELQGLRRALIVAAVFALPVFVLEMGSHMIPAFHHAVAGSIGVQNSWYIQFVLASIVLFGPGLRFFRKGVPALLRGAPDMNSLVAVGTAAAYAYSVIATFAAGVLPPGTVNVYYEAAAVIVALILLGRYLEARAKGNTSEAIKRLMGLQAKTARVRRDGATVEVPIAQVAAGDVVEVRSGERVPVDGQVIEGTSFVDESMISGEPVPVEKQPGAEIVGGTVNQNGALALRATKVGGDTVLAQIIRMVEQAQGSKLPIQALVDRITMWFVPAVMAVALATFAIWFVFGPDPALTFALVNAVAVLIIACPCAMGLATPTSIMVGTGRAAQLGVLFRKGEALQALKDARVVAVDKTGTLTKGRPELTDLVLAEGFERAAVLGKVAAVEAKSEHPIARAIVDAAQVEGARPGAIEAFESITGYGVAARVDGARVEIGADRYMARLELDVAVFAAEAARLGDEGKTPLYAAIDGHLAAMIAVADPIKNTTAAAIRALHGLGLKVAMITGDNRRTGEAIARQLGIDEVIAEVLPDGKVDAVKRLKAEHGALAYVGDGINDAPALAEADVGIAIGTGTGTDVAIEAADVVLMSGDLGGVPNAIALSQATMANIRQNLFWAFAYNVALIPVAAGVLYPVNGSLLSPVFAAGAMALSSVFVLSNALRLRRFAAPFAAR
>NC_002928.3|WP_003809026.1|1036993_1037362_+|DUF861-domain-containing-protein
MPQHDKSRLVRIDTGPMINPVAGKPSRPIAGDASFRTVTAFEGGQGKVESGVWESTSGSFQSNTTGYIEYCHIIEGEARLVDPDGTVHAVKAGDAFIMPEGYTGRWEVDRHVKKIYFVTHLA
>NC_002928.3|WP_003809025.1|1035780_1036707_-|VOC-family-protein
MTSHSTDHDTIGMPNLNLSLDHTGLIVFKLEDARQAFERLGFTLTPRSMHAGALTPGGPVVPWGSGNHCAMFRNGYFELLGLVEPDKPSTARRMLDRYEGLHIVAMDCESADAMHPQLTAAGVPAPAPATLERDAAFGPANDQTRRARFRNINLDGEAYPEARFIVIEHGTRDVLWQPHLLDHPNGATGLAAMYFAAADLSATLERFQRLLGTPSAHGDAYCFELRRGRFWVMSEAAMREHCPVLADGPVHRVAAACIEVRSLPALQEYLQARQIDYVAAPYLDGAAPSIWVAPAQASCAALQFIQAR
>NC_002928.3|WP_003809022.1|1034287_1034722_-|PaaI-family-thioesterase
MSQQAARKLEKADIEAIFARSRFISAMNLEILDIDHAGSRFSVRMPLQDTYERGAPGTKQFHGGALAALIDVVGDFAIGMLVGGGVPTMNLRIDYLRPAVGDYVDGVAVVRKAGKSAAVVDIDILCPAGKLVAIGRGTYVPITG
>NC_002928.3|WP_010927773.1|1032376_1033165_-|ABC-transporter-ATP-binding-protein
MNQAQHNGSAPVFRVQGLEVTYRSSRGPTTALEGFSTTVAEGEFLSILGPSGCGKSTLLKVAAGLLKPSAGVAELRGQAIDGPRRDVGIVFQHATLLPWQNVLDNVLLPIRTMGMDIAAGTARAHALLKTMGLEKFEQHYPHELSGGMQQRVGIARGLIHDPSLLLMDEPFAALDAMTREAMMVELQRIWSETRKSVMFITHSIPEAVFLSSKVVVLGPRPARVLREIDIDLPFPRTEETLASPKFAQLCAELRSLFSNVAH
>NC_002928.3|WP_010927778.1|1052465_1053131_-|response-regulator-transcription-factor
MHATPVLLVTDDDLLWQHWRGLDAARWLPARGRGLASLQQWQGQGRQLVVLDASVARLPAWDAPQWQELTVGLRLVVASSRPSDAQGTQVFAAGAYGYCHSHAPLASLMQVLEVVSGGGIWMGRSLVTRLLKLVDERVPSAPAPWQHDRLTERENAVALRAAHGDSNADIAGELGITERTVKAHLSAAFEKLGVSDRLQLALCVHGISTRTPAPRTGTDGR
>NC_002928.3|WP_003809053.1|1053152_1054595_-|HlyD-family-type-I-secretion-periplasmic-adaptor-subunit
MQNTQNATLAAPPARQGSLLGALWRVPRGWIMGLFDRLLDGAERKDGPSPANYVGNAEWAIRQADARGSRVLLWASLLATLALLLWAGFGYIDEVVRGEGKVVPSRQVQIVQSLDGGIVEEILVRPGEAVETGQVLLKIDPTRFASSLGENNAEYLSLLAKAARLKALATGEPFVAPEKVLQEAPAIVEMERNTWQARTSELNATVNVAREQLKQREEELRETIAKRDQASASCGLTSRELQVTRPLLKSGAVSEVDLLRLQRDVARYCGEQKGAEAQIDRIGASIKEAQSKLQEAELNIRNQARSELSETNTKLATLREGQAALADRVKLADIRSPVRGTVKSLFSNTVGGVVQPGKDIIEIVPTDDTLLLEVRVLPRDIGFLHPDQKAEVKFTAYDFAIYGGLEGHVEQIGADTVTDEKGNSFYIVRVRTNSATLGDRKLPIIPGMVAEVHILTGKRTVLQYLLKPILRAKENAFTER
>NC_002928.3|WP_010927779.1|1054597_1056772_-|type-I-secretion-system-permease/ATPase
MTTDKFSDPATRSWRADPHASHEDPLLDCLVELTRIHGVPATAQAPSSGLPLVEHRLTPALLPRAAARAQMSARTVKRTLDEISPELLPAILLLRGERACLLLGTAPGGKYLISHPELGASAVEMDADLLQEDYTGLACFVRPQFRFDARAPEVVKVRSRHWFWAAIAENRRLYRDALIAALLINVFAMAMPLFTMNVYDRVVPNNAIETLWVLALGIGLVVLFNLVLTTARAHVVDSASKRVDIRLSAQIMERVLDLRMEGRPVSVGSFAANLRSFESIRDFIASASITTLVDLPFTLLFLAALAWISPWLIAPPLVAIALILLVSLAAQARMETLTMASYQASAQRNATLVEALAGFEAVKTLNGQGAIQRNWERSTEFIAQNGGKLKLISASTVGFVQAMQQLVSVAVVIIGVFQAQESAMSMGGIIAASMIAGRCLTPFGQVAALLMQYQNARTSLGSIDNYMNLPVERPAGTEFLHRPVFQGGIEFRDVTFAYPGASQPALKKVSFKLAPGEKVGVIGRIGSGKTTLEKLALALYQPTEGAVLVDGVDVRQIDPADLRRAIGHVPQDPVLFYGSLRHNLAMGAPHADDASILAAANAAGVTEFANVHPNGFDMMIGERGESLSGGQRQSVAIARALINDPPILLLDEPSSNMDHQSESQLRKRLKAASADKTILLVTHRTALLDLVERLIVIDNGHIVADGPKEQVVEALRQGRVGRGS
>NC_002928.3|WP_003809056.1|1056749_1056965_-|hypothetical-protein
MSASNDNGFSKLDADFVRVLEDLIDALIKNGTLRLTDLPPQAQRKLTERKRHRARLAEDLDLLDDDDGQVL
>NC_002928.3|WP_010927780.1|1056975_1058445_-|TolC-family-outer-membrane-protein
MPTFSFKRTTAIVAVLFAPAAYAQQQAGTTLNQVVEQTLLSNPEIQAKYHDFRASMEGQNVARGGLRPQVNAQGFVGKEWRSNVPDRGSYNWSRPGYSVELRQLIFDGFRTSNDVKQAGYDKLGRFYELLATSDSTAYSAVQAYVDLQRYREMELLARQNYSLHEDTLKQIREHAESGVGRRVDLEQAGGRLALAQTNLMTESANLIDVQQRFQRITGMTPAVDLQPVPDVAGKLPQQPANFDDSLRMNPSFLAKQAYLQAANAGVASAKGAFSPKFEFVAATGRDREQPEPQYRDVQSSSVQLVMSYNLYRGGADSARVRQTAEQSYAARDVRDYTCRNVQQDLAVAWNNIVRLREQIPFLRDHEIATAKVRNAYREQFQIGQRSLLDLLDTENELFESRRALANGMADLQLAQYRWLALSHKILPALSVQPARDEMPEENAVLETTDEVLKLCNSPVPDVSRLAPVQVIYNSGAKPPTFVPADKARP
>NC_002928.3|WP_076879797.1|1058796_1060089_-|TIGR03862-family-flavoprotein
MSPDSLSAVAAPQAGAPSPRAARVAIIGAGPAGLMAAETLAGHGLRIDVYDAMPSVGRKFLLAGRGGLNLTHSEAPQAFGARYGARADWVAQWLAQWDAQALRAWAHGLGVETFVGTSGRVFPREMKAAPLLRAWLARLRGAGVGFHMRHRWLGWPAGEPASPQALRFGTPDGALAVRADAVVLALGGASWARLGSDGAWTATLREHGVAVAPLRPANCGFEADWSEPMRQRATGQPAKAVAMALAPDGPWRRGEFVVTDSGIEGSLVYACSAGLRDAIDVRGAATAWLDLLPDWPAERVAAAVMHPRGARSMSSHLQSRLGIKGVKAALLRECAGAEAYADAGLLARRIKALPLRLLRTRPIDEAISSAGGVERAALDARLMLAKAPDVFCAGEMLDWEAPTGGYLLTAVMASGVVAGRGVLAWLRDGL
>NC_002928.3|WP_010927782.1|1060241_1060568_+|helix-turn-helix-transcriptional-regulator
METNAAIKALVVLGHASRLTAFRLLVQAGAEGVAAGQLAQAMGIAPSSLSFHLKELVQAGLLEARQDGRFVIYAARYDTMAGLIAYLTDNCCQGAPCDAAPCTREPRA
>NC_002928.3|WP_003809064.1|1060564_1061845_+|arsenic-transporter
MITAAVIFLFTLTLVIWQPRGLGIGWSACLGAAISLATGVVHWSDIPVVWGIVWNATAAFIAIIIVSLLLDEAGFFEWAALHVARWGRGRGRMLFAWIVLLGAAVSALFANDGAALILTPIVMAMLAALGFGAGATLAFVMAAGFVADTASLPLIVSNLVNIVSADYFGIGFNRYAAVMIPVTLVSVAATLAVLLLRFGASVPARYDASQLKAPRAAIRDPRTFRAGWMVLALLLVGFFGLEPLGVPVSATAAAAAAVLLAVAGRGHFISTRKVMREAPWHIVVFSLGMYLVVFGLRNAGLTQSLADLFGWFASHGLWAATYGVGLVTALLSSVMNNLPTVLVGALSIDASSASGAAREAMVYANVIGSDLGPKITPIGSLATLLWLHVLARKGVRISWGYYFKVGIVLTLPVLLLTLGALALRLS
>NC_002928.3|WP_003809067.1|1061885_1062851_-|tripartite-tricarboxylate-transporter-substrate-binding-protein
MHSFKSALLASAVLALAAGTAGAADTYPGDKPIKIVAAFSPGSATDTSARIIAEELRKDLGANVIVENKPGAQGLIGTEYAVRQPGDGYTLTIASSSLNSINPGLFKKLPYDAQKDFTHISRLTTMPMLVLVRGDGDIKTLDQLVQKAKAGSLNYGYGSPGGQVGAVAFNNIAGIRAEGVPYKSQPPALTDLAGGQVDYVLGDLSVATPLLRAGKIRALAVSTEQRLPDLPEVPTFAETDYKAFDLVVWVGLSGPAGIPPEVAQRLNDSVNKALARPEIQEKFKGLGMTTAPNTLAQQQQFVQSQLDTWGRRMREANIQPE
>NC_002928.3|WP_003809070.1|1062894_1064031_-|CoA-transferase
MQSSDSGGALAGLRVIDASRVLAGPFCGQMLGDHGAEVIKIESPEGDECRGFGPPFVDGASAYFRAVNRNKRSMVLDLNSEAGRETLWQLLETADVLIENFKASTLRAWGIADPAEITARFPRLVHCRITGFGDDGPLGQLPGYDAAVQAIAGLLSINGEAGGPPVRLGVPVVDLTTGMNAAIAVLLALQARHRTGRGQMADVALYDSAVSVAHPFLTNYLASGKTPGPSGNGHPNIVPYNVYRTRTCPLFIAVANDRLFAKLCAQLGVAELAADARFATNGQRVVNREALDAALSQAFAQVDGEPFGQQLLAQNVPAAPILDIAAVAAAPHTAHRRMVVQQPDYTGPGIPIKLSHTPAAIRRGPPALGEMAAPPPKR

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Crispr_ID: NC_002928_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_3

2198758-2198844

Orphan

Consensus_repeat	Method
AGTGTGCCTGTCCCCGCAGGGACAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_002928_3

>merge|NC_002928|3|2198758-2198844|CRISPRCasFinder
AGTGTGCCTGTCCCCGCAGGGACAGATACCGTCTTGGCGGGCTAGCGTCGATGGCGTACGGCAGTGTGCCTGTCCCCGCGGGGACAG

>NC_002928|3|2|2198758-2198844|CRISPRCasFinder
AGTGTGCCTGTCCCCGCAGGGACAG	ATACCGTCTTGGCGGGCTAGCGTCGATGGCGTACGGC
AGTGTGCCTGTCCCCGCGGGGACAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_010928348.1\|2210397_2211000_-\|YhbY-family-RNA-binding-protein	unknown	unknown	gnl\|CDD\|198171
NC_002928.3\|WP_010928338.1\|2189079_2190057_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226706
NC_002928.3\|WP_010928341.1\|2193177_2196408_+\|autotransporter-SphB3	unknown	unknown	gnl\|CDD\|377133
NC_002928.3\|WP_010927744.1\|2209307_2210258_-\|IS481-family-transposase	unknown	unknown	gnl\|CDD\|289759
NC_002928.3\|WP_003809596.1\|2199530_2200430_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|223656
NC_002928.3\|WP_010928342.1\|2196528_2197749_-\|ISL3-like-element-IS1001-family-transposase	unknown	unknown	gnl\|CDD\|376574
NC_002928.3\|WP_003809599.1\|2200477_2201563_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|226361
NC_002928.3\|WP_003809590.1\|2197930_2198695_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|235910
NC_002928.3\|WP_010928344.1\|2201559_2203269_-\|iron-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224099
NC_002928.3\|WP_010928340.1\|2192068_2192896_+\|TatD-family-hydrolase	unknown	unknown	gnl\|CDD\|238635
NC_002928.3\|WP_010928343.1\|2198875_2199520_-\|histidine-phosphatase-family-protein	unknown	unknown	gnl\|CDD\|366010
NC_002928.3\|WP_033446709.1\|2187397_2189098_-\|single-stranded-DNA-specific-exonuclease-RecJ	unknown	unknown	gnl\|CDD\|182944
NC_002928.3\|WP_010928347.1\|2206268_2207906_-\|Tar-ligand-binding-domain-containing-protein	unknown	unknown	gnl\|CDD\|185001
NC_002928.3\|WP_010928345.1\|2203345_2204665_-\|extracellular-solute-binding-protein	unknown	unknown	gnl\|CDD\|270236
NC_002928.3\|WP_041937185.1\|2190066_2191347_+\|lipoprotein-releasing-ABC-transporter-permease-subunit	unknown	unknown	gnl\|CDD\|274034
NC_002928.3\|WP_010926447.1\|2185405_2186161_-\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|180796
NC_002928.3\|WP_010928346.1\|2204924_2206238_+\|pyrimidine-permease	unknown	unknown	gnl\|CDD\|132655
NC_002928.3\|WP_010928336.1\|2186190_2187295_-\|peptide-chain-release-factor-2	unknown	unknown	gnl\|CDD\|234799
NC_002928.3\|WP_003812422.1\|2191339_2192035_+\|lipoprotein-releasing-ABC-transporter-ATP-binding-protein-LolD	unknown	unknown	gnl\|CDD\|213222
NC_002928.3\|WP_003809615.1\|2208529_2209006_+\|transcription-elongation-factor-GreA	unknown	unknown	gnl\|CDD\|234693

