CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Target MGE spacer number	Prophage number
NC_009338	Mycolicibacterium gilvum PYR-GCK, complete sequence	4 crisprs	csa3,DEDDh,cas3,DinG,cas4,casR,WYL,Cas9_archaeal	2	6
NC_009340	Mycolicibacterium gilvum PYR-GCK plasmid pMFLV02, complete sequence	0 crisprs	NA	0	0
NC_009341	Mycolicibacterium gilvum PYR-GCK plasmid pMFLV03, complete sequence	0 crisprs	NA	0	0
NC_009339	Mycolicibacterium gilvum PYR-GCK plasmid pMFLV01, complete sequence	0 crisprs	csa3,csf1gr8,csf4gr11,csf2gr7,csf3gr5,c2c9_V-U4,Cas14u_CAS-V	0	2

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_009338_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009338_1

337343-337448

Orphan

Consensus_repeat	Method
CACGACGGCGGCGCCGACGGCACCGCCT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_009338_1

>merge|NC_009338|1|337343-337448|CRISPRCasFinder
CCCGAGGGCCACGACGGCGGCGCCGACGGCACCGCCTCGGGCGAAGGCACCGCTGACGGCGGCAGCAACCCCGAGGGTCACGACGGCGGCGCCGACGGCACCGCCT

>NC_009338|1|1|337343-337448|CRISPRCasFinder
CCCGAGGGCCACGACGGCGGCGCCGACG	GCACCGCCTCGGGCGAAGGCACCGCTGACGGCGGCAGCAACCCCGAGGGT
CACGACGGCGGCGCCGACGGCACCGCCT

Protein	Signature genes	Signature genes Name	Protein_function
NC_009338.1\|WP_011891333.1\|332146_332722_-\|VOC-family-protein	unknown	unknown	gnl\|CDD\|366361
NC_009338.1\|WP_011891332.1\|331510_332140_+\|TetR/AcrR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224228
NC_009338.1\|WP_011891328.1\|322969_326956_-\|type-VII-secretion-protein-EccC	unknown	unknown	gnl\|CDD\|274858
NC_009338.1\|WP_011891338.1\|337460_338669_+\|cupin-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|369647
NC_009338.1\|WP_011891331.1\|330505_331411_-\|DUF2236-domain-containing-protein	unknown	unknown	gnl\|CDD\|226188
NC_009338.1\|WP_013470466.1\|347331_347592_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011891343.1\|343029_344268_+\|DNA-polymerase-domain-containing-protein	unknown	unknown	gnl\|CDD\|240135
NC_009338.1\|WP_011891346.1\|346151_347321_+\|acyl-CoA/acyl-ACP-dehydrogenase	unknown	unknown	gnl\|CDD\|224871
NC_009338.1\|WP_011891327.1\|322661_322970_-\|PE-family-protein	unknown	unknown	gnl\|CDD\|376422
NC_009338.1\|WP_011891341.1\|340864_341185_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011891340.1\|339564_340836_+\|FAD-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|366721
NC_009338.1\|WP_011891344.1\|344425_344833_+\|STAS-domain-containing-protein	unknown	unknown	gnl\|CDD\|132914
NC_009338.1\|WP_011891334.1\|332830_333967_+\|alpha/beta-hydrolase	unknown	unknown	gnl\|CDD\|224561
NC_009338.1\|WP_011891342.1\|341263_342973_-\|acyl-CoA-synthetase	unknown	unknown	gnl\|CDD\|236097
NC_009338.1\|WP_011891339.1\|338665_339568_+\|sucrase-ferredoxin	unknown	unknown	gnl\|CDD\|227101
NC_009338.1\|WP_011891336.1\|334971_337158_+\|acyl-CoA-dehydrogenase	unknown	unknown	gnl\|CDD\|173841
NC_009338.1\|WP_011891345.1\|344974_346159_+\|acyl-CoA-dehydrogenase-family-protein	unknown	unknown	gnl\|CDD\|173841
NC_009338.1\|WP_011891335.1\|333963_334911_+\|2-hydroxyacid-dehydrogenase	unknown	unknown	gnl\|CDD\|240652
NC_009338.1\|WP_011891329.1\|326952_328491_-\|type-VII-secretion-protein-EccB	unknown	unknown	gnl\|CDD\|368288
NC_009338.1\|WP_011891330.1\|328487_330338_-\|type-VII-secretion-AAA-ATPase-EccA	unknown	unknown	gnl\|CDD\|188437

Protein	Function_ID	Function_description	E-value
NC_009338.1\|WP_011891333.1\|332146_332722_-\|VOC-family-protein	gnl\|CDD\|366361	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily.	1.61665e-20
NC_009338.1\|WP_011891332.1\|331510_332140_+\|TetR/AcrR-family-transcriptional-regulator	gnl\|CDD\|224228	COG1309, AcrR, Transcriptional regulator [Transcription].	0.00011917
NC_009338.1\|WP_011891328.1\|322969_326956_-\|type-VII-secretion-protein-EccC	gnl\|CDD\|274858	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This model represents the N-terminal domain or EccCa subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes. [Protein fate, Protein and peptide secretion and trafficking].	0
NC_009338.1\|WP_011891338.1\|337460_338669_+\|cupin-like-domain-containing-protein	gnl\|CDD\|369647	pfam08007, Cupin_4, Cupin superfamily protein. This family contains many hypothetical proteins that belong to the cupin superfamily.	1.2976e-30
NC_009338.1\|WP_011891331.1\|330505_331411_-\|DUF2236-domain-containing-protein	gnl\|CDD\|226188	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown].	2.60752e-84
NC_009338.1\|WP_011891343.1\|343029_344268_+\|DNA-polymerase-domain-containing-protein	gnl\|CDD\|240135	cd04865, LigD_Pol_like_2, LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.	3.4444e-112
NC_009338.1\|WP_011891346.1\|346151_347321_+\|acyl-CoA/acyl-ACP-dehydrogenase	gnl\|CDD\|224871	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism].	2.88944e-47
NC_009338.1\|WP_011891327.1\|322661_322970_-\|PE-family-protein	gnl\|CDD\|376422	pfam00934, PE, PE family. This family named after a PE motif near to the amino terminus of the domain. The PE family of proteins all contain an amino-terminal region of about 110 amino acids. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis.	6.65327e-12
NC_009338.1\|WP_011891342.1\|341263_342973_-\|acyl-CoA-synthetase	gnl\|CDD\|236097	PRK07788, PRK07788, acyl-CoA synthetase; Validated.	0
NC_009338.1\|WP_011891340.1\|339564_340836_+\|FAD-dependent-oxidoreductase	gnl\|CDD\|366721	pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.	1.06956e-29
NC_009338.1\|WP_011891344.1\|344425_344833_+\|STAS-domain-containing-protein	gnl\|CDD\|132914	cd07043, STAS_anti-anti-sigma_factors, Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.	2.08004e-07
NC_009338.1\|WP_011891334.1\|332830_333967_+\|alpha/beta-hydrolase	gnl\|CDD\|224561	COG1647, COG1647, Esterase/lipase [General function prediction only].	0.000322524
NC_009338.1\|WP_011891339.1\|338665_339568_+\|sucrase-ferredoxin	gnl\|CDD\|227101	COG4759, COG4759, Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones].	7.32501e-23
NC_009338.1\|WP_011891336.1\|334971_337158_+\|acyl-CoA-dehydrogenase	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.	3.14081e-138
NC_009338.1\|WP_011891345.1\|344974_346159_+\|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.	9.06158e-120
NC_009338.1\|WP_011891335.1\|333963_334911_+\|2-hydroxyacid-dehydrogenase	gnl\|CDD\|240652	cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric.	8.94095e-120
NC_009338.1\|WP_011891329.1\|326952_328491_-\|type-VII-secretion-protein-EccB	gnl\|CDD\|368288	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B. EccB is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterized in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope.	0
NC_009338.1\|WP_011891330.1\|328487_330338_-\|type-VII-secretion-AAA-ATPase-EccA	gnl\|CDD\|188437	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking].	0

>NC_009338.1|WP_011891336.1|334971_337158_+|acyl-CoA-dehydrogenase
MPIAILEEHNDLADSVRAFVERVAPSEVLHEALETPVPNPPPYWRSASEQGLHGVHLAESVGGQGFGILELAIVVAEFGYGAVPGPFVPSAIASALIAAHDPDAADLGGLASGDVIATYAIDSGLTATRQGENLVIRGEVRAVPAAAQASLLVLPVAIESGEEWVLIDAAQLEIEPVPSVDPLRPVAHVRANAVEVGDDRVLSNLSRAHARALMSTLLSAECVGVARWATDTASAYAKIREQFGRPIGQFQAIKHKCATMIAETERATAAVWDAARAIDEARENPDTAYEFAAAVAATLAPVAAQHTTGDCIQVHGGIGFTWEHDTNVYYRRALVLAASFGRASEYPQRVVDLATSTGMRALDLDLDPETEKLRDEIRADVAALKEIPREKRAAAIAEAGWVQPHLPVPWGRAAKPVEQIIIAQEFSSGRVKRPQMGIAAWIIPSIVAFGTDEQKERFLPPTFRGEMIWCQLFSEPGAGSDLAALSTKATKVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHQGITYFLLDMAADGVEVKPLRELTGNAMFNTVFIDDVFVPDELVLGDVNRGWEVSRNTLTNERVSLGSSEPPFLPSLDKFVEFVGEGHFDQIAQNHAGILIAEGHAAKILNMRSTLLTLAGGDPMPAAAISKLLSMKTGQGYAEFAVSSFGTDAVVGDPAQPTGRWADYLLASRSTTIYGGTSEVQLNIIAERLLGLPRDP
>NC_009338.1|WP_011891335.1|333963_334911_+|2-hydroxyacid-dehydrogenase
MRVLAHFLPGPKVTEFLSPHTDWLDIRYCAEDDDETFYRELPDAEVIWHVLRPISGDDLSKAPKLRLVHKLGAGVNTVDVDTATARGIAVANMPGANAPSVAEGTLLLMLAALRRLPELDRATRTGNGWPSDPTLGESVRDLGGCTVGLVGYGNIAKQVERILLAIGAEVVHTSTRDDGLPGWRTLPDLLSESDIVSLHLPLTGATEGLLGRKALAQMKTDAVLVNTSRGAIVDEAALVDALRAGTLAAAGLDVFAVEPVPSDNPLLGLPNVVLTPHVTWYTADTMRRYLEFALDNCERLRDGRALAHVVNDPSG
>NC_009338.1|WP_011891334.1|332830_333967_+|alpha/beta-hydrolase
MSRTTAAQAPGVTREFVGLDSTTARRAGSGGHPCQGLYHRGMGRRPKVAMIATHYQIDFSEHYLADYMATRGIGFLGWNTRFRGFESSFLLDHALVDIGVGVRWLREVQGIETVILLGNSGGGSLMAAYQANAVDKHVTPLDGMRPAAGLDDLPAADGYVASAAHPGRPDVLTAWMDASVVDENDAVATDPDLDLFNERNGPSYDAEFVTRYRAAQVARNEAITDWAEAELARVRAAGFSDRPFTVMRTWADPRMVDPLLEPTKRPPNMCYAGVPVKANRSTHGIAAACTLRNWLGMWSLRHAQTRAERHLARIDCPALVINAEQDTGVFPSDAQRIYDALAGDDKTLCAMDTDHYFTTPGARSEKADTIAKWITRRW
>NC_009338.1|WP_011891333.1|332146_332722_-|VOC-family-protein
MIKPDNTNTEFALGGINHVALVCSDMARTVDFYSNVLGMPLIKSLDLPGGMGQHFFFDAGNGDCVAFFWFAEAPDRVPGISSPEAIPGIGDIVSAVSTMNHLAFHVPAEKFDEYRQKLKAKGVRVGPVLNHDESPAQVSATLHPGVYVRSFYFLDPDGITLEFACWTKEFGDSDTATVPKTAADRRVPVNG
>NC_009338.1|WP_011891332.1|331510_332140_+|TetR/AcrR-family-transcriptional-regulator
MGCMAQVRPYRGVDAPARVAERRRRLLEAGLDLLGGQLNPPELTVRAICAQSGLAARYFYESFTDKDVFVGAVFDRVIADIATTTQAAVAAAPPREQSRQGMANIVRAISEDARVGRLLFNAHLDNPVVVRKRAESGALFALLSGQHAGSALRLERNDRITSAAHFVVGGVAQTLSAWLAGDLTFTEAQLAAQLGALIDQLADPALYRD
>NC_009338.1|WP_011891331.1|330505_331411_-|DUF2236-domain-containing-protein
MTLNESVPAALPVVERPINDVVVDVPTGRRARRGDDGMLGLGLLAGPANVIMQLARPAVGYGVLESRVESGRVDRHPIKRARTTFTYLAVSTNGTPEQQKAFRRAVNGAHAQVFSTDESPVKYHAFDKDLQLWVGACLYKGVVDVHRLFVGEMDEETADRVYVQGRALATMLQVPESMWPADREAFDRYWAASLDEVHIDDTVREYLYPIAASRLRGLRLPGPLQRRNEELALLITTGFLPQRFRDEMRLPWGPDHQRRFDRLMKVLRVANTVSPKFVRQFPFNLLLKDVDRRIRTGRPLV
>NC_009338.1|WP_011891330.1|328487_330338_-|type-VII-secretion-AAA-ATPase-EccA
MDIGSDTLAPPAGTSRVDQDVVSRFATCCRALGLSVHERRRPADLTAARAGFAALTRIASDQCDAWTGLAAAGDVTPQVIERVWQTSGATAGLLSRRIELAPQALGFTYDSGLYLRFRASTPDDFALAYTVCLSDAACYEEADQLLEGLLARRRGWFEARWVRIAMYHRAARWSDVVRMLTPLVTDATLDETSAHAARVTLGIALARLGMFAPALSYLERPEGPVTVAATDGALVKALSLRAQGEDEEALQLLQELYAVNPEHAQIEEALLDTSFGIPTTTAARIEARSNPWDPETEPGEADFVDSGAKDRKAHLLVEAEAELAEFIGLDEVKYQVARLKSSVAMAIRRQERGLAVAQRTNHLVFAGPPGTGKTTIARVVAKIYCGLGLLKKETVREVHRADLIGQHIGETEAKTNAIIDSALDGVLFLDEAYALVSTGAKNDFGLVAIDTLLARMENDRDRLVVIVAGYRKDLDTFLDANEGLRSRFTRSIDFPSYSPKELVEIAVRMAEKRDSHFEDSARSDMESLFSYLAESSSPDANGVNRRSLDIAGNGRFVRNLVERSEEEREYRLDHSDAEDFTDDELMTITAADVGQSAGPLLRGLGLAVPQHASDER
>NC_009338.1|WP_011891329.1|326952_328491_-|type-VII-secretion-protein-EccB
MSGADGDRRSFTSRTPTNENPDRVSFRRGFVTRHQVSGWRFMVRRMASGVALHDTRMLVDPLRTQSRSVLVGALILVTGLIGCFLFSLIRPAGDVGTDSILAERDTAALYVRLGDQVHPVLNLASARLITGRPDNPAMVKSSELDELPRGNMLGIPGAPGRMAVNTTRDAYWTVCDAAAGAVTGVTVIAGAPDDTGERATVLPDGHAVLAENNGRTWLLWDGRRSAIDLADRAVAGGVGIGVGVAAPQPIATGLFNAIPEAPALITPVIPNAGLPSDLGLPEPFPVGSVVVSYDEDNTLRHYVVLTDGLQPISPVVAAILRNSNSWGLASPPRLDADLVARTPQAEVVDVDAYPAERVTLVDTAAEPVICAAWSEHEGAQESSMELRSGAALPVADGVSTVALVSAGAPGGPANQVALPQGTGYFVDNAGSLFWLSDTGVRYGIDTGADADGADTVAALGLTTTPLPIPSSVLSLFAAGPTLSRGDALLAHDTLAPNPSPARVEALPGLENP
>NC_009338.1|WP_011891328.1|322969_326956_-|type-VII-secretion-protein-EccC
MSRLIFEHRKRLPAPVARKGTITIEPPPELPRVVPPSLLRRALPYLIVILIVGMIVALVATGLRLISPTTLFFPFVLLLAATALYRGTDNKMRTEEVDAERADYLRYLSVVRDNVRAHADEQRTALQWSHPEPAALNGIPGTRRQWERDPHDPDFLVLRAGLHDQPLDVTLRVKDTADEIDLEPVSHTTLRGLLDAQRTLYDVPAGIALTRVSRITVLGDDAEVTGALRAWVAQAMTWHDPSVLGIAFAGEALESEAWSWLKWLPHVDVPGRIDGVGPARYLAGDASDLRTLLAPALADRSGFTGDATGTTKHLLIVLDDPDADPSEFIGSGLAGVTVIHRSATEPDRDQYSDPERPVLRISGGRIERWQNGTWASNIDSADHLGAADARHIARRLARWDSNPDHARSATTGGAAFTTLLGIPDASALDVAALWAPRNRDDELRVPIGVTATGEPLIFDLKDEAEGGMGPHGLMIGMTGSGKSQTLMSILLSLLTTHPADRLIVIYADFKGEAGADIFRNFPQVVAVISNMAEKRSLADRFADTLRGEVARREQLLKDSGRRVQGSAFNSVTEYENAVREGHDLPPIPTLLVVADEFTLMLADHPEYADLFDYVARKGRSFRIHLLFASQTLDVGRIKDIDKNTSYRIGLKVASPSVSRQIIGVEDAYHIESGREHKGVGFLVPAPGALPVKFRSTYVDGIYEPPRVDRSIVVHAIPKPQLFSAGWVDPEPDTVIVDDGADVEVLPPRKLIATIGEQLVHYGPRAPQLWLPPLEEAIPLQGLLERSGIGAGQWRWPLGEIDRPFDMRRDPLVFDATSAAANMVIHGGPKSGKSTALQTFVLSAAALHAPGDVSFYCLDYGGGQLRVLDGLAHVGSVASPLESERIRRTFGELEQLLQARQRHGAAVNNGGYRDGYGEVFLLIDNLYAFSRDNTDTFNTRNPLLAKVTELVNTGLAYGIHVVITTPNWLEVPLAMRDGLGLRLELRLHDAHDSNVRVVGALRRPAEGVPADQPGRGLTMAAEHFLFARPAPETIPALNARFPGQSAPEVRLLPTRLSPRAFASLYPAPERVVIGQREEDLAAVSVDFADNPLLMVFGDTKTGKTTLLRHLIRTLRENSRADQVAFTVIDRRLQLVDEPIFPDNEYTPNIDRILPAMLGLAGLLEKRRPPAGLSPQELRGWDFRSSANGSGSHLHYLIIDDVDQIPDGPAVSGPYAGQRPWTPVIGLLSQASELGLRVIVTARAAGSAHAVMTAPLLRRLNELQATTLLLSGNPQDSGKIRGHRFSRLPAGRGLLLDDSNLSDTPTYVQLVDPLADDATAPAGHLGKEYS
>NC_009338.1|WP_011891327.1|322661_322970_-|PE-family-protein
MTLRVVPEGLTAASAAVEALTARMAAAHAAAAPLVTAVLPPAADAVSLQTATGLSANGVEHQSIAARGVEELGRSGVGVGDSAASYVSGDAMAATSYLIARG
>NC_009338.1|WP_011891338.1|337460_338669_+|cupin-like-domain-containing-protein
MLSRCIAIDPEVFAAEYWGRTPLLSHADALPRDFCDLLSPAMVDELIAERGVRAPFIRLAKEGQVLAKDSYLGPAGFGAEITDQVDPAKVLTQLAAGATVVLQGLHRLWPPLIDFTHRAVADIGHPVQVNAYITPPGNRGFDFHHDVHDVFVLQIAGSKRWIVHEPVHAHPLPDQSWTQFRDLIDERVTADPVIDTALTEGDALYLPRGWVHAAQALDTTSIHLTVGVSATTGVDVARAVLDELAGIDEFRAPLPLGIDPAAGDHTAAIAAKVIAQMVGHLQEDAAALSTAAAERLQARHRSRTRPEALRPLESLRAAEHAATIRVRRREGLAASVRHGADGRVSIHLTDKTVTFPALCAAALEEILGGRVAEADTLPGLDGADGAVLLRRLLREGVVVPAS
>NC_009338.1|WP_011891339.1|338665_339568_+|sucrase-ferredoxin
MTATKRLPCSEQSLARDEPMYGTASAGSSWLLLELEGGWGPSAFLESPGSIEPDLGRAIVRRAEAAGMRIAAIRRHGRRSATPRWRWFVAKADVGRHALFSGEVDEARDYLDVSLDGSDGAATDGPLVAVCAHGRHDQCCAVRGRSAVSAISAAYPESTWECSHLGGDRFAATMLILPEGLCYGRVDSADAAELVRLYCDGRLDDRFLRGRTSLPHAVQAAQHFARVAYGDDRIEAYPLVSMEGGDDTVRVVLAAGPGPIEVVLDVVMSEPLFSQCRAATAGPVRTFRLRSLSDTGMHPS
>NC_009338.1|WP_011891340.1|339564_340836_+|FAD-dependent-oxidoreductase
MSHGDYDVLVIGAGLAGLRCAALLASSGRSVAVWESGDAVGGRVRTDVVDGFRCDRGFQVLNPAYPELRRAIDVPALRLHPFLAGVAIRDTDRARHWVHPLRAPRRLPGMLTGGGLRPRDVVALMRWAAPALRPATLTEGRDDVSVADALDRSGVDGLARRVVDKFLAGVVLDDQGSTSNAFTLLLARMFALGVPGLPAEGMQALPRLMSAPIADRITLNHRVDRIVRDGRGWAVSAGGDTVRASHVVVATDPQTAETLTGAPAPPMKGVVTDWWATEDTIPGSRLLWVDGRPTPPGPLVNTAIVSAVAPGYAPAGHHLIAASALIGGDGEAPPESVTRTHAADILRVTGAQGWSLVTRHVVPEALPVQPPPLRVRRPVRTPDGLWLCGDHRDTASIQGALVSGRRVADAIDRCDRRSDTAHA
>NC_009338.1|WP_011891341.1|340864_341185_+|hypothetical-protein
MTNDRDFVEKRFNRPGEYRSAVVYSLIVVALAAAAFVVYAFGPRDSVFSAALVPAFLFAGGVGALIRTYREWKAGSGWTAWQGAGWFLLLLMLLTLAVPGSAAFAG
>NC_009338.1|WP_011891342.1|341263_342973_-|acyl-CoA-synthetase
MSKLSDLPAQALATVSQTLGKSVGKYVERGSAELHYARKMFQAGALKLEPPQDIAAFVADMVRWGEFGMIPALNARRHPHRTAVIDDFGEFTFGELDEAVNAVANGLLAKGVKGGDGVAILARNHRWFLVSVYAAGKVGARIILLNSEFSGPQIKEVSHREGAKLVIYDDEYTAAVKAAEPELGKLRSLGVNPDKDAPSGSTDETLEELIARTSSTPPPKATKHSSIIILTSGTTGTPKGANRSAPPSLAPIGGILSAVPFKSEEVTSLPAPMFHALGFLHATIAMMLGSTLVLRRRFKPATVLADIEKHRATAIVVVPVMLSRMLDELDKTSPKPDLSSLRILFVSGSQLGAELATRALKDLGPIVYNLYGSTEVAFATIAGPQHLSINPATVGPVVKGMRVKILDDNGNELPRGEIGRIFVGNFFPFEGYTGGGGKQIIDGLLSSGDVGYFDDNDLLYVSGRDDEMIVSGGENVFPAEIEDLVSGHPEVVEATALGVEDKEWGHRLRCFVVKAEGATIDEDAIKAYVRDNLARYKVPREVIFLDELPRNPTGKILKRELREMDVPES
>NC_009338.1|WP_011891343.1|343029_344268_+|DNA-polymerase-domain-containing-protein
MAARESYEIGGRTVPVTHLDKVVFGELGLTKLDLIDYYASVADGALRGVRDRPMILKRFVKGIDEEAVFQKRAPKNRPDFVDVAELKYASGTSAAEAVLRDPAGLVWAVNLGCVDLNPHPVRAEDLDHPDELRVDLDPMPGVGWRQILDVAFVAREVLEDHGLVAWPKTSGSRGFHIYARIHPRWPFKQVRLAAEAVAREVERRAPESATARWWKEERHGVFVDFNQNAKDRTVASAYSVRATPDARVSTPLFWDELAGCKPEEFTVHTVPARFAELGDPWEGMDDAAGGLEALLELSDRLGPAEKAPRGAKKSVDGRRASVMPLIEIARTKTKDEALSALAQWRDKYPAVSEKLEPADVLVDGMRGPSSIWYRIRINLQHVAEDQRPPQEELLADYSPWTHYTGAQQQRRD
>NC_009338.1|WP_011891344.1|344425_344833_+|STAS-domain-containing-protein
MYGNPTFHCAGADIRAHCRQLATVVKVAGRLDNANVERAGRYIDRFILPEKPFVLDLSEVDSFGEEAISLLFVIDDLCTAAGEEWSLIASRAVEQTLRDSGIEFPAAGSVPEALNHFADAMVARRRLLPLLTKTA
>NC_009338.1|WP_011891345.1|344974_346159_+|acyl-CoA-dehydrogenase-family-protein
MGTDADLVADTARRVVAEHDPKTVPIQQFLGACFDAGLSWVHFPEGFGGLGVSRGLQAVADGILQGAGSPVPLGLNPMGYGMAAPTVREHAQTDDVRRQLLRPLATTEHIWCQLFSEPGAGSDLAGLATSAVLDGDTWVVNGQKVWTSLAHRAKWGLLLARTDPNMPKHKGLTYFVIDMHGEGVQTRPLRQLTGHAEFNEVYMTDARIPDTFRLGAVGDGWRVAMTTLMNERSALGGSGSRRGAGTISDAVALWTSRPDLHTPVLRDRLSSLWLRSEAQRLTSKRSRAAATVGGPGPEGSVGKLVGAELNQHIYEFCMDLLGPEGILYDGYGMGDGDAADWRGPIQQRFLRSRANTIEGGTSEVMRNILAERVLGLPGDLRADAGMAWKEIPRG
>NC_009338.1|WP_011891346.1|346151_347321_+|acyl-CoA/acyl-ACP-dehydrogenase
MADTAGEWVFSDEQNQLRAAVRAFCADHVDESSVRAAMESDPPFDAKVWSRLGSELGVLGMAVPESAGGAGGNLVDQAVAVEQLGAALACGPLFGTVYLAIPALVAASGGQELLGPLVDGTRTAAFAVRDDAGAFDASSVEVQAVPTEQGWALSGTVERVVDAGAADVLLVAATTPDGVGLFVVEADSLGVQRIRLTTLDLTRPQATVGLLDAPAQLIAGPEEAERVITHALQVGAALLAVEQVGAAQHLLDLSVDYAKNRLQFGRPIGSFQAVKHRLADDLVAVEHARSTAYHAVWALSDGSDDPALAVSIAQATTSAAFVRVATDTIQVHGGIGFTWEHQAHLYYKRAYTDAALLGGAEEHRARVADFVLVVAPEKDAPRVATGMPS
>NC_009338.1|WP_013470466.1|347331_347592_+|hypothetical-protein
MLAKTTARQQISRYLGIIAVAAALVGAPLAAALQTGPATSHAQCPPGQTGVIYGCSPFCVAGKFLDTQTGLCMPVAPPPPAPAPRF

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Crispr_ID: NC_009338_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009338_2

4104312-4104400

Orphan

Consensus_repeat	Method
GGCGGTGCGGGCGGCGAGAACGTCTCGACCGA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_009338_2

>merge|NC_009338|2|4104312-4104400|CRISPRCasFinder
GGCGGTGCGGGCGGCGAGAACGTCTCGACCGATCCCGACGACGGCGGCGTCGCAGCCGGCGGTGCGGGCGGCGAGAACGTCTCGACCGA

>NC_009338|2|2|4104312-4104400|CRISPRCasFinder
GGCGGTGCGGGCGGCGAGAACGTCTCGACCGA	TCCCGACGACGGCGGCGTCGCAGCC
GGCGGTGCGGGCGGCGAGAACGTCTCGACCGA

Protein	Signature genes	Signature genes Name	Protein_function
NC_009338.1\|WP_011894705.1\|4115806_4116634_+\|carbohydrate-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223472
NC_009338.1\|WP_193373628.1\|4096061_4096706_-\|CDP-alcohol-phosphatidyltransferase-family-protein	unknown	unknown	gnl\|CDD\|223632
NC_009338.1\|WP_193373590.1\|4106079_4107792_-\|GAF-domain-containing-sensor-histidine-kinase	unknown	unknown	gnl\|CDD\|226951
NC_009338.1\|WP_011894689.1\|4096720_4097269_-\|HIT-domain-containing-protein	unknown	unknown	gnl\|CDD\|238606
NC_009338.1\|WP_011894686.1\|4093949_4095080_-\|glycosyltransferase-family-4-protein	unknown	unknown	gnl\|CDD\|340831
NC_009338.1\|WP_011894700.1\|4110422_4111412_-\|nitroreductase-family-protein	unknown	unknown	gnl\|CDD\|236122
NC_009338.1\|WP_011894704.1\|4114877_4115810_+\|sugar-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224096
NC_009338.1\|WP_011894703.1\|4113570_4114881_+\|extracellular-solute-binding-protein	unknown	unknown	gnl\|CDD\|270453
NC_009338.1\|WP_011894706.1\|4116638_4117868_+\|sn-glycerol-3-phosphate-ABC-transporter-ATP-binding-protein-UgpC	unknown	unknown	gnl\|CDD\|236947
NC_009338.1\|WP_011894693.1\|4100577_4101075_+\|DUF1990-domain-containing-protein	unknown	unknown	gnl\|CDD\|378157
NC_009338.1\|WP_011894691.1\|4099444_4099873_-\|TIGR02611-family-protein	unknown	unknown	gnl\|CDD\|131660
NC_009338.1\|WP_011894701.1\|4111474_4113139_-\|glycoside-hydrolase-family-13-protein	unknown	unknown	gnl\|CDD\|200471
NC_009338.1\|WP_011894698.1\|4108897_4109722_+\|universal-stress-protein	unknown	unknown	gnl\|CDD\|366180
NC_009338.1\|WP_013471922.1\|4101273_4101990_+\|GAF-and-ANTAR-domain-containing-protein	unknown	unknown	gnl\|CDD\|377145
NC_009338.1\|WP_011894687.1\|4095111_4096065_-\|phosphatidylinositol-mannoside-acyltransferase	unknown	unknown	gnl\|CDD\|236131
NC_009338.1\|WP_011894697.1\|4107905_4108904_+\|NAD(P)H-nitroreductase	unknown	unknown	gnl\|CDD\|236122
NC_009338.1\|WP_011894699.1\|4109753_4110404_+\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|225107
NC_009338.1\|WP_011894685.1\|4092909_4093953_-\|NUDIX-domain-containing-protein	unknown	unknown	gnl\|CDD\|240041
NC_009338.1\|WP_011894690.1\|4097270_4099358_-\|threonine--tRNA-ligase	unknown	unknown	gnl\|CDD\|237050
NC_009338.1\|WP_011894692.1\|4099869_4100520_-\|PaaI-family-thioesterase	unknown	unknown	gnl\|CDD\|239527

Protein	Function_ID	Function_description	E-value
NC_009338.1\|WP_011894705.1\|4115806_4116634_+\|carbohydrate-ABC-transporter-permease	gnl\|CDD\|223472	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism].	4.63865e-82
NC_009338.1\|WP_193373628.1\|4096061_4096706_-\|CDP-alcohol-phosphatidyltransferase-family-protein	gnl\|CDD\|223632	COG0558, PgsA, Phosphatidylglycerophosphate synthase [Lipid metabolism].	4.66141e-27
NC_009338.1\|WP_193373590.1\|4106079_4107792_-\|GAF-domain-containing-sensor-histidine-kinase	gnl\|CDD\|226951	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms].	3.06113e-44
NC_009338.1\|WP_011894689.1\|4096720_4097269_-\|HIT-domain-containing-protein	gnl\|CDD\|238606	cd01275, FHIT, FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours.	6.79578e-63
NC_009338.1\|WP_011894686.1\|4093949_4095080_-\|glycosyltransferase-family-4-protein	gnl\|CDD\|340831	cd03801, GT4_PimA-like, phosphatidyl-myo-inositol mannosyltransferase. This family is most closely related to the GT4 family of glycosyltransferases and named after PimA in Propionibacterium freudenreichii, which is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIM) which are early precursors in the biosynthesis of lipomannans (LM) and lipoarabinomannans (LAM), and catalyzes the addition of a mannosyl residue from GDP-D-mannose (GDP-Man) to the position 2 of the carrier lipid phosphatidyl-myo-inositol (PI) to generate a phosphatidyl-myo-inositol bearing an alpha-1,2-linked mannose residue (PIM1). Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in certain bacteria and archaea.	2.38169e-68
NC_009338.1\|WP_011894700.1\|4110422_4111412_-\|nitroreductase-family-protein	gnl\|CDD\|236122	PRK07877, PRK07877, Rv1355c family protein.	1.19444e-21
NC_009338.1\|WP_011894704.1\|4114877_4115810_+\|sugar-ABC-transporter-permease	gnl\|CDD\|224096	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism].	3.94712e-78
NC_009338.1\|WP_011894703.1\|4113570_4114881_+\|extracellular-solute-binding-protein	gnl\|CDD\|270453	cd14750, PBP2_TMBP, The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold. This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 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.	3.06855e-79
NC_009338.1\|WP_011894706.1\|4116638_4117868_+\|sn-glycerol-3-phosphate-ABC-transporter-ATP-binding-protein-UgpC	gnl\|CDD\|236947	PRK11650, ugpC, sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC.	6.67417e-174
NC_009338.1\|WP_011894693.1\|4100577_4101075_+\|DUF1990-domain-containing-protein	gnl\|CDD\|378157	pfam09348, DUF1990, Domain of unknown function (DUF1990). This family of proteins are functionally uncharacterized.	1.55095e-62
NC_009338.1\|WP_011894691.1\|4099444_4099873_-\|TIGR02611-family-protein	gnl\|CDD\|131660	TIGR02611, Putative_membrane_protein, TIGR02611 family protein. Members of this family are Actinobacterial putative proteins of about 150 amino acids in length with three apparent transmembrane helix and an unusual motif with consensus sequence PGPGW. [Hypothetical proteins, Conserved].	3.37763e-25
NC_009338.1\|WP_011894701.1\|4111474_4113139_-\|glycoside-hydrolase-family-13-protein	gnl\|CDD\|200471	cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), trehalose synthase (also called maltose alpha-D-glucosyltransferase), and related proteins. Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. Trehalose synthase (EC 5.4.99.16) catalyzes the isomerization of maltose to produce trehalulose. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.	0
NC_009338.1\|WP_011894698.1\|4108897_4109722_+\|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.	6.25831e-19
NC_009338.1\|WP_013471922.1\|4101273_4101990_+\|GAF-and-ANTAR-domain-containing-protein	gnl\|CDD\|377145	pfam03861, ANTAR, ANTAR domain. ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil.	1.03039e-16
NC_009338.1\|WP_011894687.1\|4095111_4096065_-\|phosphatidylinositol-mannoside-acyltransferase	gnl\|CDD\|236131	PRK07920, PRK07920, lipid A biosynthesis lauroyl acyltransferase; Provisional.	2.45037e-167
NC_009338.1\|WP_011894697.1\|4107905_4108904_+\|NAD(P)H-nitroreductase	gnl\|CDD\|236122	PRK07877, PRK07877, Rv1355c family protein.	6.27062e-15
NC_009338.1\|WP_011894699.1\|4109753_4110404_+\|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].	2.62601e-66
NC_009338.1\|WP_011894685.1\|4092909_4093953_-\|NUDIX-domain-containing-protein	gnl\|CDD\|240041	cd04685, Nudix_Hydrolase_26, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.	1.97325e-39
NC_009338.1\|WP_011894690.1\|4097270_4099358_-\|threonine--tRNA-ligase	gnl\|CDD\|237050	PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.	0
NC_009338.1\|WP_011894692.1\|4099869_4100520_-\|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).	1.48419e-09

>NC_009338.1|WP_013471922.1|4101273_4101990_+|GAF-and-ANTAR-domain-containing-protein
MNDSADVEAAHLRVAELVQGLHNRPDADSDTVVAELAEHAAAEIPGAQYAGITLTRNAKHVETPAATHHWPLLLDKIQQRYLEGPCLTAAWEEQTVHVRDLQTEERFPNYRRDALAETPIRSIMAFQLFIADESLGALNVYSEEPDVFGSEARTLGLIFAAHSSVAWNSARREAQFRRALESRDVIGQAKGMIMERYRVDAVRAFELLRKLSQDSNVPLSKVAADLVAQAQTSNGQTG
>NC_009338.1|WP_011894693.1|4100577_4101075_+|DUF1990-domain-containing-protein
MKLTDLAGKSLTYTEVGATAGALPAGYHHVNKSAVIGRGRERFERAGNDGMQWGMLRGAGLRVEATTAVAEVGAEVLVHLGPVVAPCRVVYVVDEQDRRGFAYGTLPGHAEAGEELFLVRYDPSTDLVHAEVRAFSRHATWWSRLGAPLTSAIQRAVTDRYLRAL
>NC_009338.1|WP_011894692.1|4099869_4100520_-|PaaI-family-thioesterase
MSTNDAAEAHTGTGFDAHVGGGFNPPRPTDRGGPDYGRFVEAVRTLQDHTRAADAPDDVITAAADLIEKASALLAPYDADEWSSPSGRRMDLPNRGNILSPPIDLRVTDGRVVGTACFRRYHLGRNGAAHGGAVAHLFDSLLGFTAFKLSGSKAQRTAFLHVDYRRIALIGAQLQVEAAIDDIVDRKIYVSGRLLDGEHVLADAHSLFVKLKPGQP
>NC_009338.1|WP_011894691.1|4099444_4099873_-|TIGR02611-family-protein
MTDTDKPGFTRRWARRRDRLRERPVVDLTYRISVGVVGLVVLGLGILAIPYPGPGWAIVFLGLAILATEFDWAKRLLGYARRRYDAVMDWFKQQGLWVQALGALFTCAVVVGTLWLFGALAFVGRWFGLEYGWLDSPIGIGS
>NC_009338.1|WP_011894690.1|4097270_4099358_-|threonine--tRNA-ligase
MSAPARPAPAAPIRVTAGTTAGQAVRDAGLPSRGAPDAVVVVRDADGRLRDLSWVPDTDVEVTPVAADTEDGRSVIRHSAAHVLAQAVQEMFPDAKLGIGPPITDGFYYDFDVAEPFTPEHLQALEKKMRKIVKDGQIFERRVFGSKDEARAELASEPYKLELIDDKSGADDPEVMEVGGDELTAYDNLNPRTRERVWGDLCRGPHIPTTRYIPAFTLTRSSAAYWRGDQNNASLQRIYGTAWESQEALDRHLELIEEAQRRDHRKLGVELDLFSFPDELGSGLPVFHPKGGVVRRELEEYSRRKHIEAGYEFVNTPHITKEQLYITSGHLEWYADGMFPPMQIDAEYNEDGTVRKPGQDYYLKPMNCPMHHLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVIHGLTRVRGMTQDDAHIYCTREEMRDELARLLQFVLDLLADYGLDDFYLELSTKDPDKFVGSDDLWEEATETLREVAESSGLALVPDPGGAAFYGPKISVQVRDALGRNWQMSTIQLDFNMPDRFELEYTSSDGTRRRPVLIHRALFGSIERFFGVLTEHYAGAFPVWLAPVQVVGIPVADAHAGYLDGVAAELRRRGIRVEVDASDDRMAKKIVNHTNQKVPFMLLAGDKDVEAGAVSFRFGDRTQINGVPRDQAVEAIVDWVNRRENATPTAELVVLPSGDAQSPVAGEG
>NC_009338.1|WP_011894689.1|4096720_4097269_-|HIT-domain-containing-protein
MDPEDTIVDRGVGDPDRLQRLWTPHRMTYIADAVKGGSAASSEPFSDIPNMSDEDGLVVARGDLVYAVLNLYPYNPGHLMVVPYRRVAELENLTEDESAELMAFTQKAIRVMKTVSRPHGFNVGLNLGTSAGGSLSEHLHMHVVPRWGGDANFITVIGDSKVIPQLLRDTRLLLATEWENQK
>NC_009338.1|WP_193373628.1|4096061_4096706_-|CDP-alcohol-phosphatidyltransferase-family-protein
MTRAAYAKLSRPVAKGALKVGLTPDTVTILGTAGSVLAALTLFPIGQLWWGAVAVSFFVLADMLDGAMARERGGGTRFGAVLDAACDRISDGAVFCGLLWWAAFGLQSAELVVATMICLVSSQVISYIKARAEASGLSGDGGLIERPERLVIVLVGAGLAGFPLFPLPWLLHVAMWLLAVTSLITVGQRLHSVRTSAAAMEPLSVPDKPETTEQ
>NC_009338.1|WP_011894687.1|4095111_4096065_-|phosphatidylinositol-mannoside-acyltransferase
MTRDQGAVRDGGGLLAFPSALAGQLSDWGYAAGWRLVRAAPDILARNTFEAGAVWASRNGGPDQLRRNLARVIGSAPAEVPDSLMRASLASYARYWREAFRLPSMDHAELGRKLWVRDIETVFAALEHGRGAVLALPHSGNWDMAGVWLAQNHGTFATVAERLKPESLYNRFLAYRQSLGFNVVPSSGGERPAYDVVRDWLLDNGIVCLMADRDLSRRGVEVDFFGELSRLPAGPAKLAIETGAPLFPAHCWFDGDGWGCAVYEPIDTSSSDVSAVTQALADRFAANIAAHPEDWHMMQPQWVADLSDERRAHLEGT
>NC_009338.1|WP_011894686.1|4093949_4095080_-|glycosyltransferase-family-4-protein
MRIGMVCPYSFDVPGGVQSHVLQLAEVMRVDGHEVSVLAPASPDAQDSLPDYVVSGGRAVPIPYNGSVARLRFGPATHRLVKKWIQQGRFDVLHLHEPNAPSLSMLALNIASGPIVATFHTSTTKSLTLSVFEPILRPMHEKIVGRIAVSDLARRWQMESLGSDAVEIPNGVDVGSFATAPLLPGYPRTGPTVLFLGRFDEPRKGMAVLLGALPAVVEPFPDVEILVVGRGDEDELRSQAGPLAGHLRFLGQVGDAEKASAMRSADVYCAPNTGGESFGIVLVEAMAAGTAVVASDLDAFRRVLDDGEAGRLVTVDDSAALAQGLVEVLSDAAVRRRYIECATRAVARYDWSVVGKQIMRVYETVAGSGVKVRVES
>NC_009338.1|WP_011894685.1|4092909_4093953_-|NUDIX-domain-containing-protein
MIPWITAVVIAVVVGAVLLILTWAYQTATRLDRLHVRYDLSWQALDGALARRAVVARAVAVEAYGGGPEGRRLAALADAAERAPRASREAAENELSAALARVNPSSLAVAMVAELADAEARVLLARRFHNDAVRDTLALRERPLVRMLRLGGTASLPTYFEIAEAGEMSARELAPARRRTSSRIVLLDEDGAVLLLCGSDPAGADAPTPPPRWWFTIGGATQLGESLAQAAVRELEEETGLAVAPEAMVGPVWRRDAVIDFNGAVIRSEEMYFVHRTRRFEPSDAGRSGLERTYIHDHRWCDATMIGKLVADGENVYPRQLGELLDEANRLADAPDEVPAGPVRSIR
>NC_009338.1|WP_193373590.1|4106079_4107792_-|GAF-domain-containing-sensor-histidine-kinase
MADADDHRARDGARPVRTTLSQLRLRELLTEVQDRVEQIIRGRDRLDGLVEAMLAVTSGLELDETLRTIVHTAIELVDAQYGALGVRGHDQELVEFIYEGIDEPMRERIGHLPEGRGVLGVLINDPKPIRLEDISRHADSVGFPPNHPPMRTFLGVPVRIRDEVFGNLYLTEKSDGQPFSEDDEVLVQALAAAAGIAIDNARLYAQSQARQSWIEATRDIGTELLSGIDPAGVFRRVADRAQKLSGAAATLVAVPDDPDLPVGEVAELTVAASAGETIAAAHDPIPVAGTAIGDAFVHRTPGMTDRADIGIGATVGPALLLPLRAPDAVPGVLIVLRSVGAQPFRSDELDMLAAFADQAAQAWQLASTQHRLRELGILTDRDRIARDLHDHVIQRLFAVGLSLQGSIARARSEEVQQRLSANVDDLQSVIQEIRTAIFDLHGGSSAVTRLRQRLDAAVAAFPESGVRTSMQCAGPLSVVDAGLADHAEAVVREAVSNAVRHAEASTVAVTVTVEDDLAITVTDDGRGIAADVTGSGLANLARRAQDVGGSFSVRRGAQVGTTLTWRAPLP
>NC_009338.1|WP_011894697.1|4107905_4108904_+|NAD(P)H-nitroreductase
MSATQVRIETIIDAVDVACRAPSLHNSQPWRWVATDHGVDLYADPDRMIRAADSTGREALISCGAVLDHFRVAMAAAGWSITVERLPEPSDPRHIASIRFAAATEVTAEQKRRADAILVRRTDRLPLSAPRDWDVPGETGAAGAEPDNPVRVHTVPGHKRDMLVEASQLAEVLRLYDSDYHSELFWWTADFVATEGIPRSALVSAAEGDRVGIGRTFPVTTQPERRGELESDDAAIVVLSTEDDSRESVLRCGEALSAFLLDATMTGLATCTVTHITEVPAGRDVVASVLATTSIPQVLVRVGAAPALDAIPAPTPRRPVHDVLEIRRGATC
>NC_009338.1|WP_011894698.1|4108897_4109722_+|universal-stress-protein
MLDATFVPCIVVGIDGSPAAVDAALWAVDQAVDLDIPLRLVYVIDADNEDAVDPHDQARQLATAEMAVRYALTALESTDQPVKIEVEILRGRPVQTLLEAARSAVLLCLGARGLKHSTQGRIGSTAGAVSTSAHCPVAVVRAHRPHRRPDRAVVIEITDNAGGGAVLERGLDEARRRGAPVRVLTSARSQLDVTGRWERRLAEWRRRYPDLDISAVRARDGLFDYLAAHGDGLQLLVAGRNRPGGVAPLVGTPGNAALRDTDCSILVCEPPNAL
>NC_009338.1|WP_011894699.1|4109753_4110404_+|response-regulator-transcription-factor
MVKVFLVDDHEVVRRGLIDLLGSDPELDVVGEAGSVSEALTRVPTAQPDVAVLDVRLPDGNGIELCRELLSLMPDLRCLMLTSFTSDEAMLDAILAGASGYVVKDIKGMELARAIKEVGSGRSLLDNRAAAALMAKLRGEGERTDPLSGLTDQERVLLDLLGEGLTNKQIAARMFLAEKTVKNYVSRLLAKLGMERRTQAAVFISKLDRGHGAGNA
>NC_009338.1|WP_011894700.1|4110422_4111412_-|nitroreductase-family-protein
MNAHFPDAETLRSALSLANRAPSVHNSQPWQWRVGHESVHLYANPDLLLPHTDPDARDLMLSCGAALHHCVVALAALGWQAKIHRFPNPAEPDHLAALELRRYPAADLDVTLAAAIPRRRTDRRYYSSWPVPQGDVALMGARAARAGVALRRVDDLAGLKRLVSAAAFQHRTDAGYLTELAAWSGRYAATAGVPARSVPAETAGAVSARAFAGGVLPQTPDTAADQDNAVVLALGTAGDDRLSWLRAGEATSVVLLTATALGLASCPITEPLEIAETREAVRRDVFGADGYPQMLLRVGWAPVNADPLPSTPRRNLSEVVVRLDDSSAE
>NC_009338.1|WP_011894701.1|4111474_4113139_-|glycoside-hydrolase-family-13-protein
MAPKHPWWQTAVVYQVYIRSFADGNGDGIGDIRGLRARVGYLGALGVDAIWINPWYPSPMADAGYDVADYRDIEPAYGTLTEAQDLIDAAHAVGIRVILDIVPNHTSDRHAWFEAALAGDPAARDRYHVRPGRGANGELPPNDWQSVFGGPAWTRITDGPLQGQWYLHLFAPGQPDLNWENPEVRAEFEDILAFWFDRGVDGFRIDVAHGLVKAEGLPDGAQADAPQAMLQVEAQHPAWDQDGVHDIYRGWRSVAQRYTPERIFIAEAWVSSNERLARYLRPDELHTAFQFDFLRSPWRAANLRGVIDDAITSAASVGAPPTWVLSNHDVTRTVTRFSRSQPDHLVETDWERGRWSGEEPDHELGRRRARAAALVQLALPGTAYVYQGEELGLEEIEDLPDDVRQDPTWAQSGFTDVGRDGCRIPLPWNESEPTYGFADGPDAVTWLPQPGHWAEHSVEAQERDPDSMLHLYRAALKLRPSLWRDAGEVTWLDVAAEVAAFDRGGAQCWVNTGTADVTLPAGASVVLASSPGVDGVLPGDTAVWLQTRGKDFLL
>NC_009338.1|WP_011894703.1|4113570_4114881_+|extracellular-solute-binding-protein
MKRNQFARGRRRRAVALASAPLVAASLLSGCGAQSGPPTLTWYILPDNGGSVARAEQCAEASNGAYQVRIESLPSTATAQREQMVRRLAAGDSSIDLVSMDVVFTAEFANAGFLRPYTAEETSRLTAGMLPAPIETGMWEDTLYGAPYKSNAQLLWYRKSAAAAAGVDPASPTFTWDEMLKAAVGQQKKIAVQAQRYEGYTVLINALVLSGGGALLEDVEAGRDAKPSLNTPPGLKAAEIVGTLGRSPAAPTDMSNASEEQARANFQSDQGMFMVNWPYVLAAARSAAEEGTLPQEVVDDIGWARYPRVSPDMPSAPPLGGANLGIGAYTEYPEEAVALVECINAEPKATQYMLDESEPSPYAASYDNPEIRETYENADLIRESIGDGGPRPPTPFYTDISGAIQQTWHPPASVTSETPERTDQFMADVLAGRRLL
>NC_009338.1|WP_011894704.1|4114877_4115810_+|sugar-ABC-transporter-permease
MTAPADAPIQKDPGKPSVSERAKGERRLGLYLTLPSYVVMLLVTAYPLGYALVLSLYNFRLTDPEGRSFVGLGNYLVILTDPIWWNDFVTTLAITVVTVAIELVLGFWFAFVMLRIVRGRGPLRTAILIPYGIVTVVSAFIWRYAFAIDSGFVNQWLNLTDFDWFGDRWSAIFVICLSEIWKTTPFISLLLLAGLVQVPEDMQEAAKVDGATAWQRLWKITLPNMKAAIMVALLFRTLDAWRIFDNPYVMTAGANNTETISFLAYRQNVTLVNLGMGSAVSVLLFLSVVAIAWIFIKVFKTDLSQVRGDQ
>NC_009338.1|WP_011894705.1|4115806_4116634_+|carbohydrate-ABC-transporter-permease
MTKNTKWWTIAGIVIVIYSFVPMLWMISLAFKPPSDIVSGEPSFLPSTVTFDNFAQIFSNPLFTRALINSIGIALVATVISVIIAMFAAYAIARLEFPGKKVLLSLALGIAMFPQAALVGPLFDMWRGLGIYDTWLGLIIPYLTFALPLSIWTMSAFFRQIPWEMEHAAQVDGATQWQAFRKVIVPLAAPGVFTTAILTFFFCWNDFLFAISLTSTDSARTVPAALAFFQGASYFESPVPYIMAASVIVTIPVVILVLVFQRRIVAGLTSGAVKG
>NC_009338.1|WP_011894706.1|4116638_4117868_+|sn-glycerol-3-phosphate-ABC-transporter-ATP-binding-protein-UgpC
MAAITMRNIVKKYGDGYPAVNDVSLDIADGEFVILVGPSGCGKSTLLRMIVGLEDITSGDMMIGDKRVNDMAPRDRNLAMVFQNYALYPHLTVFENIAFPLRLAGKLSDDEIRQRVNDAATTLELGEHLDRKPANLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRTEILRLQRKLGVTTVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYDQPVNLFVAGFIGSPPMNFVPARVTGNEIELPFATVPLRDEWRGSVEEGKVYIAGIRPGAFEDAEFVDTDKASRGVTFDVEIDVTEWLGNEQYAFVPFEATTEISGQLAELANELDSEQLRTQICVELDPLSRVRSGDKATLWLDSERLHLFDPHSGDNLTRVSHERPREQNPPESRGRHAATAG

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Crispr_ID: NC_009338_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009338_3

4160507-4160585

Unclear

Consensus_repeat	Method
GTAACGAACTGACGAACTGACTCA	CRISPRCasFinder

1 spacers

Cas9_archaeal,csa3

The CRISPR arrays of NC_009338_3

>merge|NC_009338|3|4160507-4160585|CRISPRCasFinder
GTAACGAACTGACGAACTGACTCAGCAGAGTCCGTTGACGAACTGGCAACGAACTGCAACGAACTGACGAACTGACTCA

>NC_009338|3|3|4160507-4160585|CRISPRCasFinder
GTAACGAACTGACGAACTGACTCA	GCAGAGTCCGTTGACGAACTGGCAACGAACT
GCAACGAACTGACGAACTGACTCA

Protein	Signature genes	Signature genes Name	Protein_function
NC_009338.1\|WP_011894751.1\|4165651_4165996_-\|DUF3703-domain-containing-protein	unknown	unknown	gnl\|CDD\|372144
NC_009338.1\|WP_011894753.1\|4166724_4167054_-\|winged-helix-turn-helix-transcriptional-regulator	csa3	COG0640_csa3_CAS-I-A	gnl\|CDD\|238042
NC_009338.1\|WP_011894755.1\|4167860_4168280_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_049777447.1\|4167310_4167604_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894752.1\|4166023_4166713_-\|cation-transporter	unknown	unknown	gnl\|CDD\|223131
NC_009338.1\|WP_011894738.1\|4151926_4152682_+\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|223816
NC_009338.1\|WP_041800184.1\|4155774_4156014_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_041800186.1\|4157179_4158325_-\|phage-major-capsid-protein	unknown	unknown	gnl\|CDD\|377449
NC_009338.1\|WP_011894756.1\|4168300_4168657_-\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|197666
NC_009338.1\|WP_041800190.1\|4163644_4163938_-\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894748.1\|4162940_4163342_-\|HNH-endonuclease	Cas9_archaeal	cas9_archaeal	gnl\|CDD\|372995
NC_009338.1\|WP_011894746.1\|4160164_4160413_-\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894749.1\|4163338_4163536_-\|excisionase-family-DNA-binding-protein	unknown	unknown	gnl\|CDD\|200128
NC_009338.1\|WP_081437677.1\|4158789_4159053_-\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_013471963.1\|4154917_4155331_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894742.1\|4156010_4156232_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894740.1\|4153829_4154513_-\|DUF305-domain-containing-protein	unknown	unknown	gnl\|CDD\|367619
NC_009338.1\|WP_011894750.1\|4164150_4165290_-\|tyrosine-type-recombinase/integrase	unknown	unknown	gnl\|CDD\|271189
NC_009338.1\|WP_011894745.1\|4159491_4160073_-\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894739.1\|4152678_4153821_+\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|182539

Protein	Function_ID	Function_description	E-value
NC_009338.1\|WP_011894751.1\|4165651_4165996_-\|DUF3703-domain-containing-protein	gnl\|CDD\|372144	pfam12487, DUF3703, Protein of unknown function (DUF3703). This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.	3.44423e-45
NC_009338.1\|WP_011894748.1\|4162940_4163342_-\|HNH-endonuclease	gnl\|CDD\|372995	pfam14279, HNH_5, HNH endonuclease. This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.	4.83809e-12
NC_009338.1\|WP_011894753.1\|4166724_4167054_-\|winged-helix-turn-helix-transcriptional-regulator	gnl\|CDD\|238042	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.	2.43864e-17
NC_009338.1\|WP_011894749.1\|4163338_4163536_-\|excisionase-family-DNA-binding-protein	gnl\|CDD\|200128	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General].	5.61996e-08
NC_009338.1\|WP_011894752.1\|4166023_4166713_-\|cation-transporter	gnl\|CDD\|223131	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism].	3.34066e-19
NC_009338.1\|WP_011894738.1\|4151926_4152682_+\|response-regulator-transcription-factor	gnl\|CDD\|223816	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].	2.82914e-79
NC_009338.1\|WP_011894740.1\|4153829_4154513_-\|DUF305-domain-containing-protein	gnl\|CDD\|367619	pfam03713, DUF305, Domain of unknown function (DUF305). Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices.	3.7097e-53
NC_009338.1\|WP_011894750.1\|4164150_4165290_-\|tyrosine-type-recombinase/integrase	gnl\|CDD\|271189	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons. This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.	4.30188e-27
NC_009338.1\|WP_011894756.1\|4168300_4168657_-\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|197666	smart00342, HTH_ARAC, helix_turn_helix, arabinose operon control protein.	1.09749e-21
NC_009338.1\|WP_041800186.1\|4157179_4158325_-\|phage-major-capsid-protein	gnl\|CDD\|377449	pfam05065, Phage_capsid, Phage capsid family. Family of bacteriophage hypothetical proteins and capsid proteins.	1.39404e-09
NC_009338.1\|WP_011894739.1\|4152678_4153821_+\|ATP-binding-protein	gnl\|CDD\|182539	PRK10549, PRK10549, two-component system sensor histidine kinase BaeS.	2.78792e-62

>NC_009338.1|WP_011894746.1|4160164_4160413_-|hypothetical-protein
MTPKPAPFDCALCDTRIGRDRPHLIVGTNTVHIRCAEQRSAHNTIYPDCHIRWHDVWDHPLQTATRGGADQLLRPDHTEEIA
>NC_009338.1|WP_011894745.1|4159491_4160073_-|hypothetical-protein
MTTNPTNPSLEDIDLLSTTATEILRRRIEQIDRDRGHQPEFLAMAREDADTARREALAAEPWADCWKAIPMTDAGTGEMTGMMALPTINGKELWGARAAFDFLDAGEDREKIEEVLSRYFSALDGNTEHLFFIFSAALCTIAEHVVPAMLDKLEHDASDYRSRVMLADAAANAWRTRVGDDLCGPGDQESGEK
>NC_009338.1|WP_081437677.1|4158789_4159053_-|hypothetical-protein
MSDLDLAITPNHQQLAARGALAAIGLDSPRIDLVLSEIRDGGMDDALAVIAVLIRNLSTALVTVNGATAARLVLERTILDAQAAGDE
>NC_009338.1|WP_041800186.1|4157179_4158325_-|phage-major-capsid-protein
MSRKEALKQRYEQLRPQVAQAQQVAEKAYSQNRSMTVEEKAFFDPVMSQLKDIERALAEVAAEEKTLDFAKKVGREVGASDSYGDAGSRQQFAFKRMAPEVVRKINRGAEGEKALATSGSVVVGQEFEASPVELGRPANSLLAVLPSKIRSVGEYAYLRQSVRTNNAAVVADGGTKPTSVYTTVRVEDKLDVVAHLSEGVPRYWFKDNDTLEQFIADELLYGLEKAVEAMALADIDGTSGIQTQAYATSPLVTLRKTLTKLETVGHAASAFVMHANDWEAIELALSSANTIEYRGLPYDASARRLYGVPVVVSLAQAEGVAHTLGEGAARLETDDEGVGVQWSESSNADDFAKNLIRARCEGRFATSVMRPLAVVKADLTA
>NC_009338.1|WP_011894742.1|4156010_4156232_+|hypothetical-protein
MTIDPEQVFEVARAAIIREVRDALGVLRADELTTRELIALANILTPAYERRQAREATPAPLLQMVHRKRRGKR
>NC_009338.1|WP_041800184.1|4155774_4156014_+|hypothetical-protein
MSTTRYPVDSTTRRCCGGIGRHSRTCPTRQVTDHPAVVHTVGSAIVVDQLDGAPLNSDQARELASALLVAAAEVDGRQR
>NC_009338.1|WP_013471963.1|4154917_4155331_+|hypothetical-protein
MNRWIWAAAAGASAAMLTSPTATADLVGFTSPSGNIGCILTDEMVRCDIASRSWDPPPRPADCPDVTGYGQGITLSPTGPAAFVCAGDTTLGSGPALPFGQYEAGGGMSCNSEPSGMRCSNSDGHGFVLAREAYQVF
>NC_009338.1|WP_011894740.1|4153829_4154513_-|DUF305-domain-containing-protein
MQHRGFRFGFAAIAASALVVSACSNGSTDSSSDSATTSAAASATSSVASGATAHNGSDVMFAQGMIPHHQQAIEMSDMLLGKQDIDPEVVSLAEQIKSAQGPEIEQMQGWLQEWGVGSTPPGDGTMPGHHMPDHQMPHGGGMGPMPGMPAGGHGMMSQADMTALQNAQGPEAGRLFLTQMITHHEGAIMMAQREIESGQFPAAVDMARSIISSQQSEIDQMRAMLAG
>NC_009338.1|WP_011894739.1|4152678_4153821_+|ATP-binding-protein
MSVTRRSPAASTRRWRRPGIGLRLLAAQAIVLAVGAATTAVVAAVVGPPLFQEHLHRAGVPMNSPEEMHAEEAYGYATVMSIGGALAVSALAALAVSVYVSRRLQRSVTEVACAAALVAEGRYDIRVSPPRLGDDFDALATAFNQMASRLQSVESTRRRLFGDLAHEIRTPVAVLDAYVEALEDGVRTLNPDTVAVLRDQTGRLVRFSGDVAALAKAEESSVTMTYTEVDLDGLVRRAVAAARERYETKGVALQVMSARELPLLRADEQRLSQVLDNLLDNALRHTARGGRVEIHCHTEGARVRIAVTDDGEGIAAEHLSSVFERFYRADAARDREHGGAGLGLAIAKALVEAHGGSVTAASDGAGTGATFTVELPTTRP
>NC_009338.1|WP_011894738.1|4151926_4152682_+|response-regulator-transcription-factor
MSTMDHPQGSPSEHSRGYRALVVDDEVPLAEVVASYLQREQFDAVVADNGVDAIALARDFDPDVVILDLGLPGIDGLEVCRSLRTFSDAYVVMLTARDTELDTVLGLTVGADDYVTKPFSPRELVARIRAMLRRPRLLQSPPTGADREVTPPRRFGALSIDVAAREVRIADDPILLTRTEFDILQALSGRPGIVLSRRQLLEIIRDEPWVGNDQLVDVHIGHLRRKLGDDAARPRYIATVRGVGYRMGTGA
>NC_009338.1|WP_011894748.1|4162940_4163342_-|HNH-endonuclease
MSRRQGITPAVYNTVMDRGNGLCRYCEFPASEIDHIVPVARGGGNDLANLVPACRECNSEKRDLLPEEWADKRRADGKPWPIPTFIQRVKFLCHWYLPASQRHKGRFTLREPEKFRGLVVAARDCAELDGGAA
>NC_009338.1|WP_011894749.1|4163338_4163536_-|excisionase-family-DNA-binding-protein
MAETLATRRRYAKLTEAADYLGVTDRTIRQMIADGRLTGYRSGKRLVRVDLNEIDDAMQPFGGAA
>NC_009338.1|WP_041800190.1|4163644_4163938_-|hypothetical-protein
MDSTAAKIIDLIATPATPGGPSLRDQWGRTAIEVRDYEDPVARSEEFELELQGGRDPNQPSEVPMAVRTIQPYVIPLFGEDGRIGLRQIVTRLEKRR
>NC_009338.1|WP_011894750.1|4164150_4165290_-|tyrosine-type-recombinase/integrase
MARGTGRKDRAPGTFGSVDKLATGYRARYFGPDGRRHKAPVLFLTKTDARAWLAQRHSEIVAQQWTPPNAVEVPKTTFTEYADQWLLTRQVAGRPLKDRTREHYQALLDDHITATFGALPLASITADDVRQWYARTLTDKPTMRSHAYGLLRTILATAVSDGKISVNPCSIRGAGTAKRVHKVRPATVGEIGTIADAMPAQWSLMVLLAAWLAMRFGELTELRRKDIDLADEVVRVRRAVVRTDDGFKVTTPKSDAGIRDIAIPPHLIPPIEAHLSQHVGAKADALLFPAVGGGHLAPATLYRRFYTARERANRKDLRWHDLRHSGAVLAAATGATLAELMARLGHSTPQAALRYQHAAQGRDRQIAALLSKIAENGGA
>NC_009338.1|WP_011894751.1|4165651_4165996_-|DUF3703-domain-containing-protein
MTRISAQARAVYDTEMQAARATASADQRWHHLERAHIVSQPFAWLHTRNHIAMLRLALTQHDRREAFGQVIRILVAAPGSLTGRYPEGNTGRVAAGLTTPMPVPRDLAAVMRSA
>NC_009338.1|WP_011894752.1|4166023_4166713_-|cation-transporter
MTDPAAEELKPLIASSAGCTDAGCTATAATVSPARRAVLTRRVRLFVLATITYNLIEAVVAISAGTIASSAALIGFGLDSLIEVASATAVAWQFAGRDPEERERTALRIIAVSFFALATYVTVESARALFGAAEAAPSPAGIVLAAVSLAVMPFLSYAQRRAGRELGSASAVADSKQTLLCTYLSGVLLVGLLLNALFGWSWADPIVALVIAGVAVKEGRQAWRGEHCC
>NC_009338.1|WP_011894753.1|4166724_4167054_-|winged-helix-turn-helix-transcriptional-regulator
MRTVFHGDALARFGHALSDPVRARLLLALREGPGYPAELADVLGATRQNVSNHLACLRGCGLVVAAPEGRRMRYELADVRLAHALGALLELVLVTDPSACPASPADDCC
>NC_009338.1|WP_049777447.1|4167310_4167604_+|hypothetical-protein
MQQIGHGGQPLRPVFRRVHPPHRVLIDLVALFPREAHCDGRYHPKGLQMDSIVEGRLTCWGLSEQGRWWGLVTYPITHGGQKDSVTHWVPASVLRLK
>NC_009338.1|WP_011894755.1|4167860_4168280_+|hypothetical-protein
MIRKMLVASALGAALCCAPVASAQPGPIYWDDPVRYSTDVPGMNYDAHLTGPCTNMDRFTFGRGPGGEALQCRWIPNQWPPIYTGFWQTSYELFGVQDIGAPCPKPQSAAQAPDGRPLVCLGAQGWQAGKYNGVGFTPM
>NC_009338.1|WP_011894756.1|4168300_4168657_-|helix-turn-helix-transcriptional-regulator
MMRANDKTTIQPRMLRRALDFMHENAQYDITIRDIASAADVTPRAIQYAFREHLDTTPLEYLRRIRLERAHRELMSADPSFDTVTSIAGRCGFSHPGRFSSAYKQVFGTEPSRTLRSS

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Crispr_ID: NC_009338_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009338_4

4292367-4292501

Orphan

Consensus_repeat	Method
CGGGGACCGCCACCGGGACGCGGACCACCG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_009338_4

>merge|NC_009338|4|4292367-4292501|CRISPRCasFinder
CGCGGGCCTGCACCGGGACGGGGGCCACCACCCGGGCGGGGACCGCCACCGGGACGCGGACCACCGACGGGACGGGGCGGCATGTTGCCGGGCGTCGCGCCGGGACGGGGACCGCCACCGGGGCGCGGACCACCG

>NC_009338|4|4|4292367-4292501|CRISPRCasFinder
CGCGGGCCTGCACCGGGACGGGGGCCACCA	CCCGGGCGGGGACCGCCACCGGGACGCGGACCACCGACGGGACGGGGCGGCATGTTGCCGGGCGTCGCGCCGGGA
CGGGGACCGCCACCGGGGCGCGGACCACCG

Protein	Signature genes	Signature genes Name	Protein_function
NC_009338.1\|WP_011894880.1\|4281542_4282490_-\|metallophosphoesterase	unknown	unknown	gnl\|CDD\|224327
NC_009338.1\|WP_011894885.1\|4286691_4287303_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|369777
NC_009338.1\|WP_193373592.1\|4288798_4289809_-\|bifunctional-oligoribonuclease/PAP-phosphatase-NrnA	unknown	unknown	gnl\|CDD\|223691
NC_009338.1\|WP_011894882.1\|4283253_4284888_+\|CocE/NonD-family-hydrolase	unknown	unknown	gnl\|CDD\|225487
NC_009338.1\|WP_011894898.1\|4301062_4302427_-\|cobyrinate-a,c-diamide-synthase	unknown	unknown	gnl\|CDD\|234896
NC_009338.1\|WP_011894886.1\|4287486_4288806_-\|MATE-family-efflux-transporter	unknown	unknown	gnl\|CDD\|240541
NC_009338.1\|WP_011894897.1\|4299854_4301066_-\|uroporphyrinogen-III-C-methyltransferase	unknown	unknown	gnl\|CDD\|381169
NC_009338.1\|WP_011894899.1\|4302524_4303139_-\|cob(I)yrinic-acid-a,c-diamide-adenosyltransferase	unknown	unknown	gnl\|CDD\|235662
NC_009338.1\|WP_011894888.1\|4289783_4290290_-\|30S-ribosome-binding-factor-RbfA	unknown	unknown	gnl\|CDD\|234787
NC_009338.1\|WP_011894893.1\|4295385_4295910_+\|hypothetical-protein	unknown	unknown	unknown
NC_009338.1\|WP_011894891.1\|4293617_4294679_-\|transcription-termination/antitermination-protein-NusA	unknown	unknown	gnl\|CDD\|237061
NC_009338.1\|WP_011894881.1\|4282643_4283246_+\|DUF3558-family-protein	unknown	unknown	gnl\|CDD\|378803
NC_009338.1\|WP_011894884.1\|4285737_4286550_+\|enoyl-CoA-hydratase	unknown	unknown	gnl\|CDD\|235733
NC_009338.1\|WP_011894896.1\|4298189_4299821_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|129794
NC_009338.1\|WP_011894895.1\|4296395_4298162_-\|proline--tRNA-ligase	unknown	unknown	gnl\|CDD\|236405
NC_009338.1\|WP_011894894.1\|4295906_4296392_+\|ferritin-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|373114
NC_009338.1\|WP_011894890.1\|4293187_4293550_-\|YlxR-family-protein	unknown	unknown	gnl\|CDD\|377288
NC_009338.1\|WP_013472051.1\|4285472_4285739_-\|DUF2277-domain-containing-protein	unknown	unknown	gnl\|CDD\|378364
NC_009338.1\|WP_011894892.1\|4294681_4295218_-\|ribosome-maturation-factor-RimP	unknown	unknown	gnl\|CDD\|234627
NC_009338.1\|WP_011894883.1\|4284876_4285476_-\|DUF1802-family-protein	unknown	unknown	gnl\|CDD\|370138

Protein	Function_ID	Function_description	E-value
NC_009338.1\|WP_011894880.1\|4281542_4282490_-\|metallophosphoesterase	gnl\|CDD\|224327	COG1409, Icc, Predicted phosphohydrolases [General function prediction only].	1.90561e-37
NC_009338.1\|WP_011894885.1\|4286691_4287303_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|369777	pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases.	6.11764e-24
NC_009338.1\|WP_193373592.1\|4288798_4289809_-\|bifunctional-oligoribonuclease/PAP-phosphatase-NrnA	gnl\|CDD\|223691	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only].	1.1386e-64
NC_009338.1\|WP_011894882.1\|4283253_4284888_+\|CocE/NonD-family-hydrolase	gnl\|CDD\|225487	COG2936, COG2936, Predicted acyl esterases [General function prediction only].	5.68743e-101
NC_009338.1\|WP_011894898.1\|4301062_4302427_-\|cobyrinate-a,c-diamide-synthase	gnl\|CDD\|234896	PRK01077, PRK01077, cobyrinate a,c-diamide synthase.	0
NC_009338.1\|WP_011894886.1\|4287486_4288806_-\|MATE-family-efflux-transporter	gnl\|CDD\|240541	cd13136, MATE_DinF_like, DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli DinF is a membrane protein that has been found to protect cells against oxidative stress and bile salts. The expression of DinF is regulated as part of the SOS system. It may act by detoxifying oxidizing molecules that have the potential to damage DNA. Some member of this family have been reported to enhance the virulence of plant pathogenic bacteria by enhancing their ability to grow in the presence of toxic compounds. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR).	2.52047e-94
NC_009338.1\|WP_011894897.1\|4299854_4301066_-\|uroporphyrinogen-III-C-methyltransferase	gnl\|CDD\|381169	cd11642, SUMT, Uroporphyrin-III C-methyltransferase (also known as S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT). SUMT is an enzyme of the cobalamin and siroheme biosynthetic pathway. It catalyzes the first of three steps leading to the formation of siroheme from uroporphyrinogen III; it transfers two methyl groups from S-adenosyl-L-methionine to the C-2 and C-7 atoms of uroporphyrinogen III to yield precorrin-2 via the intermediate formation of precorrin-1. Precorrin-2 is also a precursor for the biosynthesis of vitamin B12, coenzyme F430, siroheme and heme d1. This family includes proteins in which the SUMT domain is fused to other functional domains, such as to a uroporphyrinogen-III synthase domain to form bifunctional uroporphyrinogen-III methylase/uroporphyrinogen-III synthase, or to a dual function dehydrogenase-chelatase domain, as in the case of the multifunctional S-adenosyl-L-methionine (SAM)-dependent bismethyltransferase/dehydrogenase/ferrochelatase CysG, which catalyzes all three steps that transform uroporphyrinogen III into siroheme.	3.73289e-101
NC_009338.1\|WP_011894899.1\|4302524_4303139_-\|cob(I)yrinic-acid-a,c-diamide-adenosyltransferase	gnl\|CDD\|235662	PRK05986, PRK05986, cob(I)yrinic acid a,c-diamide adenosyltransferase.	7.29513e-115
NC_009338.1\|WP_011894888.1\|4289783_4290290_-\|30S-ribosome-binding-factor-RbfA	gnl\|CDD\|234787	PRK00521, rbfA, 30S ribosome-binding factor RbfA.	1.86031e-44
NC_009338.1\|WP_011894891.1\|4293617_4294679_-\|transcription-termination/antitermination-protein-NusA	gnl\|CDD\|237061	PRK12327, nusA, transcription elongation factor NusA; Provisional.	0
NC_009338.1\|WP_011894881.1\|4282643_4283246_+\|DUF3558-family-protein	gnl\|CDD\|378803	pfam12079, DUF3558, Protein of unknown function (DUF3558). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 177 to 195 amino acids in length.	1.86435e-06
NC_009338.1\|WP_011894884.1\|4285737_4286550_+\|enoyl-CoA-hydratase	gnl\|CDD\|235733	PRK06190, PRK06190, enoyl-CoA hydratase; Provisional.	3.14662e-145
NC_009338.1\|WP_011894896.1\|4298189_4299821_-\|MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	1.93618e-58
NC_009338.1\|WP_011894895.1\|4296395_4298162_-\|proline--tRNA-ligase	gnl\|CDD\|236405	PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.	0
NC_009338.1\|WP_011894894.1\|4295906_4296392_+\|ferritin-like-domain-containing-protein	gnl\|CDD\|373114	pfam14530, DUF4439, Domain of unknown function (DUF4439). This domain has a ferritin-like fold.	1.78864e-33
NC_009338.1\|WP_011894890.1\|4293187_4293550_-\|YlxR-family-protein	gnl\|CDD\|377288	pfam04296, DUF448, Protein of unknown function (DUF448).	3.27448e-22
NC_009338.1\|WP_013472051.1\|4285472_4285739_-\|DUF2277-domain-containing-protein	gnl\|CDD\|378364	pfam10041, DUF2277, Uncharacterized conserved protein (DUF2277). Members of this family of hypothetical bacterial proteins have no known function.	2.25651e-31
NC_009338.1\|WP_011894892.1\|4294681_4295218_-\|ribosome-maturation-factor-RimP	gnl\|CDD\|234627	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed.	1.20933e-41
NC_009338.1\|WP_011894883.1\|4284876_4285476_-\|DUF1802-family-protein	gnl\|CDD\|370138	pfam08819, DUF1802, Domain of unknown function (DUF1802). The function of this family is unknown. This region is found associated with a pfam04471 suggesting they could be part of a restriction modification system..	2.97965e-63

>NC_009338.1|WP_011894888.1|4289783_4290290_-|30S-ribosome-binding-factor-RbfA
MPDPARAKRLAKRISTIVASAIEYEIKDPRLAGVTITDAKVTNDLHDATLYYTVLGRSLDEEPDYEGAAAGLEKAKGVLRTKVGASLGVRFTPTLAFARDTVPDAAHRMEALLAQARAADEDLARVREGAKHAGDSDPYRVLGEGDLEGPATGGPDVEDEGGANSHDR
>NC_009338.1|WP_193373592.1|4288798_4289809_-|bifunctional-oligoribonuclease/PAP-phosphatase-NrnA
MAPTRTIAESTTDGRAAGGHVDARAAAELLAAACSVSIVCHVFPDADTIGAGLALALVLDEAGKSVEVSFAEPDTLPDSLRSLPGGHLLVPPATMRRDADLVVTVDIPSVNRLGALRDLADGDRDVLVIDHHASNQLFGTANLVDAGADSTTMLVAELLDAWDKPLGLDVAHCLYAGLTTDTGSFRWASARAHRLAARLVEAGVDNAAVSRTLMDTHPFAWLPMLSRVLGSAELVADAVGGRGFVYAIVGHDEWANARSEEVESIIDIVRTTAQAEVAAVLKEIEPQRWSASLRSKSVDVSAVAATFGGGGHRLAAGFTATGSADDVVAALRTALG
>NC_009338.1|WP_011894886.1|4287486_4288806_-|MATE-family-efflux-transporter
MADPVAPATGRRIAGLAFPALGVLAAEPVYLLFDLAIVGRLGALSLAGLAIGALIMGVLSSQLTFLSYGTTARAARFYGAGDRNAAVEEGVQATWLAVGIGTVIVAAVQVTAVPLVSALAAGGEIAETALPWVRIASLAVPAILIAAAGNGWMRGVQDTMRPLRYVVVGFGLSAVLCPLLVFGWLGCPELGLPGSAVANVAGQYLAAALFCRALFVEKVPLRVRPAVLRAQVVMGRDLILRTMAFQACFISAGAVAARFGAASVAAHQVVLQLWSFLALVLDSLAIAAQSLVGAALGAGQLTHAKAVAWRVTIFSAVAGVVLAVVFALGSQLIPSAFTDDQSVLDRIGVPWWFLVAQLPVAGIVFAIDGVLLGAGDATFMRNATLASALAGFLPLVWLSLAFGWGLLGIWAGLSTFMVLRLVFVGWRALSGRWLVPGTR
>NC_009338.1|WP_011894885.1|4286691_4287303_+|class-I-SAM-dependent-methyltransferase
MDGSERPVNHHGDHPGFSGLTGQLCAVAFLLTGRETGRLAADLTAVSATDHVLDIGCGPGNACRIAAARGARVTGVDPSAAMLRVARIVTHGASVTWVRGGAEALPVPDAGATVAWALATVHHWPDVDAGLAEIHRALGPGARFLAVERQTEPDATGISSHGWTGAQAETFAAMCESAGLTTVRVGSGRAGKRRVWTVHATRP
>NC_009338.1|WP_011894884.1|4285737_4286550_+|enoyl-CoA-hydratase
MDTTIGASAGGRYGERVSTSTDVLLVDTRDRIQTLTLNRPGSRNALSAALRSRLFEALRQAQADDEVDVVILTGADPVFCAGLDLKELGDTTELPDISPKWPPMTKPVIGAINGAAVTGGLEIALYCDILIASDQARFADTHARVGLLPTWGLSVRLPQKVGVGMARRMSMTGDYLSADEALRCGLVTQVVPHAELQDTARQVATSIVGNNQKAVRALLASYHDIDDAQNGAALWQEAAAAREWMKSTSGDDIAESRSNVIERGRTQVRP
>NC_009338.1|WP_013472051.1|4285472_4285739_-|DUF2277-domain-containing-protein
MCRNITELRGLEPAATADEIEAAARQYVRKVSGITRPSGANTDAFEAAVAEVTESTRRLLSGLAPRKQPPKTVPPLRRPEVRARLNLA
>NC_009338.1|WP_011894883.1|4284876_4285476_-|DUF1802-family-protein
MTATPVESRGTATPTRPALKEWSAAIHALLDGRQTVLLRKGGIGEKRFDIPAEASGSRFLLFPTVAHSHAERVRPEHRDLLEPAAADSTEDEVVVRAGASVVASIPVERPENLESIAMHHIWTGESVQSDRLDFRPRHRLTALVVATVPLVEPVRLARTPDYRGCSSWVRLPVDPRWGEPVHSEAELDRVARLVRDSVG
>NC_009338.1|WP_011894882.1|4283253_4284888_+|CocE/NonD-family-hydrolase
MSSELARRARRALSRVFDLPPPVCDFVVHRELRVPMRDRVELVADHYAPHTASPAGTLLVRGPYGRGLPFATMFASFYAARGYHVVFQSVRGTFGSGGEFDPFVNEVDDGADTAAWLRDQPWFTGTFATIGLSYLGFTQWALLTDPPPELAAAVITVGPDDVSGPRWGAGSFGLNDFLGWSDLVGRQEDPNRVRTLLRQARAQRRVTSASLRLPLAAASRELLGDGALWFESWLDHPDTDDPFWTRLRLRDGLERAEVPVLLLTGWQDLFVDQTVEHYRMLAGRGVPTGLTIGPWTHGDMMTKAAPTMLRESLDWLATHLKGEPPQRRSPVRIHLSRRGWLNLPDWPPAMPSLVLHPQPGGGLAPGAPGAADATFVYNPGDPTPTVGGRLLSPVGGYRDDTALARRADVLTFTGTALASDLPVVGVPVLDVAHTCATPHNDLFVRISQVDAHGRSRNVSDGYVASAPDSGTVTVELDPVAWTFPAGSRIRVLIAGGSHPRFLRNLGTGEHAGTATDFATARHTVHLGEGTRLTLPAGPPPPSAD
>NC_009338.1|WP_011894881.1|4282643_4283246_+|DUF3558-family-protein
MVAKLRLFSALCALVAAVVVVCQVNPAGLTTPAGVDLRSTFAPLPDATPPPYASTTIKSPVIDLTDPDPFNPCRDIPLDAVQRIGLAYTPPTQEDSLRCKYDAGNYQMAVETFVWRTYEESLPPDAVELDINGHRAAQFWIMKPTDWNNRWWITCMVAFQTSYGVIQQSLFYSPIYSEPDPDCMQTNLQRAHELSPYYIY
>NC_009338.1|WP_011894880.1|4281542_4282490_-|metallophosphoesterase
MSTDERRPTLWAVSDLHTGHTGNKPVTESLHPASPDDWLIVAGDVAERTDEIRWALDLLRKRFAKVIWIPGNHELWTTQRDPMQIYGKSRYDYLVTMCDEMGIVTPEHPYPVWTEEGGPATIVPMFLLYDYSFLPQGAGTKAEGLAIAREKNIVGTDEYLLSSEPYATRDAWCRDRVNYTRGRLEDLDWMMPTIQVNHFPMVREPCDAMFYPEFSLWCGTTATADWHTRYNAICSVYGHLHIPRTTWYDGVRFEEVSVGYPREWRRRRPYRWLRQILPDPKYPAGYLNEFGGHFQITQEMRDNAAKMQQRIKDRG
>NC_009338.1|WP_011894890.1|4293187_4293550_-|YlxR-family-protein
MIQRETSARMRESTINPFAGPVRTCIGCRRRELAVELLRLVAVDSANGSGNRSSAVTVDAARKLPGRGAWLHPDPGCLQAAIRRRAFGRALRITGSPDITAVSEHLLPQEQPEAPGQENR
>NC_009338.1|WP_011894891.1|4293617_4294679_-|transcription-termination/antitermination-protein-NusA
MNIDMAALHAIEADKGITVDVVVETIKSALLTAYRHTEGHEADAHIDIDRKTGVVKVMARQTDEDGNVLHEWDDTPEGFGRIAATTARQVILQRLRDAENEKNYGEFSAREGDIVAGVIQRDARANARGLVVVRMGSETKGSEGVIPAAEQVPGERYEHGDRLRCYVVGVARGAREPVITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVTSRAPGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDEDPARFVANALSPAKVVSVTVIDEAARAARVIVPDFQLSLAIGKEGQNARLAARLTGWRIDIRSDDADKNGGDGPGGHDRSASRPDAGRGVG
>NC_009338.1|WP_011894892.1|4294681_4295218_-|ribosome-maturation-factor-RimP
MAERSTDFRPGLPSQRQVVELLDGEFARAGYDIEDVVIDAATRPPRIVVIADGDRGLDLDAVAELSRLASEQLDTLDTPPYVLEVTSPGVDRPLTEEKHYRRAQGRLAEVTLADGSTLTGRIGAVQNATVALVVREARSNLTVRDIALDAVVKAVVQVEFSPPSPRELELAGVSGKET
>NC_009338.1|WP_011894893.1|4295385_4295910_+|hypothetical-protein
MLLVPSRPPTLSRRRVLVGAAALAALSVTAAGCGTPPPPPDLDDLTTALDRARSDGDLAAEVATGARGTLADALTTIAAQRAAHAEALSEEIVRLTGHAAPTPSTAAASTTTTSAASVPDPTVDDVIGALRASADSATAAAGSLTGYRAGLLASIAASCTASFTVALAGAGSTP
>NC_009338.1|WP_011894894.1|4295906_4296392_+|ferritin-like-domain-containing-protein
MTSPTPAPTDAALPTRPEDAAAGALFDALAAEHATIYGYGVVSAHSTPELNYLVSAAIAEHRARREAAIALCEQQGVDPAVPEAGYQMPFEVDTPADATNLAVQMEEDAAEAWRAVVEQATDPGVRAFGVTALTECAVTAAQWRAVRGDTTVTVAFPGGSE
>NC_009338.1|WP_011894895.1|4296395_4298162_-|proline--tRNA-ligase
MITRMSELFLRTLRDDPADAEVPSHKLLIRAGYVRPVGPGLYSWLPLGLKVLRKIEHIVRSEMDAIGGQEILFPALLPRAPYETTNRWTEYGDTLFRLQDRRDNDYLLGPTHEEMFTLTVKGEYSSYKDFPLRLYQIQNKYRDEARPRAGILRGREFLMKDSYSFDVDDDGLKNAYHAHREAYQRIFDRLKVRYVIVSAVSGAMGGSASEEFLAESEVGEDTFVRCAQSGYAANVEAVVTTAPDPIPLDGLPEAVVYDTPDTPTIATLVDWANTADLPSFAGRAVTAADTLKNVLLKVREPGGDWELLAIGVPGDREVDDKRLGAALDPAEYAMADDADFAAHPFLKKGYIGPKALLANGVRYLVDPRVVDGTAWITGADETGRHVVDLVAGRDFTPDGTIEAAEVREGDPSPDGAGPLVAARGIEIGHVFQLGRKYADAFNADVLGENGKPVRLTMGSYGIGVSRLVAVIAEQHHDELGLRWPGSVAPFAVHVVIANKDAEARAGATELATALDRAGADVLLDDRTASPGVKFKDAELLGVPWIVVVGRGWADGVVELRDRFSGEKREIPVGPDTTAAEQILAAITG
>NC_009338.1|WP_011894896.1|4298189_4299821_-|MFS-transporter
MTALNDAERAAIQRDAEGRGKRGSDRASGRALPARVTGSGESAGGRGGDAGRRGRTPAWMPSRRFFAAVIAIGGMQLLATMDSTIAIVALPKIQDELGLSDAGRSWVITAYVLTFGGLMLLGGRLGDTIGRKRTFIVGVALFTIASVLCGIAWDEATLVIARLLQGVGAAIASPTALALIATTFPKGPARNAATAVFAAMTGVGSVMGLVVGGALTEVSWRLAFLVNVPIGLIMIYLARKTLRETNRERLKLDAAGALLATMGCTAAVFGFSMGPEAGWMSPVTIGSGIAAVGCLIAFLWVERTAENPVVPFELFLDRNRVATFAAVFLAGGVMFTLTVTIGLYVQDIMGYSALRAGVGFIPFVIALGIGLGVSSALVSKYPPRVLVIGGGVLVLAAMIYGSTLDANIPYFPNLVLPITIGGLGIGMIVVPLMISAIAGVGFDQIGPVSAIALMLQNLGGPVVLAIIQAVITSRTLYLGGTTGPVKDMNAAQMHALDQGYSYGLLWVAAVAVIVGAVALFIGYTAQQVAHAQEVKDAIDAGEL
>NC_009338.1|WP_011894897.1|4299854_4301066_-|uroporphyrinogen-III-C-methyltransferase
MSTYDNAYLVGLRLSGKKVVVVGGGTVAQRRLPLLVSNGADVHVVTKAATPAVEAIDGITLTLREFRDEDLDGAWYVIAATDDPAVNAAIVAGAERRRIFCVRADIAVEGTAVTPATFEYEGLEVGVLAGGEHRRSAAIRTAIREALQQGVVTDESGDAPGVVKGGVALVGGGPGDPELITVRGRRLLAHADVVVADRLAPQELLAELSPEVEVIDASKIPYGRAMAQDAINAVLVDRAKAGKFVVRLKGGDPFVFARGYEEVIACAEAGIPVTVVPGVTSAIAVPALAGVPVTHRGLTHEFVVVSGHLAPDHPESLVNWDALAAMSGTIVLLMAVERIELFVKVLLKGGRPADTPVLVVQHGTTSSQRTLRAGLSEVPERIRSDGIRPPAIVVIGAVAGFGT
>NC_009338.1|WP_011894898.1|4301062_4302427_-|cobyrinate-a,c-diamide-synthase
MSTPAVVIAAPSSGSGKTTVATGLMGALRRAGHRVAPFKVGPDFIDPGYHALATGRPGRNLDPVLVGEPLIGPLYRHGSDDADIAIVEGVMGLFDGRISDGGAGPARGSTAHVAGLLGAPVVLVVDARGQSHSVAALLHGFATFDQTVRLAGVILNRVGSSRHDEVLRQACDHAGVAVLGSIPRADELAVPSRHLGLVTAEEHGRHATAAVAAMTELVARHVDLAAVTAVAGGDVADAPWTPAQFAAGPTATVALAAGKAFTFGYAEHREILCAAGADVVTFDPLCDPLPAHTSALVLPGGFPEEFVTELSANEPVRSQIRALAAAGAPIHAECAGLTYLVDELDGHPMCGVLAGSASFTPSLTLGYRDAVAVAESSLHAVGERVTGHEFHRTAVQFASDRQAAWQYRGRGGAAVEDGAVLGGVHAGYLHTHAAAHPQAIARFVAAAATTKLAG
>NC_009338.1|WP_011894899.1|4302524_4303139_-|cob(I)yrinic-acid-a,c-diamide-adenosyltransferase
MPQGQPLTVPDDGLTTRARRNAPLLAVHTGPGKGKSTAAFGMALRAWNQGFDIAVFQFVKSAKWKVGEESALTELGRAHDERGVGGPVEWHKMGSGWSWTRKSGTEVDHAAAAADGWAEISRRLAEQRHDFYVLDEFTYPLKWGWVDVDDVVETLARRPGNQHVVITGRDAPQALLDAADLVTEMTKVKHPMDAGRKGQKGIEW

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP032325	Azospirillum brasilense strain MTCC4035 plasmid p4, complete sequence	116652-116676	3	0.88
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NC_007974	Cupriavidus metallidurans CH34 megaplasmid, complete sequence	755574-755598	3	0.88
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP046333	Cupriavidus metallidurans strain FDAARGOS_675 plasmid unnamed3	2121212-2121236	3	0.88
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	CP042595	Streptomyces albogriseolus strain LBX-2 plasmid pSALBX2, complete sequence	195301-195325	3	0.88
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP026517	Deinococcus sp. NW-56 plasmid unnamed1, complete sequence	170075-170099	3	0.88
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP011771	Croceicoccus naphthovorans strain PQ-2 plasmid p1, complete sequence	66144-66168	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_LR134450	Tsukamurella tyrosinosolvens strain NCTC13231 plasmid 8, complete sequence	65827-65851	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP022369	Azospirillum sp. TSH58 plasmid TSH58_p05, complete sequence	57362-57386	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_HG938354	Neorhizobium galegae bv. orientalis str. HAMBI 540 plasmid pHAMBI540a, complete sequence	478320-478344	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NC_009620	Sinorhizobium medicae WSM419 plasmid pSMED01, complete sequence	523702-523726	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NC_016585	Azospirillum lipoferum 4B plasmid AZO_p1, complete sequence	385871-385895	4	0.84
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013554	Rhizobium phaseoli strain N931 plasmid pRphaN931b, complete sequence	282754-282778	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013588	Rhizobium phaseoli strain N161 plasmid pRphaN161c, complete sequence	258104-258128	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NC_017081	Phycisphaera mikurensis NBRC 102666 plasmid pPSMK1, complete sequence	8782-8806	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013529	Rhizobium phaseoli strain R723 plasmid pRphaR723b, complete sequence	277106-277130	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013539	Rhizobium phaseoli strain R630 plasmid pRphaR630b, complete sequence	266373-266397	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013565	Rhizobium phaseoli strain N831 plasmid pRphaN831b, complete sequence	282754-282778	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NZ_CP013582	Rhizobium phaseoli strain N261 plasmid pRphaN261b, complete sequence	277106-277130	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	KX641262	Mycobacterium phage Nazo, complete genome	18532-18556	5	0.8
NC_009338_2	2.1\|4104344\|25\|NC_009338\|CRISPRCasFinder	4104344-4104368	25	NC_023692	Mycobacterium phage BigNuz, complete genome	18532-18556	5	0.8
NC_009338_3	3.1\|4160531\|31\|NC_009338\|CRISPRCasFinder	4160531-4160561	31	NZ_AP019820	Enterobacter hormaechei subsp. hoffmannii strain OIPH-N069 plasmid pN069_3, complete sequence	19527-19557	7	0.774

1. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP032325 (Azospirillum brasilense strain MTCC4035 plasmid p4, complete sequence) position: , mismatch: 3, identity: 0.88

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
tcccgaccacggcgccgtcgcaggc	Protospacer
******* ****** ******** *

2. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NC_007974 (Cupriavidus metallidurans CH34 megaplasmid, complete sequence) position: , mismatch: 3, identity: 0.88

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
tgccgacgacggcggcgtcgcggac	Protospacer
* *******************.* *

3. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP046333 (Cupriavidus metallidurans strain FDAARGOS_675 plasmid unnamed3) position: , mismatch: 3, identity: 0.88

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
tgccgacgacggcggcgtcgcggac	Protospacer
* *******************.* *

4. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to CP042595 (Streptomyces albogriseolus strain LBX-2 plasmid pSALBX2, complete sequence) position: , mismatch: 3, identity: 0.88

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
tgccgacgacggcggcgtcggcgcc	Protospacer
* ******************  ***

5. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP026517 (Deinococcus sp. NW-56 plasmid unnamed1, complete sequence) position: , mismatch: 3, identity: 0.88

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
tctccacgacggcggcgtcgcaggc	Protospacer
**.* ****************** *

6. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP011771 (Croceicoccus naphthovorans strain PQ-2 plasmid p1, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
cgccggcgacggcggcgtcgcagcg	Protospacer
. ***.******************

7. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_LR134450 (Tsukamurella tyrosinosolvens strain NCTC13231 plasmid 8, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
cgccgatgacggcggcgccgcagcc	Protospacer
. ****.**********.*******

8. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP022369 (Azospirillum sp. TSH58 plasmid TSH58_p05, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
caccgacgacggcgccgtcgcaggc	Protospacer
. ************ ******** *

9. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_HG938354 (Neorhizobium galegae bv. orientalis str. HAMBI 540 plasmid pHAMBI540a, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcatcgccgcc	Protospacer
  **************.**** ***

10. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NC_009620 (Sinorhizobium medicae WSM419 plasmid pSMED01, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgacgcc	Protospacer
  ******************  ***

11. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NC_016585 (Azospirillum lipoferum 4B plasmid AZO_p1, complete sequence) position: , mismatch: 4, identity: 0.84

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
cgccgacgacggcgacgtcgcagtc	Protospacer
. ************.********.*

12. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013554 (Rhizobium phaseoli strain N931 plasmid pRphaN931b, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

13. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013588 (Rhizobium phaseoli strain N161 plasmid pRphaN161c, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

14. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NC_017081 (Phycisphaera mikurensis NBRC 102666 plasmid pPSMK1, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
cagcgacgacggcggcgtcgccgcg	Protospacer
.  ****************** **

15. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013529 (Rhizobium phaseoli strain R723 plasmid pRphaR723b, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

16. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013539 (Rhizobium phaseoli strain R630 plasmid pRphaR630b, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

17. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013565 (Rhizobium phaseoli strain N831 plasmid pRphaN831b, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

18. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NZ_CP013582 (Rhizobium phaseoli strain N261 plasmid pRphaN261b, complete sequence) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
aaccgacgacggcggcgtcgcgctc	Protospacer
  *******************. .*

19. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to KX641262 (Mycobacterium phage Nazo, complete genome) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
ccccgacgacggcggcgtcgagatc	Protospacer
.******************* ...*

20. spacer 2.1|4104344|25|NC_009338|CRISPRCasFinder matches to NC_023692 (Mycobacterium phage BigNuz, complete genome) position: , mismatch: 5, identity: 0.8

tcccgacgacggcggcgtcgcagcc	CRISPR spacer
ccccgacgacggcggcgtcgagatc	Protospacer
.******************* ...*

21. spacer 3.1|4160531|31|NC_009338|CRISPRCasFinder matches to NZ_AP019820 (Enterobacter hormaechei subsp. hoffmannii strain OIPH-N069 plasmid pN069_3, complete sequence) position: , mismatch: 7, identity: 0.774

gcagagtccgttgacgaactggcaacgaact	CRISPR spacer
gcgttgtccggtgacgaactggcaacgatgg	Protospacer
**.  ***** *****************

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

588273 : 612652

Acanthamoeba_polyphaga_mimivirus(33.33%)

integrase,transposase

attL 596843:596858|attR 616003:616018

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_085977995.1\|588273_589502_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_036349499.1\|589576_590701_-	epoxide hydrolase	NA	NA	NA	NA
WP_011891540.1\|591078_591576_-	nuclear transport factor 2 family protein	NA	NA	NA	NA
WP_011777805.1\|591569_592751_-	aromatic ring-hydroxylating dioxygenase subunit alpha	NA	NA	NA	NA
WP_011855460.1\|592747_593833_-	hypothetical protein	NA	NA	NA	NA
WP_011559050.1\|593847_594873_-	2,3-butanediol dehydrogenase	A0A0G2Y405	Acanthamoeba_polyphaga_mimivirus	3.1e-15	29.5
WP_041799743.1\|594930_595758_-	glucose 1-dehydrogenase	NA	NA	NA	NA
WP_011855462.1\|595777_597154_-	Rieske 2Fe-2S domain-containing protein	NA	NA	NA	NA
596843:596858	attL	NA	NA	NA	NA
WP_011891542.1\|597216_597726_-	3-phenylpropionate/cinnamic acid dioxygenase subunit beta	NA	NA	NA	NA
WP_011891543.1\|598283_599744_-	aldehyde dehydrogenase family protein	NA	NA	NA	NA
WP_011767827.1\|599939_600230_-	4Fe-4S binding protein	NA	NA	NA	NA
WP_011559041.1\|600226_601999_-	FAD-binding protein	NA	NA	NA	NA
WP_011777800.1\|602121_602631_-	3-phenylpropionate/cinnamic acid dioxygenase subunit beta	NA	NA	NA	NA
WP_085976237.1\|603662_604855_-\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4
WP_085981117.1\|604993_606222_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_011891548.1\|607548_609192_-\|integrase	site-specific integrase	NA	NA	NA	NA
WP_011777793.1\|609216_609531_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011777792.1\|609527_610595_-\|integrase	tyrosine-type recombinase/integrase	NA	NA	NA	NA
WP_110797900.1\|611755_612652_+\|transposase	IS5 family transposase	A0A0N9SHJ4	Paenibacillus_phage	1.9e-16	42.7
616003:616018	attR	NA	NA	NA	NA

DBSCAN-SWA_2

624742 : 641999

Mycobacterium_phage(20.0%)

integrase,transposase

attL 629579:629594|attR 638909:638924

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_011891562.1\|624742_626149_-\|transposase	IS1380 family transposase	A0A222ZN33	Mycobacterium_phage	2.7e-86	44.3
WP_085981119.1\|627985_629132_+\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	2.7e-31	32.4
629579:629594	attL	NA	NA	NA	NA
WP_063840634.1\|629737_630133_+	winged helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011891568.1\|630129_632097_+	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	2.9e-102	39.2
WP_085977995.1\|632310_633539_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_011891571.1\|634140_635004_-	TniQ family protein	NA	NA	NA	NA
WP_011891572.1\|635006_636020_-	TniB family NTP-binding protein	NA	NA	NA	NA
WP_036372924.1\|636007_637960_-\|integrase,transposase	DDE-type integrase/transposase/recombinase	NA	NA	NA	NA
WP_109489628.1\|638097_638727_-\|transposase	TnsA-like heteromeric transposase endonuclease subunit	NA	NA	NA	NA
WP_011891575.1\|638908_639373_-\|transposase	transposase	U5P429	Shigella_phage	1.2e-09	30.5
638909:638924	attR	NA	NA	NA	NA
WP_041799750.1\|639785_640016_-	hypothetical protein	NA	NA	NA	NA
WP_085976237.1\|640807_641999_+\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4

DBSCAN-SWA_3

685483 : 748811

Corynebacterium_phage(42.86%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_085981120.1\|685483_686765_+\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	8.9e-60	50.6
WP_011891543.1\|687422_688883_-	aldehyde dehydrogenase family protein	NA	NA	NA	NA
WP_011767827.1\|689078_689369_-	4Fe-4S binding protein	NA	NA	NA	NA
WP_011559041.1\|689365_691138_-	FAD-binding protein	NA	NA	NA	NA
WP_011777800.1\|691260_691770_-	3-phenylpropionate/cinnamic acid dioxygenase subunit beta	NA	NA	NA	NA
WP_011891550.1\|694208_695234_-	dihydrodipicolinate synthase family protein	NA	NA	NA	NA
WP_011559038.1\|695401_695788_-	SCP2 sterol-binding domain-containing protein	NA	NA	NA	NA
WP_011891551.1\|695833_696724_-	VOC family protein	NA	NA	NA	NA
WP_011891552.1\|696742_697741_-	dihydrodipicolinate synthase family protein	NA	NA	NA	NA
WP_011891592.1\|698668_699904_+\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	8.5e-108	52.1
WP_011891554.1\|700881_702123_-	FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_011891555.1\|702119_702320_-	ferredoxin	NA	NA	NA	NA
WP_011891556.1\|702348_703152_-	3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase	NA	NA	NA	NA
WP_011891557.1\|703148_703454_-	hypothetical protein	NA	NA	NA	NA
WP_011891594.1\|703450_704047_-	3-phenylpropionate/cinnamic acid dioxygenase subunit beta	NA	NA	NA	NA
WP_011891595.1\|704043_705498_-	aromatic ring-hydroxylating dioxygenase subunit alpha	NA	NA	NA	NA
WP_011891596.1\|705972_706773_+	IclR family transcriptional regulator	NA	NA	NA	NA
WP_011777780.1\|706772_707276_+	hypothetical protein	NA	NA	NA	NA
WP_011891597.1\|707717_708953_-\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	1.0e-81	44.1
WP_011891598.1\|709290_710343_+\|transposase	IS110 family transposase	NA	NA	NA	NA
WP_011891602.1\|712306_712750_-	hypothetical protein	NA	NA	NA	NA
WP_011891603.1\|713908_714676_+	pirin family protein	NA	NA	NA	NA
WP_011891604.1\|714653_715985_+	gluconolaconase	NA	NA	NA	NA
WP_011891605.1\|716114_717221_+	phosphodiester glycosidase family protein	NA	NA	NA	NA
WP_011891606.1\|717617_718019_-	DUF2510 domain-containing protein	NA	NA	NA	NA
WP_041799755.1\|718717_719953_-\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	6.1e-82	43.5
WP_011891609.1\|720816_721746_-	hypothetical protein	NA	NA	NA	NA
WP_011891610.1\|721712_722285_-	hypothetical protein	NA	NA	NA	NA
WP_011891611.1\|722281_723265_-	RDD family protein	NA	NA	NA	NA
WP_011891612.1\|723261_723891_-	hypothetical protein	NA	NA	NA	NA
WP_011891613.1\|723860_725423_-	MCE family protein	NA	NA	NA	NA
WP_011891614.1\|725426_726572_-	virulence factor Mce family protein	NA	NA	NA	NA
WP_011891615.1\|726568_728200_-	virulence factor Mce family protein	NA	NA	NA	NA
WP_011891616.1\|728212_729784_-	virulence factor Mce family protein	NA	NA	NA	NA
WP_011891617.1\|729780_730812_-	virulence factor Mce family protein	NA	NA	NA	NA
WP_011891618.1\|730808_732026_-	MCE family protein	NA	NA	NA	NA
WP_011891619.1\|732031_732904_-	ABC transporter permease	NA	NA	NA	NA
WP_011891620.1\|732905_733703_-	ABC transporter permease	NA	NA	NA	NA
WP_049777181.1\|733916_735599_-	long-chain-fatty-acid--CoA ligase	A0A2H4PQM9	Staphylococcus_phage	1.3e-31	27.6
WP_041799757.1\|735742_736429_+	FCD domain-containing protein	NA	NA	NA	NA
WP_011891623.1\|736436_736877_-	SRPBCC family protein	NA	NA	NA	NA
WP_011891624.1\|736914_737643_-	DUF72 domain-containing protein	A0A1V0CNL1	Kaumoebavirus	4.2e-22	30.0
WP_011891625.1\|737693_738785_+	peptidase M42	NA	NA	NA	NA
WP_013470333.1\|738768_739437_-	TetR family transcriptional regulator	NA	NA	NA	NA
WP_041799759.1\|739670_740105_-	hypothetical protein	NA	NA	NA	NA
WP_011891628.1\|740162_740972_-	ABC transporter ATP-binding protein	G3M9Y6	Bacillus_virus	1.3e-24	31.3
WP_011891629.1\|740955_741993_-	ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_041799761.1\|741989_742862_-	ABC transporter permease	NA	NA	NA	NA
WP_011891631.1\|742927_744019_-	NAD(P)-dependent alcohol dehydrogenase	NA	NA	NA	NA
WP_011891632.1\|744198_745746_+	Re/Si-specific NAD(P)(+) transhydrogenase subunit alpha	NA	NA	NA	NA
WP_011891633.1\|745758_747198_+	Re/Si-specific NAD(P)(+) transhydrogenase subunit beta	NA	NA	NA	NA
WP_011891634.1\|747263_748811_+\|transposase	IS1182-like element ISMgi4 family transposase	NA	NA	NA	NA

DBSCAN-SWA_4

3364869 : 3383240

Red_sea_bream_iridovirus(16.67%)

integrase,transposase

attL 3354447:3354463|attR 3387608:3387624

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
3354447:3354463	attL	NA	NA	NA	NA
WP_036372924.1\|3364869_3366822_-\|integrase,transposase	DDE-type integrase/transposase/recombinase	NA	NA	NA	NA
WP_109489628.1\|3366959_3367589_-\|transposase	TnsA-like heteromeric transposase endonuclease subunit	NA	NA	NA	NA
WP_085981130.1\|3368294_3370004_+	macro domain-containing protein	F1SVT2	Red_sea_bream_iridovirus	4.7e-24	45.7
WP_041799926.1\|3370170_3371526_-\|transposase	IS1380-like element ISMgi1 family transposase	A0A222ZN33	Mycobacterium_phage	4.1e-241	92.2
WP_011894058.1\|3371898_3372879_+	hypothetical protein	A0A1P8DIG7	Virus_Rctr197k	2.4e-12	54.0
WP_085975375.1\|3373353_3374492_-\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	6.3e-33	34.8
WP_011894059.1\|3374748_3375219_-	hypothetical protein	NA	NA	NA	NA
WP_041800102.1\|3375295_3375559_-	hypothetical protein	NA	NA	NA	NA
WP_011891592.1\|3375727_3376963_+\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	8.5e-108	52.1
WP_011894061.1\|3376959_3378357_-	GTPase domain-containing protein	NA	NA	NA	NA
WP_041800104.1\|3378349_3382021_-	50S ribosome-binding GTPase	NA	NA	NA	NA
WP_085978014.1\|3382078_3383240_+\|transposase	IS3 family transposase	U5P429	Shigella_phage	5.4e-32	34.5
3387608:3387624	attR	NA	NA	NA	NA

DBSCAN-SWA_5

4574893 : 4583556

Lactococcus_phage(14.29%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_041800248.1\|4574893_4577062_-	class 1b ribonucleoside-diphosphate reductase subunit alpha	V9VI16	Lactococcus_phage	8.2e-207	51.0
WP_011895150.1\|4577028_4577475_-	class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI	G3MBF1	Bacillus_virus	5.0e-10	31.7
WP_013472213.1\|4577525_4577780_-	redoxin NrdH	V5UN81	Mycobacterium_phage	3.6e-21	67.6
WP_011895152.1\|4578360_4578912_-	NAD(P)H-dependent oxidoreductase	A0A2P0ZL77	Lactobacillus_phage	5.8e-08	35.4
WP_085978064.1\|4579029_4579626_+	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA
WP_011895154.1\|4579622_4580696_+	DNA polymerase IV	F1C5A5	Cronobacter_phage	3.3e-23	29.6
WP_011895155.1\|4580749_4581466_+	GAF domain-containing protein	NA	NA	NA	NA
WP_011895156.1\|4581513_4582680_+	AAA family ATPase	A0A077SLJ9	Escherichia_phage	1.6e-52	34.9
WP_011895157.1\|4582683_4583556_-	SDR family oxidoreductase	W8CYX9	Bacillus_phage	6.6e-06	35.9

DBSCAN-SWA_6

4918194 : 4943604

Acinetobacter_phage(75.0%)

integrase,transposase

attL 4935243:4935302|attR 4946102:4946409

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_085976237.1\|4918194_4919386_+\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4
WP_011895461.1\|4919771_4921064_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_131805205.1\|4921082_4921382_-	hypothetical protein	NA	NA	NA	NA
WP_011895462.1\|4921848_4922748_-	alpha/beta hydrolase	NA	NA	NA	NA
WP_011895463.1\|4922800_4923235_-	PaaI family thioesterase	NA	NA	NA	NA
WP_011895464.1\|4923283_4923877_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA
WP_041800306.1\|4924057_4925551_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA
WP_011895466.1\|4925547_4926645_+	zinc-binding dehydrogenase	NA	NA	NA	NA
WP_011895467.1\|4926704_4927256_+	carboxymuconolactone decarboxylase family protein	NA	NA	NA	NA
WP_052537336.1\|4927287_4927836_-	hypothetical protein	NA	NA	NA	NA
WP_011895469.1\|4928015_4928885_-	metal-dependent hydrolase	NA	NA	NA	NA
WP_011895470.1\|4928987_4929629_+	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA
WP_085981140.1\|4929720_4930362_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA
WP_085976237.1\|4932518_4933711_-\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4
4935243:4935302	attL	NA	NA	NA	NA
WP_011895474.1\|4935295_4935601_+\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_049777473.1\|4935755_4937054_+\|transposase	IS256-like element IS1295 family transposase	NA	NA	NA	NA
WP_142360580.1\|4937341_4938184_+	hypothetical protein	NA	NA	NA	NA
WP_085976237.1\|4940241_4941434_-\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4
WP_011895480.1\|4941690_4943604_-\|integrase	tyrosine-type recombinase/integrase	A0A221SAN4	Ralstonia_phage	7.2e-05	28.1
4946102:4946409	attR	NA	NA	NA	NA

Anti-CRISPR protein detection

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

2. NC_009339

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

87258 : 192284

Mycobacterium_phage(31.82%)

protease,integrase,transposase

attL 75894:75909|attR 196727:196744

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
75894:75909	attL	NA	NA	NA	NA
WP_041801085.1\|87258_88494_-\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	1.9e-83	45.3
75894:75909	attL	NA	NA	NA	NA
WP_049777491.1\|90373_90553_-	hypothetical protein	NA	NA	NA	NA
WP_011896123.1\|90682_90943_+	protein-tyrosine-phosphatase	NA	NA	NA	NA
WP_011767946.1\|91223_92459_-\|transposase	IS256 family transposase	A0A220NQR7	Corynebacterium_phage	1.6e-106	52.2
WP_085981176.1\|93767_94906_-\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	6.3e-33	34.8
WP_011896127.1\|95536_96298_-	hypothetical protein	NA	NA	NA	NA
WP_085981180.1\|97060_97576_+	hypothetical protein	NA	NA	NA	NA
WP_011896129.1\|97885_99799_-	bifunctional copper resistance protein CopD/cytochrome c oxidase assembly protein	NA	NA	NA	NA
WP_041801145.1\|99914_100685_-	cytochrome c biogenesis protein CcdA	NA	NA	NA	NA
WP_011896131.1\|100821_101778_+	L,D-transpeptidase family protein	NA	NA	NA	NA
WP_011896132.1\|101851_102235_+	winged helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011896133.1\|102231_104190_+	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	9.0e-104	39.7
WP_011896134.1\|104612_104894_+	hypothetical protein	NA	NA	NA	NA
WP_011896135.1\|105499_106096_+	hypothetical protein	NA	NA	NA	NA
WP_011896136.1\|106400_107222_-	cyclase	NA	NA	NA	NA
WP_041801093.1\|107218_109777_-	heavy metal translocating P-type ATPase	E4ZFI9	Streptococcus_phage	3.5e-108	36.1
WP_041801146.1\|109959_110454_-	hypothetical protein	NA	NA	NA	NA
WP_011896139.1\|110616_112362_-	cytochrome c oxidase subunit I	R9VX24	Flavobacterium_phage	9.4e-12	39.4
WP_011896140.1\|112872_113892_+	M23 family metallopeptidase	A0A2D1G842	Mycobacterium_phage	1.3e-24	52.2
WP_041801148.1\|114131_114515_+	BlaI/MecI/CopY family transcriptional regulator	NA	NA	NA	NA
WP_011896142.1\|114514_115459_+	M56 family metallopeptidase	NA	NA	NA	NA
WP_041801094.1\|116214_117153_-	cytochrome c oxidase assembly protein	NA	NA	NA	NA
WP_041801095.1\|117238_117856_-	TlpA family protein disulfide reductase	NA	NA	NA	NA
WP_011896145.1\|118237_118582_-	hypothetical protein	NA	NA	NA	NA
WP_011896146.1\|118578_119172_-	heme-copper oxidase subunit III	NA	NA	NA	NA
WP_041801097.1\|119510_120557_+	C40 family peptidase	A0A1W6DXV0	Rhodococcus_phage	2.0e-17	46.4
WP_011896149.1\|121430_122747_+\|transposase	IS256 family transposase	A0A2P1JQX9	Mycobacterium_phage	4.9e-231	92.3
WP_011777812.1\|123388_123865_+	hypothetical protein	NA	NA	NA	NA
WP_011777813.1\|123938_124307_-	hypothetical protein	NA	NA	NA	NA
WP_011777814.1\|124345_124753_-	DUF302 domain-containing protein	NA	NA	NA	NA
WP_011777815.1\|124770_126753_-	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	5.3e-104	40.0
WP_011782545.1\|126745_127123_-	winged helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011777817.1\|127277_127541_+	SHOCT domain-containing protein	NA	NA	NA	NA
WP_011777818.1\|127546_128326_+	hypothetical protein	NA	NA	NA	NA
WP_011777819.1\|128338_128746_+	hypothetical protein	NA	NA	NA	NA
WP_011777820.1\|129168_129891_+	hypothetical protein	NA	NA	NA	NA
WP_011777821.1\|129940_131185_+	ImmA/IrrE family metallo-endopeptidase	A0A0U4JD08	Gordonia_phage	3.3e-11	36.6
WP_011777822.1\|131207_132407_+\|integrase	tyrosine-type recombinase/integrase	S6C485	Thermus_phage	7.4e-08	30.1
WP_011777823.1\|132415_134641_+\|integrase	tyrosine-type recombinase/integrase	NA	NA	NA	NA
WP_011782546.1\|134637_135072_+	hypothetical protein	NA	NA	NA	NA
WP_041321994.1\|135272_136037_+\|protease	CPBP family intramembrane metalloprotease	NA	NA	NA	NA
WP_011767854.1\|136617_137346_+	lytic murein transglycosylase	NA	NA	NA	NA
WP_011896150.1\|137542_138334_+	CbtA family protein	NA	NA	NA	NA
138037:138052	attR	NA	NA	NA	NA
WP_011767814.1\|138682_139348_-	thioredoxin	NA	NA	NA	NA
138037:138052	attR	NA	NA	NA	NA
WP_011896151.1\|139825_141370_+	fused MFS/spermidine synthase	NA	NA	NA	NA
WP_049777496.1\|141401_142718_-	L,D-transpeptidase family protein	NA	NA	NA	NA
WP_011767811.1\|143044_144406_-	hypothetical protein	NA	NA	NA	NA
WP_011767810.1\|144402_144852_-	hypothetical protein	NA	NA	NA	NA
WP_011767808.1\|145431_145992_-	RES domain-containing protein	NA	NA	NA	NA
WP_011767807.1\|145988_146330_-	DUF2384 domain-containing protein	NA	NA	NA	NA
WP_081437720.1\|146713_147568_+	hypothetical protein	NA	NA	NA	NA
WP_011767805.1\|147681_147915_+	DUF2188 domain-containing protein	NA	NA	NA	NA
WP_041321980.1\|148247_148430_-	type II toxin-antitoxin system prevent-host-death family antitoxin	NA	NA	NA	NA
WP_011767804.1\|148475_148814_-	hypothetical protein	NA	NA	NA	NA
WP_011767803.1\|148888_149641_-	TniQ family protein	NA	NA	NA	NA
WP_011767802.1\|149804_150083_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011767801.1\|150096_152646_-	TniQ family protein	NA	NA	NA	NA
WP_011767800.1\|152642_153824_-	ATP-binding protein	NA	NA	NA	NA
WP_011767799.1\|153820_155968_-\|integrase,transposase	DDE-type integrase/transposase/recombinase	NA	NA	NA	NA
WP_011767798.1\|155964_156687_-\|transposase	TnsA-like heteromeric transposase endonuclease subunit	NA	NA	NA	NA
WP_011896153.1\|157300_158620_-	AAA family ATPase	NA	NA	NA	NA
WP_041801098.1\|158603_159836_-	hypothetical protein	NA	NA	NA	NA
WP_011896155.1\|160026_161274_-	hypothetical protein	V9SI46	Achromobacter_phage	2.2e-07	27.5
WP_011896156.1\|161270_162377_-	sigma 54-interacting transcriptional regulator	M4SLY4	Vibrio_phage	1.6e-12	27.6
WP_011896157.1\|162511_162868_-	hypothetical protein	A0A222ZSS2	Mycobacterium_phage	8.6e-13	41.5
WP_011896158.1\|163093_163987_-	hypothetical protein	NA	NA	NA	NA
WP_142389927.1\|164143_164695_-	hypothetical protein	NA	NA	NA	NA
WP_011896160.1\|165040_166978_-	hypothetical protein	NA	NA	NA	NA
WP_041801100.1\|167150_168254_+	hypothetical protein	NA	NA	NA	NA
WP_011896162.1\|168382_169216_-	phosphoadenosine phosphosulfate reductase family protein	A0A0N7CD74	Skermania_phage	1.9e-23	30.4
WP_099248873.1\|169212_169686_-	hypothetical protein	NA	NA	NA	NA
WP_011896164.1\|169682_170573_-	hypothetical protein	NA	NA	NA	NA
WP_011896165.1\|170824_171502_+	hypothetical protein	NA	NA	NA	NA
WP_011896166.1\|171523_171949_+	hypothetical protein	NA	NA	NA	NA
WP_011896167.1\|171945_172812_+	hypothetical protein	A0A0N7CDP5	Skermania_phage	2.1e-28	32.4
WP_011896168.1\|172817_173531_+	hypothetical protein	NA	NA	NA	NA
WP_158022119.1\|173905_174340_-	hypothetical protein	NA	NA	NA	NA
WP_011896170.1\|175240_175771_-	DinB family protein	NA	NA	NA	NA
WP_041801102.1\|175823_176213_+	cytidine deaminase	NA	NA	NA	NA
WP_085981177.1\|176666_177813_+\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_011896174.1\|177832_178294_-	hypothetical protein	NA	NA	NA	NA
WP_081437722.1\|178373_179468_+	prolyl aminopeptidase	NA	NA	NA	NA
WP_011896176.1\|179727_180252_+	glyoxalase	NA	NA	NA	NA
WP_081437723.1\|180476_180986_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_085978045.1\|180924_182149_+\|transposase	IS3 family transposase	A0A2P1JR32	Mycobacterium_phage	9.4e-59	43.2
WP_049777502.1\|182164_182443_+	hypothetical protein	NA	NA	NA	NA
WP_041801157.1\|182556_184044_+\|integrase,transposase	DDE-type integrase/transposase/recombinase	B5TA80	Burkholderia_phage	6.6e-06	23.6
WP_011896180.1\|184040_184856_+	AAA family ATPase	NA	NA	NA	NA
WP_041801105.1\|184888_185071_-	hypothetical protein	NA	NA	NA	NA
WP_041801106.1\|185185_185701_+	transferase	NA	NA	NA	NA
WP_158022120.1\|185954_186098_-	hypothetical protein	NA	NA	NA	NA
WP_011896182.1\|186108_186492_-	hypothetical protein	NA	NA	NA	NA
WP_011896183.1\|186594_187644_-	DUF2637 domain-containing protein	A0A1D8EVB7	Mycobacterium_phage	9.3e-07	34.1
WP_011896184.1\|187893_188379_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_011896185.1\|188447_188780_-	Lsr2 family protein	S5W0B7	Mycobacterium_phage	8.8e-12	38.7
WP_011896186.1\|188793_190902_-	type VII secretion protein EccE	NA	NA	NA	NA
WP_041801108.1\|190898_192284_-\|protease	type VII secretion-associated serine protease mycosin	V5UPA7	Mycobacterium_phage	8.1e-67	41.6
196727:196744	attR	NA	NA	NA	NA

DBSCAN-SWA_2

218671 : 249382

Saccharomonospora_phage(33.33%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_011896210.1\|218671_219922_-\|transposase	transposase	I4AZI9	Saccharomonospora_phage	1.5e-136	62.6
WP_041801115.1\|219925_220324_-\|transposase	IS200/IS605 family transposase	I4AZI8	Saccharomonospora_phage	6.6e-62	82.4
WP_011896212.1\|220680_220968_-	hypothetical protein	NA	NA	NA	NA
WP_099249241.1\|221556_222834_-\|transposase	transposase	A0A1P8DJG9	Virus_Rctr71	1.2e-59	41.9
WP_011896214.1\|222882_223311_+\|transposase	IS200/IS605 family transposase	I4AZM1	Saccharomonospora_phage	6.6e-44	65.2
WP_158022122.1\|223671_223926_+	hypothetical protein	NA	NA	NA	NA
WP_041801116.1\|223990_224242_+	hypothetical protein	A0A0A7HCT4	Mycobacterium_phage	9.9e-16	56.0
WP_011896216.1\|224309_224744_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_041801117.1\|224776_225736_+	hypothetical protein	NA	NA	NA	NA
WP_041801118.1\|225759_226614_-	DUF1942 domain-containing protein	NA	NA	NA	NA
WP_041801119.1\|226957_227173_+	hypothetical protein	NA	NA	NA	NA
WP_158022123.1\|227156_227348_+	hypothetical protein	NA	NA	NA	NA
WP_041801120.1\|228658_229054_+	hypothetical protein	NA	NA	NA	NA
WP_049777512.1\|229046_229436_+	XRE family transcriptional regulator	NA	NA	NA	NA
WP_081437725.1\|229472_230186_-	RES domain-containing protein	NA	NA	NA	NA
WP_011896224.1\|230113_230698_-	hypothetical protein	NA	NA	NA	NA
WP_011896225.1\|230864_231557_+	hypothetical protein	NA	NA	NA	NA
WP_011896226.1\|231558_232539_+	nucleotidyl transferase AbiEii/AbiGii toxin family protein	NA	NA	NA	NA
WP_041801166.1\|232562_234890_-	sulfatase-like hydrolase/transferase	NA	NA	NA	NA
WP_041801121.1\|235061_235997_+	AraC family transcriptional regulator	NA	NA	NA	NA
WP_085976237.1\|236023_237215_+\|transposase	IS3 family transposase	A0A0P0I4A4	Acinetobacter_phage	8.9e-46	37.4
WP_158022132.1\|237529_238684_+	diguanylate cyclase	A0A127AWB9	Bacillus_phage	3.4e-10	34.9
WP_158022124.1\|238698_239868_-	endonuclease/exonuclease/phosphatase	NA	NA	NA	NA
WP_049777515.1\|240030_240513_-	hypothetical protein	NA	NA	NA	NA
WP_081437726.1\|240663_243012_-	hypothetical protein	NA	NA	NA	NA
WP_011896233.1\|243015_243828_-	hypothetical protein	NA	NA	NA	NA
WP_011896234.1\|243824_244112_-	hypothetical protein	NA	NA	NA	NA
WP_011896235.1\|244342_245527_+	Fic family protein	D7RWK9	Brochothrix_phage	3.9e-09	23.4
WP_011896236.1\|246160_246637_-	hypothetical protein	NA	NA	NA	NA
WP_011896237.1\|246660_247083_-	hypothetical protein	NA	NA	NA	NA
WP_158022125.1\|247181_247598_+	hypothetical protein	NA	NA	NA	NA
WP_011896239.1\|247591_247882_-	hypothetical protein	NA	NA	NA	NA
WP_011896101.1\|247975_249382_-\|transposase	IS1380 family transposase	A0A222ZN33	Mycobacterium_phage	4.2e-87	44.1

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_009338

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NC_009339

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection