CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
LS483411	Haemophilus influenzae strain NCTC11426 genome assembly, chromosome: 1	1 crisprs	DEDDh,DinG,cas3,cas14j,RT	0	1	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: LS483411_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LS483411_3

1461034-1461120

Orphan

Consensus_repeat	Method
AAATAATTATCCTTAGTCATATTTATTTT	CRISPRCasFinder

1 spacers

The CRISPR arrays of LS483411_3

>merge|LS483411|3|1461034-1461120|CRISPRCasFinder
AAATAATTATCCTTAGTCATATTTATTTTATCGTGAGCGTAAGCCCACTCATTTAACTCAAATAATTATCCTTGTCATATTTATTTT

>LS483411|3|3|1461034-1461120|CRISPRCasFinder
AAATAATTATCCTTAGTCATATTTATTTT	ATCGTGAGCGTAAGCCCACTCATTTAACT
CAAATAATTATCCTTGTCATATTTATTTT

Protein	Signature genes	Signature genes Name	Protein_function
LS483411.1\|SQG88503.1\|1469366_1470056_-\|molybdate-transporter-subunit	unknown	unknown	gnl\|CDD\|181841
LS483411.1\|SQG88490.1\|1455542_1456175_-\|class-II-aldolase	unknown	unknown	gnl\|CDD\|181241
LS483411.1\|SQG88494.1\|1460058_1460838_+\|sodium-dependent-transporter	unknown	unknown	gnl\|CDD\|271367
LS483411.1\|SQG88489.1\|1454763_1455540_-\|hydroxypyruvate-isomerase	unknown	unknown	gnl\|CDD\|226149
LS483411.1\|SQG88502.1\|1468324_1469380_-\|molybdate-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|182993
LS483411.1\|SQG88493.1\|1458491_1459250_+\|glycerol-3-phosphate-regulon-repressor	unknown	unknown	gnl\|CDD\|224268
LS483411.1\|SQG88492.1\|1457415_1458321_-\|dehydrogenase,-with-NAD(P)-binding-Rossmann-fold-domain	unknown	unknown	gnl\|CDD\|224995
LS483411.1\|SQG88495.1\|1461152_1462391_-\|putative-fimbriae-protein	unknown	unknown	gnl\|CDD\|366088
LS483411.1\|SQG88504.1\|1470217_1470982_-\|molybdate-transporter-subunit	unknown	unknown	gnl\|CDD\|182641
LS483411.1\|SQG88497.1\|1463029_1463650_-\|fimbriae-protein	unknown	unknown	gnl\|CDD\|226069
LS483411.1\|SQG88487.1\|1452285_1453752_-\|gluconate-transporter,-high-affinity-GNT-I-system	unknown	unknown	gnl\|CDD\|308194
LS483411.1\|SQG88500.1\|1466679_1467387_-\|periplasmic-chaperone	unknown	unknown	gnl\|CDD\|225663
LS483411.1\|SQG88498.1\|1463665_1466248_-\|fimbrial-biogenesis-outer-membrane-usher-protein	unknown	unknown	gnl\|CDD\|225729
LS483411.1\|SQG88488.1\|1453760_1454708_-\|putative-sugar-epimerase	unknown	unknown	gnl\|CDD\|187549
LS483411.1\|SQG88501.1\|1467465_1468071_-\|major-fimbrial-subunit	unknown	unknown	gnl\|CDD\|226069
LS483411.1\|SQG88491.1\|1456171_1457413_-\|4-hydroxy-3-methylbut-2-enyl-diphosphate-reductase	unknown	unknown	gnl\|CDD\|225930
LS483411.1\|SQG88486.1\|1450883_1452227_-\|phospholipase/carboxylesterase	unknown	unknown	gnl\|CDD\|226584
LS483411.1\|SQG88499.1\|1466358_1466646_-\|Uncharacterised-protein	unknown	unknown	unknown
LS483411.1\|SQG88485.1\|1450185_1450722_-\|cyclase-family-protein	unknown	unknown	gnl\|CDD\|224790
LS483411.1\|SQG88496.1\|1462383_1463016_-\|fimbrial-protein	unknown	unknown	gnl\|CDD\|226069

Protein	Function_ID	Function_description	E-value
LS483411.1\|SQG88503.1\|1469366_1470056_-\|molybdate-transporter-subunit	gnl\|CDD\|181841	PRK09421, modB, molybdate ABC transporter permease subunit.	7.38258e-138
LS483411.1\|SQG88490.1\|1455542_1456175_-\|class-II-aldolase	gnl\|CDD\|181241	PRK08130, PRK08130, putative aldolase; Validated.	9.08322e-138
LS483411.1\|SQG88494.1\|1460058_1460838_+\|sodium-dependent-transporter	gnl\|CDD\|271367	cd10336, SLC6sbd_Tyt1-Like, solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain. SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. These NTTs are widely expressed in the mammalian brain, involved in regulating neurotransmitter signaling and homeostasis, and the target of a range of therapeutic drugs for the treatment of psychiatric diseases. Bacterial members of the SLC6 family include the LeuT amino acid transporter. An arrangement of 12 transmembrane (TM) helices appears to be as a common topological motif for eukaryotic and some prokaryotic and archaeal NTTs. However, this subfamily which contains the majority of bacterial members and some archaeal members, appears to contain only 11 TMs; for example the functional Fusobacterium nucleatum tyrosine transporter Tyt1.	3.03933e-93
LS483411.1\|SQG88489.1\|1454763_1455540_-\|hydroxypyruvate-isomerase	gnl\|CDD\|226149	COG3622, Hfi, Hydroxypyruvate isomerase [Carbohydrate transport and metabolism].	1.03794e-152
LS483411.1\|SQG88502.1\|1468324_1469380_-\|molybdate-transporter-ATP-binding-protein	gnl\|CDD\|182993	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC.	0
LS483411.1\|SQG88493.1\|1458491_1459250_+\|glycerol-3-phosphate-regulon-repressor	gnl\|CDD\|224268	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism].	6.92802e-96
LS483411.1\|SQG88492.1\|1457415_1458321_-\|dehydrogenase,-with-NAD(P)-binding-Rossmann-fold-domain	gnl\|CDD\|224995	COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism].	5.61656e-96
LS483411.1\|SQG88495.1\|1461152_1462391_-\|putative-fimbriae-protein	gnl\|CDD\|366088	pfam00419, Fimbrial, Fimbrial protein.	5.85729e-06
LS483411.1\|SQG88504.1\|1470217_1470982_-\|molybdate-transporter-subunit	gnl\|CDD\|182641	PRK10677, modA, molybdate transporter periplasmic protein; Provisional.	1.17437e-99
LS483411.1\|SQG88497.1\|1463029_1463650_-\|fimbriae-protein	gnl\|CDD\|226069	COG3539, FimA, P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion].	6.14364e-15
LS483411.1\|SQG88487.1\|1452285_1453752_-\|gluconate-transporter,-high-affinity-GNT-I-system	gnl\|CDD\|308194	pfam02447, GntP_permease, GntP family permease. This is a family of integral membrane permeases that are involved in gluconate uptake. E. coli contains several members of this family including GntU, a low affinity transporter, and GntT, a high affinity transporter.	5.51824e-164
LS483411.1\|SQG88500.1\|1466679_1467387_-\|periplasmic-chaperone	gnl\|CDD\|225663	COG3121, FimC, P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion].	1.29307e-79
LS483411.1\|SQG88498.1\|1463665_1466248_-\|fimbrial-biogenesis-outer-membrane-usher-protein	gnl\|CDD\|225729	COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion].	0
LS483411.1\|SQG88488.1\|1453760_1454708_-\|putative-sugar-epimerase	gnl\|CDD\|187549	cd05238, Gne_like_SDR_e, Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has the characteristic active site tetrad and NAD-binding motif of the extended SDR, and is related to more specifically defined epimerases such as UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), which catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup includes Escherichia coli 055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55 antigen synthesis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	2.45124e-162
LS483411.1\|SQG88501.1\|1467465_1468071_-\|major-fimbrial-subunit	gnl\|CDD\|226069	COG3539, FimA, P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion].	2.64029e-16
LS483411.1\|SQG88491.1\|1456171_1457413_-\|4-hydroxy-3-methylbut-2-enyl-diphosphate-reductase	gnl\|CDD\|225930	COG3395, COG3395, Uncharacterized protein conserved in bacteria [Function unknown].	0
LS483411.1\|SQG88486.1\|1450883_1452227_-\|phospholipase/carboxylesterase	gnl\|CDD\|226584	COG4099, COG4099, Predicted peptidase [General function prediction only].	3.13401e-105
LS483411.1\|SQG88485.1\|1450185_1450722_-\|cyclase-family-protein	gnl\|CDD\|224790	COG1878, COG1878, Kynurenine formamidase [Amino acid transport and metabolism].	3.59148e-33
LS483411.1\|SQG88496.1\|1462383_1463016_-\|fimbrial-protein	gnl\|CDD\|226069	COG3539, FimA, P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion].	1.60205e-07

>LS483411.1|SQG88494.1|1460058_1460838_+|sodium-dependent-transporter
MVIRNVTLPGAMEGITFYLKPDFSKITPQLFIFVLGQVFFALSLGFGVLITLSSYLNKEENLIHTAVITGFTNTIIAVLAGFMIFPSLFTFGIEPNAGPTLVFQSLPIVFSHLWAGKFFAIIFFGLLLIAALTTSITIYEVIITALQEKLRMRRGKAIIFTLGGIFLLGNIPAILGGNLWKSVTIFGKSIFDFYDYASGNILFMLTALGCAIFVGFVLKDEAKKELSSTKYSTFIKIWFNYVKFVVPVIILVIFISNLF
>LS483411.1|SQG88493.1|1458491_1459250_+|glycerol-3-phosphate-regulon-repressor
MIPAERQKTLLNLISKQGVISINNLVNILGVSHMTVRRDIQKLEEDGKVISVSGGVQLLERLSSEPTHDDKSLLATTEKTAISKKAVELIQEHSTIYLDAGTTTLEIAKQIANRNDLLVITNDFVIAHYLMVNSQCNIMHTGGLINKSNRSSVGEFAAQFLHQISVDIAFISTSSWNLKGLTTPDEQKIPVKKAIIQFSQKNILVTDSSKYGKVATFLLYPLSSLDTIICDKGLPENAQARIAEMNVELFLV
>LS483411.1|SQG88492.1|1457415_1458321_-|dehydrogenase,-with-NAD(P)-binding-Rossmann-fold-domain
MENQNYSVAVIGLGSMGMGAAVSCINAGLTTYGIDLNPVALEKLKAAGAKAVAANGYDFAHELDAVVILVVNAAQANAVLFGENGIAKKLKAGTAVMVSSTMAAQDAQIISQKLTELGLIMLDAPVSGGAAKALKGEMTVMASGSKQAFELLQPVLDATAAKVYNIGEEIGLGATVKIVHQLLAGVHIAAGAEAMALASKAGIPLDVMYDVVTNAAGNSWMFENRMKHVVEGDYTPLSMVDIFVKDLGLVNDTAKSLHFPLHLASTAYSMFTEASNAGYGKEDDSAVIKIFSGVNLPKKGA
>LS483411.1|SQG88491.1|1456171_1457413_-|4-hydroxy-3-methylbut-2-enyl-diphosphate-reductase
MLGVIADDFTGASDIASFLVENGLSTVQMNGVPTQSLNSKVNAIVISLKSRSNPVNQAIEQSLRAYQWLKENGCTQFYFKYCSTFDSTAKGNIGPVTDALLDELNEDFTVITPALPVNGRTIFNGYLFVSDLLLSESGMKNHPITPMTDANLMRLMDAQAKGKTGLVAYSDVIKGASRVQERFAELKAQGYRYAVVDAVDNSQLEVLAEAVADFKLVTGGSGLAAYMAARLSGGKKGVNAFTPNKGKTVVLSGSCSVMTNKQVEKYREKAPHFQLDVEQAIHNENYVEQLYQWVIANLDSEFAPIVYATVQPDVLKAIQHQFGVDQASHAIESIFAKLAAKLKQAGVVNFITAGGETSSIVVQELGFTGFHIGKQIAPGVPWLKAVEEDIFLALKSGNFGKEDFFEYAQGMFL
>LS483411.1|SQG88490.1|1455542_1456175_-|class-II-aldolase
MTDLAQKELMVQLGRSFYERGYTVGGAGNLSVRLDDNRVLVTPTGSSLGRLSVERLSVLDMEGNLLGGDKPSKEAVFHLAMYKKNPECKAIVHLHSTYLTALSCLDNLDPNNAIEPFTPYYVMRVGKMQVIPYYRPGSPKIAEELSNRALTGKAFLLANHGVVVTGSDLLDAADNTEELEETAKLFFILKGQKIRYLTDDEIKDLEHRGK
>LS483411.1|SQG88489.1|1454763_1455540_-|hydroxypyruvate-isomerase
MPKFAANLTMMFNEVPFLERFEVAANAGFKYVEYLWPYDYPAKELKAKLDQYGLTQVLFNTSAGDVTKGEWGIAATPGREAEARQHIDQALEYAITLNCPTVHIMAAVVPEGANREDYKQTFVENIRYAAEKFKPHGINICLEALSPEVKPNYFLKSQYDTLDIVELVDRDNVFVQLDYFHAQNVDGNLSRLTDKLNGKFAHVQIASVPARHEPDEGEINYQYIFDKLDEIGYTGYVGCEYKPRGETVAGLDWFQKYK
>LS483411.1|SQG88488.1|1453760_1454708_-|putative-sugar-epimerase
MKVVITGGQGFLGQRLAKTLLAQNDVHIDDLILIDVVKPIAPNNDPRVRCYEMDLRYPTGLDELITEETDAIFHLAAIVSSHAEQDPDLGYEINFLATRNILEICRKNNPKVRFIFSSSLAIFGGELPETILDSTAFTPQSTYGTQKAMCELLINDYSRKGFVDGIVIRLPTICIRPGKPNKAASSFVSSIMREPLHGEDAVCPVSEELRLWLSSPNTVVANFIHALQLPSLPLRSWHTINLPGFSVTVKQMLSDLTQVKGEAILEHIKFEFDESINNIVASWPARIDNTQALALGFKVDSNFQNVIQQFIEYDM
>LS483411.1|SQG88487.1|1452285_1453752_-|gluconate-transporter,-high-affinity-GNT-I-system
MFGLPIPIIGLLIAVFVLVFLVLRTRVHAFIAMLIAASIAGLVGGMSADETLNSITKGFGGTLGSIGIVIGLGVMMGSVLEVSGAAEKMAYSFIKMLGQKKEEWALAITGYVVSIPIFVDSAFVILYPVAKALAKNGKRSLLTLGVALAGGLVVTHHTVPPTPGPLGVAGLFGVDIGAMLLTGVCMAVLPVVGIVLYAKWLDKKYPNFNQEVFTEEELKQKYDSYIESREKKELPSLGLSLLPIVLPIILIFIKAVVHLFVKDVPEALTSIPYQIVSFLGHPVIALALSVLISVYTLLPKADKNTTALHLEEGVKTAGIILLVTGAGGALGAVLRDSGAGKQLAEQIANLPISPILIPFIVSTLVRFIQGSGTVAMITAASISAPILAQIPGVNMLLAAQAATMGSLFFGYFNDSLFWVVNRMMGINDVKKQMVVWSVPTTIAWGIGGISVILANLIFGNDGSVFDLLFPIVMLASILFYIKLQNKNL
>LS483411.1|SQG88486.1|1450883_1452227_-|phospholipase/carboxylesterase
MLKKICILLSLLAAFHVLAQDKVFKNIKPIQVTLLAEITAQGQKVNAVALEYEDNILSGSDLRKTYQISTALNGEEFIPRTILRAYVNNEPTLSAQPKIGKFVIIELDNQDKNADLYSLKTENNQSMQFKGRDKDGNVIVIEKKQINKVPQYYGEKLIYQINQIGYLKLTNGKTLDKIQLMQPAIFEHVKTPWLDQFAVKSVYLKDKANFLNYRIFTPHFETEKTYPLTIFLHGSGQVGSDNIAHLLSSKGAISTLQYEEGVVLAPQYQSVFDPFDDITKGHQGGIHWQTENRRDLVLKIIDETLMQYPQIDKTRIYLVGLSRGSEGAVKLLLTRPHFFAGALLMSGREAYTYEWVDGNATKENLSSIKDIPMWFFHSKEDKISPVEGSRINVNILKELHAPNVKYTEFTTEKVGDNGIANDNAHNTWDAVFNSPEVIQWLLHQKRR
>LS483411.1|SQG88485.1|1450185_1450722_-|cyclase-family-protein
MDAARYFVKDGLSINELPIEYFCHKDVVLLEVPKDEAEGITKEDLEPYADILAQVSFAFLRTGFEKYRTENPLIYQNEGPYIATSAGKYLSDNYPNLKGVGIDFLALGSPSSRVPDTENPKNYHQAILGYHSGRFTTVIEDMHLSELPKGAKIKQFINAPLRIVGLDSSQLVLLKLNK
>LS483411.1|SQG88495.1|1461152_1462391_-|putative-fimbriae-protein
MNKFVKTFQKLTALFIILNAIPQEVQADKQGVWHNECDTGGNHGCIRFPGGQSVVHYPKGPVLTERYLFPRDNPSLTLKPINMEKLIQALGKHEITMETYKIPKKSSSRNNSCFASELRLDEFIWNKIPNTSPTIFQLKEFPYLGFTFRIKTRLSGQPARVGENTRLQDWHNINDYFYTFRSGCGFTGEELRITPIMEITPIDLSHLVHGFQFPSGDIDLKLQNSYFGAFSLNGYSRSGPKPVVTEDAGTAINGSNVTIRLTAVTCNIKGVADYTRDFGTKKSSDITTPIKTSDVDIRVNCGSNAYINPWIVFTDANNLGNRSDTLKMIYKNNGAQTANVGIKLKQKNGNYISFGPDSPKKGTQNQIKLTKEFPQQNTYIISFTPELIKLDNSKKIEGGELEGRATYTLSYQ
>LS483411.1|SQG88496.1|1462383_1463016_-|fimbrial-protein
MRKTSLWAGVLFLLFGLPQGYAANHGKVTFSGKVLAARLCNITTETAGKTVDLGRVRSHQFTGEGTTVGGTDFTLSVRNCGEMPNTKNANRLKYYFVSPYAELKVITTNGLNVQYYLKNTVQNSGNKDSVGIQIFATSGSEAGKVIKVTKQTLPTDNSASSGYTGTQLGAKANGDTFDITLTAKFYAVTAGSSDKAGKVASEMTFEVFYE
>LS483411.1|SQG88497.1|1463029_1463650_-|fimbriae-protein
MKKLKKQGLFRQIIGLFSLLFVAPFSSASDGWVKFTVTIKNGGTCQVHSGYENKQVDLGTVYANELSTANQTAGEKDFDLWVEECGDLINETNKLKFVLMNTTNKTDLLAKGVLPNLETGANKDSVGVQLLTKQGNPVEIKYNASSSPTETLVLSPNGNTLGAEVVIGKKHAFKLPLKARFYAITNGKDDKAGDVRAEVIFAAFYE
>LS483411.1|SQG88498.1|1463665_1466248_-|fimbrial-biogenesis-outer-membrane-usher-protein
MREFSFNPHLSLIGFLIGLAFFPLYTKAENVPNTPKESLNVEDEDVEFSAGFLNMGGNGSNIDVARFQQKNSVLPGEYPAAVWVNGKEKGEMTLRFRDNENANIPFAQLCFTPELEALLDLESAAIKRSPSENECVFIQEAIPDGKAVFNTGQQRLEFTIAQALTINRPRDYIAPSRWQTGDVAAFADYNINHSRYANQGSQSSQMFLNLRTGVNLGNWAFRHSGSKSWSQSEGQSYNTPYQTYETYVQRDFAPIRGLVTLGDFYTSGQVVEGFALRGIDISSDDRMLSPSQLGFAPRVQGIANSNAVVSIYQNGNIIYQTNVTPGPFVIDDLYSSGYNGDLTVEIKEADGKVRSFIVPFSNVAPLIRMGQFRYQLAAGRYRSGEEIYPDNVAQSMLQYGLYNNITINTGVTYSKNYLSGALGLGLNTPIGAFSVDSTWTRSTFLPHSLVDENGAMNTQPSVRKGYSLHGNYSINFNRTRTNITLAAYRYSSRDFYSLSDVINANHVIGKSFFSVLSPRPKNQYQLSIIQDFDKWGSLYLVGATRNYWNKSGSYHQYQLSYANRFKWLSYQIGFSQTIDRQSGQRDNQIYLSMSVPLGHNHSLSSNYARNSAGNSSSQIGINGSFGKNSQWSYGVYGNSGQEGYRNMSANMSYRNSYFDFDASASRDNRGSRQMSSNLSGVVVAHRHGLTFGESVGDSFAVVHADGAAGAEVNSGQGQMLDWFGNAIVPYTQPYRINEIGIDPQNLPLNIEFDGTEKKIIPRANSIHVIDFETKRNRLVLFNLTRTNGELLPMASEAYDEQGQFVGYVVQNGVLFAGGLQQPKGTIKVSWGNGEQNQCHFDYSVNLENATQMQQYEKVCQ
>LS483411.1|SQG88499.1|1466358_1466646_-|Uncharacterised-protein
MKYIHFTVGLRPPYEVFGDAMKYIHFTVGLRPPYEALGDAMKYIHFTVGLRPPYEVFGDAMKYIHFTMGLRPPYEVLGRCDEIYSSNGYAQYLML
>LS483411.1|SQG88500.1|1466679_1467387_-|periplasmic-chaperone
MLSFSKKSIFISAILSCLFATFSAHASVIILGTRLIYPGNQSSLNVQLNNQDSSPALVQSWIEDKQGSQAQVPFIITPPVTRVEGNQGQTLRITFTGTQALPQDRESLYYFNLLDIPPKPSKAYLKDNPNYLQFSVRSRLKLFYRPSNLPYPPAEAYKKVSWQAKGGKLWADNPTPYYLTFTQATVGGKSAPEAVMVAPFSQGEFDVKGVNNGQKVKWSLINDYGGDVAGESTIN
>LS483411.1|SQG88501.1|1467465_1468071_-|major-fimbrial-subunit
MKKTILALLALGVVGANSAFATAVTTQNQPATHAKITVNGEVVTQTCEISTNDRNKVVTLDKVGTNSLKQTGNVAAQQLVTIHLENCTVTNGVHTPHVGTVHQTTQNKVSVTFNHTEKVDTANQFTLKNIETNDPATNVNIQFANINGNGLKIGQNDADAKLSVTDLSTTPAINFLARYYATGQSQAGKVKAEAELDLAYE
>LS483411.1|SQG88502.1|1468324_1469380_-|molybdate-transporter-ATP-binding-protein
MLQINVKKQLGQLALQANIQVPDQGVTAIFGLSGSGKTSLINLVSGLIQPDEGFIRLNDRTLVDMESQECLPTHLRKIGYVFQDARLFPHYSVKGNLRYGMKNVSQDDFNYIVDLLGITHLLKRYPLTLSGGEKQRVAIGRALLTDPDILLMDEPLSALDVPRKRELMQYLERLSKEINIPILYVTHSLDELLRLADRVVLMENGIVKAYDSVEKIWNSAIFAPWKGESEQSSVLALPVYLHNPPYKMTALSLGEQALWIHQVPANVSERVRVCIYSSDVSITLQKPEQTSIRNILRGKITQIEIQDSRVDLAVLVEGHKIWASISKWAQNELRFAVGQDVYVQIKAVSVM
>LS483411.1|SQG88503.1|1469366_1470056_-|molybdate-transporter-subunit
MEISAINLSLSVAVSSMLWSLPLAIFVAWLLARKNFYGKSLITGVIHLPLVLPPVVIGYLLLVAMGRNGFIGKYLYQWFGLSFGFSWKGAVLSSAVVAFPLVVRAIRLSLENIDIKLEQAAQTLGASAWRVFFTITLPLSLPGVLAGLVLGFARSLGEFGATITFVSNIAGETQTIPLAMYSFIQTPSAEEQTARLCLLAIILSLISLLLSEWLSKRMQKKLGQGNVAD
>LS483411.1|SQG88504.1|1470217_1470982_-|molybdate-transporter-subunit
MKKLTKISTALLIAGLGFSFAASAKVTVFAAASMTDALQQVAKDYAKQNPKNEVVFSFASSSTLAKQIEEGAPADIFVSASNKWMKYLSEKDLTVKETEKVLVGNDLVLIAPAKSAVNSVDIAKGEWINALKDSYLSVGDPAHVPAGQYAEEALTKLNLWDKVKDRLARGKDVRGALALVERAEAPYGIVYSTDSKVSQQVKTVGVFPADSHKPVVYPVSIVKGHDNSDSRDFLKYLESDAAKKVLVGYGFSAK

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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
LS483411_2	2.1\|618042\|34\|LS483411\|CRISPRCasFinder	618042-618075	34	MH572422	Microviridae sp. isolate SD_MC_8, complete genome	4166-4199	9	0.735

1. spacer 2.1|618042|34|LS483411|CRISPRCasFinder matches to MH572422 (Microviridae sp. isolate SD_MC_8, complete genome) position: , mismatch: 9, identity: 0.735

aaggcgaaagatttcgtggtacttaatggcgatg	CRISPR spacer
tatccgaatgattttgtggtacttaatggtaaaa	Protospacer
 *  **** *****.**************..* .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1024754 : 1125348

Mannheimia_phage(25.93%)

portal,head,capsid,holin,tail,protease

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
SQG88089.1\|1024754_1025219_+\|protease	metalloprotease	NA	NA	NA	NA
SQG88090.1\|1025236_1026022_+	haloacid dehalogenase-like protein	NA	NA	NA	NA
SQG88091.1\|1026058_1027858_-	long chain fatty acid CoA ligase	A0A1V0SBX8	Catovirus	7.4e-44	26.0
SQG88092.1\|1028050_1029070_-	glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA
SQG88093.1\|1029320_1029947_+	guanylate kinase	K4JYM5	Abalone_herpesvirus	7.5e-20	35.6
SQG88094.1\|1030009_1030276_+	RNA polymerase subunit omega	NA	NA	NA	NA
SQG88095.1\|1030819_1032934_+	bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase	A0A1B1IUF0	uncultured_Mediterranean_phage	2.5e-11	38.8
SQG88096.1\|1032930_1035012_+	ATP-dependent DNA helicase	NA	NA	NA	NA
SQG88097.1\|1035042_1035852_+	glutamate racemase	NA	NA	NA	NA
SQG88098.1\|1036062_1037208_+	L-lactate dehydrogenase, FMN-linked	NA	NA	NA	NA
SQG88099.1\|1043313_1043541_+	Uncharacterised protein	NA	NA	NA	NA
SQG88100.1\|1043550_1044063_+	Uncharacterised protein	NA	NA	NA	NA
SQG88101.1\|1044326_1045256_+	DNA-binding transcriptional activator, homocysteine-binding	NA	NA	NA	NA
SQG88102.1\|1045265_1045601_+	branched-chain amino acid permease	NA	NA	NA	NA
SQG88103.1\|1045646_1045985_+	branched-chain amino acid permease	NA	NA	NA	NA
SQG88104.1\|1045981_1046311_+	branched-chain amino acid permease	NA	NA	NA	NA
SQG88105.1\|1046413_1046647_+	L-lactate dehydrogenase	NA	NA	NA	NA
SQG88106.1\|1046722_1048303_-	peptide chain release factor 3	A0A1S5SF82	Streptococcus_phage	4.3e-32	27.3
SQG88107.1\|1048533_1049322_+	enoyl-ACP reductase	NA	NA	NA	NA
SQG88108.1\|1049401_1051381_+	ribonuclease II	Q0GXV6	Lactococcus_phage	1.1e-24	25.1
SQG88109.1\|1051807_1059013_+	hemophilus surface fibril	NA	NA	NA	NA
SQG88110.1\|1059249_1059891_+	allophanate hydrolase subunit 1	NA	NA	NA	NA
SQG88111.1\|1059887_1060817_+	allophanate hydrolase subunit 2	NA	NA	NA	NA
SQG88112.1\|1060803_1061541_+	lactam utilization protein	NA	NA	NA	NA
SQG88113.1\|1061584_1062778_+	Mn2+ and Fe2+ transporter of the NRAMP family	NA	NA	NA	NA
SQG88114.1\|1062858_1064193_-	argininosuccinate synthetase	A0A140XAJ5	Dickeya_phage	8.4e-53	79.4
SQG88115.1\|1064369_1065242_-	phosphoribosylaminoimidazole-succinocarboxamide synthase	A0A0M4JBD3	Mollivirus	7.4e-50	35.7
SQG88116.1\|1065407_1067756_-	penicillin-binding protein 1b	NA	NA	NA	NA
SQG88117.1\|1067762_1068161_-	Uncharacterised protein family (UPF0231)	NA	NA	NA	NA
SQG88118.1\|1068117_1068462_-	iron-sulfur cluster insertion protein ErpA	A0A2H4N7M3	Lake_Baikal_phage	1.7e-26	48.6
SQG88119.1\|1068598_1069405_+	methionine aminopeptidase	NA	NA	NA	NA
SQG88120.1\|1069497_1072089_+	uridylyltransferase	NA	NA	NA	NA
SQG88121.1\|1072878_1073946_+	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase	NA	NA	NA	NA
SQG88122.1\|1074242_1074791_-	oligoribonuclease	Q8B5Y0	Diachasmimorpha_longicaudata_entomopoxvirus	1.6e-29	40.7
SQG88123.1\|1074861_1075902_+	ribosome small subunit-dependent GTPase A	NA	NA	NA	NA
SQG88124.1\|1076060_1076318_+	phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr)	NA	NA	NA	NA
SQG88125.1\|1076397_1078125_+	PEP-protein phosphotransferase of PTS system (enzyme I)	NA	NA	NA	NA
SQG88126.1\|1078184_1078685_+	glucose-specific enzyme IIA component of PTS	NA	NA	NA	NA
SQG88127.1\|1079032_1079398_+	putative outer membrane protein	A0A1I9LJU6	Stx_converting_phage	5.9e-09	34.2
SQG88128.1\|1079461_1080127_+	DNA-binding response regulator in two-component regulatory system with QseC	NA	NA	NA	NA
SQG88129.1\|1080123_1081479_+	sensory histidine kinase in two-component regulatory system with QseB	W8CYF6	Bacillus_phage	5.4e-15	26.5
SQG88130.1\|1081828_1083772_+\|holin	choline transporter of high affinity	A0A2I7QNT1	Vibrio_phage	2.0e-18	24.8
SQG88131.1\|1083808_1085284_-	aminopeptidase A	Q6GYZ8	Mycoplasma_phage	3.2e-45	35.7
SQG88132.1\|1085391_1086495_+	permease	NA	NA	NA	NA
SQG88133.1\|1086491_1087568_+	permease	NA	NA	NA	NA
SQG88134.1\|1087761_1090032_+	5- methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase	NA	NA	NA	NA
SQG88135.1\|1090681_1091692_-\|portal	portal vertex protein	Q19UT6	Mannheimia_phage	2.3e-119	61.5
SQG88136.1\|1091701_1092682_-	Terminase, ATPase subunit	Q19UT5	Mannheimia_phage	3.8e-103	56.1
SQG88137.1\|1092700_1093483_-	Terminase, ATPase subunit	A0A0M3LRV4	Mannheimia_phage	7.5e-102	75.4
SQG88138.1\|1093651_1094458_+\|capsid	capsid scaffolding protein	A0A0M3LNM2	Mannheimia_phage	3.3e-60	58.1
SQG88139.1\|1094479_1094680_+\|capsid	major capsid protein	Q94MH4	Enterobacteria_phage	8.8e-07	51.7
SQG88140.1\|1095090_1095597_+\|head	putative phage head completion	A0A0M3LNL8	Mannheimia_phage	1.1e-32	51.0
SQG88141.1\|1095596_1095806_+\|tail	Probable bacteriophage tail protein X	NA	NA	NA	NA
SQG88142.1\|1095807_1096029_+\|holin	holin	NA	NA	NA	NA
SQG88143.1\|1096021_1096540_+	phage-like lysozyme	A0A0M3LPQ1	Mannheimia_phage	5.6e-37	46.6
SQG88144.1\|1096524_1096794_+	Uncharacterised protein	NA	NA	NA	NA
SQG88145.1\|1097044_1097341_+	putative zinc finger DksA/TraR C4-type	A0A0M3LS11	Mannheimia_phage	2.6e-07	51.7
SQG88146.1\|1097340_1097568_+\|tail	bacteriophage tail completion protein gpS-like protein	K4NZQ8	Burkholderia_phage	9.3e-05	54.5
SQG88147.1\|1097852_1098248_+\|tail	phage-related tail protein	NA	NA	NA	NA
SQG88148.1\|1098349_1099186_+\|tail	phage-related tail protein	V5YUN9	Pseudomonas_phage	2.4e-37	40.7
SQG88149.1\|1099309_1099540_+\|tail	phage-like tail protein	NA	NA	NA	NA
SQG88150.1\|1099923_1101297_-	Na+-dependent transporters of the SNF family	NA	NA	NA	NA
SQG88151.1\|1101355_1101991_-	DNA glycosylase and apyrimidinic (AP) lyase	NA	NA	NA	NA
SQG88152.1\|1102170_1102878_-	inner membrane NADH-quinone reductase	NA	NA	NA	NA
SQG88153.1\|1102879_1103503_-	oxidoreductase	NA	NA	NA	NA
SQG88154.1\|1103502_1104579_-	inner membrane oxidoreductase	NA	NA	NA	NA
SQG88155.1\|1104583_1107190_-	electron transport complex protein RnfC	NA	NA	NA	NA
SQG88156.1\|1107190_1107772_-	electron transport complex protein RnfB	NA	NA	NA	NA
SQG88157.1\|1107859_1108438_-	inner membrane subunit	NA	NA	NA	NA
SQG88158.1\|1108721_1109783_-	inner membrane peptidase	A0A2H4UUF9	Bodo_saltans_virus	7.4e-20	31.7
SQG88159.1\|1109982_1110648_+	Uncharacterized protein conserved in bacteria (DUF2057)	NA	NA	NA	NA
SQG88160.1\|1110715_1112872_+	inner membrane protein	NA	NA	NA	NA
SQG88161.1\|1112969_1113512_-	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase	A0A140XBD6	Dickeya_phage	3.1e-22	44.5
SQG88162.1\|1113521_1114457_-	arabinose-5-phosphate isomerase	A0A2P0VNK5	Tetraselmis_virus	1.8e-41	35.2
SQG88163.1\|1115080_1115752_-	regulator of cell morphogenesis and cell wall metabolism	NA	NA	NA	NA
SQG88164.1\|1117300_1117783_+	molybdopterin biosynthesis, protein C	NA	NA	NA	NA
SQG88165.1\|1117784_1118030_+	molybdopterin synthase, small subunit	NA	NA	NA	NA
SQG88166.1\|1118030_1118483_+	molybdopterin synthase, large subunit	NA	NA	NA	NA
SQG88167.1\|1118537_1121183_-	paraquat-inducible protein B-like protein	NA	NA	NA	NA
SQG88168.1\|1121166_1122249_-	paraquat-inducible protein A-like protein	NA	NA	NA	NA
SQG88169.1\|1122600_1123239_+	structural transport element	NA	NA	NA	NA
SQG88170.1\|1123266_1125348_+\|protease	carboxy-terminal protease	A0A0R6PIZ1	Moraxella_phage	7.1e-83	32.3

DBSCAN-SWA_2

1745409 : 1774521

Haemophilus_phage(50.0%)

tail,transposase,plate,head

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
SQG88753.1\|1745409_1747254_+	abc transporter atp-binding protein	F2Y2R6	Organic_Lake_phycodnavirus	4.8e-22	29.3
SQG88754.1\|1747331_1747610_-	copper chaperone MerP-like protein	NA	NA	NA	NA
SQG88755.1\|1748057_1749698_+	phage protein	B7SDN0	Haemophilus_phage	8.5e-249	78.2
SQG88756.1\|1749778_1751401_+	Mu-like prophage FluMu protein gp29	B7SDN1	Haemophilus_phage	7.0e-203	68.3
SQG88757.1\|1751384_1752692_+\|head	phage head morphogenesis protein, SPP1 gp7 family	A0A0M3LSH7	Mannheimia_phage	1.6e-160	67.2
SQG88758.1\|1752814_1753231_+	Mu-like prophage FluMu G protein	B7SDN8	Haemophilus_phage	2.1e-47	66.7
SQG88759.1\|1753513_1754551_+	Mu phage protein I	B7SDN9	Haemophilus_phage	7.2e-68	46.7
SQG88760.1\|1754550_1755474_+	Mu bacteriophage protein T	B7SDP1	Haemophilus_phage	1.4e-134	75.2
SQG88761.1\|1755537_1755843_+	Uncharacterised protein	B7SDP3	Haemophilus_phage	6.9e-19	47.0
SQG88762.1\|1755852_1756284_+	Mu-like prophage protein GP36	B7SDP4	Haemophilus_phage	1.3e-36	60.9
SQG88763.1\|1756267_1756930_+	Mu-like prophage protein gp37	A0A0M3LQJ7	Mannheimia_phage	1.2e-44	45.0
SQG88764.1\|1756901_1757084_+	Uncharacterised protein	A0A0M3LQM9	Mannheimia_phage	1.0e-09	63.3
SQG88765.1\|1757076_1758492_+\|tail	bacteriophage Mu tail sheath family protein	B7SDP8	Haemophilus_phage	1.1e-156	62.6
SQG88766.1\|1758501_1758873_+	Uncharacterised protein	A0A0M3LRV6	Mannheimia_phage	1.2e-36	65.0
SQG88767.1\|1758872_1759214_+	Uncharacterised protein	A0A0M3LSI2	Mannheimia_phage	1.8e-20	50.5
SQG88768.1\|1759481_1760024_+\|tail	phage tail length determination protein	A0A0M3LPB6	Mannheimia_phage	7.1e-35	55.2
SQG88769.1\|1760011_1761610_+\|tail	phage tail length determination protein	A0A0M3LPB6	Mannheimia_phage	5.4e-99	60.6
SQG88770.1\|1761762_1763097_+	putative phage virion protein	F6MIL2	Haemophilus_phage	6.3e-109	45.6
SQG88771.1\|1763086_1764211_+	bacteriophage Mu P family protein	F6MIL3	Haemophilus_phage	1.4e-146	72.7
SQG88772.1\|1764220_1764856_+\|plate	phage baseplate assembly protein V	A0A0M3LPA3	Mannheimia_phage	4.7e-62	58.3
SQG88773.1\|1764925_1765276_+	phage GP46 family protein	A0A0M3LQK5	Mannheimia_phage	1.2e-43	73.3
SQG88774.1\|1765290_1766355_+\|tail	Mu phage tail protein gp47	F6MIL6	Haemophilus_phage	2.6e-129	67.1
SQG88775.1\|1766354_1766948_+	Uncharacterized protein conserved in bacteria (DUF2313)	F6MIL7	Haemophilus_phage	1.7e-66	63.0
SQG88776.1\|1766951_1768931_+\|tail	tail fiber protein	Q7Y5S2	Haemophilus_phage	1.1e-24	79.0
SQG88777.1\|1768924_1769560_+	HP1	Q94MX9	Haemophilus_virus	2.2e-27	50.0
SQG88778.1\|1769552_1769822_+	Uncharacterised protein	NA	NA	NA	NA
SQG88779.1\|1770225_1770345_+	mu com-like protein	NA	NA	NA	NA
SQG88780.1\|1770406_1771045_+	D12 class N6 adenine-specific DNA methyltransferase	F6MIM2	Haemophilus_phage	4.7e-78	66.7
SQG88781.1\|1771316_1771535_+	Uncharacterised protein	NA	NA	NA	NA
SQG88782.1\|1772332_1773469_-\|transposase	transposase	A0A1B0VCD8	Salmonella_phage	1.6e-121	56.7
SQG88783.1\|1773514_1773931_+\|transposase	ISSoc3 transposase	A0A1S5RHE3	Helicobacter_phage	4.2e-51	66.4
SQG88784.1\|1773990_1774521_-	antimicrobial peptide transporter subunit	A0A2K9L3Z8	Tupanvirus	3.6e-07	28.3

DBSCAN-SWA_3

1792311 : 1800851

Escherichia_phage(71.43%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
SQG88799.1\|1792311_1792965_+	BexA	M1HXU1	Acanthocystis_turfacea_Chlorella_virus	9.3e-05	25.6
SQG88800.1\|1793176_1793662_+	superoxide dismutase, Cu, Zn	Q9MC02	Salmonella_phage	2.3e-45	59.7
SQG88801.1\|1793751_1794030_-	putative heavy metal transport/detoxification protein	NA	NA	NA	NA
SQG88802.1\|1794038_1794401_-	putative mercuric transport protein MerT	NA	NA	NA	NA
SQG88803.1\|1794375_1795485_-	transglutaminase domain-containing protein	NA	NA	NA	NA
SQG88804.1\|1795738_1798159_+	dimethyl sulfoxide reductase, anaerobic subunit A	A0A077SK27	Escherichia_phage	4.8e-224	50.5
SQG88805.1\|1798169_1798787_+	oxidoreductase, Fe-S subunit	A0A077SL61	Escherichia_phage	3.7e-72	57.3
SQG88806.1\|1798788_1799628_+	oxidoreductase, membrane subunit	A0A077SK59	Escherichia_phage	1.3e-19	33.2
SQG88807.1\|1799739_1800351_+	twin-argninine leader-binding protein for DmsA and TorA	A0A077SLS7	Escherichia_phage	3.0e-21	32.5
SQG88808.1\|1800350_1800851_+	ferredoxin	A0A077SLP0	Escherichia_phage	9.2e-13	31.4

Anti-CRISPR protein detection

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