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_010928348.1\|2210397_2211000_-\|YhbY-family-RNA-binding-protein	gnl\|CDD\|198171	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.	5.40171e-31
NC_002928.3\|WP_010928338.1\|2189079_2190057_-\|hypothetical-protein	gnl\|CDD\|226706	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown].	1.57718e-20
NC_002928.3\|WP_010928341.1\|2193177_2196408_+\|autotransporter-SphB3	gnl\|CDD\|377133	pfam03797, Autotransporter, Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C-terminus of the proteins it occurs in. The N-terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs.	1.2867e-46
NC_002928.3\|WP_010927744.1\|2209307_2210258_-\|IS481-family-transposase	gnl\|CDD\|289759	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481. This is the upstream region of the conjoined ORF AB of insertion element 481. The significance of IS481 in the detection of Bordetella pertussis is discussed in. The B portion of the ORF AB carries the transposase activity in family rve, pfam00665.	3.75329e-40
NC_002928.3\|WP_003809596.1\|2199530_2200430_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|223656	COG0583, LysR, Transcriptional regulator [Transcription].	7.08863e-33
NC_002928.3\|WP_010928342.1\|2196528_2197749_-\|ISL3-like-element-IS1001-family-transposase	gnl\|CDD\|376574	pfam01610, DDE_Tnp_ISL3, Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165.	9.11286e-79
NC_002928.3\|WP_003809599.1\|2200477_2201563_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|226361	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism].	3.76041e-148
NC_002928.3\|WP_003809590.1\|2197930_2198695_+\|SDR-family-oxidoreductase	gnl\|CDD\|235910	PRK07024, PRK07024, SDR family oxidoreductase.	4.78988e-141
NC_002928.3\|WP_010928344.1\|2201559_2203269_-\|iron-ABC-transporter-permease	gnl\|CDD\|224099	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism].	3.58657e-90
NC_002928.3\|WP_010928340.1\|2192068_2192896_+\|TatD-family-hydrolase	gnl\|CDD\|238635	cd01310, TatD_DNAse, TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.	1.42767e-89
NC_002928.3\|WP_010928343.1\|2198875_2199520_-\|histidine-phosphatase-family-protein	gnl\|CDD\|366010	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1). The histidine phosphatase superfamily is so named because catalysis centers on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.	5.12316e-70
NC_002928.3\|WP_033446709.1\|2187397_2189098_-\|single-stranded-DNA-specific-exonuclease-RecJ	gnl\|CDD\|182944	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ.	0
NC_002928.3\|WP_010928347.1\|2206268_2207906_-\|Tar-ligand-binding-domain-containing-protein	gnl\|CDD\|185001	PRK15041, PRK15041, methyl-accepting chemotaxis protein.	7.95515e-118
NC_002928.3\|WP_010928345.1\|2203345_2204665_-\|extracellular-solute-binding-protein	gnl\|CDD\|270236	cd13518, PBP2_Fe3_thiamine_like, Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.	3.04415e-40
NC_002928.3\|WP_041937185.1\|2190066_2191347_+\|lipoprotein-releasing-ABC-transporter-permease-subunit	gnl\|CDD\|274034	TIGR02212, releasing_system_transmembrane_protein_lolC., lipoprotein releasing system, transmembrane protein, LolC/E family. This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC. [Protein fate, Protein and peptide secretion and trafficking].	9.67778e-160
NC_002928.3\|WP_010926447.1\|2185405_2186161_-\|SDR-family-oxidoreductase	gnl\|CDD\|180796	PRK07023, PRK07023, SDR family oxidoreductase.	5.47641e-103
NC_002928.3\|WP_010928346.1\|2204924_2206238_+\|pyrimidine-permease	gnl\|CDD\|132655	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40).	0
NC_002928.3\|WP_010928336.1\|2186190_2187295_-\|peptide-chain-release-factor-2	gnl\|CDD\|234799	PRK00578, prfB, peptide chain release factor 2; Validated.	0
NC_002928.3\|WP_003812422.1\|2191339_2192035_+\|lipoprotein-releasing-ABC-transporter-ATP-binding-protein-LolD	gnl\|CDD\|213222	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.	2.7791e-114
NC_002928.3\|WP_003809615.1\|2208529_2209006_+\|transcription-elongation-factor-GreA	gnl\|CDD\|234693	PRK00226, greA, transcription elongation factor GreA; Reviewed.	7.10406e-83

>NC_002928.3|WP_003809590.1|2197930_2198695_+|SDR-family-oxidoreductase
MQHVFITGASSGLGQALARRYAADGARLGLLGRRAQALEALASSLPGQHRCYAVDVRDRAALHAAAQDFIAHCGGRVDVVIASAGVSAGTLTEAGEDYAVFKEIVDTNLLATVATFEPFIAGMRAARAGRLVGIASVAGVRGLPGAGAYSASKAAVATYCESLRLELAQAGVRVVTIAPGYVKTAMTAHNPYAMPFLMEADAFAGRAHAAIARGVSYRVIPWQMGVVAKLMRLLPDAVYDRLARDAPRKPRRGQ
>NC_002928.3|WP_010928342.1|2196528_2197749_-|ISL3-like-element-IS1001-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPIGRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYKQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFSLKIRAAFPGNAR
>NC_002928.3|WP_010928341.1|2193177_2196408_+|autotransporter-SphB3
MAQASARGMGLRITSLAAALLGVYGAAGAAENRLECIGACPPGQPVAGAHYSGTNLSANREWVVYGEGSNAVFTLQGGSVTASGGLMGAVNAADGARVYLNQVSVRTDAGNGWEAPGVRAEYGALVNVRGGSIATVGGGSYGVQSLDSGTMIELNGTDIRTTDAYSDGLRAEFGGSIRAVGLTINTTGEHAVGAMGADDGTIALRDSRITTSGVDAYGLGTESQVLSPGGVLQVSNTAIQTSGKNAHGVYLQGGSSLNMSGGSIRTTGSGAAGLRVSNGSSVALNGVEVVASGPSLLSTLSATRQQSIVVGAGSNLTRNDGRLLLVRRVAGGELGQVTLTLKSGSYAAGNIENLAADGSRESSALTIVDVQSGAQWAGLVIDDTTAIVNGSQSGQHSGFSTAGDMVLEGGSAPVTFTGVSNIGGSSSLGAGSQTTFGGATTIGQSLAVLPGGSVAFNGPLTIGESVTGGQGTALSFNAPAIIGANVQGAGGAAFTFSGPAQVGGSVQGLDGASFRFSTSAPTAIAGGLSLAGGSSLGGGSPTTPIVVTGGADAVSGAILGGNLDIGGALRMTGASLAPGNSIGTVTVGSVGALSGSTYLAEVNAKGQSDLLVVRSGNVDLAGVSLVVGQENGTGGYVLNHDYTIIKTEAGKIVGEFAAASLDESLASTLVKLDPVKYGAQATQVSLSPDADKLAAARAGLTRNQSAVLDGALSVAGRNASADAVMLMSDTGQRAGALDQLSGEVHGSAVSALYSNTQLLNRTVARRMSANLGAGLLAGAPTAQAAGPAAASAMPGTAAYPLWADVVGNWSSFDAKDNAAKAKSNTAGLFIGGDVAVGAGWRVGGALGFTDGRIKADAVDSRSDVTSYTAALYGGNSWAAGKGKLNFLAGVGYTHHDIDSRRSVDVGGAQTLKADYKANTTQLFAELGYQVPVGASSSVEPYAGLAWFNNHSDSFDEDGGPAALHGSGQTDQITTFTLGLRGNTALQLGATETRLSAGLGWRHANGDVDATRKLAFIQGGGTAFTVAGSPVARDAAVLDLAAEVDVGRNAALGLAYGGQFGNGNKENTGSLYLKVRF
>NC_002928.3|WP_010928340.1|2192068_2192896_+|TatD-family-hydrolase
MLIDTHCHLDAAEFDADRMAVARAAREAGVQAIVIPAVERANFATVRQLAHAVDSGAYALGIHPLYVARARDEDLDSLRRAIESALPDPRFVAIGEIGLDFFVAEIASGAPRERQERFYAAQLDLAAEYGLPVLLHVRRSQDILLKHLRRRPGVPGGIAHAFNGSAQQAGAFVEQGFALGLGGAMTYPRALQIRRHAADIGLDHLVLETDAPDIPPAWLYEPERRNTPGQLPRIAAELAALRGQAVADVARATTTTALRVLPRLGALLQDRAATP
>NC_002928.3|WP_003812422.1|2191339_2192035_+|lipoprotein-releasing-ABC-transporter-ATP-binding-protein-LolD
MTEPNDTGPALQAEHLGKVYDEGPARIEVLSDVSLSVARGEMVAIVGASGSGKSTLLHILGLLDVPSSGTVSVDGVPAAGLSEKRKSALRNRSLGFVYQFHHLLPEFSALDNVAMPLIVRRENRDRARAQAREVLELVGLAAREEHFPGQLSGGERQRVALARALVTRPACVLADEPTGNLDRHTAHNMFELLTRVNRESGTAFVIVTHDPELAARADRQLHMENGRLQPD
>NC_002928.3|WP_041937185.1|2190066_2191347_+|lipoprotein-releasing-ABC-transporter-permease-subunit
MLKIPYELWIGARYAGMARIRQRRGRRDRFISFIAATSMAGIALGVAALIVVLSVMNGFQKEVRDRMLSVLPHIELYIPGAAPERVLQQWRQFAQAARANPEVKGEAPFVAAQGMLVRGQALRGVQVRGIDPATEGNVSNIPRQMVSGKLSDLVAGGFGAVLGSDLADGLGVKTGDTVLMLAPQGSISPAGFAPRMRQFTVVGIFSSGHYEYDSTLVFIDDEDAAKVFRESGTAGVRLRVADMQRAPEVAAELTKVLPPYVMAADWSRNNRTWFAAVQTEKRMMFLILALIVAVAAFNLLSSLVMAVKDKQSDIAILRTLGAGPGEVARIFLVQGALIGVVGTLLGVAGGIAIAYNVDVIVPFIERLLGVQFLPREVYFISALPSDPQADDIITIGLTSLVLSLLATLYPSWRASRLQPAQVLRHD
>NC_002928.3|WP_010928338.1|2189079_2190057_-|hypothetical-protein
MALTGTRTTIAAMLIVIPGALPAAAVAPELARLLPQHAPTLHGWLQAASARVQAFDAARQGCTPFEGWQLEQAGYQPQPGLPLGAGLGPLRAAGGTPGQPVWLADLAHLMLGADQAALLDPALLDLRADESAQLFEAAAPLFADSGFGATPIDAARWRLTLPAGMAPQTASPAAVAGQRLRAWWTQDVAMRPWRRLLNEIQMVWYEHPVNEARAARGAAPINALWLYGGATPWPAGAPAPARVCDELAAAQRAGDWAAWLDALAVLDAAQLAPLAGPHGRPVQPLQLLLLGDDRRAALTLKPRAGLARWLPAPKHNWNAWWSRPV
>NC_002928.3|WP_033446709.1|2187397_2189098_-|single-stranded-DNA-specific-exonuclease-RecJ
MVSPRLIIRTADLQACQHLEAAGIHPLLSRLWAARGVIHPEQTRMAWPALLPPDRLTHSAHAAAVLADAIEQGKRLLIVADYDCDGATACAVGLRALSAMGADVDFLVPNRFETGYGLSPAVVELACRHRRGKPDIIITVDNGIASVDGVAAANAAGIGVVITDHHLPGDTLPEALAIVNPNQPGCGFGSKHLAGVGVIFYMMLALRAELRRRGVYAPDGGPRLDALSDLVALGTVADVVKLDANNRLLVTQGLQRMRAGRMQPGVRALFAVAGREPRTASGFDLGFALGPRINAAGRLADMSLGIACLTTDDEAQALEMARELDNINRERRTIEAEMRDQALAAMEAPDAAAGATVCVFDPGWHQGVVGLVASRLKEKFWRPTLAFAPAGEDELRGSGRSIPDVHLRDALDLVSKRHPGLIRKFGGHAMAAGLTLGSGDFAAFAPAFDAAVRELTGRDRFEPLLETDGSLESGYANAEVAGLLQQQVWGAGFAAPLFLDEFTVRSQRLVGGKHLKLALERGHQRFDAIWFGHDQSLPERIQAAYRLEQNIWNGMVSVQLVIEHAA
>NC_002928.3|WP_010928336.1|2186190_2187295_-|peptide-chain-release-factor-2
MEAERQNQLVARLEDYAEREQALRRYLDYDAKSERLQVVNAELEDPAIWNDPKHAQDLGREKKSLEDVVETLTELGSGLADSCELVELALADSDDATLEAIEHDVDRFQEKLETLEFRRMFANPADPLNCFVDIQAGAGGTEAQDWASMLLRQYLKYAERKGFKAEILEESEGDVAGLKSATIKIEGEYAFGYLRTETGVHRLVRKSPFDSSGGRHTSFASVFVYPEVDESFEVEVNPADLRIDTYRASGAGGQHINKTDSAVRITHAPSGIVVQCQNDRSQHRNRAEAMQMLKSKLYELEMRNRMTEQQKLEDSKTDVGWGHQIRSYVLDQSRIKDLRTNVEISNTQKVLDGDLDPFIQASLKQGV
>NC_002928.3|WP_010926447.1|2185405_2186161_-|SDR-family-oxidoreductase
MTDTVAILTGASRGLGAALARGLLAPGTRLITLARRADPDLEAAARTRGASLEQVQVDLSDPAAAGAAAKRLCAALPRDARRYLLINNAGTVSPVAQAAGLTDGAAIAGALNLNVTAVVLLTARFVAALQGLPADRRVLNISSGAGRNPNAGWGVYCAAKAALDMYSRVLKQEQGQDGVRVVALAPGIVDTDMQGAIRASDPADFPALERFREFHATGKLSAPADVAARILAYLDRDDFGTTEIDDIRNYQ
>NC_002928.3|WP_010928343.1|2198875_2199520_-|histidine-phosphatase-family-protein
MTEIWFIRHGETDWNRQRRLQGWQDIPLNESGREQARLLAERLRDTASEHPFAALYSSDLKRAHDTAASLSAALQLRVRTEPGIRERGFGVLEGLEMENLEQQAPQAAQAWRSRDPLRALEGGETLGQFQARIIATVDDLAARHASERILAVTHGGALDIIWRHASGVPLDAPRYAALLNVSINRVAIAQRKWEVLGWGDVEHIGAETGNDVTP
>NC_002928.3|WP_003809596.1|2199530_2200430_-|LysR-family-transcriptional-regulator
MEIYQIRAFVTVARLGNLTKAAEALSLTQPAVTAQLKALEQSLGVALFDRAAGRLSLAKAGEALLPTAEALLVLGAQLKSEARQLQGQLQGVIDLGVPSEQPDFLRLGELAAALRQRLPLVELKTHVLPSTALLEQVGTARLAGALTIVAHPPRGVTWHALRSVRYRIALPASLADTLKRAGWRDIAQLPWLDGPSGSHLHLLLRDMFERHGLAPRVVMQNDDQSNLDALVRAGAGCALLREETALAGAAAGDFIVWGQARADATLGFIAPPEQAGEPMLVALISMIQKIWKPGAAVAT
>NC_002928.3|WP_003809599.1|2200477_2201563_-|ABC-transporter-ATP-binding-protein
MKKVSVECRNIRLSYGRNEVLKDISIHIEPGEFFALLGPSGSGKSTLLRLIAGFNRQSHGQLLVDGRDIGATPPWDRNIGMVFQNYALWPHMTVWDNVAFGLVERRLPRAEIRDKVAAALELVGLADFGRRRPNQLSGGQQQRVALARTIVIEPQVLLLDEPLSNLDKKLRVQMRQDLLSLQRRLGITTIFVTHDQEEAMTTADRMAVLDHGVVQQIGAPSTLFDYPVNRFVANFVGTMNVLEGEVRERSRGGVVLAVDGVGELHLPVNGDAPQAGRLAASFRPHTVLIEMADGTGDARYVWLPGVVESSEFLGEFTRYQVQVGEQRLTADQHHLAGLSPFPVGAPVAVGLEPTQIRLLAA
>NC_002928.3|WP_010928344.1|2201559_2203269_-|iron-ABC-transporter-permease
MTSTGTFRLPAGPALAALLVLAFLALFLVFPVGTVFYTAFVNADGSFTLGHFGAVFNQPLMKEAFFNSLYVAGWSSLLASLIAVPLAYFTVRFEFRGALLIQTLGVLPLIMPPFVGAMAMQLIFGRSGSVNLLLDDWLGITLPFMDGLNGVIFVESLHYFPFILMNLVVALRNIDGSMEEAAFNLGSRGFRLFCRIIFPLALPGYLAGTSLVFVKVFDDLGTPLVLGTTNMLAPQAYLRITQVGLEDPLGYVISVIMIGFSILALWLSARVLKGKDYSTLQKGGNAIHKRRLRPVESVLAYAWIGAVLLLVLSPHLGVLLLSLASVWSYAPLPDGYTLAHYTAVFTESQGMIANTLLYCGLAAGVDVVLGTAIAYLMLRTRLPARQWLDFIASAALAIPGIVLAIGYLRTFRGVEIPGTGVLLTSSWVLIMIAYSVRRLPYALRSCVAALQQINVSLEEAAESLGASRLRTIRRIVVPLMAGGMLAGFVTSFITAAVELSATIMLVTRDSQAPMSYGIYLYMQSAAGRGPGAALGVLAVVAVGIGTYVSHLLVERASARQRPARSGESS
>NC_002928.3|WP_010928345.1|2203345_2204665_-|extracellular-solute-binding-protein
MQALQRQLAAIMAACAPALAGTVTVITSFPKDLTQAYKAAFEKAHPDIKLEILNKNTVSGIAFVRATPAGQRPEVFWASAPDAFEVLGRDKLLAKAPDVANPAVPDKIGSYPINDPSGMYMGQALAGYGIIYNTRYIKANKLPAPVEWKDLLAPHWFGHVGITAPSRSGTMHLTVETILQGEGWNDGWGTLLRMSGNASAVTERSFGVPDGVNNGQFGAGPVIDFFGLSSKYSKFPVDFVYPSETAIVPANIALIEGAKNTEEGKKFIAFTLSQAGQELLLEPKISRLPVLPYAALAGKIPPGYPDPAEIAKRSKVHFDADLSQARYYVVQSLFDQTITFRLKELQAATKAIYDAEAKLGERAGQGKAAELLAQARQLAWTPLVDAQRAADPAFLKLFAGNKKDAAVNQQITQLEGEWNGKARANYEQAQKLAREAAAL
>NC_002928.3|WP_010928346.1|2204924_2206238_+|pyrimidine-permease
MSNTYFPRWRLADDTVPGAVIAPDERLSWPKNIAMGAQHVVAMFGSTVLAPLLMGFDPNVAILMSGIGTLIFFLFVGGRVPSYLGSSFAFIGGVVAVTGYVAPGANANIGVALGAIIACGLVYALIGLVVWAASARGNGARWIEAMMPPVVTGAVVAVIGLNLAPIAAKGAMGSSGFEASMALMTILCVGGIAVYTRGMVQRLLILVGLVLACVIYAVCANGLGLGAPMDFAKVAAAPWFGLPSFAAPVFEPQAMGLIVPVAIILVAENLGHVKAVAAMTGQDLDRCVGRAFVGDGVATMVSGAVGGTGVTTYAENIGVMAVTRIYSTLVFVVAAVIALVLGFSPKFGALIQTIPGPVLGGMSVVVFGLIAIAGARIWVVNQVDFSDNRNLIVAAVTLVLGAGDFSVKLGDFSMNGIGTATFGAIILYALLGLARRR
>NC_002928.3|WP_010928347.1|2206268_2207906_-|Tar-ligand-binding-domain-containing-protein
MPMLERIKVRTAMVAVFACFLAVLMLSGALTWRNAGRSAAEIEGLNQVAVNQVDPLFEASGAALRARVALLEALANLQANHLDPVATLHQQAGAAQRQAATQFQRYVDVPKEPAAAELAATLQTRWRAYQSVLDELAAAVDAGQAEPALAAMNRAQQAEHAFQRDMEAFLARVQAHSDEVRSGAEDTHVVARWSAIALAALGVLLTLAGWLFVRRAVLRPLLEAGHHFDRIADGDLTARIEVRSANEIGALFAALKRMQEGLTRTIAVMRRGVDEINVGAAEISAGNANLSSRTEEQAAALEETAATMEELATTVKQNADNAAQANQLAAVSMQVAQRGGESVAQVVQTMHGISASSRQIADIVTVIDGIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRSLAQRAAQAAKEIKALIESSVATVRAGSQQVASAGGTMDEVVASVQRVADIMGEISAASAQQASGIDQVSLAISQMDETTQQNTALVEQAAAAATAMEEQARHLAAAAAVFRTQGGAIIDVAAAPLAGPAGGHAALPPAAAR
>NC_002928.3|WP_003809615.1|2208529_2209006_+|transcription-elongation-factor-GreA
MSAIPLTVRGAERLQQELHRLKTVERPAVISAIAEARAQGDLSENAEYDAARERQGFIEGRISELEGTLSNAHLIDPTALDAEGRAVFGATVEIEDLDSGDRLTYQIVGDVEADIKSNLISVSSPVARALIGKSEGDVVEVKVPAGVREYEVIGVRYL
>NC_002928.3|WP_010927744.1|2209307_2210258_-|IS481-family-transposase
MNNHKHARLTRLGRALLVNRVMQQNWTMRQASQAAGVSLRTGYKWLARFRSEGLDGLLDRSSRPHRSPKACAPEQVEHFAQQRRQRLPLWRIAREAGRSLATVARYMERIGLSRLASLEPPAPVRRYERASPGELLHIDTKRLGRIRGVGHRITGDRAQNRNRGIGWDAVHLAIDDFSRVSFARILDDEGGDQCAEFLRQATAYYASLGVRIDRVMTDNGSGYVSRTFRAVCVELGIRHIRTRPYTPKTNGKAERLVQTCLREWAYARPYTSSAERQAALQPFIDRYNWCRPHSALGHQPPITRIPDVNNLLRIDT
>NC_002928.3|WP_010928348.1|2210397_2211000_-|YhbY-family-RNA-binding-protein
MPISELTSRERSDLRSAAHPLRPVVLIGDNGLTDAVLKEIDLALTAHELIKVRAGGDDREAREAMLATICDTLSCAAVHHLGKTLILFRPDLRAAAAKAAADTPAKRRPSEPHTPKKMAAEGKRLTKTRPARKAAEAAAPAAGARPGRDDLNQAGRPARPSTRKASPGHAIPRRSGSALSLRAGARGGLAGRKPARANKQ

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Crispr_ID: NC_002928_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_4

3091381-3091477

Orphan

Consensus_repeat	Method
GTGCCTGTCCCGGCGGGGACAGGCACCC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_002928_4

>merge|NC_002928|4|3091381-3091477|CRISPRCasFinder
GTGCCTGTCCCGGCGGGGACAGGCACCCAGCCGCAGATGTCAGTCCCCATGCCGCTGGCGCATGACGGCGTGCCTGTCCCGGCGGGGACAGGCACCC

>NC_002928|4|3|3091381-3091477|CRISPRCasFinder
GTGCCTGTCCCGGCGGGGACAGGCACCC	AGCCGCAGATGTCAGTCCCCATGCCGCTGGCGCATGACGGC
GTGCCTGTCCCGGCGGGGACAGGCACCC

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_003810628.1\|3090356_3091307_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176131
NC_002928.3\|WP_010928781.1\|3085912_3086857_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223674
NC_002928.3\|WP_161780343.1\|3088531_3088891_-\|hypothetical-protein	unknown	unknown	unknown
NC_002928.3\|WP_010926762.1\|3083437_3085072_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224048
NC_002928.3\|WP_010926672.1\|3116867_3117722_-\|pyridoxine/pyridoxal/pyridoxamine-kinase	unknown	unknown	gnl\|CDD\|181269
NC_002928.3\|WP_010928780.1\|3081146_3081908_-\|TcpQ-domain-containing-protein	unknown	unknown	gnl\|CDD\|132874
NC_002928.3\|WP_010928793.1\|3117718_3118522_-\|YggS-family-pyridoxal-phosphate-dependent-enzyme	unknown	unknown	gnl\|CDD\|143483
NC_002928.3\|WP_010928782.1\|3091538_3092759_-\|ISL3-like-element-IS1001-family-transposase	unknown	unknown	gnl\|CDD\|225995
NC_002928.3\|WP_010928779.1\|3079572_3081150_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|274177
NC_002928.3\|WP_003810643.1\|3082085_3083441_-\|amidase	unknown	unknown	gnl\|CDD\|223232
NC_002928.3\|WP_010928792.1\|3113794_3116767_-\|GAF-domain-containing-protein	unknown	unknown	gnl\|CDD\|237425
NC_002928.3\|WP_010928791.1\|3109247_3111266_+\|4-alpha-glucanotransferase	unknown	unknown	gnl\|CDD\|237737
NC_002928.3\|WP_041937240.1\|3092946_3094395_+\|RNA-polymerase-factor-sigma-54	unknown	unknown	gnl\|CDD\|235648
NC_002928.3\|WP_010928785.1\|3095097_3096630_+\|glycogen-synthase-GlgA	unknown	unknown	gnl\|CDD\|273969
NC_002928.3\|WP_010928784.1\|3094423_3094840_-\|hypothetical-protein	unknown	unknown	unknown
NC_002928.3\|WP_010926763.1\|3086909_3088484_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|173867
NC_002928.3\|WP_003810639.1\|3085064_3085895_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224094
NC_002928.3\|WP_010928794.1\|3118581_3119913_+\|transcriptional-regulator-PtsJ	unknown	unknown	gnl\|CDD\|185378
NC_002928.3\|WP_010928786.1\|3103179_3105375_+\|1,4-alpha-glucan-branching-protein-GlgB	unknown	unknown	gnl\|CDD\|235445
NC_002928.3\|WP_010928778.1\|3078294_3079569_-\|type-4b-pilus-protein-PilO2	unknown	unknown	gnl\|CDD\|369114

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_003810628.1\|3090356_3091307_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176131	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	1.58441e-67
NC_002928.3\|WP_010928781.1\|3085912_3086857_-\|ABC-transporter-permease	gnl\|CDD\|223674	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	1.35623e-122
NC_002928.3\|WP_010928780.1\|3081146_3081908_-\|TcpQ-domain-containing-protein	gnl\|CDD\|132874	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system. VirB9 is a component of the type IV secretion system, which is employed by pathogenic bacteria to export virulence proteins directly from the bacterial cytoplasm into the host cell. Unlike the more common type III secretion system, type IV systems evolved from the conjugative apparatus, which is used to transfer DNA between cells. VirB9 was initially identified as an essential virulence gene on the Agrobacterium tumefaciens Ti plasmid. In the pilin-like conjugative structure, VirB9 appears to form a stabilizing complex in the outer membrane, by interacting with the lipoprotein VirB7. The heterodimer has been shown to stabilize other components of the type IV system. This alignment model spans the C-terminal domain of VirB9. CagX is a component of the Helicobacter pylori cag PAI-encoded type IV secretion system. Some other members of this family are involved in conjugal transfer to T-DNA of plant cells.	6.01599e-30
NC_002928.3\|WP_010926762.1\|3083437_3085072_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224048	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].	0
NC_002928.3\|WP_010926672.1\|3116867_3117722_-\|pyridoxine/pyridoxal/pyridoxamine-kinase	gnl\|CDD\|181269	PRK08176, pdxK, pyridoxine/pyridoxal/pyridoxamine kinase.	9.55334e-159
NC_002928.3\|WP_010928782.1\|3091538_3092759_-\|ISL3-like-element-IS1001-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	5.26988e-80
NC_002928.3\|WP_010928785.1\|3095097_3096630_+\|glycogen-synthase-GlgA	gnl\|CDD\|273969	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type. This family consists of glycogen (or starch) synthases that use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose (EC 2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate. [Energy metabolism, Biosynthesis and degradation of polysaccharides].	0
NC_002928.3\|WP_010928779.1\|3079572_3081150_-\|hypothetical-protein	gnl\|CDD\|274177	TIGR02520, putative_Type_IV_pilus_protein, type IVB pilus formation outer membrane protein, R64 PilN family. Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. This protein family appears to encode a secretin for pilus formation, although it is quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Scoring between the trusted and noise cutoffs are examples of bundle-forming pilus B (bfpB). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking].	2.34702e-55
NC_002928.3\|WP_003810643.1\|3082085_3083441_-\|amidase	gnl\|CDD\|223232	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis].	6.98538e-115
NC_002928.3\|WP_010928792.1\|3113794_3116767_-\|GAF-domain-containing-protein	gnl\|CDD\|237425	PRK13557, PRK13557, histidine kinase; Provisional.	1.03293e-100
NC_002928.3\|WP_041937240.1\|3092946_3094395_+\|RNA-polymerase-factor-sigma-54	gnl\|CDD\|235648	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.	0
NC_002928.3\|WP_010928791.1\|3109247_3111266_+\|4-alpha-glucanotransferase	gnl\|CDD\|237737	PRK14507, PRK14507, malto-oligosyltrehalose synthase.	1.32174e-140
NC_002928.3\|WP_010928793.1\|3117718_3118522_-\|YggS-family-pyridoxal-phosphate-dependent-enzyme	gnl\|CDD\|143483	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity.	4.92186e-110
NC_002928.3\|WP_010926763.1\|3086909_3088484_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|173867	cd08502, PBP2_NikA_DppA_OppA_like_16, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	0
NC_002928.3\|WP_003810639.1\|3085064_3085895_-\|ABC-transporter-permease	gnl\|CDD\|224094	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism].	1.14667e-85
NC_002928.3\|WP_010928794.1\|3118581_3119913_+\|transcriptional-regulator-PtsJ	gnl\|CDD\|185378	PRK15481, PRK15481, transcriptional regulatory protein PtsJ; Provisional.	0
NC_002928.3\|WP_010928786.1\|3103179_3105375_+\|1,4-alpha-glucan-branching-protein-GlgB	gnl\|CDD\|235445	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB.	0
NC_002928.3\|WP_010928778.1\|3078294_3079569_-\|type-4b-pilus-protein-PilO2	gnl\|CDD\|369114	pfam06864, PAP_PilO, Pilin accessory protein (PilO). This family consists of several enterobacterial PilO proteins. The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body. This family does not seem to be related to pfam04350.	8.4282e-07

>NC_002928.3|WP_003810628.1|3090356_3091307_+|LysR-family-transcriptional-regulator
MRPQADLSTRQLRAFVMLADLRHFTKAAQACHLSQPAFSALIQSLEATLAMQLFDRSTRRVVLTQEGELFEPLARRLLADLGHAMTHIASFVELRRGRVHVAALPSLAAGWLPKVLHEFHAEHPDIELMLSDVLSDECIELVRSGQADFALASRGIRASDPAVLHARELCSDTFHLICRKDHPLAREPRLTLKHLAPWPFIHLTRNSSVRQTVEAALRPQVAKTILEVAQLATVAGMIEAGLGISVVPTFTLYQFERPGLLIRPISLPGLTRQIYIVRRQEERLSIAAQALYDLVVAKLGTPAAAKPRRRRTEKGR
>NC_002928.3|WP_161780343.1|3088531_3088891_-|hypothetical-protein
MSDVLVPLFRVAHARTGDKGDRSNISVIAWDRALYPLLVEQLTPEVVLAQFAHRRPAGAQRYLLPKLGAMNFVLDAVLDGGVNGALNLDAHGKALSYLILKTEIAVPSDLVCRLAGSPG
>NC_002928.3|WP_010926763.1|3086909_3088484_-|ABC-transporter-substrate-binding-protein
MRYLKSTYAAVLLAIGTAVPHATTLAQEVKVAAEAPLRLLDPVGTTAYITRNHAYMVYDTLFALDAQLKPQPQMVSTWSVSPDKLVYRFTLRDGLKFHDGSPVTAADCVASIKRWAQRDLTGLRMMAAAKEITAKDDKTFEIVLEQPFGAVIEGLSKASSLPAFIMPKRIADAPASQAITEVIGSGPFRFVASEYRPGLQVVYERNTDYVPRSEPPSGLAGGKVVNVDRVVWLSLPDIQTEANALAKGEVDYVQTVYPDVVQTLQASKDVVIQKLASTTTPTLRLNWLQPPFNNQKVRQALLHAVSQRDYMDAQVGDPKAYRVCWAMFGCDSPLASTAGVVSQDDEADLNAAKALLKESGYKNEKAVVLHATDYPPTSAIAPFTAQILRSIGMKAEVQSMDWATFLTRRGKQDPVEKGGWSVAYGSWNTLDLMSPIANLNLDGRGKEGYAGWTESAEMESLRTQYAQATEPASRQQIAAKIQQLAYDQVFYIPLGTYSNYAARRSNVTPLLDAPVTVFWGISKN
>NC_002928.3|WP_010928781.1|3085912_3086857_-|ABC-transporter-permease
MQILRLLFLRLASAIPVVLVVVTVVFLLVRLTGDPATILAGDMASPEVVASVRADLGLDRPLLGQYAQWLWDLLQGNLGTSIVTKQPVATLIGERLESTLVLSLSALVVTVLLAVPLGVLAAWRHNTLVDRVVMIYAVIGFSLPSFVVGYLLILMFSVWLGWLPVQGYVSITDDIWLAAQHLVLPTLALAIFYMSLISRVTRASVLEALNEDFVRTAKAKGVPSLRILSQHVLRNAAIPIVTVIGIGLAFLISGVVITESVFNLPGLGRLTIDAVLSRDYPVVQGVILFFACVYILVNLLIDMLYVVIDPRIRY
>NC_002928.3|WP_003810639.1|3085064_3085895_-|ABC-transporter-permease
MTSILRHNRLALLGGGVLLLMVAISVAASWIASMDPAMMQPRMRLTPPGEAFLLGTDALGRDVYSRVVHGSRMSLAIGALVVVITIAIGTLIGLVAGASRIMDRVLMRIMDGVMAIPGILLAVALVSLFGASLASVVIAIAVPEIPRVVRLVRSVVLSVREEPYVEAAVGLGVPYPKVVWRHILPNCFAPLIVQASYVFAAAILLEAVLGFLGVGFPPEIPTFGNILAEARPVFQRAPWATVAPGLLLAVTVLAVNLLGDGLRDSLDPKLARRAND
>NC_002928.3|WP_010926762.1|3083437_3085072_-|ABC-transporter-ATP-binding-protein
MIENTPKQRVLEVSGLAIRAGARTLVQDVTLSLAQGEILCLVGESGSGKSLTASAVMGLLPGNLGVSAGSIRLDGEDLTAASPARMQALRGDRMAMVFQEPMTSLNPLMRVGRQIAEVLQVHRPDLGAGQVRARVLELMGDVRLPTPEALMDAFPHQLSGGQRQRIMIAMALALEPALIIADEPTTALDVTTQAQVLKLFRQLLAKHSSAVLFITHDFDVVRDIADHVAVMQLGRIVEQGPAGQVLDAPRHDYTRKLLAAVPSGVPKTQQNASSDELLSVSGLNLVYESRGLLGPARRTHAVADVGFTLKKGETLGVVGESGSGKSTLGRCITRAHAPTSGRIVFDGVDIAGLSGKALRAVRRRVQMVFQDPYRSLNPRRRILHALIEGPIESGVDRKAACARAAELMALVGLPADGLQRYPHQFSGGQRQRICIARALAMEPDLIVADEAVSALDVSVQAQVLELFEDLQKRLGFAMIFITHDLRVAAQVCDRIGVMQKGRLLELGPVRQVIHAPQHPYTRHLFDSLPGRVGQAAEPAMELQA
>NC_002928.3|WP_003810643.1|3082085_3083441_-|amidase
MTSTDQHIARAGVAELARGIARGAFTPAEVTDVFLRRIQDLNPAIGAFVAVYEDEARHAARQATQALAQGQRLSPLHGIPFAVKDIVDVAGRFTTYGSRTGAGRQAGATAEYVRALLDAGMILLGKTHTVEFAFGGWGTNQRMGTPRNPLRADVPCATGGSSSGSGAAVGAQMVPFAVGTDTGGSIRIPSAFCGLTGMRPSMGRHSGAGVMSLSHTLDTIGPLARTVEDVQMLDDLLTGKTATDTAQPGSQAVARVRDARIGVLGAQWLGAIEPEVAHAYAQSLRAFEAMGATLVELALPFDREAFAQLTSTLIACEGLQFAGKYVHDPLSGMDEDVRARFLVGDRYDAAAYAELLGRRSAMIDTFTQAMAGVKALLMPTTPCVAQPLAGLEQSPYNPAVYTRMPAWLGCCALAVPNGSGAHGLPTSLQIVGLPESDRLVMSLGRAYQEYA
>NC_002928.3|WP_010928780.1|3081146_3081908_-|TcpQ-domain-containing-protein
MVRSLSIVCLLAVLQACAGPRPAAVAAAWDEAPAGQYRFDWQLSGDPAVAPLQVFDDARRIWLQFAPGQPIPAIFAHGAGGERPVPYLRRDPYIVVDGAWPALSLRGGRYVARIQRSGAPIPAGAPVVRAEGPAPVPATPSAVAPAEAAEAAPPAPRFRAAPPDLTLRAVLARWARAAGWTFEAEHWALDVDIPLAGKAELPGDFKTAVRALLAATELSEPPAQPCFYANRVLRVVPLAQACDRTRAAAPGLT
>NC_002928.3|WP_010928779.1|3079572_3081150_-|hypothetical-protein
MKARRLAMAGLSLALGGCSLSQQMQAMRDAATSLRARLLEGQQAVGRAGERPAREAAQDVARPWLAGRAQPLAREVLLPPALRADVDTTLLFAGKATLLVLAERLHRATGIAVRVHPDALLPRAAFLPRLAGPAELAAEPPAQAELRAGPRPLADTLDALAAQLYVHWRYHRGAIEFYRTETRVFDVRTLALAASAQARLGRAGSGETGSFGHASSTVLSADAGKALQAVRDRVAAFLTRAGVIAEIEAGGSTLAVTDTPEALARIEKYLQGENRALTRRVRLVFEELTVRTTAAAEGGIDWQAVYASARAAASYVMPGGAGAAGALGARVLAGPWRDARALIAALSTMGAVLRHRSIPMLTLNRRAVTHAVRTTFSYVDQVQRLSPTAAAPGGRDAVPGLAVQQKRETVGTFLTLLPKARDDGRILLSISYDNTIAQPLRTLTFGEGGQQVSLQQIAIDGSGIVQQVELLPGQPVILSGFDHSEDQYERHRLFPDAPLAAGGHDRTARERVTTVVMVTAQIDEG
>NC_002928.3|WP_010928778.1|3078294_3079569_-|type-4b-pilus-protein-PilO2
MRAATHPPLVLQQTQGGPMLAFGLTWFAVLGSHAALQGRARARALRATHYLVGGRHAVAAGCARLPRRYGALALHSAAQAYASLHPDGAQAGVASLPDGQGWLIAVQDGAVLASADRLFADVAQAQACLRTLLAQRPDLREVPAQAALDTLLARPDPSARLAPLASRWSRAPVAARAVVLALAVAGGASLWRGLRQGPPPAAPDPRAVWRAAQAEFLRGWPVHTSSELARVLDTLQALPLRVAGWALRQAQCVPGPAWHCDADYHRVDAAATSLAFAAAVPPGWQMRLHTLEHTRVAWTLAGDQHGLDRTAPASPADTLALAATLQRASAAFTHVSVGAAQALAGPAWDGPPELAPPAAPELRRREVVLDGPLRSLALVWPLPAPIGWATVSLRVVPDAIATLRASVLSLHLQGSLYEQTTSRS
>NC_002928.3|WP_010928782.1|3091538_3092759_-|ISL3-like-element-IS1001-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPISRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR
>NC_002928.3|WP_041937240.1|3092946_3094395_+|RNA-polymerase-factor-sigma-54
MFPRPGASLSEENLSHVLQDLRLRQQTTLAPRLQQSIHLLQMSALEFTTTVQQALATNPFLEDADETEAQDDAPAPPAASEPPATSEPPPEPPSYAGDYPTRSAAAQPGVASDAAAWVPATLSLHERLSQALGAYVLSERDRALAEFIVDGLDDDGYLRQELAQLAGVADFDPPPDASEWQAALHLVQQLDAPGLAARDLPECLALQIRACSRLDPAVRDAALAIVAAHLPRLARSDYPGMRRALRCSEPVLRQACGVIRGLDPKPGRRYAHEPPSYVVPDVVVSKQRQQWLVVPNRGAMPHARLHQAYADLFRRARMDERSPMAQELQEARWLVRNVEQRYATIRRVAEAIVQRQQMFFEFGQIALRPLMLREVADELEMHESTVSRATANKYMSTPRGVFEFRHFFSRELSTESGGTCSAAAVRALIREYIDAEDPRMPLSDVTLAKRLAGDGIVVARRTVSKYRLQLRLPAADTRRQYY
>NC_002928.3|WP_010928784.1|3094423_3094840_-|hypothetical-protein
MADRHAACEMEGPYLEDIDMKQRSLIYLVAGAMAALLAHGGALAQSGTAPTTPSTTPNDSTAVPPNRPVPPGQVPPAPGTTTHDGMPKTPQQHMNEHRGNDTRGDMPRRQPDINDNPPATPAQGASPPPGYPNTGGSK
>NC_002928.3|WP_010928785.1|3095097_3096630_+|glycogen-synthase-GlgA
MTTIRTLVVAAEAFPLAKTGGLGDAVSGMVQALGHRPGGVDVQCELLMPAYRGTLDMVYRPRTVARLGGLPGGPASLVRGHCPGSGLSVLLLRNDALYDRPGIYVDDSGQGYPDNARRYAALAHAAARLAQGLPGLRPPHVVHAHDWHAALAPLLIHAAGLHYVKTLLTIHNLAFQGTFPAELASALGIPLACRHDDGALSDDSVNFLKAGIRYATRVTTVSRAYAREILTPAFGCGLHGLLRARGADLSPVPNGIDTALWNPAADPHLGGLRFDALDMRNKACCKAALQAELGLQPRADATVLAMGSRLTGQKMADVAIAALPALLEAHEHLQFALIGRGEPALETALRALAARYPGRCAVHIGYDEPLAHRLHAGADLLLHGSRFEPFGLTPLYAMRYGTLPVASRVGGMVDTIRDPGPAVEESCAGQGTGFLFDGSEPADMQLAVARALRALAKPAVCDAMRRNAMQADFSWRASAQAYAGLYASLASAPQRGRVPAPTLPLLANAA
>NC_002928.3|WP_010928786.1|3103179_3105375_+|1,4-alpha-glucan-branching-protein-GlgB
MMRDSPSIQGTLDAATQHALLAGRHADPFSVLGPHQAGAHTVVRVLAPGARTVMAVLPGGQRTPLLPMQPGLFENTVPGLQPGAPAAYRLCIEWEGGIQHTADPYAFGPVLDTAQLDHCAAGGWRYLAGLLGAHAASVDGCAGTRFALWAPNARRVAVVGDFNGWDGRRHAMRLRYPAGVWELFLPDVGPGARYKFQVLGADGHTVLKADPLARQAEAPPATASIVPDERPFAWTDEAWMEQRAARQRCDAPISIYEVHAGSWFDDAGAPRWQSLAARLPEYARSLGFTHIELLPVMAHPFGGSWGYQPLGLFAPAAAHGAPADFAHFVDRCHEAGLGVILDWVPAHFPDDAHGLARLDGTPLYEHADPHEGRHPDWNTLIYNYGRREVRAFLIASAIHWLRHYHVDGLRVDAVASMLYRDYSRPAGQWIPNRHGGRENLEAIDFLRELNAAVGVQCPGAITVAEESTAWPGVTAPVANGGLGFDYKWNMGWMHDTLRYMRRDPIHRRHHHHDLSFGMVYAYAERFVLPLSHDEVVHGKGSLLGKMPGERAAQLAQLRLYYAFMWAHPGKKLLFMGGEFGQQGEWNHDAMLQWSLLDDPAHRGLQRLVADLNHVYATLPELHCRDADPSGFAWIVGDDADNSVLAFARVDASHCLVAVCNFTPVPRPGYRFGVPHAGDWRVRVDTGATRYGGAGGGPPICLRSEPIPAHGHPQSLVLDLPGFTALYLRHSE
>NC_002928.3|WP_010928791.1|3109247_3111266_+|4-alpha-glucanotransferase
MSENQALARLCALAGVSPRWTDVWGRTRAVAPPVLRAVLAALDLPAATPAQAADTLARWRARRPAMLTARAGGMLRVPGDAAAPYAIELDNGQVAHGLAEPDGAGGLALRAPRQPGYHTLRLGSASIALAVAPPRAPTLARLLASPRPRRWGVAAQIYSLRGTADPDGGHGDFGALAELAVAAAGHGADAVALSPAHALFAAAPRRCSPYSPSTRLFLNILYADPLDTFSDAECAAARRPSSGADAPLIDWPQAAGARLAMLRRLHRGLAADDPRAAELARFRAEGGQALRDHALFEALHAANGATDWRGWPAAWRRPAAALAAGCAREHAREMDFHVFAQWLARRSLAHAQAAARAAGMGVGLIADLAVGVDPAGSQTWAQPDAMLGGLNVGAAPDLRHPGGQDWRLTACSPATLATQGYAAYIDMLRRALASAGGVRIDHVLGLARLWVIPEGAPPDQGAYLAFPVEDLLRLAALEAWRHRAVLIGENLGTVPRDFNARLRAHGVLGMDVLWLQRETGPGGAGRFRPPGRWPASAVAMTSTHDLPTLRGWWQARDLDWCVPAHEADAQRRQRDQDRRALWRQAAPPGLAATAPPAEPPCAALLSHVARSRAPLMLVPLEDLAGLAEQPNVPGCPDHPNWRRRMPATAAAMLVQPAARLALAAIAAHRGRP
>NC_002928.3|WP_010928792.1|3113794_3116767_-|GAF-domain-containing-protein
MLRKGDRVSSPWTNTLARLEDERVMLQRIAAGVPLTDVLLHVMQAVEAQSSVELLTSIAFVDDSGMRLRHVATPSLPAAYVQATDGAAIGPGVASWGAAAFLGTPVYVEDLTVHPNWPPWREAATQHGLRACWSTPIKATDGRTLGVFSNYYRQPRLPTREDIEAIALVTRTAALAIERHLTEQALRNSSVRWRGMFERMQEGFFLAEAQRDSTGSVDDFTLLEINPAFETQSGLAVGQTLGPMLRVMSPAAADSIMRIFVGVIESGEPAQFEVEAPGPPQACYECRAGKEGHDRVAALFLNVTARKLAESELWERQYRKNFLLTLGDRMREIHQQDQIEQMVCEELGRHLELGAVAVMESVPQRGDRIAASWGPRPPYDGRSMLESAPLTPDYYEAVRKGRTAYLSPYLAGPAGNQQPSAIVVPLRRWGRADGTLLVRPDPTHPLKGTDIAFIEEAAERMCEAIERSQYARVLEQRVEHAIAERDRIWRLSPELLAVADHGGRLVSVNPAVRAILGWSPEQFLAMGLDEGVHPEDLASMQATLEAEPAEGMQPVRHLESRLLHKDGSYHWITWSLSRAEGNVYLAGRDDTDLKAQAEVLRQTEDALRQSQKLEAVGRLTGGIAHDFNNMLQGISGALYLIDRKLRRSKPEEVGKYVRTAQESTDRAARLTQRLLTFSRQQAIDPQVFDPGDILRSMDELFRRYTGEQVRLTLKLPAQSWRVRCDMNQFENAVLNLVINACDAMPAGGDLEIEVAHRELDAAAVQTNPCAEAGEFVEVCVSDMGCGMAPDVLARVFEPFFTTKPMGQGTGLGLSMIYGFAQQAGGMVTIASVQAEGTAVRLFLPRHVGEPVALPAPESSEPPAAPAHAAVVALVEDDEHVRDMVRAALEELNLTVLTAADGDAGHRLLQSDARIDLLLSDVGLPGMNGHALAQAARALRPALRIILMTGYADERENGWARQERDVSLIRKPFSPGELTARVCRLLAASQD
>NC_002928.3|WP_010926672.1|3116867_3117722_-|pyridoxine/pyridoxal/pyridoxamine-kinase
MMKLAAPNPQALAPLPIDVVSIQSQVVYGQVGNSVAVPVFNGFGLRVAAVPTVVLSNTPHYPSMHGGAVPLDWFEGYLADLGARGALAGVRVVQLGYLGGPAQAEALGRWIAGLVAVRPDLRVHIDPVIGDHDSGVYVAPGMVAAYRDHLLPLAQGLTPNGFELECLTGLPTGTMEQTIAAARTLLGGRARWVIVTSAAPATWPPGRVRVAVVTHDDAQVLEHAHVDTAPKGTGDMFGAALTGHLLAGQPVAEAARRAALQVIEALERTREAGCGELLLAGPLR
>NC_002928.3|WP_010928793.1|3117718_3118522_-|YggS-family-pyridoxal-phosphate-dependent-enzyme
MHADTAQDAPDAAARYPRADSVADFEHNLAAVRARMAAACQRAGRDPAGVRLLPVSKTVDEARIRMSYAAGCRELGENKVQEAYRKWEAMADLADLRWSVIGHLQTNKAKLVARFAAEFQALDSVRLAEALERRLQAEGRALDVYVQVNTSGEASKYGLHPDEAAAFIRQLPSYGALRVRGLMTLAVLSADAARVRQLRTLRDRLRQEAPAGVSLDELSMGMSGDYEIAIEEGATVVRVGQAIYGARALPNDYYWPDSGAADRAEDE
>NC_002928.3|WP_010928794.1|3118581_3119913_+|transcriptional-regulator-PtsJ
MSITGASAAEIFDSVRQLAQARRLLPGQALPPVRELAQTLGVNRNTVAAAYKRLVGAGLALSQGRRGTIIRGPSEPGEQDGAHPGSPLIDLASGNPDPARLPDPLAIMAGRASPPRLYGEATVDPRLQAYASQWYAGDCPAAFEVDLTHGAIDAIERLLGANLAAGDTVAVEAPGFLGSINALRALGLHAEGVALDAAGMLPDALERALADGAQAVLLTPRAQNPTGASLTRARARALRQVLQRYPHVMVIADDHFAHLSASPYHSPIPAAALRWALVRSVSKALGPDLRLAFVASDPDTSRRLRLRLASGTTWVSHLLQDVVAGCLASAPVQARMAQARRAYAQRRTWLADALRAEGIAAQWPADGLNLWVPLAQDSPALLLELAHRGWRLRNGRSFGVREDVHGLRITIATLEHATARRLARDLRLCLDALDGLKKYPTLL

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Crispr_ID: NC_002928_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_5

3767340-3767421

Orphan

Consensus_repeat	Method
CTGTCCCCGCCGGGACAGGCACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_002928_5

>merge|NC_002928|5|3767340-3767421|CRISPRCasFinder
CTGTCCCCGCCGGGACAGGCACCCGTCGTGCGCCATGAGCGCCACTGCCAAGACGGCGTCTGTCCCCGCCGGGACAGGCGCC

>NC_002928|5|4|3767340-3767421|CRISPRCasFinder
CTGTCCCCGCCGGGACAGGCACC	CGTCGTGCGCCATGAGCGCCACTGCCAAGACGGCGT
CTGTCCCCGCCGGGACAGGCGCC

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_003814065.1\|3760589_3760943_-\|cytochrome-c	unknown	unknown	gnl\|CDD\|225418
NC_002928.3\|WP_003814092.1\|3774351_3775251_+\|NAD-kinase	unknown	unknown	gnl\|CDD\|179379
NC_002928.3\|WP_010929087.1\|3775266_3776928_+\|DNA-repair-protein-RecN	unknown	unknown	gnl\|CDD\|223571
NC_002928.3\|WP_003821187.1\|3764487_3767238_+\|insulinase-family-protein	unknown	unknown	gnl\|CDD\|223685
NC_002928.3\|WP_010927279.1\|3776960_3778181_-\|ISL3-like-element-IS1001-family-transposase	unknown	unknown	gnl\|CDD\|225995
NC_002928.3\|WP_010929082.1\|3761103_3761991_+\|MoxR-family-ATPase	unknown	unknown	gnl\|CDD\|223786
NC_002928.3\|WP_003814085.1\|3771762_3772005_-\|hypothetical-protein	unknown	unknown	unknown
NC_002928.3\|WP_003814063.1\|3760214_3760577_-\|cytochrome-c	unknown	unknown	gnl\|CDD\|225418
NC_002928.3\|WP_065956704.1\|3757099_3758062_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|340821
NC_002928.3\|WP_003821191.1\|3758279_3759536_-\|NADP-dependent-isocitrate-dehydrogenase	unknown	unknown	gnl\|CDD\|180792
NC_002928.3\|WP_010929083.1\|3763188_3763743_-\|N-acetyltransferase	unknown	unknown	gnl\|CDD\|224168
NC_002928.3\|WP_003814072.1\|3763780_3764155_-\|hypothetical-protein	unknown	unknown	unknown
NC_002928.3\|WP_010929081.1\|3759738_3760164_+\|DUF1841-family-protein	unknown	unknown	gnl\|CDD\|370177
NC_002928.3\|WP_003821189.1\|3762012_3763185_+\|VWA-domain-containing-protein	unknown	unknown	gnl\|CDD\|226346
NC_002928.3\|WP_010929085.1\|3768662_3770588_-\|molecular-chaperone-DnaK	unknown	unknown	gnl\|CDD\|234715
NC_002928.3\|WP_003814083.1\|3771066_3771621_-\|nucleotide-exchange-factor-GrpE	unknown	unknown	gnl\|CDD\|237621
NC_002928.3\|WP_010929084.1\|3767428_3768562_-\|molecular-chaperone-DnaJ	unknown	unknown	gnl\|CDD\|236757
NC_002928.3\|WP_010929086.1\|3772086_3773175_-\|ferrochelatase	unknown	unknown	gnl\|CDD\|234585
NC_002928.3\|WP_003821185.1\|3770678_3771059_-\|thioredoxin-family-protein	unknown	unknown	gnl\|CDD\|239245
NC_002928.3\|WP_003814090.1\|3773232_3774237_-\|heat-inducible-transcriptional-repressor-HrcA	unknown	unknown	gnl\|CDD\|234621

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_003814065.1\|3760589_3760943_-\|cytochrome-c	gnl\|CDD\|225418	COG2863, COG2863, Cytochrome c553 [Energy production and conversion].	6.05638e-23
NC_002928.3\|WP_003814092.1\|3774351_3775251_+\|NAD-kinase	gnl\|CDD\|179379	PRK02155, ppnK, NAD kinase.	0
NC_002928.3\|WP_010929082.1\|3761103_3761991_+\|MoxR-family-ATPase	gnl\|CDD\|223786	COG0714, COG0714, MoxR-like ATPases [General function prediction only].	2.85673e-44
NC_002928.3\|WP_003821187.1\|3764487_3767238_+\|insulinase-family-protein	gnl\|CDD\|223685	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only].	3.06874e-64
NC_002928.3\|WP_010929085.1\|3768662_3770588_-\|molecular-chaperone-DnaK	gnl\|CDD\|234715	PRK00290, dnaK, molecular chaperone DnaK; Provisional.	0
NC_002928.3\|WP_003814063.1\|3760214_3760577_-\|cytochrome-c	gnl\|CDD\|225418	COG2863, COG2863, Cytochrome c553 [Energy production and conversion].	2.60442e-23
NC_002928.3\|WP_065956704.1\|3757099_3758062_-\|hypothetical-protein	gnl\|CDD\|340821	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins. Lipopolysaccharide heptosyltransferase (2.4.99.B6) is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family also contains lipopolysaccharide 1,2-N-acetylglucosaminetransferase EC 2.4.1.56 and belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.	3.67712e-14
NC_002928.3\|WP_003821191.1\|3758279_3759536_-\|NADP-dependent-isocitrate-dehydrogenase	gnl\|CDD\|180792	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.	0
NC_002928.3\|WP_010929083.1\|3763188_3763743_-\|N-acetyltransferase	gnl\|CDD\|224168	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane].	1.00531e-60
NC_002928.3\|WP_010929081.1\|3759738_3760164_+\|DUF1841-family-protein	gnl\|CDD\|370177	pfam08897, DUF1841, Domain of unknown function (DUF1841). This family of proteins are functionally uncharacterized.	1.92899e-74
NC_002928.3\|WP_003821189.1\|3762012_3763185_+\|VWA-domain-containing-protein	gnl\|CDD\|226346	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown].	0
NC_002928.3\|WP_010927279.1\|3776960_3778181_-\|ISL3-like-element-IS1001-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	6.63558e-80
NC_002928.3\|WP_003814083.1\|3771066_3771621_-\|nucleotide-exchange-factor-GrpE	gnl\|CDD\|237621	PRK14139, PRK14139, heat shock protein GrpE; Provisional.	1.18525e-78
NC_002928.3\|WP_010929084.1\|3767428_3768562_-\|molecular-chaperone-DnaJ	gnl\|CDD\|236757	PRK10767, PRK10767, chaperone protein DnaJ; Provisional.	0
NC_002928.3\|WP_010929086.1\|3772086_3773175_-\|ferrochelatase	gnl\|CDD\|234585	PRK00035, hemH, ferrochelatase; Reviewed.	7.84073e-159
NC_002928.3\|WP_003821185.1\|3770678_3771059_-\|thioredoxin-family-protein	gnl\|CDD\|239245	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.	1.07863e-05
NC_002928.3\|WP_003814090.1\|3773232_3774237_-\|heat-inducible-transcriptional-repressor-HrcA	gnl\|CDD\|234621	PRK00082, hrcA, heat-inducible transcription repressor; Provisional.	1.1274e-145
NC_002928.3\|WP_010929087.1\|3775266_3776928_+\|DNA-repair-protein-RecN	gnl\|CDD\|223571	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair].	0

>NC_002928.3|WP_003821187.1|3764487_3767238_+|insulinase-family-protein
MRLPLLSRRLNALLVSSFLAFQAGAASLPAGVSEVSSIEGITEYRLANGLRVLLAPDASKPTTTVNMTYLVGSRNENYGQTGMAHLLEHMLFKGTPAIRNALGEFSRRGLQANGSTSSDRTNYFASFAANPETLKWYLGWQADAMVNSLIAKEDLDSEMTVVRNEMESGENNPFRVLMQKMQAAAYQWHNYGKSTIGARSDVENVDIAQLRAFYHEYYQPDNAVLIVAGKFDPQTALADIQSSLGKLPKPKRTLPPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSGRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVRDAKLDDVQRAAVAYLVRSNRTEGRYIPTEKPQRAPLAQRADLAAVFKDYKGDPNFKAVEAFDPSPANIDKRTLRRTLDLPNGQVELALLPKATRGDRVQAELLIQFGDAEALRGQRVPLAAAAALLDRGTDKLSRQAIQDRLDQLQAEAAINGSGTNLVVNISTLGKNLPDVMALVLDVVRNASFPQDQVEEYKRQAITMVQDAMTDPTALASRALARHNNPWPADDVRYVPTFDEALEQLRSLSRDDLAAVSGKLYGAGRIKFSAVGEFDPAAVEAVLRKGLDGWRSAPAYTRLPDPYRAVPAQQFDIATPDKANAFYISRMPLQLQDTNADYPALYLANFLLGTSETSRLWHRVRETEGLSYNVRSNLSVSSYEPSANWTIYAIYAPQNRARLEKAISEELARALKDGFTDQEVRDGVVALLNYRNLARAQDDVLADTWVNYMQTGRSFQWSADMDRKLEALTPDQVNAALRKYLKPDAFSTAVAGDFTKKSAP
>NC_002928.3|WP_003814072.1|3763780_3764155_-|hypothetical-protein
MLTDIVTRALSQLLGNSLSGDVIKGRFRYAYASDDGRFVAILGHDLTTYVVDVDAQRYFAECAGVPCGFAGHVLEMEGAQEHGHPWPAVNDLFDLDMDGDEIAWRRCPGAVALAATRQAQSRVA
>NC_002928.3|WP_010929083.1|3763188_3763743_-|N-acetyltransferase
MNATPSPAPTGATLVDCTHDRHAAAILDIFNDAILTSTALYDYQPRALASMEAWFLAKRQGGFPVVGFEDAAGVLMGFASYGTFRAWPAYKYSVEHSVYVDRRYRGRGLGEALLRALIERARLQQVHVLVGGIDATNAGSVALHRKLGFVHAGTITQAGFKFGRWLDLAFYQLTLDTPLRPVDG
>NC_002928.3|WP_003821189.1|3762012_3763185_+|VWA-domain-containing-protein
MLIDFFYHLRAHKLPVSVQEYLTLLEALRQRLMAPTLDDFYFLARTALVKDESLYDRYDAAFGAYYRGIAAALPADRDIPLDWLIKEFEKTLTPEEKAAIEAHGWDKLMELFKQRLEEQQERHAGGSKWIGTGGTSPFGNGGYHPEGIRVGGDSAGNRTAVKVWDMRQFRDYDDQLELGTRNFKVALRRLRRFARQGADLELDLDDTIASTARNAGHLDLRLVPERRNTVKVLMLLDVGGSMDDHIARVEELFSAARSEFRHLDVYYFHNCPYENLWQNNRRRQNERFDTWDVLRKYNADWRLIIVGDATMSPYEILQPGGSVEHYNKEAGAVWLRRLLDAWPKAAWLNPEPTASWRYRQSIALLRDIMQDRMYPVTVAGLEQAMRQLSK
>NC_002928.3|WP_010929082.1|3761103_3761991_+|MoxR-family-ATPase
MPTSASSSSAPAQPARFEGTDRYVATDDLKLAVNAALTLQRPLLIKGEPGTGKTILAEEVARALDRPLLQWHIKSTTKAHQGLYEYDAVSRLRDSQLGDEKVRDIRNYIVQGTLWQAFEAPEPVVLLIDEIDKADIEFPNDLLRELDRMEFHVYETRQTVQARHRPLVIITSNNEKDLPDAFLRRCFFHYIRFPDRDTMRDIVGVHYPDIRQDVLRAALDTFFALREAPGLKKKPSTSELLDWLRLLLAEAIPAAEIDAHAATAVPVLAGALLKNEQDVHLLERLGAMARGAQRR
>NC_002928.3|WP_003814065.1|3760589_3760943_-|cytochrome-c
MKLRISMTRTVSVLAVLASCAIAGPAAAADAAPVGNAQNARDKVSMCIGCHGIPGYKASFPELYHVPMIAGQNAKYIEAALNEYRKGARSHPTMDAVAGSLSDQDIADLAAYYSSLK
>NC_002928.3|WP_003814063.1|3760214_3760577_-|cytochrome-c
MKRFTFALAGIVLATAGVSAQAQDVVAGKAVFDKFNCASCHGADAKTSVQPEYPVLAGQHADYLAHALKAYKRGAAGSAATANVRKNPIMGAFAAQLSDQDIRNVAAWLAAQPSDLGVRQ
>NC_002928.3|WP_010929081.1|3759738_3760164_+|DUF1841-family-protein
MFNPSRDQVREFFIETWRKHRATEVLTPLESMALDWILEHPEYHGDLESPEAMTAEYPVEHGRTNPFLHLSMHLAIAEQLSIDHPRDIRAAYQRLVGRGDAHQAAHEIMECLGQVVWEAQRLGTPLDSDAYIELIRQRAER
>NC_002928.3|WP_003821191.1|3758279_3759536_-|NADP-dependent-isocitrate-dehydrogenase
MSYQHIKVPTGGQKITVNADYSLNVPDQVIIPVIEGDGTGADITPVMIKVVDAAVQKAYAGKRKIHWMEVYAGEKATKVYGPDVWLPEETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRYFKGVPSPVREPEKTDMVIFRENSEDIYAGIEYMAESEQAKDLIQYLQTKLGATKIRFPNTSSIGIKPVSREGTERLVRKALQYAIDNDRASVTLVHKGNIMKFTEGGFRDWGYALAQNEFGAQPIDGGPWCKFKNPKTGREIIVKDSIADAFLQQILLRPAEYDVIATLNLNGDYISDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHMGWTEAADLIIASMEKSILSKKVTYDFARLLEGATQVSCSGFGQVMIDNM
>NC_002928.3|WP_065956704.1|3757099_3758062_-|hypothetical-protein
MCPPYDKAAALRGLAGARRVALLMAPRLGDTLLMMNMARNLAAHGREVSIFGDYIHGLRDWFPGLDIRPSLSEEQAGQVLPGYDCAAQMHVGWPYALHAHQPNYFYYDAHVVITGRGFVKLFQIRDFCREQLGLAQAGADNGLRPPPQVQPHRSHPRRVALHPTSTGAQRCWAPRHFKELGLRLLHEGYEPNYIVAPHERAEWSWVLDHGLHLPQFPSLSEVAGFIHASGWFIGNESGIGHLASNVGVPTLSLTGRPTRTRAWRPAWSTSRIVYPALIPGGRWRDRLWREWLSPRRVMSAFHKLQADDRRQPVGVPWGKI
>NC_002928.3|WP_010929084.1|3767428_3768562_-|molecular-chaperone-DnaJ
MAKRDYYEVLGVAKNASDEDLKKAYRKLAMKYHPDRNPDSKEAEEKFKEAKEAYEVLGDEQKRAAYDRYGHAGVDPNAAGMGGGMGGGMGGGFADAFGDIFGEIFGAGRRGGGGPQVYRGADLKYALEITLEQAASGFDTEIRVPSWENCDTCHGSGAKAGTSPKTCRTCGGSGAVRMQQGFFSVQQTCPTCHGTGKEITDPCPSCDGVGRTRRNKTLQVKIPAGIDDGMRIRSSGNGEPGINGGPPGDLYVEIHIKQHKIFQRDGDDLHCELTIPFTTAALGGELQVPTLGGKAEISIPEGTQSGKTFRLRAKGIRGVRGSYPGDLYCHVVVETPVRLSDEQKAILRQFEASLNDGGDRHSPQSKSWTDRVKEFFS
>NC_002928.3|WP_010929085.1|3768662_3770588_-|molecular-chaperone-DnaK
MSKIIGIDLGTTNSCVAVLDGGQVKIIENAEGARTTPSIVAYMDDGETLVGAPAKRQAVTNPKNTLYAVKRLIGRKFDEKAVQKDIDLMPYSIVKADNGDAWVEVHGKKLAPPQVSAEVLRKMKKTAEDYLGEEVTEAVITVPAYFNDSQRQATKDAGRIAGLEVKRIINEPTAAALAFGLDKTEKGDRKIVVYDLGGGTFDVSIIEIADVDGEMQFEVLSTNGDTFLGGEDFDQRIIDYIISEFKKEQGVDLSKDVLALQRLKEAAEKAKIELSSSQQTEINLPYITADASGPKHLNLKITRAKLEALVEELIERTIEPCRVAIKDAGVKVSDIDDVILVGGMTRMPKVQDKVKEFFGREPRKDVNPDEAVAAGAAIQGSVLSGERKDVLLLDVTPLSLGIETLGGVMTKMIQKNTTIPTRYSQTFSTADDNQPAVTIKVFQGEREIAAGNKGLGEFNLEGIPPAPRGLPQIEVTFDIDANGILHVSAKDKGTGKENKITIKANSGLSEDEIQRMVKDAEANAEEDHRLAELAQARNQADALVHATRKSLTEYGEKLEAAEKESIEAAIKDLEDILKTGDKAEIDAKVEALSTASQKLGEKMYADMQAQQQAQQQQAADNAKPVDDNVVDADFKEVKRDQ
>NC_002928.3|WP_003821185.1|3770678_3771059_-|thioredoxin-family-protein
MAAAPFDPAEVFQVFGMRRVDSASFDEQVVQAPGDDLRCVFLWGQDCYNCGIFKQTALLQRQALLALELSWFEADVYADEALGRRFSLHGVPTFVLYRSGKRLGRVTGWPGLPQFSAAMQRLRDGT
>NC_002928.3|WP_003814083.1|3771066_3771621_-|nucleotide-exchange-factor-GrpE
MTAPQEPVDSTPESGENAATPGLEDDLSAELAALRAELEAAQATVKAQQEQVLRAAAEAENVRRRAQEDVAKARKFGIESFAESLVPVKDSLEAALAQPDQAAQAWREGVEVTLKQLTAAFERNLLKEIAPAQGDKFDPHLHQAISSVPADQPANTVLQLLQKGYVIADRTLRPALVVVSAGQG
>NC_002928.3|WP_003814085.1|3771762_3772005_-|hypothetical-protein
MNPPRKPTIGTSGPPGHANLEEDQLERELDEALLETFPASDPIAITSEDERDEPDDKVDEALEDTFPASDPPAPAQPGKK
>NC_002928.3|WP_010929086.1|3772086_3773175_-|ferrochelatase
MFLRLFKYLWPERYLPEIPAQDPFDENPPPCGPGRVGVLLVNLGTPDEPTRGAIRRYLGEFLSDPRVIEIPRYLWMPILHGLVLAMRPKKLAPRYAGIWMEEGSPLLVYSQRQAAGVRQGLAARGVHAEVELAMRYGKPSIPAAITALRERGCDHILAVPLYPQYAASTTATVVDAVTRHAGRLRDQPALRFVKRFHNDPAYVEAQAGRIAEFWQAHGRPQKLVMSFHGLPRYSIELGDPYYRDCLDTARLLRERLGLREDEVEVTFQSRFGSARWLEPYTEPTLAELARQGVTEVDVVCPGFVADCLETLEEISQECRDAFVAAGGRQFRYIPALNDCPPWIEGLTDLVERQLRGWPTGNP
>NC_002928.3|WP_003814090.1|3773232_3774237_-|heat-inducible-transcriptional-repressor-HrcA
MDDRARALLKALIERYIADGQPVGSRTLSKVFDLSPATIRNVMADLEELGLIHSPHTSAGRVPTPRGYRMFVDSLLAVRAYQFEPAHIGELLPVSEPSRAVNAAAALLSNLTQFAGVVLTPKRTQIFRQIEFIRLSDKRVLLIIVTPEGDVQNRILSAQRDYTEAELLEAGNFFNVHFSGKSFDAVRRTLSTELAQLRDDISRLMQAAVEAGAEAADDGEAVVISGERKLLDVTDIASDMDRLRKMFSLFEKKTDLLQLLDVSSRAQGVQIYIGGDSQLVPMEEVSVITAPYGVDGKVIGTLGVIGPTRMAYERVIPIVDITARLLSNALSHNQ
>NC_002928.3|WP_003814092.1|3774351_3775251_+|NAD-kinase
MYFPIVALIGRYQDTGLDAPLTALAQMLTQAGRRVLVEAETARNAGVSGYPVADWDEIGRTATLAVVMGGDGTVLGAARHLAPYGVPLIGINHGRLGFITDIPLQDAHDALGRVLEGNYQAEDRMLLQGGVWRGEQQMYSASAVNDVVLNRAGRGGMIEVRVELDGAFMYTQRADGLIIATPTGSTAYSLSANGPILHPGMNAMVLVPVAPQTLSNRPIVIPDSGVLNMTLTAMGRVEIGASVHFDMQTWSDLQPGDRITVQRAPHTIRFVHPEGYSFFSTLRRKLHWNLMPQATDNLE
>NC_002928.3|WP_010929087.1|3775266_3776928_+|DNA-repair-protein-RecN
MLRTLHIRDFVIVEQTELHFGDGFTVFSGETGAGKSILIDALALTLGERGDASMLREGAARADITAVFDAPPALRDWLAERELDSGDELALRRVIDSQGRSRAYINGMPATIAQLRELGDGLVDIHGQHAHQSLMRPEAQRDLLDAHGGHAELRQTVAQAWKQWRALARQLDTAEQDAEALAAERDRLQWQSDELDRLGLGPDEWDALQTEHTRLSHAQSLLDGASRILEALDGEHDSAQYRLNGAAHQLQQMLRHDPALQGIGDELESARIAITEAVSDLNNYVSRVELDPQRLADVEARLSAVFETARKFKCEPHGLPALRDSLHGKLAEMQAASDVQALRAQAEAAQARYEAAAARLSAARRKIAKDLGKQVTQAMQTLSMQGGRFEAALTGGAPSAHGSEQVEFLVAGHAGSTPRPLAKVASGGELSRISLALSVIASRAARVPTLIFDEVDSGVGGAVAEAVGKLLRELGQRHQVLCVTHLPQVAACAHAQYRVSKVESGGSTRSRIAELDAEARVEEVARMLGGIKITATTRDHAREMLGGHTAPAA
>NC_002928.3|WP_010927279.1|3776960_3778181_-|ISL3-like-element-IS1001-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPIGRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR

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Crispr_ID: NC_002928_6

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_6

3920365-3920449

Orphan

Consensus_repeat	Method
CTGTCCCCGCGGGGACAGGCACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_002928_6

>merge|NC_002928|6|3920365-3920449|CRISPRCasFinder
CTGTCCCCGCGGGGACAGGCACCCTGTCATACGCCATGAACGCTTGACGGCCAAGACGGTATCTGTCCCCGCGGGGACAGGCACC

>NC_002928|6|5|3920365-3920449|CRISPRCasFinder
CTGTCCCCGCGGGGACAGGCACC	CTGTCATACGCCATGAACGCTTGACGGCCAAGACGGTAT
CTGTCCCCGCGGGGACAGGCACC

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_010929159.1\|3911147_3912131_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein-BugE	unknown	unknown	gnl\|CDD\|270295
NC_002928.3\|WP_019247543.1\|3915273_3916659_+\|N-acetylmuramoyl-L-alanine-amidase	unknown	unknown	gnl\|CDD\|182376
NC_002928.3\|WP_003814358.1\|3930751_3931495_+\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224715
NC_002928.3\|WP_010929160.1\|3917526_3919416_+\|DNA-mismatch-repair-endonuclease-MutL	unknown	unknown	gnl\|CDD\|234630
NC_002928.3\|WP_010929162.1\|3920459_3921509_-\|phosphoribosylformylglycinamidine-cyclo-ligase	unknown	unknown	gnl\|CDD\|235439
NC_002928.3\|WP_010929166.1\|3927394_3929497_-\|TRAP-transporter-large-permease-subunit	unknown	unknown	gnl\|CDD\|129868
NC_002928.3\|WP_010929161.1\|3919412_3920354_+\|tRNA-(adenosine(37)-N6)-dimethylallyltransferase-MiaA	unknown	unknown	gnl\|CDD\|234626
NC_002928.3\|WP_010929167.1\|3929667_3930708_+\|TRAP-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270320
NC_002928.3\|WP_010929164.1\|3923158_3924514_+\|polynucleotide-adenylyltransferase-PcnB	unknown	unknown	gnl\|CDD\|130997
NC_002928.3\|WP_003814332.1\|3916801_3917440_-\|VTT-domain-containing-protein	unknown	unknown	gnl\|CDD\|182775
NC_002928.3\|WP_010927027.1\|3926003_3927398_-\|MmgE/PrpD-family-protein	unknown	unknown	gnl\|CDD\|377179
NC_002928.3\|WP_041937284.1\|3921761_3922463_+\|DnaA-regulatory-inactivator-Hda	unknown	unknown	gnl\|CDD\|236347
NC_002928.3\|WP_003814344.1\|3922459_3923158_+\|HAD-IB-family-hydrolase	unknown	unknown	gnl\|CDD\|319796
NC_002928.3\|WP_010929165.1\|3924510_3925002_+\|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-diphosphokinase	unknown	unknown	gnl\|CDD\|172582
NC_002928.3\|WP_010929158.1\|3910186_3911083_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176107
NC_002928.3\|WP_003814327.1\|3913263_3914655_-\|class-II-fumarate-hydratase	unknown	unknown	gnl\|CDD\|234779
NC_002928.3\|WP_003814329.1\|3914806_3915343_+\|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE	unknown	unknown	gnl\|CDD\|223873
NC_002928.3\|WP_003814321.1\|3908325_3910080_-\|gamma-glutamyltransferase	unknown	unknown	gnl\|CDD\|223482
NC_002928.3\|WP_003814325.1\|3912266_3913247_+\|AEC-family-transporter	unknown	unknown	gnl\|CDD\|223751
NC_002928.3\|WP_003814351.1\|3925020_3925977_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270296

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_010929159.1\|3911147_3912131_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein-BugE	gnl\|CDD\|270295	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	3.25651e-157
NC_002928.3\|WP_019247543.1\|3915273_3916659_+\|N-acetylmuramoyl-L-alanine-amidase	gnl\|CDD\|182376	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA.	1.25625e-84
NC_002928.3\|WP_003814358.1\|3930751_3931495_+\|GntR-family-transcriptional-regulator	gnl\|CDD\|224715	COG1802, GntR, Transcriptional regulators [Transcription].	5.58304e-45
NC_002928.3\|WP_010929160.1\|3917526_3919416_+\|DNA-mismatch-repair-endonuclease-MutL	gnl\|CDD\|234630	PRK00095, mutL, DNA mismatch repair endonuclease MutL.	0
NC_002928.3\|WP_010929162.1\|3920459_3921509_-\|phosphoribosylformylglycinamidine-cyclo-ligase	gnl\|CDD\|235439	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional.	0
NC_002928.3\|WP_010929166.1\|3927394_3929497_-\|TRAP-transporter-large-permease-subunit	gnl\|CDD\|129868	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit. The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family (TC 2.A.56)- DctM subunit TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterized. This system is the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997). DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. DctQ is an integral cytoplasmic membrane protein with 4 putative transmembrane a-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein with 12 putative TMSs. These proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].	2.19046e-96
NC_002928.3\|WP_010929161.1\|3919412_3920354_+\|tRNA-(adenosine(37)-N6)-dimethylallyltransferase-MiaA	gnl\|CDD\|234626	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed.	1.00887e-155
NC_002928.3\|WP_010929167.1\|3929667_3930708_+\|TRAP-transporter-substrate-binding-protein	gnl\|CDD\|270320	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold. DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.	1.18155e-85
NC_002928.3\|WP_010929164.1\|3923158_3924514_+\|polynucleotide-adenylyltransferase-PcnB	gnl\|CDD\|130997	TIGR01942, pcnB, poly(A) polymerase. This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca).	7.39002e-147
NC_002928.3\|WP_003814332.1\|3916801_3917440_-\|VTT-domain-containing-protein	gnl\|CDD\|182775	PRK10847, PRK10847, DedA family protein.	1.10927e-69
NC_002928.3\|WP_010927027.1\|3926003_3927398_-\|MmgE/PrpD-family-protein	gnl\|CDD\|377179	pfam03972, MmgE_PrpD, MmgE/PrpD family. This family includes 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyzes the third step of the 2-methylcitric acid cycle.	3.67215e-107
NC_002928.3\|WP_041937284.1\|3921761_3922463_+\|DnaA-regulatory-inactivator-Hda	gnl\|CDD\|236347	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.	8.14329e-101
NC_002928.3\|WP_003814344.1\|3922459_3923158_+\|HAD-IB-family-hydrolase	gnl\|CDD\|319796	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C. This family includes Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C, PgpC (previously named yfhB) which catalyzes the dephosphorylation of phosphatidylglycerol-phosphate (PGP) to phosphatidylglycerol (PG). This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.	3.35754e-64
NC_002928.3\|WP_010929165.1\|3924510_3925002_+\|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-diphosphokinase	gnl\|CDD\|172582	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.	1.33001e-89
NC_002928.3\|WP_010929158.1\|3910186_3911083_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176107	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	1.752e-38
NC_002928.3\|WP_003814327.1\|3913263_3914655_-\|class-II-fumarate-hydratase	gnl\|CDD\|234779	PRK00485, fumC, fumarate hydratase; Reviewed.	0
NC_002928.3\|WP_003814329.1\|3914806_3915343_+\|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE	gnl\|CDD\|223873	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only].	5.46598e-54
NC_002928.3\|WP_003814321.1\|3908325_3910080_-\|gamma-glutamyltransferase	gnl\|CDD\|223482	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism].	0
NC_002928.3\|WP_003814325.1\|3912266_3913247_+\|AEC-family-transporter	gnl\|CDD\|223751	COG0679, COG0679, Predicted permeases [General function prediction only].	2.66124e-42
NC_002928.3\|WP_003814351.1\|3925020_3925977_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	gnl\|CDD\|270296	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. Bug27 binds non-carboxylated solute nicotinamide, in contrast to BugD (aspartic acid transporter) and BugE (glutamate transporter) which both bind aliphatic carboxylated ligands. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity.	6.01101e-118

>NC_002928.3|WP_010929161.1|3919412_3920354_+|tRNA-(adenosine(37)-N6)-dimethylallyltransferase-MiaA
MTPRAIICLAGPTAAGKSASTLALAQRWPLEIINVDSATIYRGMDIGTAKPSAAERAQVPQHLLDIRDPAQSYSAAKFRADALRLIAEIHARGRIPLLAGGTMLYYKALREGLDDLPQADPALRAELEARAARLGWPALHAELALLDPATAARLSPNDSQRIQRALEICRLAGQPMSALLQGERRGDAPSPYRYVTLSLEPSERAALHARIAQRFDAMLAAGLVEEVRGLHARPDLHPGLPSVRCVGYRQMWSYLDGDIDLDTAREQGVAATRQLAKRQLTWLRAQPERVIIDCLAGDAVARTVDAMARALPD
>NC_002928.3|WP_010929160.1|3917526_3919416_+|DNA-mismatch-repair-endonuclease-MutL
MSDRRPIATLPDLLISQIAAGEVIERPASVLKEILENAIDAGARAIEVRLEGGGIRRIAVTDDGSGIPPEELPLALTRHATSKIRSLDELESVASMGFRGEALASIASVADLTIISRTRGAEHAWQIDGGSLQVSPASGPPGTTIDVRQLFDRVPARRKFLRSEATEFGHCVDAMERIALAHPEVAFRLFHHDRAQRQWLPADHGQRIRDVLGAEFVDHVLPVQAAAGAIALMGMVTRPTAARARADRQYLYVNGRFVRDRTVSHALRSAYADVLHGDRQPAYVLYLDIDPGAVDVNVHPAKHEVRFRDSGAVHRFVSQVVGQTLAQTGGAEAVPAGVPDGAAPDAAYAGEPAAAAPGLAEPRAPYPAAYPSPGQSPYQGSPARPHTQVPFRLHGEPAGIPATDWQSLYRPLPGDAAPAATALRAAPATPLPTADEHPLGQALAQLHGIYILAQNSRGLVLVDMHAAHERVVYEQLKRALDDRALPRQDLLVPVVFHAAEKDVALVEEHETQLNELGFEMRPSGPASIAVRSVPALLARGDIESLARAVLRDLGAVGVSRLLTEQRNELLSTMACHGSVRANRRLTLEEMNALLRQMEITERADQCNHGRPTWVQWSVNDLDKLFLRGQ
>NC_002928.3|WP_003814332.1|3916801_3917440_-|VTT-domain-containing-protein
MLDFFNMVLHIDQTLGIWVEQYGVWVYLVLFLIVFAETGLVVLPFLPGDSLLFIAGAFGATGHMDPVLTAALLIVAAISGNTVNYTIGRYIGPRVFSMNLRFLDRNALMRTHAFYEKHGGKTIVMSRFIPVIRTFAPFVAGVADMRLARFQLFNIGGALLWVISLVAAGYFFGNIPLVREHLNTIVLIGLGAAIVPVVIGALVRLLQVRRGQ
>NC_002928.3|WP_019247543.1|3915273_3916659_+|N-acetylmuramoyl-L-alanine-amidase
MVERDCPPAHGALSPRAAARRRLISVAATLLVLPVVPRLAHAATILAVRTWPADEYTRVTLELDSELKAEHFTLENPHRLVVDIEGLSVNAALNDLVSKVRHDDPYIQGLRVAQNRPNVVRLVFDLKQSVAPQVFTLKPVADYQYRLVLDLYPKVAQDPLMAILNKQSGPDVDDPLARVLDEIARNQPAPDQPAAPLARGQEPAPALPAPPIKPLPAPGRSASRKRMLTIALDPGHGGEDPGAIGRSGLREKDVVLRIARRLKTLIDAQPYMRAYLTRDDDYFVPLHVRVQKARRVRADLFVSIHADAFIKPTANGSSVFALSERGASSTQARWLADKENAADLIGGVNLGSHDRQVAKVLLDLSTTAQINDSLKVGSAFLDEIKKINRLHKNRVEQAGFAVLKAPDIPSILVETAFISNPKEEALLRSAAHQEKLAQAMMTGIDRYFTANPPLARVGDVS
>NC_002928.3|WP_003814329.1|3914806_3915343_+|bifunctional-alanine-racemase/tRNA-(adenosine(37)-N6)-threonylcarbamoyltransferase-complex-ATPase-subunit-type-1-TsaE
MSAPPTTLCLHLPDEAATEDLARQLAPLVDGRRGGQPGGQIHLQGDLGAGKTAFTRALLRECGIQGRIKSPSYALLESYKVSNLYFYHLDFYRFSDSREWLDAGFRDLLRDDAVVLIEWPERAAGLLPPPDLLISLAYADQGRDASLTAHTARGQTWLNAIVPPPTARSLPAPPPADA
>NC_002928.3|WP_003814327.1|3913263_3914655_-|class-II-fumarate-hydratase
MKTRTEKDTFGPIEVPEQHLWGAQTQRSLHFFAISTEKMPVPLVAAMARLKRAAAKVNAELGELDPQVADAIMRAADEVVAGKWPDEFPLSVWQTGSGTQSNMNMNEVLANRASELLGGERGEGRKVHPNDHVNRGQSSNDTFPTAMHVAAAVEVEHRVLPALKALRGTLAAKSAAFYDIVKIGRTHLQDATPLTLGQEISGYVAQLDLAEQQIRATLAGLHQLAIGGTAVGTGLNAHPQFSAKVSAELAHDTGSAFVSAPNKFQALASHEALLFAHGALKTLAAGLMKIANDVRWLASGPRSGLGEISIPENEPGSSIMPGKVNPTQCEAVTMLAAQVMGNDVAINVGGASGNFELNVFKPLVIHNFLQSVRLLADGMVSFDKHCAAGIEPNRERITELVERSLMLVTALNPHIGYDKAAQIAKKAHKENLSLKEAALALGHLTEAQFAEWVVPGDMTNARR
>NC_002928.3|WP_003814325.1|3912266_3913247_+|AEC-family-transporter
MSENSSLRRDAEAPLLSIFLPGSMSVALLVLPDFMLVALGWALRHKLGFSREFFAGTERMVYFVLFPALLFQSILRTPISAGHAMQLLQATAALMACGVALAWLAGPVLRPAPVALASAAQCGYRFNTYIGLALAASLAGGPGQTIMALIVGFAVPMANVAAVYGLARHSGNGLLRELARNPLLVSTLLGLACNLAGLSLPGPIDTVMARLGAAALALGIMCVGASLAWEGGKGHGRLIGWMLAVKLAAMPSAALGIAWALGLPALETRMLVLFSALPTASAAYVLAMRMGGDGRMVAVLISLGTLASAATIPLWLTAAAGLGAPN
>NC_002928.3|WP_010929159.1|3911147_3912131_-|tripartite-tricarboxylate-transporter-substrate-binding-protein-BugE
MNKVRTLVQAIAVATGLVAAAGAQAADAYPSKAIRVIVPFAPGGSTDIIARLVTQRMSQELGQPMVVENKGGAGGAIGASEAARAEPDGYTLSIATVSTMAVNPACRPKDLPYDPIKDFQPVTNFANTANVVAVNPKFPAKDFKGFLEELKKNPGKYSYGSLGTCGVLHLMGESFKMATGTDIVHVPYKGSGPAVADAVGGQIELIFDNLPSSMPQIQAGKLRAMAIAWPTRIDAIKDVPTFADAGFPVLNQPVWYGLLAPKGTPMDVVNKLRDAAVVALKDPKVIKALDDQGSAPSGNTPEEFAKEIKEQYDWAQDVVKKQNIKLD
>NC_002928.3|WP_010929158.1|3910186_3911083_+|LysR-family-transcriptional-regulator
MRLRHIEIFEAIRRTGSLTEAAALHISQPAASKLLAHAEAQLGFKLFERVKGRLVATRETEILAPEVARLNQDLGSVRRLAASLRDRPHGHLRLGCAPALGLGLLPGVVRASRDAQPGITFDIHTHHSAELVQGLLAHELDLAITFDANDHPGLTRTSLGHTELVHLSRRPGAGTTRLQELGGETLIVLDARDASGSLLQMALDAQGLAPRVAIQVQTHYVACALAEAGCGDAVVDAITARAMLRPGMALRRLEPALRVPISVMTRSQDALSTLHHDFIERLRQACSVLQAQPAPQPE
>NC_002928.3|WP_003814321.1|3908325_3910080_-|gamma-glutamyltransferase
MPLRTLLAALCAAAICQAPAWAREAPGVAREDVNPEIASARSERAQAHAQRYMIATANPLASEAGYRILRAGGSATDAIIAAQLVLNLVEPQSSGIGGGAFMVHYDRGAGELRVYDSRETAPAAARPDRFLREGKPLSYAESVNNGRAVGTPGLLRGLELAHRQHGKLPWQALFEPAIAMAEQGFAVSPRLHESIAGDKALAAQPAAARYFYGPDGQAWPVGHRLRNPEFAATLRSIAREGADAFYRGPIARDIVAAVRAHPTPGDLAEADLAGYRAVVREPVCGLYRGYRLCGAPPPSSGPLAVLQMLGELEQYPLARMRPGSVEAVHYFSEAGRLAFADRDFYVADPAFVDVPVRALLDPAYLRQRGALIRPDRSMKTALPGDPQGLLAERARDDAIEVPSTSHLVAVDAAGNVVSMTSTIEAAFGSKIFVRGFLLNNEMTDFSSSYRDPEGRLVANRVEPGKRPRSSMAPMIVFRAGKPVLALGSPGGSAIINYVAKTLVGVLDWKLDVQQAIALPNLGSRNKETELERGTALEALAPALRRMGHEVRITDFPSGIQGIVIGPHGLAGGADPRREGLALGD
>NC_002928.3|WP_010929162.1|3920459_3921509_-|phosphoribosylformylglycinamidine-cyclo-ligase
MTNQHSAPLTYRDAGVDIDAGDALVDRIKPLAARTMRPGVLVGIGGFGALFEVPKKFREPVLVSGTDGVGTKLRLAFDWNRHDTVGIDLVAMSVNDILVQGAEPLYFLDYFACGKLSVDTAAAVVGGIARGCELAGCALIGGETAEMPGMYPDGEYDLAGFAVGAVDKSAIIDGKSIQPGDVVLGLASSGAHSNGYSLVRKILERAGARPDQDFHGQPLVDVVMAPTRIYVKQVLAALDRHGPAIKGLAHITGGGLLDNVPRILQPGMAAQLQRDGWEMPKLFQWLQQQGSVADAEMHRVFNCGIGMVLVVAADQADAVAATLREQGEIVNRIGEIVPQQDGMAQTVVV
>NC_002928.3|WP_041937284.1|3921761_3922463_+|DnaA-regulatory-inactivator-Hda
MNRQLLLDVLPAPAPTLNNYIAGPNGQALAAAHALTAGRAIYLWGPAGCGRTHLLRGLSARPEAIYIDAARAAQSLRELAEADSTAPMPRLVAVDDVHRMDDARQAGLFALYNRWRESAATGRAFALAVSGDRAPMSLPLREDLRTRLGWDLVFRLDPLSDADKLAALTAQAAERGLQLAPEVINWMLTHHERDIRKLAALLDALDRYSLATGRPITTPLLRAMLADPHSQAT
>NC_002928.3|WP_003814344.1|3922459_3923158_+|HAD-IB-family-hydrolase
MTTRRLALFDLDHTLLPLDSDYQWADFLARTGRAGDPAEARRRNDDLMERYNRGELTAEQAAEFMLGLLAAHSPVELAAWHEEFMRDVIRPSLTAQAVDVVRGHLAAGDLCALVTATNSFVTAPIARAFGVQHLIATDPEYRDGRYTGRIEGTPSFREGKVVRVNQWLAGMGLALGDFAESYFYSDSVNDVPLLEAVTRPIAANPSPGLREIAQARGWQVIDLFDHLEDAKS
>NC_002928.3|WP_010929164.1|3923158_3924514_+|polynucleotide-adenylyltransferase-PcnB
MITETIRKFVGRLFAPALRGPQRIGAERHGIDRRNVSRHAIKVCDVLRQHGYEAYIVGGAVRDLIVGLEPKDFDVATNATPEQIRPLFRRARIIGRRFQLVHVVFGQEIIETSTFRAPASDDQETDEHGRILRDNVFGSQEEDAARRDFTMNALYYDPHTEEVIDYHQGVQDLKKRQVRIIGDPVKRYREDPVRMLRAVRFAAKLNGSIDTATRQPIRTMASLIENVPASRLFDEMLKLLTCGHAMDCLRQLRNDGLHHGLLPLLDVVLEQPGGENFVELALERTDARVRAGKTISPSFLFAALLWQLVDVRWKQLRAQGEHNIPALVQAADSVLDEQTEKLAIQRRFSSDMREIWFMQPRFERRAGKTIYRMLEQPRFRAACDFLQLRAAAGEFDSVLAQWWMDLANGDDATRAEMIEETAHLPREASDAPAQKRRRPRRRPSNRPREPQ
>NC_002928.3|WP_010929165.1|3924510_3925002_+|2-amino-4-hydroxy-6--hydroxymethyldihydropteridine-diphosphokinase
MNGSPASALAYVGLGANLGDAAATLRSVLAELAAAPGILACKASRLYRTAPVDAQGPDFVNAVAALDTTLAPLDLLDLLQALEQRHGRERPYRNAPRTLDLDLLLYGEQAIDHPRLSVPHPRIHERAFVLAPLCELAPGLRLAQGDCAALLAALEDQAIEPLR
>NC_002928.3|WP_003814351.1|3925020_3925977_-|tripartite-tricarboxylate-transporter-substrate-binding-protein
MKKRIWGTLLAAAMTVGSGAAHAGYPDKAVRIVVPFAAGGGVDALARPFAKELGDILGQSIVVENKPSNTGQIGATDVARAAADGYTLLLSSAAFATTPAFYPQVPYDPVKDFSPVMIMAAAPQVLVASNRFKAASLPDVLAQARQSDRINFALSASTGIQALATAMLAGQGGVTFMTIPYKGAGAAFMDLISGEVDLMIDNPASSLVHVRAGKLRVLATTGSKRMAILPDVPTVAETLPGFEARNWFVLAAPQGTPPAVIQKLNEASARALNTPAMRQMLERDGIDLVADSPAHAAAFLQDEIAKWGKVVKEGNLQP
>NC_002928.3|WP_010927027.1|3926003_3927398_-|MmgE/PrpD-family-protein
MTMNQAVSPLAGTPAVSAELARFAATSRWEDVPQAVRHEGRRSLLNYFAVALAAARDPVLDTATRTYARFASDARASLVGRARRLDMLNAAALNAMAANVYDFDDTHHPTIIHPTAPVAPALFALAETRPLSGAQLLHAFVLGVEATCRIGNAMSPGHYARGWHITSTCGVFGAALGAARCLGLPGDAMVAALGCAAVQAGGLVETLGTAAKSISVGNAARNGLLSALLAAEGFDGPPQPLEGVRGYLRVAADAPDIAAVSAGLGERWEVLNNTYKPYPCGVVLNPVIDACLALAADPRIAGGGWAAIERIELTGHPLLKQRTDRPGVATGRQSQVSAQHAVAVALVRGRAGLPEFSDEAVADAGLRALGLRLGFRDDASMSVDAVKVRIAFQDGTLLEREVQAARGSRERPLQDGEIEEKLRELCRHGGARVDADRLIEAVWTLDEAGDAAAVMRLAAEQPAA
>NC_002928.3|WP_010929166.1|3927394_3929497_-|TRAP-transporter-large-permease-subunit
MSSIEMPAPVMPIEPAELAGASPYPLAIDQDFCLIRWMAAISRACGALATVALLLMALSMCYEIFSRYLFNAPTAWATEISGYLLVATVFFGLAAAQASNSHVQVELWIDRLSAPVRLRVELLCQWLALLFCVVLGWQMASFNVREYLNDTRDWGLLSTPQWMPELAVSVGIVVFCMSILVDIYRLSPPAQAWRRWLTPTLLALLAAALVALGANAVPMAAGGRFDWGMALIVAALLACAWAWSGVRTLAHVVLVVGGCAVLYGLARGQSLGWVAFLLVASMMLLLFLGVRIGVALGLVGLFGVYFLLSRPQLSLLAERAWSSTNTFTLTAVPMFIFMGGLLLRSGITAGMFDALVRWFGRAPGGLAHASAGASAVFAAVSGSSLATAATLGKVACPDMIERGYSPRLTYGVAAAGATLGILIPPSIPMIIYGTTVGASVTHLFLAGMLPGLLLMACFMLGALVWALAVPGSAPVARAYTLREKLSASRGMVPFVAIIGAVLGSMYTGVATPTEAAAIGAVSAFVLCLVRRQLSWRALFEIAHDSAKVTALLLLIVVGAGIFSWVFDYLRLPREVVNLIQGADLSPALIVAAMVLAYLVLGMFVESIAMMLMTLPVTYPIAMSLGLDPIWFGVFLVLMIELGLITPPVGMVLFVLRSMNEKARFTDIIRGALPFVLIILLFLCLIYIYPQIVMWLPQQVK
>NC_002928.3|WP_010929167.1|3929667_3930708_+|TRAP-transporter-substrate-binding-protein
MSQRFPLPRGFQAALAAAALCTASWSGAAAQTYDLTMAVITSPGDGYSILTASVPERVAKATDGKVKVTVSDSLVPPAQIATAVREGRVDMSAALHTYLAADEPRMGIFNLPGLINNIQEYKQVCDAFWCEDTRKIWKDKWNAIVLAEGAWCTQQLFSKDPIHKVEDFKGKRLRVHNPQTAEVVNALGGKPVAMPTTEIFPALERGVIDGLFISTCVGGSLEFWRIAKNVQNWSLGPINGWAILANPDSWQKLPADVQKQVQGAMDALQQEAFGNYDTFVSNAQQEMMKKGVTFWVAPEEERAKLMQQQYIGPSYEAWNKRAKQVGFDGPAYLDRVRTTLGKSASN
>NC_002928.3|WP_003814358.1|3930751_3931495_+|GntR-family-transcriptional-regulator
MPFPFCNTNRMTSPAAPEGEFKVQRVASVLRHSVTESIRNAILVGRFRPGERLPERELCEMTGVSRTLVREALRQLESEGLIVVIPHRGPVVERLSPEQARGIYQVREELEGLACQLFAEHATEPQLAALQEAFQALKRALTRGTPLEQIAAKNAFYQQLLDGAGNEALTTTLRLLNSRVMLLRSTSMQAPGRAKHSVAELSNLLQALVARDGKAARKAGSLHVRNAASVAIAILQDSLADAAATAE

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Crispr_ID: NC_002928_7

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_002928_7

4130977-4131070

Orphan

Consensus_repeat	Method
GTGCCTGTCCCCGCCGGGACAGGCAC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_002928_7

>merge|NC_002928|7|4130977-4131070|CRISPRCasFinder
GTGCCTGTCCCCGCCGGGACAGGCACCCGGGCCCAGGAAAACCCCCACGCTGCGCCCGCTGTGCGGGCGTGCCTGTCCCCGCCGGGACAGGCAC

>NC_002928|7|6|4130977-4131070|CRISPRCasFinder
GTGCCTGTCCCCGCCGGGACAGGCAC	CCGGGCCCAGGAAAACCCCCACGCTGCGCCCGCTGTGCGGGC
GTGCCTGTCCCCGCCGGGACAGGCAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_002928.3\|WP_003814704.1\|4133473_4134874_-\|PLP-dependent-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|224089
NC_002928.3\|WP_003814701.1\|4132470_4132941_-\|universal-stress-protein	unknown	unknown	gnl\|CDD\|366180
NC_002928.3\|WP_157734664.1\|4139162_4139435_+\|GtrA-family-protein	unknown	unknown	gnl\|CDD\|377229
NC_002928.3\|WP_010929257.1\|4125822_4127052_-\|CoA-transferase	unknown	unknown	gnl\|CDD\|367110
NC_002928.3\|WP_010929261.1\|4137651_4138107_-\|multidrug/biocide-efflux-PACE-transporter	unknown	unknown	gnl\|CDD\|226610
NC_002928.3\|WP_010929258.1\|4128113_4128632_+\|MgtC/SapB-family-protein	unknown	unknown	gnl\|CDD\|224204
NC_002928.3\|WP_003814713.1\|4138103_4139207_-\|ChbG/HpnK-family-deacetylase	unknown	unknown	gnl\|CDD\|212118
NC_002928.3\|WP_003814694.1\|4127247_4128003_-\|TerC-family-protein	unknown	unknown	gnl\|CDD\|223930
NC_002928.3\|WP_010929253.1\|4119402_4120596_-\|acetyl-CoA-C-acyltransferase	unknown	unknown	gnl\|CDD\|180775
NC_002928.3\|WP_010929256.1\|4125040_4125826_-\|crotonase/enoyl-CoA-hydratase-family-protein	unknown	unknown	gnl\|CDD\|181723
NC_002928.3\|WP_010927085.1\|4135973_4136633_+\|LysE-family-translocator	unknown	unknown	gnl\|CDD\|224199
NC_002928.3\|WP_010929259.1\|4128628_4130746_-\|elongation-factor-G	unknown	unknown	gnl\|CDD\|234569
NC_002928.3\|WP_010927279.1\|4131107_4132328_-\|ISL3-like-element-IS1001-family-transposase	unknown	unknown	gnl\|CDD\|225995
NC_002928.3\|WP_003814706.1\|4135062_4135977_+\|DMT-family-transporter	unknown	unknown	gnl\|CDD\|223769
NC_002928.3\|WP_041937294.1\|4121716_4122889_-\|acyl-CoA-dehydrogenase-family-protein	unknown	unknown	gnl\|CDD\|173841
NC_002928.3\|WP_010929260.1\|4136722_4137646_+\|alpha/beta-fold-hydrolase	unknown	unknown	gnl\|CDD\|378820
NC_002928.3\|WP_010929255.1\|4123074_4123992_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176106
NC_002928.3\|WP_003814685.1\|4124002_4124974_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270234
NC_002928.3\|WP_003820700.1\|4133029_4133374_-\|TIGR01244-family-phosphatase	unknown	unknown	gnl\|CDD\|225984
NC_002928.3\|WP_003814676.1\|4120661_4121690_-\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|366103

Protein	Function_ID	Function_description	E-value
NC_002928.3\|WP_003814704.1\|4133473_4134874_-\|PLP-dependent-aminotransferase-family-protein	gnl\|CDD\|224089	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism].	1.52472e-110
NC_002928.3\|WP_003814701.1\|4132470_4132941_-\|universal-stress-protein	gnl\|CDD\|366180	pfam00582, Usp, Universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity.	9.38587e-30
NC_002928.3\|WP_157734664.1\|4139162_4139435_+\|GtrA-family-protein	gnl\|CDD\|377229	pfam04138, GtrA, GtrA-like protein. Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyzes the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b). This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose.	1.3327e-06
NC_002928.3\|WP_010929257.1\|4125822_4127052_-\|CoA-transferase	gnl\|CDD\|367110	pfam02515, CoA_transf_3, CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.	6.62375e-118
NC_002928.3\|WP_010929261.1\|4137651_4138107_-\|multidrug/biocide-efflux-PACE-transporter	gnl\|CDD\|226610	COG4125, COG4125, Predicted membrane protein [Function unknown].	1.97335e-52
NC_002928.3\|WP_010929258.1\|4128113_4128632_+\|MgtC/SapB-family-protein	gnl\|CDD\|224204	COG1285, SapB, Uncharacterized membrane protein [Function unknown].	1.18053e-44
NC_002928.3\|WP_003814713.1\|4138103_4139207_-\|ChbG/HpnK-family-deacetylase	gnl\|CDD\|212118	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria. This subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear.	1.3947e-92
NC_002928.3\|WP_003814694.1\|4127247_4128003_-\|TerC-family-protein	gnl\|CDD\|223930	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism].	1.14565e-78
NC_002928.3\|WP_010929253.1\|4119402_4120596_-\|acetyl-CoA-C-acyltransferase	gnl\|CDD\|180775	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase.	2.86943e-175
NC_002928.3\|WP_010929256.1\|4125040_4125826_-\|crotonase/enoyl-CoA-hydratase-family-protein	gnl\|CDD\|181723	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein.	3.47115e-155
NC_002928.3\|WP_010927085.1\|4135973_4136633_+\|LysE-family-translocator	gnl\|CDD\|224199	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism].	4.25651e-32
NC_002928.3\|WP_010929259.1\|4128628_4130746_-\|elongation-factor-G	gnl\|CDD\|234569	PRK00007, PRK00007, elongation factor G; Reviewed.	0
NC_002928.3\|WP_010927279.1\|4131107_4132328_-\|ISL3-like-element-IS1001-family-transposase	gnl\|CDD\|225995	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	6.63558e-80
NC_002928.3\|WP_003814706.1\|4135062_4135977_+\|DMT-family-transporter	gnl\|CDD\|223769	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].	8.05606e-10
NC_002928.3\|WP_041937294.1\|4121716_4122889_-\|acyl-CoA-dehydrogenase-family-protein	gnl\|CDD\|173841	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26. Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.	3.96966e-84
NC_002928.3\|WP_010929260.1\|4136722_4137646_+\|alpha/beta-fold-hydrolase	gnl\|CDD\|378820	pfam12146, Hydrolase_4, Serine aminopeptidase, S33. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. The majority of the members in this family carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in UniProtKB:Q7ZWC2.	6.02976e-19
NC_002928.3\|WP_010929255.1\|4123074_4123992_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176106	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	1.19908e-60
NC_002928.3\|WP_003814685.1\|4124002_4124974_-\|tripartite-tricarboxylate-transporter-substrate-binding-protein	gnl\|CDD\|270234	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter.	2.06741e-117
NC_002928.3\|WP_003820700.1\|4133029_4133374_-\|TIGR01244-family-phosphatase	gnl\|CDD\|225984	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown].	3.40043e-35
NC_002928.3\|WP_003814676.1\|4120661_4121690_-\|acyl-CoA-dehydrogenase	gnl\|CDD\|366103	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.	1.19321e-12

>NC_002928.3|WP_010929259.1|4128628_4130746_-|elongation-factor-G
MTRRTSIERYRNIGISAHIDAGKTTTTERILFYTGITHKLGEVHEGAATMDWMEQERGITITSAATTAFWRGMAGNYPEHRINIIDTPGHVDFTIEVERSMRVLDGACMVYDSVGGVQPQSETVWRQANKYGVPRIAFVNKMDRVGADFFRVQRQIVERLKGDAVPIQIPVGAEDHFEGVVDLVKMKAIIWDDASQGVRFEYRDIPPELQAQAEQWREKMIEKAAEANEALLEKYLSGQPLSEDEIKSGLRARTVANEIVPMLCGSAFKNKGVQAMLDAVIDYLPSPADVPAIIGHDERDREIERHPADDEPFSALAFKIMTDPFVGQLVFFRVYSGVVKSGDSVLNPLKSKKERLGRILQMHANERREISEVYAGDIAAAVGIKEITTGDTLTDPAHVIILERMTFPEPVISQAVEPRTKADQEKMGIALNRLAQEDPSFRVRTDEESGQTIISGMGELHLEILVDRMKREFGVEANVGKPQVAYRETIRSTVTDVEGKFVKQSGGRGQYGHVVLKLEPQEQGKGYEFVDAIKGGVVPREFIPAVDRGVRETLNTGVLAGYPVVDVKVTLVFGSYHDVDSNENAFRMAASMAFKEGMRRAKPVLLEPMMHVEVETPEDFTGNVMGDLSSRRGMVQGMEDIAGGGGKLVRAEVPLAEMFGYSTSLRSLTQGRATYSMEFKHYAEAPRQVAEQIIAARGSGAAARG
>NC_002928.3|WP_010929258.1|4128113_4128632_+|MgtC/SapB-family-protein
MDTVWMEIWTTVRNEFADIPDVAEATRIVLRLGMAVALGGLLGYERERSGKAAGLRTHMLVALGAALFVLVPLQGGMEVGDLSRVLQGVIAGIGFLGAGAIIKLGNEGEIRGLTTSAGIWLTAAIGVAAGMGREATALASTLIALFVLAALRHLEKRIAARDDKRVVAQPPP
>NC_002928.3|WP_003814694.1|4127247_4128003_-|TerC-family-protein
MDYLVSLAQQPAAWAALATLIAMEVVLGIDNLIFISILTNKLPPQHQTKARRIGIGMALILRLALLGTVAFIVQLTQPVFELFGHGFSWRDVILVAGGLFLVWKATKEIHHHVDPNPGDDMFGGKAATLGFAAAVAQILMLDLVFSIDSIITAVGMTEHIPIMFVAVIVAVAVMLLAAEPLARFIERNPTVVMLALAFLMMIGMTLIAEGFGAHVPKGYIYAAMAFSALVEGLNMMARRAREGRGAGAAGG
>NC_002928.3|WP_010929257.1|4125822_4127052_-|CoA-transferase
MSGPLEGVRILDVTTVLMGPYATQILGDLGADVIKVEPPAGDNVRGIGPGRHADMGGIFLHANRSKRSIALDLKNPAGREALLKVAATCDVLVYNVRPQAMARLGLSYAEVAQANPSILYVGMYGYDQRGPYAARAAYDDLIQGAVGIPSLSVEAGSDIPRYAPSAMVDRIVGISAANAVTAGLYHRARTGQGQAIDVPMFETMAHLILGDHMMGQTFEPPLGPPGYPRILNADRRPYATRNGHICVLLYADKHWKAFFELIGQPGRDAADPRFRDIGTRTQHIHAIYRLVSDAIASRTTEEWLAAFEAADIPAMPVHTMASLLRDPHLEAIGFFGMVDHPSEGAVRMMAVPSRWSGTPPQPRGHAPRLGEHSVDVLKEAGYDDEAIAALVRNGAGHRRGPPASGGNRS
>NC_002928.3|WP_010929256.1|4125040_4125826_-|crotonase/enoyl-CoA-hydratase-family-protein
MTDFLRHERHGGVLLLTMDRERTRNALSDADAVEALVQACARIGADLSVRAVVLTGSHGVFSSGGNLKTLSDTVGAGLGEPVHSRQAYRSGIQRIPLALYNLEVPTIAAVNGPAIGAGCDLACMCDIRLAARQASFAESFVKLGLTPGDGGAWLLPRIVGMSRACELAFTGRSIDAARARELGLVPEVFDADALLPAALALAQEIAQHSGHALRLTKRLLREGQHTRLDTLLELSAGFQALAHHTQEHAGALDAHLSRKRG
>NC_002928.3|WP_003814685.1|4124002_4124974_-|tripartite-tricarboxylate-transporter-substrate-binding-protein
MHSRTLALALLSVAALAQGGSARAASDYPAHPVKIIVSLPPGSGADTTARFLSKHLAERFKQPFVVENRPGGNSFIAAQAVATAPPDGYTLFVASNSPMTTNAAVFKNLPYDAVKDFAPVAPIARFPMALVVPANSPYRSVADLVAAARAAPGQLNFASGTATYQVVLELFHEQNGIKATHVPYKGTSAALADVAGGVVQYSVADVSAALPLIRGGKLRPLAVTSTRRIKDLPDVPTMQESGNKGFEAYAWTAAFFPAKVDPAIVARVSDAVQALVRSQEGKAFMEQLGGEPFVGGPDTLAAFQRDELASMRRIAKLANIQQE
>NC_002928.3|WP_010929255.1|4123074_4123992_+|LysR-family-transcriptional-regulator
MELRQLKQLLVLSETLNFHRAAERLHMAQPPLSTAIKKLEQELGVQLFERLPAGLQPTPAAEVVLRYARATLFYADEIQRAAQEGASGKQGMLKVGFVGSSIYSLMPQLLSAFRKDYPRVDLVIEESTTVDLLRRLDAHTLDVALVRFPVLEPSTARITLLQADHLMLAVPAGSRYAQRDDVALDELADEPFIGYSRTHVPGMHALIMYAFQQYGVVPHIAQEAIQVQTILSLVESGLGLAIVPKVACRQAGSGVRLVNVPQLAETIKVGIALAVHPDNATPTTANFVDMACRLMQTEPAAGQAR
>NC_002928.3|WP_041937294.1|4121716_4122889_-|acyl-CoA-dehydrogenase-family-protein
MGAILGTIIEALQLAAIPAHDEALRPAVRAFLDEALREMPADRRARSWMGHDAEFSRALARQGWLGLTLPVEYGGAGRSNFARFVLSEELLAAGAPVSAHWIADRQTAPLILRFGSPAQRAFYLPRIIRGEAFFAIGMSEPDTGSDLASVRTRATPVADGWLLNGRKIWTTNAHRSHYMCALVRTSGASEDRHRGLSQMIFDLALPGIEIRPIRDIAGDAHFCEVLFDNVLLPHDALVGEEGSGWRQVMAELALERSGPERIYSSMVLLDGWLAHLRRDAAPQRAQVCLAGRLAARLAVLRSMSLAVSQRLEQGADASLAAVLVKDLGTEFEQAVPELIGQALHASPQPAPDDVLMRTLAYLTLINPTFSLRGGTRHILRGIIARELGLR
>NC_002928.3|WP_003814676.1|4120661_4121690_-|acyl-CoA-dehydrogenase
MVSTMQQDLYETFARALAGLCPLERVRELEAAADPRAGAARAWNEVDALGYGDALSPAEHGGAGLSLADAEGLLRAAGAMALPFPFADTLLARALLRAAGQAVPDGPIALGVALPHGAGWRCAPIAGVALAQAVAVEHDGCLALWPAPDAVQPGLFRPRASGAPAWRGTPAQAGRAGAPAGAVQAWRNAADAAGMAGAMQAVLDRCVAYVQERQQFGRALGRFQAVQQDISMLAEQVAAVAMAARLACASGALFPDPALAACARLRACEAVPVVCALAHAVHGAIGITEELPLGLYTARLHEWRATGMSEDDCAELLGRRVLADGERTLLDVVRGMVSAAHA
>NC_002928.3|WP_010929253.1|4119402_4120596_-|acetyl-CoA-C-acyltransferase
MSVHPDPVVIVAARRTPIGAFQGALAHYSAPQLGAHALAAAVRQAGLQPDAAQEALMGCCLFAGLGQAPARQAVLGAGLPTDVQATTLSKMCGSGMKAAMLAHDMLRAGSADVVLAGGMESMSNAPHLIPKARQGYRLGDGQLLDHMYRDGLQDAYEGRLMGHYADLAAREYGFSREQQDAYAHESVLRAQRSVAEGEFAEEIAPIAGLARRGAPAAMVAVDETPGLCDVSRLASLKPVFNADGTVTAGNASSISDGAAALVLTRQAHAERLGLAPQARIVGHATAALPPGQFPAAPVRAIARLFERVGWDRDSVDLFEINEAFAVVTMIALRELGLPAERVNVNGGACALGHPVGATGARLIVTLMHALRRRGLRRGVACLCLGGGEATAIAIERA
>NC_002928.3|WP_010927279.1|4131107_4132328_-|ISL3-like-element-IS1001-family-transposase
MLDRKLLESLGGWQGYGVERVEWPEDPGRTLSIYLKPTAKVMLCEQCGARCRQVHETTVRRVRDLPLFEYRVVLHVPRRRLWCEQCGGPRLERLAWLGRYQRVTDRLAQACSQLLQSSNVQAVARFFELGWHTVKTLDKARLRASVREPDWSKIEYLAMDEFALHKGHRYATVVVDPIGRQVLWIGPGRSRETARAFFEQLPPGAAQRIKAVAIDMTTAYELEIQAHSPQAEIVYDLFHVVAKYGREVIDRVRVDQANQLRQDRPARRIIKSSRWLLLRNRDNLDRQQAVRLDELLQANQPLLTVYVLRDELKRLWFYQRPAWARQAWNHWYEQAEQSGIAALNTFAQRLKGYLHGILARCRHPLNTSIVEGINNTIKVIKRRAYGYRDQEYFFLKIRAAFPGNAR
>NC_002928.3|WP_003814701.1|4132470_4132941_-|universal-stress-protein
MFKKILIPTDGSPLSAQAANAGICFARSTGAEVVALHVTQPFAATIGFDGMAAAYAITDEDYEKASAEQAEKYLKLILDRAETAGVKAESRAVSNFNVADGIVQAAGEAGCDLIFIGSHGRSGLSRLLLGSVTAKVLSLAHTAVLVYRVKEDKDKK
>NC_002928.3|WP_003820700.1|4133029_4133374_-|TIGR01244-family-phosphatase
MSAAIKPLTENFAVAPQLGPADMADVAAAGYKSVIINRPDFEGGPDQPTAADVSQAAQALGLQVEYQPVVGSAMTAADVARFAELLRTMPGPVLAYCRTGTRCTNLFAAAQQLG
>NC_002928.3|WP_003814704.1|4133473_4134874_-|PLP-dependent-aminotransferase-family-protein
MRQADATLVTQLADDLARRIDEHGLRPGTRLPSIRRMAEQSGVSRFTVVEAYDRLVARGLVQSRRGAGFFVRARSASLTALASARVPQAAPETPVRVDVSWLLRNMFRETAAGMPGGAGLLPPEWLDPDMVAAAVRAVGRTVRGNLVSYGSPQGYAPLRQQLASMLQADGVPAHPERNLLTTNGVTHGLDIVARHLIKPGDTVLVEDPAWFVIFGRLAAFGARPVGVPRGPDGPDLAMLDRLAAEHKPRLYIINGAVHNPTGHTLSAGAAYDILRLAERHDFMVVEDDTYADLHPGGAMKLAALDRLERVILVGGFSKMLAASLRVGYIAAGAETLQRLTDLKMLAGLTSPELGERVVHRVLVEGQYRRHIERVRARVNEARLRSIQALQQLGLSVPHEPHAGMFVWADCGRDSEPVARNAAERGMLLAPGTLFSPSGAPSTMLRFSVAMVDTPGIWQSIAAVMAQ
>NC_002928.3|WP_003814706.1|4135062_4135977_+|DMT-family-transporter
MSPPSAQASAPSASPHAPSWEGYGYGLIGVLVFALTLPMTRLAVGELSPLLVGLGRALLAAVPAAALLWLTRSRRPDRAEWSGIVLAAVGIVVGWPVASTLAMASVPAAHGAVFNGLLPLSTAVFAAWRSGERPSPAFWSFAVLGAVLVAGYALRQGHGALQPGDLWLLLAVVLGGMGYAEGARASRTLGGWRTICWALVVSVPALLPAVLWLAHDAAWPSLPVAGAFAYLAFGSMFLGFFAWYRGLAIGGIARVGQIQLLQPFLTVVAAALLFNEQVEPITYVFAVAVVLVIAGGRRAMVRKA
>NC_002928.3|WP_010927085.1|4135973_4136633_+|LysE-family-translocator
MIGSDLSSLDQAPLASLSVLMPLVLFTLVNSLTPGPNNVMLASSGLTFGFRRTIPHLLGISVGFSIMLLMVGLGLGATLERLPWLYSTLKYGGAAYLLYLAWKIATSGPMESGAERGKPLTFIQAALFQWVNPKAWVMIVSVVATYTPQHGYFANLIIATLVCGVVNLPSVGVWAAFGMALRRWLHRPAAVRAFNVGMAVLLVVSLYPVGLDLLALYTG
>NC_002928.3|WP_010929260.1|4136722_4137646_+|alpha/beta-fold-hydrolase
MVCLPFRLSWRRMAAVLLLAAGALGFNQLDAWQRQAIFSPQTDQQRWWREPPAGTEVFDLALPNGDKVHAWYWQSPRRDAPTVLYLHGARWNLNGSAFRMEGWTGMGYSMLAIDYRGFGQSTPLLPSEQSASQDAAAALQELARRQPDPARRFIYGHSLGGAIAIDLAARPDLPPFAGLIVESSFTSIGAMLGTMKWGWVPGATLLVTQPFASVDKLAALTTLMLLLHGTADRVVPHTMSDELYRAAQQVPADLKRLVKIEGASHSGAIRSGRIYEDAVADFVRDAGRGYAGRQGAPTPLTASRPGT
>NC_002928.3|WP_010929261.1|4137651_4138107_-|multidrug/biocide-efflux-PACE-transporter
MSSSSKQTPKTIKERFLHAFFFEIIAIGLSAPVAAWAMDQPLFDMGVLTAVIAWIALLWNMVYNAGFERLERRFGVVRTMPVRVAHAVGFELGLVLIIVLLAAWWLAISFWEAFMLDIGLLMFYLPYAFFYNLAYDKLRARWWGRIEPAGA
>NC_002928.3|WP_003814713.1|4138103_4139207_-|ChbG/HpnK-family-deacetylase
MTSERYDEGQQPAHHVGPQRGQAGPFHAGDRDGPMGGGRGASDGNEPGNLSQQAAHVEEVSPLRNQAGDVRCRRIAVCGDDFGMNEAIDGALIELAGAGRLSAVSCMPLAPAFAADAPALARLDVDLGVHVDFTEAFAGAAPAAPGLAALLWRAYAGQLDPDWIDARLASQFDAFERAFGRAPDYVDGHQHVHQLPGILPRLRALLKRRYAGQRIWLRHTAPGLQFGLPLAEAAKARLIGALGAGALARAAGQEGWQTNRRMLGVYGFTGGPRRYAGLLHHWLMNARDGDLLMCHPGWPQVHGAAHASQRAAEYEVLAHPELGTWLARNGLRIVRLSQVRGRQASQESGKVRNVPHSGSFRRLASRL
>NC_002928.3|WP_157734664.1|4139162_4139435_+|GtrA-family-protein
MVGWLLAFVVSFTGHFRLTFRHLAASWTIAARRFFLVSALGFAINELSYAWLLHATSLPYDVLLALVLIGLAFLTFVASRLWAFRHRHAP

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_002928_1	1.2\|822523\|24\|NC_002928\|PILER-CR	822523-822546	24	NC_002928.3	822385-822408	0	1.0
NC_002928_1	1.2\|822523\|24\|NC_002928\|PILER-CR	822523-822546	24	NC_002928.3	822595-822618	0	1.0

1. spacer 1.2|822523|24|NC_002928|PILER-CR matches to position: 822385-822408, mismatch: 0, identity: 1.0

ggactggcaccggcaagatttcac	CRISPR spacer
ggactggcaccggcaagatttcac	Protospacer
************************

2. spacer 1.2|822523|24|NC_002928|PILER-CR matches to position: 822595-822618, mismatch: 0, identity: 1.0

ggactggcaccggcaagatttcac	CRISPR spacer
ggactggcaccggcaagatttcac	Protospacer
************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

3294265 : 3302331

uncultured_Mediterranean_phage(28.57%)

tRNA

The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_010928873.1\|3294265_3295150_-	peptidoglycan DD-metalloendopeptidase family protein	A0A292GJG6	Xanthomonas_phage	4.6e-15	49.5
WP_010928874.1\|3295167_3295947_-	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	4.8e-32	46.9
WP_003811017.1\|3295931_3296690_-	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	6.2e-69	51.2
WP_003811015.1\|3296815_3297463_+	glycerol-3-phosphate 1-O-acyltransferase PlsY	NA	NA	NA	NA
WP_010928875.1\|3297507_3298548_-\|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD	A0A0R6PI74	Moraxella_phage	7.9e-91	51.3
WP_010928876.1\|3298682_3299975_+	NCS2 family permease	A0A0R6PHV4	Moraxella_phage	1.9e-65	35.8
WP_010928877.1\|3300180_3301206_+	LLM class flavin-dependent oxidoreductase	NA	NA	NA	NA
WP_010928878.1\|3301341_3301725_+	thiol reductase thioredoxin	V9SJ74	Achromobacter_phage	1.8e-08	25.8
WP_003811006.1\|3301743_3302331_-	YigZ family protein	A0A1X9I5T8	Streptococcus_phage	2.1e-16	46.8

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_002928

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection