CRISPRimmunity

Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_005090	Wolinella succinogenes DSM 1740, complete genome	2 crisprs	cas4,DEDDh,csa3,cas2,cas1,cas9,cas3	0	7	0	0

1. NC_005090

CRISPR-Cas detection and classification

Crispr_ID: NC_005090_1

• CRISPR_ID: NC_005090_1
• CRISPR_location: 1386269-1386899
• CRISPR_type: TypeII
• Repeat_type: NA
• Spacer_info: 9 spacers
• Cas_protein_info: cas2,cas1,cas9

Consensus repeat of NC_005090_1

Consensus_repeat	Method
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	PILER-CR
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CRISPRCasFinder
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CRT

spacers of NC_005090_1

>1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TCGCCAAAGAAGTTACCAATCTAATTGAGC
>1.2|1386371|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
AAGGTTGATCTTGTTTTCATTGCAACAAGG
>1.3|1386437|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
GAATACATCGACACGGCTAGCACCATAACA
>1.4|1386503|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
AGCTTGAGGATGGTACATATACCCTCACAA
>1.5|1386569|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
AGCTACATAGCCTGCAACTGAGTCGAAATA
>1.6|1386635|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
AAAAGAATGGTACAAGAAGTACGCTAACAC
>1.7|1386701|31|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CCAAGCAATCATGCCTGAGGGAGGAAGTATA
>1.8|1386768|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
ATTTCAGGGGCAAGGAAATAGAAGCTGATG
>1.9|1386834|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CATCAGTATGCTCAGAGCAGACGACAAAGA

CRISPR arrays and Neighbor proteins around NC_005090_1

CRISPR arrays

The CRISPR arrays of NC_005090_1

>merge|NC_005090|1|1386269-1386899|PILER-CR,CRISPRCasFinder,CRT
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATTCGCCAAAGAAGTTACCAATCTAATTGAGCGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATAAGGTTGATCTTGTTTTCATTGCAACAAGGGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATGAATACATCGACACGGCTAGCACCATAACAGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATAGCTTGAGGATGGTACATATACCCTCACAAGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATAGCTACATAGCCTGCAACTGAGTCGAAATAGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATAAAAGAATGGTACAAGAAGTACGCTAACACGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATCCAAGCAATCATGCCTGAGGGAGGAAGTATAGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATATTTCAGGGGCAAGGAAATAGAAGCTGATGGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAATCATCAGTATGCTCAGAGCAGACGACAAAGAGTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT

>NC_005090|1|1|1386269-1386899|PILER-CR
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	TCGCCAAAGAAGTTACCAATCTAATTGAGC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAGGTTGATCTTGTTTTCATTGCAACAAGG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	GAATACATCGACACGGCTAGCACCATAACA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTTGAGGATGGTACATATACCCTCACAA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTACATAGCCTGCAACTGAGTCGAAATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAAAGAATGGTACAAGAAGTACGCTAACAC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CCAAGCAATCATGCCTGAGGGAGGAAGTATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	ATTTCAGGGGCAAGGAAATAGAAGCTGATG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CATCAGTATGCTCAGAGCAGACGACAAAGA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT

>NC_005090|1|1|1386269-1386899|CRISPRCasFinder
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	TCGCCAAAGAAGTTACCAATCTAATTGAGC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAGGTTGATCTTGTTTTCATTGCAACAAGG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	GAATACATCGACACGGCTAGCACCATAACA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTTGAGGATGGTACATATACCCTCACAA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTACATAGCCTGCAACTGAGTCGAAATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAAAGAATGGTACAAGAAGTACGCTAACAC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CCAAGCAATCATGCCTGAGGGAGGAAGTATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	ATTTCAGGGGCAAGGAAATAGAAGCTGATG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CATCAGTATGCTCAGAGCAGACGACAAAGA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT

>NC_005090|1|1|1386269-1386899|CRT
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	TCGCCAAAGAAGTTACCAATCTAATTGAGC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAGGTTGATCTTGTTTTCATTGCAACAAGG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	GAATACATCGACACGGCTAGCACCATAACA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTTGAGGATGGTACATATACCCTCACAA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AGCTACATAGCCTGCAACTGAGTCGAAATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	AAAAGAATGGTACAAGAAGTACGCTAACAC
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CCAAGCAATCATGCCTGAGGGAGGAAGTATA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	ATTTCAGGGGCAAGGAAATAGAAGCTGATG
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT	CATCAGTATGCTCAGAGCAGACGACAAAGA
GTTATAGCCGCCTACTCAGCCATTCCTCGCTATAAT

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_005090.1|WP_041571852.1|1391726_1392446_+|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_011139278.1|1371021_1371885_+|dimethyl-sulfoxide-reductase-anchor-subunit	unknown	unknown	gnl|CDD|225839
NC_005090.1|WP_011139293.1|1394532_1395519_+|lipopolysaccharide-heptosyltransferase-II	unknown	unknown	gnl|CDD|340821
NC_005090.1|WP_041571851.1|1386967_1387273_-|CRISPR-associated-endonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|226043
NC_005090.1|WP_011139282.1|1374843_1376490_+|HAMP-domain-containing-histidine-kinase	unknown	unknown	gnl|CDD|223715
NC_005090.1|WP_011139294.1|1395561_1395822_+|heavy-metal-associated-domain-containing-protein	unknown	unknown	gnl|CDD|225328
NC_005090.1|WP_173355311.1|1373398_1374847_+|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl|CDD|173853
NC_005090.1|WP_011139288.1|1387250_1388195_-|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|187851
NC_005090.1|WP_011139284.1|1377196_1377622_-|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_158305207.1|1377054_1377225_-|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein	unknown	unknown	gnl|CDD|378065
NC_005090.1|WP_011139280.1|1372584_1373268_+|response-regulator-transcription-factor	unknown	unknown	gnl|CDD|223816
NC_005090.1|WP_011139291.1|1392430_1392751_+|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_011139286.1|1384568_1386251_+|N-6-DNA-methylase	unknown	unknown	gnl|CDD|280533
NC_005090.1|WP_041571847.1|1371896_1372547_+|molecular-chaperone-TorD-family-protein	unknown	unknown	gnl|CDD|225916
NC_005090.1|WP_011139283.1|1376476_1376917_-|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein	unknown	unknown	unknown
NC_005090.1|WP_011139296.1|1397209_1398478_-|citrate-synthase	unknown	unknown	gnl|CDD|180164
NC_005090.1|WP_011139289.1|1388201_1391381_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	cd09643_cas9_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|273840
NC_005090.1|WP_011139295.1|1395838_1397182_-|3-deoxy-7-phosphoheptulonate-synthase-class-II	unknown	unknown	gnl|CDD|366662
NC_005090.1|WP_011139292.1|1393119_1394448_-|histidine--tRNA-ligase	unknown	unknown	gnl|CDD|273080
NC_005090.1|WP_041571850.1|1383461_1384376_-|methylenetetrahydrofolate-reductase	unknown	unknown	gnl|CDD|238299

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_005090.1|WP_011139288.1|1387250_1388195_-|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	1.5e-95	314.2	0.0
NC_005090.1|WP_011139289.1|1388201_1391381_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	cd09643_cas9_CAS-II-A:CAS-II-B:CAS-II-C	1.3e-245	812.4	8.3
NC_005090.1|WP_041571851.1|1386967_1387273_-|CRISPR-associated-endonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	2.2e-37	122.5	0.2

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_005090.1|WP_011139292.1|1393119_1394448_-|histidine--tRNA-ligase	gnl|CDD|273080	TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. [Protein synthesis, tRNA aminoacylation].	1.72077e-153
NC_005090.1|WP_011139278.1|1371021_1371885_+|dimethyl-sulfoxide-reductase-anchor-subunit	gnl|CDD|225839	COG3302, DmsC, DMSO reductase anchor subunit [General function prediction only].	4.04593e-11
NC_005090.1|WP_011139293.1|1394532_1395519_+|lipopolysaccharide-heptosyltransferase-II	gnl|CDD|340821	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins. Lipopolysaccharide heptosyltransferase (2.4.99.B6) is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family also contains lipopolysaccharide 1,2-N-acetylglucosaminetransferase EC 2.4.1.56 and belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.	1.49645e-84
NC_005090.1|WP_041571851.1|1386967_1387273_-|CRISPR-associated-endonuclease-Cas2	gnl|CDD|226043	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms].	4.22363e-35
NC_005090.1|WP_011139282.1|1374843_1376490_+|HAMP-domain-containing-histidine-kinase	gnl|CDD|223715	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms].	6.43147e-26
NC_005090.1|WP_011139294.1|1395561_1395822_+|heavy-metal-associated-domain-containing-protein	gnl|CDD|225328	COG2608, CopZ, Copper chaperone [Inorganic ion transport and metabolism].	2.87943e-08
NC_005090.1|WP_173355311.1|1373398_1374847_+|ABC-transporter-substrate-binding-protein	gnl|CDD|173853	cd00995, PBP2_NikA_DppA_OppA_like, The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand binding domains of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	1.77687e-55
NC_005090.1|WP_011139288.1|1387250_1388195_-|type-II-CRISPR-associated-endonuclease-Cas1	gnl|CDD|187851	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer intergration. Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.	1.31403e-137
NC_005090.1|WP_158305207.1|1377054_1377225_-|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein	gnl|CDD|378065	pfam08843, AbiEii, Nucleotidyl transferase AbiEii toxin, Type IV TA system. This family was recently identified as belonging to the nucleotidyltransferase superfamily. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338.	3.08158e-05
NC_005090.1|WP_011139280.1|1372584_1373268_+|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].	2.41465e-34
NC_005090.1|WP_011139286.1|1384568_1386251_+|N-6-DNA-methylase	gnl|CDD|280533	pfam02384, N6_Mtase, N-6 DNA Methylase. Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.	2.47133e-35
NC_005090.1|WP_041571847.1|1371896_1372547_+|molecular-chaperone-TorD-family-protein	gnl|CDD|225916	COG3381, TorD, Uncharacterized component of anaerobic dehydrogenases [General function prediction only].	5.75306e-20
NC_005090.1|WP_011139296.1|1397209_1398478_-|citrate-synthase	gnl|CDD|180164	PRK05614, gltA, citrate synthase.	0
NC_005090.1|WP_041571850.1|1383461_1384376_-|methylenetetrahydrofolate-reductase	gnl|CDD|238299	cd00537, MTHFR, Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.	7.08983e-67
NC_005090.1|WP_011139295.1|1395838_1397182_-|3-deoxy-7-phosphoheptulonate-synthase-class-II	gnl|CDD|366662	pfam01474, DAHP_synth_2, Class-II DAHP synthetase family. Members of this family are aldolase enzymes that catalyze the first step of the shikimate pathway.	0
NC_005090.1|WP_011139289.1|1388201_1391381_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	gnl|CDD|273840	TIGR01865, conserved_hypothetical_protein, CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.	0

Protein sequences

>NC_005090.1|WP_011139286.1|1384568_1386251_+|N-6-DNA-methylase
MRELLQMFDYIKRYHSDIFESLALALQFFIFKLEQKEALLEFVSLHHRRKEFRPLYEYDLKELMGEELYTRADPNLNVGKILKTIAETPLTPEIIEQFIHTITIKRTLNKLYVYSTPQEVNELIISLLDIAPKDEVYNPCYGMGTLFLSLSKRSKTIRLFGEELDGRLAKIAKLMARVGGIQEMHLFVNDILKKPVFKNEKGFRQFDKIVCNPPFSAHLGIEYLKNDERFSRYGILAKSSPELVFLTHALMHLKQRGVFIVRNQTLQKSFLEEKLRERMVEDRVIEAIIELPKNIFPHQSHDFSILVLAAHSDSILHIDATSERFWQKDGKYNRLIGIEEILALYRQKRESEYSKLTPIEEIDIHDLRAQNYLRFCALKPQKTLSLASLKPLIFRGQRVYGGSKDVPLEYLDIGIQDFAPYCFTDHRGTLRSSGDREKILRYALKPYDILLPLRGSSPKVTLLGEGYRDKLAIANAGIIVIRLPQKEKAIALYLYLFSKEGQKLVSGLYESSAASIITPENLLELALPASFEHDSSKRFATLERLAKEIASLEEEIDRIR
>NC_005090.1|WP_041571850.1|1383461_1384376_-|methylenetetrahydrofolate-reductase
MIETLIHKLQKDHFLTLEVAPHASPTLTPLIHSIQSVGLEKRVDGFVCTDSPLAKLRHSSILATIKLQQSLQKPVICTLSMRDRNSLALQGELMGANEFDVRAILALTGDAIRLGDQPQAKGVFEGKSTLLLEIIQSFNRGIDLQGQPLKSPLRPLYPLAVINSYSQSPESLKKRLRQKIEAGAIGIVTQPIYDLEVAKTLLGWVHEINQELGTFSELVLGYFPVVSYRTAHFLYSKLPGVYIPNEWLSQLEAASKINPEEERRVGLELSRNIWLGLWDFHPKIHFMSANNTKLASEILPPPPT
>NC_005090.1|WP_011139284.1|1377196_1377622_-|hypothetical-protein
MRTIDLARLTGSSLRTAASAKKLVKEGKGLAGSQSKVLMVANFYANHLLSKGYRRKLQYNTAQPIPSADILAAFAGEKHLAWIAERVFSDFLVDDLIAMIQDLQIPLLDVEKSFHASLSQKPAMQKFIQSIHRVCQTKKTL
>NC_005090.1|WP_158305207.1|1377054_1377225_-|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein
MFAKQKRLFELARLILDVQFPRSLWAFGGGTALSAMYWQHRLSTDIDIFLYGGKIF
>NC_005090.1|WP_011139283.1|1376476_1376917_-|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein
MPSNALTAKPWSPMNVFGYADICVERIEEIIAKKIFYRYKELKPRDIIDIGVALKKNKNLLATLERNPHFSLDLLADFAGRIEAANQNGRLLEVVRQEADVLQMQGRYKEMAYEAPHTIVSKIDSLLDRASLALWERQERKGFSGS
>NC_005090.1|WP_011139282.1|1374843_1376490_+|HAMP-domain-containing-histidine-kinase
MKKIKIEYKLFLLFGVAFIGMIFLAHKALSVSEENITSTRTLFENSTTIQSLQEHYIEPLNLLREMSLSLVMSPNESFRRSIEQELISSIAKLDERFLSLDPESQTAWQEYLRLLNQTRLYVSQGFEEGAFVNANTTERTRYYELLERLKALQSKEITQAKGNFAHIQERAKILKYEVILAVVILSILVFLLGYFLSRHIVSSILTLQEGLQDFFDYLERKIPRPKPISLQSRDELEEMSKLLNHNILKAARDIEQDILFVENAISVVTQLKSGHLSSRLETMAQAHELKLLKNVINDMIDNLESKIKEEIEKRSEQEKLLIQQSKLASMGEMIGNIAHQWRQPLSELGAILMNLQVKHHFKDLTEETFKAQVERTNEITAFMSHTISDFQNFFTPSKIKEPFSVRLACEKAIAIIEASLRYHNIILEFRERGDRIAYGYPNEYSQVVLNILSNAKDALISREISHPRIHIELINGKNYSVVKIEDNAGGIRAHPMEKIFEPYFTTKHSRQGTGIGLYMSKMIIEKNMDGIITVENTAEGARFKIKIR
>NC_005090.1|WP_173355311.1|1373398_1374847_+|ABC-transporter-substrate-binding-protein
MPYVYVSRLINEGLVRLAENDQGWEYSLATDCPKLSPTLYECTLRQGVRFQDGTPFNADSVIKNFDYFLAQPFNYTDIHRSLKAVEKVSPYKIRLILSQPYGMLFRDLARIFFYSDAYLRQYGWGGAETGANIKSAGSYGLGPYILVEGMITGRKQTPKAILKANPYYWEKGFPKIETITVFTELETQSALESLLEREGELDFMPIPFNKKIETLLSPYTKLIITPSTNNFTIYFNLHKHDSKVFDPKVRQALNCALNQENLLNFTYKKEGRPNTGAYTHEDCPFSLRELHEILRGLKFKVATQDSLLFLWRGIEYQLSRYGVELEFLLTTSEKEIYDLAQKNHQQTQEWDMLIQGTQDWYGRHPWPIFIRYQEGNPWSFVTGDIKMREAINQLFRHEQGTPEFEALCQTIIQRAKEKAYMLFIPTPHAVYGMNKELHFTPHGIGLQPLWKAEVTSEHWSLRGDKPYPESLQKPILPQRITP
>NC_005090.1|WP_011139280.1|1372584_1373268_+|response-regulator-transcription-factor
MEAWQESLKNLTLLYVEDEEGIRRPMVDTLSYYLKEVYEAEDGEAGLECYYTHRPDIIFTDLKMPHRDGLWMVREIRKHDKHTPIAMITAHSDKEYLLSAVELKMEKYLIKPIALEELLHVLRLCIEDIEEERGIVLECGSVRFDLKNRLFIKEERETPLTQKESDFLALLLRKKGQLIPYEEIESQVWRGEFMSTDALRTLVKNLRKKLGIPCIKNHSLAGYSFEG
>NC_005090.1|WP_041571847.1|1371896_1372547_+|molecular-chaperone-TorD-family-protein
MDYEAFALGAKILSGFFIEPPSLKRFELLKQQGLLQGWFITSPHFANTQGKELWEQSLRYDDSSEIAADFTHLFIADEEYLKAPPYASYYLESSGETFTQESDELSKLYASLNFTPTLYPHEPCDHLASELEFLALLLEQNIANPSPNALLLSFLEYRLTPWSNECLAYLQKNALTPFYQGVGYLTQDLLETLKESLGIKAQKRTIYRSIRVESQE
>NC_005090.1|WP_011139278.1|1371021_1371885_+|dimethyl-sulfoxide-reductase-anchor-subunit
MTLSNLILGELPLVLFTVMTQAVVGFSFVYALSTRAKTSTLASRKRFGLTFLFLLAIALLPSLFHLGDPTHAPYLLMRLGAFESGGAWHIAWLPNEILGVGVLFALGIWLFYTGTLLALYLLPLAGIVTLFFMSGIYGSMQNTVLTWNFSLTLWLFGSSALFLGGLLYRILHDLTHEDRLGAFLFSLIGFALLCLSLAFYTLHVGQSQIEGIGSAYTLLGEHYALFLGTGVILSVLALLLWFLKDFSTLPFGSPRSIGAIALLFGLLGVFSTRVLFYGLIHTHLWLG
>NC_005090.1|WP_041571851.1|1386967_1387273_-|CRISPR-associated-endonuclease-Cas2
MRLMVMFDLPTGTKKERKAYTLFRKFLIKEGFEMMQFSVYVRICRGADMALAYEDRIRRNIPPKGHVRSLVLTNSQYERMHILLGGPKSQEKIGAKQLVLF
>NC_005090.1|WP_011139288.1|1387250_1388195_-|type-II-CRISPR-associated-endonuclease-Cas1
MAAWRTVVIATSCHLRVRDRQLVIESREGERTQLPLADIGVVIVENPQVTLSAALLSALAQEGTALMSCDSSHLPDGVFAPFGTHSRHTRAARVQAVWSEPFKKRCWQKIVRAKVSSQAEVLRRVGAEDAARRLENLVGKVTSGDTTGVEAQAAQVYWRSLFVNFKRWDGGLDARNGGLNYGYAVLRGALGRAIAGAGLIPAFGLHHAGELNSFNLADDLIEPFRPFVDLLVWGLFLERTGDDPLTREERMRIAQILGESCIMTERYETLLSATQIIARSLVSAGEQKESRRLILPWMGEDDVQGEVYEADGDV
>NC_005090.1|WP_011139289.1|1388201_1391381_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9
MIERILGVDLGISSLGWAIVEYDKDDEAANRIIDCGVRLFTAAETPKKKESPNKARREARGIRRVLNRRRVRMNMIKKLFLRAGLIQDVDLDGEGGMFYSKANRADVWELRHDGLYRLLKGDELARVLIHIAKHRGYKFIGDDEADEESGKVKKAGVVLRQNFEAAGCRTVGEWLWRERGANGKKRNKHGDYEISIHRDLLVEEVEAIFVAQQEMRSTIATDALKAAYREIAFFVRPMQRIEKMVGHCTYFPEERRAPKSAPTAEKFIAISKFFSTVIIDNEGWEQKIIERKTLEELLDFAVSREKVEFRHLRKFLDLSDNEIFKGLHYKGKPKTAKKREATLFDPNEPTELEFDKVEAEKKAWISLRGAAKLREALGNEFYGRFVALGKHADEATKILTYYKDEGQKRRELTKLPLEAEMVERLVKIGFSDFLKLSLKAIRDILPAMESGARYDEAVLMLGVPHKEKSAILPPLNKTDIDILNPTVIRAFAQFRKVANALVRKYGAFDRVHFELAREINTKGEIEDIKESQRKNEKERKEAADWIAETSFQVPLTRKNILKKRLYIQQDGRCAYTGDVIELERLFDEGYCEIDHILPRSRSADDSFANKVLCLARANQQKTDRTPYEWFGHDAARWNAFETRTSAPSNRVRTGKGKIDRLLKKNFDENSEMAFKDRNLNDTRYMARAIKTYCEQYWVFKNSHTKAPVQVRSGKLTSVLRYQWGLESKDRESHTHHAVDAIIIAFSTQGMVQKLSEYYRFKETHREKERPKLAVPLANFRDAVEEATRIENTETVKEGVEVKRLLISRPPRARVTGQAHEQTAKPYPRIKQVKNKKKWRLAPIDEEKFESFKADRVASANQKNFYETSTIPRVDVYHKKGKFHLVPIYLHEMVLNELPNLSLGTNPEAMDENFFKFSIFKDDLISIQTQGTPKKPAKIIMGYFKNMHGANMVLSSINNSPCEGFTCTPVSMDKKHKDKCKLCPEENRIAGRCLQGFLDYWSQEGLRPPRKEFECDQGVKFALDVKKYQIDPLGYYYEVKQEKRLGTIPQMRSAKKLVKK
>NC_005090.1|WP_041571852.1|1391726_1392446_+|hypothetical-protein
MKPRKSKAAIDFHLRQGRNLGVVSRAIEQEDDYLQVVAKIDERTTNICRSMHLRVIPLSHLKKQYNSIIQAKSVDEAKTTTNLSLERAGAWSHKLPANLGIPPYHFGCRTILRQMSDIQVKQMKLDEFGREYEVGDEIDKKILNKHLKKTRYRSVDELLRETMGNISREGVHHEHGDRRTILGSNGVLVVLSRDGKIITAFPPDTDSTKYYDKWTAHTYFDKVEHRLSLLTRIQKWLGL
>NC_005090.1|WP_011139291.1|1392430_1392751_+|hypothetical-protein
MARTLIIENDCYNWDISESGEPPEYEGGDEPLGNYGIWRTNKERILYLFSCDVSNAQIEESKMDSRFLEVCEFTHPQSGVRFTGTWIDALKFIQKTLTEAQKRGHY
>NC_005090.1|WP_011139292.1|1393119_1394448_-|histidine--tRNA-ligase
MKEQALITPRTLSGFKDRLPQEAMAKSRLLRTVSEVFEGFGFVPIETPHLEYAEILVKQGSDEIQKELYRFFDHGGRDVALRFDQTVPLARFISQHRNALGLPFKRYAIGNVFRGERAQRGRYREFTQCDFDFIGSESIGSDAEIIQVIYASLKALGIERFTISMNNRKILNGICDYFGVKEQTSDVLRIIDKLDKIGEESVIKELVEELGLSQESARGILGFTSLKQERSSEEFFAKVASYEGLSDSLREGMGEMRALYAILDTLEMDRACYKINFSIARGLGYYTGIVYETTLDALPSIGSVCSGGRYDNLTQSFSKERMSGVGASIGVDRLLAALEELGLLEGRGTSAQVLVACMEESQLAYSYKVAERLRTLGIKSEVYPEAVKPKRSLAYANSKGHPYVAVIGEDELKQGVVTLKDMQWGDQKPCISIEAAAEILLG
>NC_005090.1|WP_011139293.1|1394532_1395519_+|lipopolysaccharide-heptosyltransferase-II
MKILVRLPTWLGDAVMATPALELLHDRFPHAQFTYIGSPVSCALFERDSRVSRLIVDDSKKAKSRLKGILHIARRAGRHDIALTFQNNFLSALLLFLTRTPRRLGYAKEWRSFLLSDSLQTPSSLHQVERYAKLLEPLIGALSEIPSLNITHQPRPKPLPVPKLIGINPGAAYGSAKRWPEAHFAHLISSLLQEGYGVMLFGGEGEREGNERILRSLEPSPLLLDLTAQTDLSQLIDVIGTLDLFITNDSGPMHLACALGIPLIALFGPTDSKETSPWKPMSETLLLSKHLPCAPCKKRICPLGHHHCMTLLAPQEVLAAASQVLGDS
>NC_005090.1|WP_011139294.1|1395561_1395822_+|heavy-metal-associated-domain-containing-protein
MKKSFEVMNVKCGGCANRVKEALKEEFGEVEVDVEQKSLTLEIEDAQEEALKKKLKELGYPVVGDENGFFTKAKSFISCAIGKAQS
>NC_005090.1|WP_011139295.1|1395838_1397182_-|3-deoxy-7-phosphoheptulonate-synthase-class-II
MQNEWNPQSWREKPIRQQPTYKDREHLKNIERELKQYPPLVFAGEARSLKKRLADVTEGRAFLLQGGDCAESFSEFNAINIRDMFKVILQMAVVLTFAGSCPIVKVGRLAGQFAKPRSSDEEVMDGVSLPSYRGDIINSIEFTPEAREPNPKRMLKAYNQSAATLNLIRAFAQGGLADLHEVHRWNLGFIESSFGERYQALCDRITETLSFMEACGITSATTPMLHETEFYTSHEALLLNYEEALTRKDSLTGDWYDCSAHMLWIGERTRELEGAHMEFLRGVNNPVGVKVGPGATKEELLGICDILNPLNEAGRLNFIVRMGAEKIGEKLPALLRIIKEEGRKVLWSIDPMHGNTVKASSGYKTRAFNQVLSEVRSFFDIHKAEGTYAGGIHLEMTGQDVTECIGGSQKITEEGLACNYNTQCDPRLNATQALELAFLIAEILKKR
>NC_005090.1|WP_011139296.1|1397209_1398478_-|citrate-synthase
MGTVTFTNNETGEKFEFEILNPTRGPQLVDFSKFYETTGMFTFDPGYGSTANCKSEISFVDGKKGELVYYGHPIEELVEKYKFVDVIKLLIGNGYIFPTKEESDQFERELVRRSYIHEGLRKIIDAFPDGAHPMANLSSSVSALSTFYYDHIDMEYEAEYQTMARRIIAKTPTLAAFAYRSSVGSPFVYPDADRGYVENFLYMLRAYPHGKLKEEISPIEVSALDTIFMLHADHGQNASTATVRNVASTGVHPYAALSAGLSALWGKAHGGANESVMDQLEMIGDVKNVDRYIAKAKDKNDSFRLMGFGHRVYKSYDPRARILRKLKDDLDQKGVKMNQRLVEIAEKIEEVATQDEYFLSRSLYPNVDFYSGIILTALKIPKSMFTPIFAIGRMPGWCGQVLELLQEPNVKITRPRQMYVGK

Crispr_ID: NC_005090_2

• CRISPR_ID: NC_005090_2
• CRISPR_location: 1531926-1533569
• CRISPR_type: TypeII
• Repeat_type: NA
• Spacer_info: 22 spacers
• Cas_protein_info: cas4,cas2,cas1,cas9

Consensus repeat of NC_005090_2

Consensus_repeat	Method
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	PILER-CR
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CRISPRCasFinder
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CRT

spacers of NC_005090_2

>2.1|1531963|37|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CCGCATACAGGGCAAACCACATCTATCAATACGCTAT
>2.2|1532037|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TCGGTAAGCTCAATTAAGCCCTGTAATAGTTGCTTC
>2.3|1532110|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TAAACCTAGAAAACGGAATACTCGCCGCGCCTGAAA
>2.4|1532183|37|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TCGACAATCACGGTGACGATTTCATGAGCACGCAAGA
>2.5|1532257|38|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CTCTTCAAATTCTACAAATGAGGCGGGTTCTACTTTCA
>2.6|1532332|39|NC_005090|PILER-CR,CRISPRCasFinder,CRT
ATCAACCCAAACTTTTTTAGTATATAAGCGACTCTTCAA
>2.7|1532408|34|NC_005090|PILER-CR,CRISPRCasFinder,CRT
GTTTCGCAGAGTAGCATGAGTGCCACCCTGTATT
>2.8|1532479|37|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TCTGTGTAAATATCTGCATTAAACCCAAGTCTTGATA
>2.9|1532553|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TAGATTTATTGTTTTCCTTCTTCACCCCGCCCACG
>2.10|1532625|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CATAAGAGTGGCGTTCCTCATACTCATATTAGTTTC
>2.11|1532698|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TTCTTTCTTGCCCCTTAACTGTTTTTGTTGTGGTAG
>2.12|1532771|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
ACAACATCAATCTGAGCATCGACGCAGAAGAGTTT
>2.13|1532843|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
GAGCTCACCGAAGCTTTTCAGTCTGCGCTAGCACC
>2.14|1532915|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CTGATACTCATAGAGCCTACGAGGCACGGGCTGTA
>2.15|1532987|38|NC_005090|PILER-CR,CRISPRCasFinder,CRT
ACTCCGCAAGAGCGAATCTATCGAACTACAATGTGAGG
>2.16|1533062|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CAAAAGGGCATTTTAGAGATCTACCCGCTGATGAGC
>2.17|1533135|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CCGCTTGAAACATTGTATCGAACCACTACCGCAGG
>2.18|1533207|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TTTTTATCTCTTTGTAGTCAAAACAAATATCAGTTT
>2.19|1533280|36|NC_005090|PILER-CR,CRISPRCasFinder,CRT
CCTCAATATGGATGCTTGATTTTGCCATCTTTCCCC
>2.20|1533353|35|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TTGGGAACTGCTCCCAACAGGGTTGTTTCCTTCTT
>2.21|1533425|34|NC_005090|PILER-CR,CRISPRCasFinder,CRT
TTTGACCGAGTGAAATTTCGGGTGCTCAATTCGA
>2.22|1533496|37|NC_005090|CRT
TTTGAAATCTCCCGACAGACTGTCAAAAAGCGATTCC

CRISPR arrays and Neighbor proteins around NC_005090_2

CRISPR arrays

The CRISPR arrays of NC_005090_2

>merge|NC_005090|2|1531926-1533569|PILER-CR,CRISPRCasFinder,CRT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCCGCATACAGGGCAAACCACATCTATCAATACGCTATGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTCGGTAAGCTCAATTAAGCCCTGTAATAGTTGCTTCGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTAAACCTAGAAAACGGAATACTCGCCGCGCCTGAAAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTCGACAATCACGGTGACGATTTCATGAGCACGCAAGAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCTCTTCAAATTCTACAAATGAGGCGGGTTCTACTTTCAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACATCAACCCAAACTTTTTTAGTATATAAGCGACTCTTCAAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACGTTTCGCAGAGTAGCATGAGTGCCACCCTGTATTGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTCTGTGTAAATATCTGCATTAAACCCAAGTCTTGATAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTAGATTTATTGTTTTCCTTCTTCACCCCGCCCACGGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCATAAGAGTGGCGTTCCTCATACTCATATTAGTTTCGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTTCTTTCTTGCCCCTTAACTGTTTTTGTTGTGGTAGGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACACAACATCAATCTGAGCATCGACGCAGAAGAGTTTGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACGAGCTCACCGAAGCTTTTCAGTCTGCGCTAGCACCGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCTGATACTCATAGAGCCTACGAGGCACGGGCTGTAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACACTCCGCAAGAGCGAATCTATCGAACTACAATGTGAGGGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCAAAAGGGCATTTTAGAGATCTACCCGCTGATGAGCGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCCGCTTGAAACATTGTATCGAACCACTACCGCAGGGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTTTTTATCTCTTTGTAGTCAAAACAAATATCAGTTTGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACCCTCAATATGGATGCTTGATTTTGCCATCTTTCCCCGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTTGGGAACTGCTCCCAACAGGGTTGTTTCCTTCTTGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTTTGACCGAGTGAAATTTCGGGTGCTCAATTCGAGCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAACTTTGAAATCTCCCGACAGACTGTCAAAAAGCGATTCCGCAACACTCTATAATAATCCCATCCAGCTTTAACAAA

>NC_005090|2|2|1531926-1533495|PILER-CR
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCATACAGGGCAAACCACATCTATCAATACGCTAT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGGTAAGCTCAATTAAGCCCTGTAATAGTTGCTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAAACCTAGAAAACGGAATACTCGCCGCGCCTGAAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGACAATCACGGTGACGATTTCATGAGCACGCAAGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTCTTCAAATTCTACAAATGAGGCGGGTTCTACTTTCA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ATCAACCCAAACTTTTTTAGTATATAAGCGACTCTTCAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GTTTCGCAGAGTAGCATGAGTGCCACCCTGTATT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCTGTGTAAATATCTGCATTAAACCCAAGTCTTGATA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAGATTTATTGTTTTCCTTCTTCACCCCGCCCACG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CATAAGAGTGGCGTTCCTCATACTCATATTAGTTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTCTTTCTTGCCCCTTAACTGTTTTTGTTGTGGTAG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACAACATCAATCTGAGCATCGACGCAGAAGAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GAGCTCACCGAAGCTTTTCAGTCTGCGCTAGCACC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTGATACTCATAGAGCCTACGAGGCACGGGCTGTA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACTCCGCAAGAGCGAATCTATCGAACTACAATGTGAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CAAAAGGGCATTTTAGAGATCTACCCGCTGATGAGC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCTTGAAACATTGTATCGAACCACTACCGCAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTTTATCTCTTTGTAGTCAAAACAAATATCAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCTCAATATGGATGCTTGATTTTGCCATCTTTCCCC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTGGGAACTGCTCCCAACAGGGTTGTTTCCTTCTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTGACCGAGTGAAATTTCGGGTGCTCAATTCGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC

>NC_005090|2|2|1531926-1533495|CRISPRCasFinder
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCATACAGGGCAAACCACATCTATCAATACGCTAT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGGTAAGCTCAATTAAGCCCTGTAATAGTTGCTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAAACCTAGAAAACGGAATACTCGCCGCGCCTGAAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGACAATCACGGTGACGATTTCATGAGCACGCAAGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTCTTCAAATTCTACAAATGAGGCGGGTTCTACTTTCA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ATCAACCCAAACTTTTTTAGTATATAAGCGACTCTTCAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GTTTCGCAGAGTAGCATGAGTGCCACCCTGTATT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCTGTGTAAATATCTGCATTAAACCCAAGTCTTGATA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAGATTTATTGTTTTCCTTCTTCACCCCGCCCACG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CATAAGAGTGGCGTTCCTCATACTCATATTAGTTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTCTTTCTTGCCCCTTAACTGTTTTTGTTGTGGTAG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACAACATCAATCTGAGCATCGACGCAGAAGAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GAGCTCACCGAAGCTTTTCAGTCTGCGCTAGCACC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTGATACTCATAGAGCCTACGAGGCACGGGCTGTA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACTCCGCAAGAGCGAATCTATCGAACTACAATGTGAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CAAAAGGGCATTTTAGAGATCTACCCGCTGATGAGC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCTTGAAACATTGTATCGAACCACTACCGCAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTTTATCTCTTTGTAGTCAAAACAAATATCAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCTCAATATGGATGCTTGATTTTGCCATCTTTCCCC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTGGGAACTGCTCCCAACAGGGTTGTTTCCTTCTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTGACCGAGTGAAATTTCGGGTGCTCAATTCGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC

>NC_005090|2|2|1531926-1533569|CRT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCATACAGGGCAAACCACATCTATCAATACGCTAT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGGTAAGCTCAATTAAGCCCTGTAATAGTTGCTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAAACCTAGAAAACGGAATACTCGCCGCGCCTGAAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCGACAATCACGGTGACGATTTCATGAGCACGCAAGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTCTTCAAATTCTACAAATGAGGCGGGTTCTACTTTCA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ATCAACCCAAACTTTTTTAGTATATAAGCGACTCTTCAA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GTTTCGCAGAGTAGCATGAGTGCCACCCTGTATT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TCTGTGTAAATATCTGCATTAAACCCAAGTCTTGATA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TAGATTTATTGTTTTCCTTCTTCACCCCGCCCACG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CATAAGAGTGGCGTTCCTCATACTCATATTAGTTTC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTCTTTCTTGCCCCTTAACTGTTTTTGTTGTGGTAG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACAACATCAATCTGAGCATCGACGCAGAAGAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	GAGCTCACCGAAGCTTTTCAGTCTGCGCTAGCACC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CTGATACTCATAGAGCCTACGAGGCACGGGCTGTA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	ACTCCGCAAGAGCGAATCTATCGAACTACAATGTGAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CAAAAGGGCATTTTAGAGATCTACCCGCTGATGAGC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCGCTTGAAACATTGTATCGAACCACTACCGCAGG
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTTTATCTCTTTGTAGTCAAAACAAATATCAGTTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	CCTCAATATGGATGCTTGATTTTGCCATCTTTCCCC
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTGGGAACTGCTCCCAACAGGGTTGTTTCCTTCTT
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTGACCGAGTGAAATTTCGGGTGCTCAATTCGA
GCAACACTTTATAGCAAATCCGCTTAGCCTGTGAAAC	TTTGAAATCTCCCGACAGACTGTCAAAAAGCGATTCC
GCAACACTCTATAATAATCCCATCCAGCTTTAACAAA

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_005090.1|WP_011139435.1|1533725_1534310_+|hypothetical-protein	unknown	unknown	gnl|CDD|375883
NC_005090.1|WP_011139432.1|1529853_1530852_+|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	gnl|CDD|187766
NC_005090.1|WP_041572204.1|1535967_1537500_-|AAA-family-ATPase	unknown	unknown	gnl|CDD|223571
NC_005090.1|WP_041571864.1|1524149_1524623_+|pyridoxamine-5'-phosphate-oxidase-family-protein	unknown	unknown	gnl|CDD|378988
NC_005090.1|WP_011139440.1|1538365_1539031_-|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_011139427.1|1520995_1521934_-|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl|CDD|225117
NC_005090.1|WP_011139425.1|1518630_1519056_+|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_011139428.1|1522049_1524044_+|TonB-dependent-receptor	unknown	unknown	gnl|CDD|238657
NC_005090.1|WP_011139443.1|1540896_1543710_+|excinuclease-ABC-subunit-UvrA	unknown	unknown	gnl|CDD|234734
NC_005090.1|WP_011139439.1|1537496_1538369_-|NAD(+)/NADH-kinase	unknown	unknown	gnl|CDD|172567
NC_005090.1|WP_011139444.1|1543830_1544280_+|rhodanese-like-domain-containing-protein	unknown	unknown	gnl|CDD|238724
NC_005090.1|WP_011139437.1|1534636_1535968_-|fibronectin/fibrinogen-binding-protein	unknown	unknown	gnl|CDD|224212
NC_005090.1|WP_011139436.1|1534320_1534632_-|hypothetical-protein	unknown	unknown	unknown
NC_005090.1|WP_011139434.1|1531132_1531714_+|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl|CDD|273040
NC_005090.1|WP_011139431.1|1525627_1529857_+|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12	cas9	cd09704_cas9_CAS-II-B	gnl|CDD|274401
NC_005090.1|WP_041571865.1|1540081_1540831_+|sulfite-exporter-TauE/SafE-family-protein	unknown	unknown	gnl|CDD|376667
NC_005090.1|WP_011139426.1|1519034_1520843_+|excinuclease-ABC-subunit-UvrC	unknown	unknown	gnl|CDD|234792
NC_005090.1|WP_011139430.1|1524600_1525383_-|AraC-family-transcriptional-regulator	unknown	unknown	gnl|CDD|225117
NC_005090.1|WP_041572206.1|1539120_1539924_-|J-domain-containing-protein	unknown	unknown	gnl|CDD|197617
NC_005090.1|WP_011139433.1|1530855_1531146_+|CRISPR-associated-endonuclease-Cas2	cas2	mkCas0128_cas2_CAS-I:CAS-II:CAS-III	gnl|CDD|187856

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_005090.1|WP_011139431.1|1525627_1529857_+|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12	cas9	cd09704_cas9_CAS-II-B	0	1201.2	30.4
NC_005090.1|WP_011139432.1|1529853_1530852_+|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	1.3e-75	249.1	1.6
NC_005090.1|WP_011139434.1|1531132_1531714_+|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	4.2e-27	90.2	0.2
NC_005090.1|WP_011139433.1|1530855_1531146_+|CRISPR-associated-endonuclease-Cas2	cas2	mkCas0128_cas2_CAS-I:CAS-II:CAS-III	5.2e-14	47.2	0.0

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_005090.1|WP_011139435.1|1533725_1534310_+|hypothetical-protein	gnl|CDD|375883	pfam18457, PUD1_2, Up-Regulated in long-lived daf-2. This entry includes C. elegans PUD-1 and PUD-2, two proteins up-regulated in daf-2(loss-of-function) (PUD), are homologous 17-kD proteins with similar beta-sandwich folds that further associate with each other into a V-shaped heterodimer.	2.27935e-53
NC_005090.1|WP_011139432.1|1529853_1530852_+|CRISPR-associated-endonuclease-Cas1	gnl|CDD|187766	cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.	2.493e-86
NC_005090.1|WP_041572204.1|1535967_1537500_-|AAA-family-ATPase	gnl|CDD|223571	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair].	1.24885e-83
NC_005090.1|WP_041571864.1|1524149_1524623_+|pyridoxamine-5'-phosphate-oxidase-family-protein	gnl|CDD|378988	pfam12900, Pyridox_ox_2, Pyridoxamine 5'-phosphate oxidase. Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyzes the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins.	1.55671e-27
NC_005090.1|WP_011139427.1|1520995_1521934_-|helix-turn-helix-transcriptional-regulator	gnl|CDD|225117	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription].	9.91948e-23
NC_005090.1|WP_011139431.1|1525627_1529857_+|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12	gnl|CDD|274401	TIGR03031, cas_csx12, CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to pfam01844, HNH endonuclease.	0
NC_005090.1|WP_011139428.1|1522049_1524044_+|TonB-dependent-receptor	gnl|CDD|238657	cd01347, ligand_gated_channel, TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.	4.08317e-54
NC_005090.1|WP_011139443.1|1540896_1543710_+|excinuclease-ABC-subunit-UvrA	gnl|CDD|234734	PRK00349, uvrA, excinuclease ABC subunit UvrA.	0
NC_005090.1|WP_011139444.1|1543830_1544280_+|rhodanese-like-domain-containing-protein	gnl|CDD|238724	cd01447, Polysulfide_ST, Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.	5.37179e-41
NC_005090.1|WP_011139437.1|1534636_1535968_-|fibronectin/fibrinogen-binding-protein	gnl|CDD|224212	COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].	4.41845e-29
NC_005090.1|WP_011139439.1|1537496_1538369_-|NAD(+)/NADH-kinase	gnl|CDD|172567	PRK14077, pnk, NAD(+) kinase.	4.57164e-88
NC_005090.1|WP_011139434.1|1531132_1531714_+|CRISPR-associated-protein-Cas4	gnl|CDD|273040	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.	2.34925e-16
NC_005090.1|WP_041571865.1|1540081_1540831_+|sulfite-exporter-TauE/SafE-family-protein	gnl|CDD|376667	pfam01925, TauE, Sulfite exporter TauE/SafE. This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane during taurine metabolism as an exporter of sulfoacetate. This family used to be known as DUF81.	2.34495e-33
NC_005090.1|WP_011139426.1|1519034_1520843_+|excinuclease-ABC-subunit-UvrC	gnl|CDD|234792	PRK00558, uvrC, excinuclease ABC subunit UvrC.	0
NC_005090.1|WP_011139430.1|1524600_1525383_-|AraC-family-transcriptional-regulator	gnl|CDD|225117	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription].	7.21546e-23
NC_005090.1|WP_041572206.1|1539120_1539924_-|J-domain-containing-protein	gnl|CDD|197617	smart00271, DnaJ, DnaJ molecular chaperone homology domain.	3.06474e-07
NC_005090.1|WP_011139433.1|1530855_1531146_+|CRISPR-associated-endonuclease-Cas2	gnl|CDD|187856	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.	1.10495e-05

Protein sequences

>NC_005090.1|WP_011139434.1|1531132_1531714_+|CRISPR-associated-protein-Cas4
MTSYKLPINLIRQYLFCPRVVYFLEVLNIPKASPVWVKEGSAHHRKQTELFKRRTLARFHLENAKLSTNVMLFHENFNFYGICDILIISEESVYPVEIKLHGEKITKAQKAQIVAYGVLAEAIYRKKLEMGFVLFEKNSKTIPIKISDGDKAEINNFVKKIIEMIELGNLPHSSADGSKCTQCEFLNYCNDRF
>NC_005090.1|WP_011139433.1|1530855_1531146_+|CRISPR-associated-endonuclease-Cas2
MKLFFEVIVSYDIEDNRNRKKLFEELKDMGLSPIQKSVFWGHLKLAEIKILPNLFCKYCSDGDKAFFVKARLSSEIVKNGFGYTSKIFEIKEYDII
>NC_005090.1|WP_011139432.1|1529853_1530852_+|CRISPR-associated-endonuclease-Cas1
MTKHLYIDEYGSFVGKTSERLTVSQGGELKAEIPLSRLKSVNILKGGISLSSDIIEACSLRGIKIFFLDFRNVAHTAITSTANHAVANVRKAQFLTIESNHGREIARTLIVGKLKNQRATLQYFYKYLKNTDKQSKKLESAIEKIKETIESLKNIELSNNKHWSQIIMGKEGGMAAIYFDAIGAELLEECDFTTRIGRGAEDIMNSALNYGYAILTSFVWQSIINAGLEAYAGVLHTNRPGKPSLVLDVMEEYRAWVVDRNIIKLRSSLAGKKELDAELKKKIITEINATMNKKHLYNGKNLSLQGVMQRQVYRLVGAFMQQNRYKSYIFKW
>NC_005090.1|WP_011139431.1|1525627_1529857_+|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12
MLVSPISVDLGGKNTGFFSFTDSLDNSQSGTVIYDESFVLSQVGRRSKRHSKRNNLRNKLVKRLFLLILQEHHGLSIDVLPDEIRGLFNKRGYTYAGFELDEKKKDALESDTLKEFLSEKLQSIDRDSDVEDFLNQIASNAESFKDYKKGFEAVFASATHSPNKKLELKDELKSEYGENAKELLAGLRVTKEILDEFDKQENQGNLPRAKYFEELGEYIATNEKVKSFFDSNSLKLTDMTKLIGNISNYQLKELRRYFNDKEMEKGDIWIPNKLHKITERFVRSWHPKNDADRQRRAELMKDLKSKEIMELLTTTEPVMTIPPYDDMNNRGAVKCQTLRLNEEYLDKHLPNWRDIAKRLNHGKFNDDLADSTVKGYSEDSTLLHRLLDTSKEIDIYELRGKKPNELLVKTLGQSDANRLYGFAQNYYELIRQKVRAGIWVPVKNKDDSLNLEDNSNMLKRCNHNPPHKKNQIHNLVAGILGVKLDEAKFAEFEKELWSAKVGNKKLSAYCKNIEELRKTHGNTFKIDIEELRKKDPAELSKEEKAKLRLTDDVILNEWSQKIANFFDIDDKHRQRFNNLFSMAQLHTVIDTPRSGFSSTCKRCTAENRFRSETAFYNDETGEFHKKATATCQRLPADTQRPFSGKIERYIDKLGYELAKIKAKELEGMEAKEIKVPIILEQNAFEYEESLRKSKTGSNDRVINSKKDRDGKKLAKAKENAEDRLKDKDKRIKAFSSGICPYCGDTIGDDGEIDHILPRSHTLKIYGTVFNPEGNLIYVHQKCNQAKADSIYKLSDIKAGVSAQWIEEQVANIKGYKTFSVLSAEQQKAFRYALFLQNDNEAYKKVVDWLRTDQSARVNGTQKYLAKKIQEKLTKMLPNKHLSFEFILADATEVSELRRQYARQNPLLAKAEKQAPSSHAIDAVMAFVARYQKVFKDGTPPNADEVAKLAMLDSWNPASNEPLTKGLSTNQKIEKMIKSGDYGQKNMREVFGKSIFGENAIGERYKPIVVQEGGYYIGYPATVKKGYELKNCKVVTSKNDIAKLEKIIKNQDLISLKENQYIKIFSINKQTISELSNRYFNMNYKNLVERDKEIVGLLEFIVENCRYYTKKVDVKFAPKYIHETKYPFYDDWRRFDEAWRYLQENQNKTSSKDRFVIDKSSLNEYYQPDKNEYKLDVDTQPIWDDFCRWYFLDRYKTANDKKSIRIKARKTFSLLAESGVQGKVFRAKRKIPTGYAYQALPMDNNVIAGDYANILLEANSKTLSLVPKSGISIEKQLDKKLDVIKKTDVRGLAIDNNSFFNADFDTHGIRLIVENTSVKVGNFPISAIDKSAKRMIFRALFEKEKGKRKKKTTISFKESGPVQDYLKVFLKKIVKIQLRTDGSISNIVVRKNAADFTLSFRSEHIQKLLK
>NC_005090.1|WP_011139430.1|1524600_1525383_-|AraC-family-transcriptional-regulator
MIPLEHRYAQIEKAITYIDENFRAHPSVDEIAQNVGMSKYHFIRVFKEYAGVTPKQFLHCVTLNYAKEHIKESRSILESSLDIGLSSSSRLHELFVNLIGVTPREWRERGRGVLVTYGFGQTPFGEALIGFTDKGICYLGLMSDNKLEILGRFYELWGEAILEYDEKAAQKYLGYIFDRGEEGSPWNLGTNSQVNAWKALINLSRHLEDRVEGLIPCCGIISRSGAMSGHRWRIERGAALSLLDDIREKGSFGFSDNIDL
>NC_005090.1|WP_041571864.1|1524149_1524623_+|pyridoxamine-5'-phosphate-oxidase-family-protein
MQHRTKTHLLTKEEIKEALNLAQVGRIGIVCSDGFPYVLPLHFVYADEKIYLHGLPKGKKIEGIKQNPNVCFEIDQMVSLLKEGVENPCDVNTEFNSVILQGKASLVGDFEEKKSALKRIVEKFTPLLINQEIPDKMIQGTAIIRIDILNSTGRYYR
>NC_005090.1|WP_011139428.1|1522049_1524044_+|TonB-dependent-receptor
MKTAHSLFSSLVALSMLHTSALANDEALSLENVTITAQKQKENLQEVPLSVTVFQESDLEDRNIRSLQELAPYVPNFFLFDLGNMGALSPTIRGLSTNVTLGSPTVGLYVDGVPYTSTIGYDVMMEEVERIEVLRGPQGSLYGKNAEMGVVSVITKQPNNEFRAKAGVTLGSDNLREYTASASGPLVRDRLYLGIAGKHYEKDGFIDNTYTGEKYDDREHNYGKIQLRYTPSESLDISLISSRLKYDDKALSMNAYPVLDKRKISSDAGFNKSVVETHALHVKYAPNDYQIESITTYKKDRDYRLSDMDFTSSVGYHTLQDVAQRNLSEELRLSTQKDHYNWLLGLYGDHGKSQGGYEAFSPWPGYAGVFRQSQKSRSLGIFAHAGYQFDSHWKLSGGVRYDRDKKSIDDPSYGVQGDESFSEVSPKIALEYRFSPETSAYISATKGYHSGGFYVYSAPGYSNQYDKETLWSYEAGVKNSLFGNRLMLNASLYYMDIDDMQVLSVVNSYGQGYVSNAAKATSKGAELELAFRASESVTLLAGAGYNRTTFGEFSDFAGDYKGNTNPFAPRYNYSLGAQYRSIEGFYARVDWMGYGKMYLDNANAYEKDAYGLMNAKVGYEADSFDLYLYAKNLFDKNYDSEGYYGRYTYLSKPREVGVQGVYRF
>NC_005090.1|WP_011139427.1|1520995_1521934_-|helix-turn-helix-transcriptional-regulator
MSYRLNIENLREFMSETSDSCEHLVFPQKRGIYRAQKEWIASGITLFKCTLRAEDEVVIEQKESAFFGGAFIHVVLEGGVSFETSQPKGSFEYRRGYTTAMEALHPSGITRVARGVSVHSIGIHIHEDFLRSREIEWKKIAKEPRLLPSNPKVEWIAKSLYQGRGGAQSDADRLRVESQILEILSCELQREETRGGMERVKLSGYDLEALHKARVILEQNLKNPPSLIELSRAIHLNEFKLKFGFKRLFGVAPYEMLFLFRMQRARGLLEEGIFSVGEVAKEVGYAQQSSFSAAFFRHFGVLPKEVAKSWKD
>NC_005090.1|WP_011139426.1|1519034_1520843_+|excinuclease-ABC-subunit-UvrC
MQSETLLETLQNLPDQSGVYHYFDSRSKLLYVGKAKSLKKRVKSYFQFTPTLAPSPKLSPRIHKMISEAAFIRYIVVENEHDALILENSLIKQLKPKYNILLRDDKTYPYIYFDENESFPRLEITRKILPHKGVRYFGPYTTGARELLESLYELLPLVQKKGCLKAQKACLFYQIHRCLAPCESKISKERYGEIFKEALGLLQNHSKLISRLKERMEKLAENLRFEEAGELRDRIEKIKRIEAFSGIDLARLEDLDILAIATSGKHSMLTRLFMREGKVVSSTSTPLKAQEGLDEEEAYRRAILHYYDSFMPLPPKQILLPLELESKRELEAHLEGLFGRKIPLHHPKQGSKKALIDLALKNAEELLRLEGEKEEIPLLESLQELLGLESLPRRIEAFDTSHLRGEACVGAMVVYEEGFCKESYRRYALEGRDEYSQMREMLGRRAEAFDRESPPDLWLLDGGLGQIRLAQEIIESLGANVEIIAIAKEKIDAKAHRAKGAAKDILRTPTEEIRLLPSDKRLQLLQKIRDEVHRFAITYHRQQKLKKDRQIDLLEIKGIKKGKLKRLLDFFGSFEAIREASFEELCKVVSEGEARAILEASF
>NC_005090.1|WP_011139425.1|1518630_1519056_+|hypothetical-protein
MAHLSEAPQYTKLQKQSTWNRFKNLLPFSLRQSILFMYERGGVLFFALNHPGYLKEFNYKLSLIKSLLKEAAALLPDLRSINDVKAFVSHQALGTEEKDSLSDYHYTENSQATFSNLATTPEIHDKIEEIREIIHCNQKPS
>NC_005090.1|WP_011139435.1|1533725_1534310_+|hypothetical-protein
MATHQKASVEIVNQSGHKLLSVKIIHKYSDIASYTKQLDWTSIPNGAKSSNAQEVDYNTGAFTTGRDWWEVTWVNDLGEVYLTDPHNFRNLLDFGEKIGKFLSAPAMAIGSKVAITSPEPTSKTIGAAVAATGFIAELLLNSGTTDGYKQHILRSEDTKVTTQVIIKGNEVEFKSKSGSSHTGFRKVHTFPLPY
>NC_005090.1|WP_011139436.1|1534320_1534632_-|hypothetical-protein
MAVSPIGNVTYINQNMQTSSIQHANAQQRLDFQAMVNLQEMDDKLDEIEEVRPTEETEALDPDREKEKEQSAKHQEEEESEKEEPEEEAPAPPRSSHILDITV
>NC_005090.1|WP_011139437.1|1534636_1535968_-|fibronectin/fibrinogen-binding-protein
MNLSLLRRFSEQLASHQTLVNLKRTGDNLFKLECDNALYYIDLTRGRSTAFIAPPLFGMKQYQAPFDLSLQRYAARANILWARVEGGNRILQIGLENRGSYKSLRSILQLEFTGRNTNAILLDEAGVVIDALRHIGNERSFREVKIGQKLDSLPEPSKPLAERALPEGLGIQELLEMEYQKRLERELLERQKGAILSIEKKRERLLLSLSQITNEEELAQEAKRLRGQGALLLANLYKLSSFSSCVKLESQEGEVSLEMPPLARSFSEAAQIFFESSKKLEQKAKNLHIEREMLEDKILFYNRQIALIKAAKSVEDVMILAPKKQRAFKSEEKKEEFESFFIEGVKVSFGKNERENVKLLQSAKAEDTWLHVRDIPSSHMILRGGKGKIHANILQKAAEILVGFLDVSGGNYWVDFTKRKFVKITEGAQVVYAKHETITVKKE
>NC_005090.1|WP_041572204.1|1535967_1537500_-|AAA-family-ATPase
MISRLLIKNSPAFAHESLELHEGFNVFSGASGAGKSLLMESILALFGLRESNAELIEGVLEIPYSLEEWGVAHEEETTFSILKKEKVRYFVNSQSLSKKRVAEIASGFIKHVNPKNGEELEPARLLGLLDGFILHQEPSFKELLESYAERFLELTRVKEELKRVAEEESRVEELKEFARFEIAKIRQINPKKGEHEELMRLKKSLSKKEKIQESCEKVERFLEGERSVNAFLELLGREKEFFESVMNELRALIEEERGHLLELEEMDAESLLDRLEKLADLNRRYGGEEEALAYLVQKQKELERYENLTFSKEALQKELTQLEKSTKALSSRLHESRLSYVPKLESLLNERLGALLLPCAKLALEESTLHAKGQDWVRLMLGNAKAESVSSGEFNRLRLALLALEARHSKRLGVLILDEIDSNLSGEESEGVARVLQELSRSYQILAISHQPHMPSYAHRHFLVKKEAKGSTIERLDREGQILEIARIVSGSEITPEALEFAKKRLESKP
>NC_005090.1|WP_011139439.1|1537496_1538369_-|NAD(+)/NADH-kinase
MILMQPLSSLSKVGVILRPSSPSLKEFFLQVRSLFEREGIEVMLDSISGGMIGIYGCDFQRLCSESDMLVSIGGDGTLISVVRRSYPYGKPILGINMGRLGFLTDVRQDEVEAFVQKLKAGEYRIDSRLMLEGELSSPKGTQRFFAFNEAIVTRRPISGMIHVKASIGEEPFNTYFGDGLIVATPTGSTAYNISAGGPVVYPYSKNMILTPICAHSLTQRPLVLPSEFEVELEMLEGEFANIVVDGQEIMDFGYGDRLRLKVAERPALLVHKKEHNYFQVLREKFSWGDA
>NC_005090.1|WP_011139440.1|1538365_1539031_-|hypothetical-protein
MEEEVEIEEKKRSSAVFYIFLFTFLLLVVLGSVYYVFWAKSKDKPLFGGGNAPMEKPILPALSGESTSPELERLKIELESKQKQIERLSTSLAGAKSEQDSVKIKLQYTLKPKERIITECYAMNVGFWAIPENCALSLAANVNKELEEDKRVVAFEVQGIVDSTPYRGLSPELKQEGLASFRAREAIRMIQEKLPRAVVFEGPSVQEANHRGYRIKAYFVE
>NC_005090.1|WP_041572206.1|1539120_1539924_-|J-domain-containing-protein
MKLELFEKYIQISIQRDSEFLKRAISFATRHFSQSYRLSSSILILDDGERLKKDYFLNWAYHIGLQKESRQKSVPFERLLENSELPIRIKIMDEASVLEYVQVAMRFIQPERIALCLNRPSRLARRYLISAFEEYIVSYGKQELYLDSTRTQFWEKLMGILSQKVIHNVVLDFDYDSFKAHNRFEGFESWDYMTKEERLIRQSLKVLSCKVNDDWSTIKNRYLELAREFHPDNVYGQDSSIVQGYTERFRSIQEAYERLKVSLRQIA
>NC_005090.1|WP_041571865.1|1540081_1540831_+|sulfite-exporter-TauE/SafE-family-protein
MEYPILLGLGLFAGILAGFFGIGGGTFIVPAMILMGHDIKTAVGISIMQMTFSSLFGSYVNFKKSNLDLKDGLYVGIGGFLGAMWSGTVVDNVPSKFLEIAFFFIVIYSIYRFSRNPAAGTNDPNHPTPSRWLLIAIGAFTGVFAISLGIGGGMMLAPLLGYYLGYSSKKVIPIALFFVIFSSVSGFASLAYHGYVDYEHGLIVGLASLFGVQTGIYLLQKIDAKRHKYALLLMYIVVLLVMLKKILGL
>NC_005090.1|WP_011139443.1|1540896_1543710_+|excinuclease-ABC-subunit-UvrA
MIDKISVWGAKENNLKNINLEIPKNRLVVFTGLSGSGKSTLAFDTLYAEGQRRYIESLSSYARQFLDRVGKPNVDKIDGLTPAIAIDQKTTSKNPRSTVGTITEIYDYLRLLYARIGTQHCHLCGEPISQMSASDIIEQVLSLPQDSKAIILAPIIKEKKGTFADKIESLRHKGYVRAQVNGVMVRLDEEINLAKTKKHTIKIVIDRVVINEANKERIAQDVEKALKESYGEVEVEILGQTPDEPSRLIHYSEHLACFDCKVSFEPLEPLSFSFNSPKGACPECDGLGIRYSIDVKKIIDPHLPLGKGGIKVIYGFNKGYYSELFHAFCAQEGIDPQKSFEELEEHQKKWVLHGSASDVTFTWKSSTLKRPWRGIIQIAYDMFKDEKELNDYMSEKVCDLCHGHRLKLSSLAVRVAQRGMGEILDMPIEECYSFFEDEANFLYLSEQKRFIAAPILKEIRERLYFLYDVGLGYLSLGRDARTISGGESQRIRIASQIGSGLTGVMYVLDEPSIGLHERDTLRLIKTLRSLQEKGNSVIVVEHDKETIEHADFIVDIGPGAGKFGGEVVFAGTLEELKAQSTLTAQYLKGEKRIEYFHRRPQQDWLEIKNVTINNIKNLNVKIPLANFVCITGVSGSGKSSLILQTLLPVAQELLNNARKVKKVDGVEIEGLERLDKVIYLDQSPIGRTPRSNPATYTGVMDEIRSLFAETKEAQIRGYGVGRFSFNVKGGRCEKCQGEGEIKIEMHFLPDIMVKCDSCHGSRYNLQTLEVAYKGKNIADVLGMSVDEALEFFAPIPKIAQKLQTLSDVGLGYITLGQNAITLSGGEAQRIKLAKELGRKDTGQTLYILDEPTTGLHFADVDRLTKVLHHLTDLGNSVIVIEHNLDMIKNADYVIDIGPEGGSKGGRIVDEGTPEEVAKRWRERGSHTGEFLAKELGM
>NC_005090.1|WP_011139444.1|1543830_1544280_+|rhodanese-like-domain-containing-protein
MFRLFVTALIIALGLAQAQAADMGEKFDATFKAQVKAAKADMVMLSPKDAYKLLQENPDITLIDVRDPDELKAMGKPDVKNYKHMSRGKLEPLLAKSGLDPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMDKWLEEGLPSLD

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_005090_1	1.4|1386503|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386503-1386532	30	NZ_CP019050	Klebsiella pneumoniae subsp. pneumoniae strain RJA166 plasmid pRJA166c, complete sequence	69457-69486	6	0.8
NC_005090_1	1.4|1386503|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386503-1386532	30	NC_030948	Ralstonia phage RSP15 DNA, complete genome	73210-73239	6	0.8
NC_005090_1	1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386305-1386334	30	NC_010631	Nostoc punctiforme PCC 73102 plasmid pNPUN01, complete sequence	335604-335633	7	0.767
NC_005090_1	1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386305-1386334	30	NZ_CP045196	Acinetobacter indicus strain TQ23 plasmid p23TQ-37k, complete sequence	7129-7158	8	0.733
NC_005090_1	1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386305-1386334	30	NZ_CP044020	Acinetobacter indicus strain HY20 plasmid pAI02, complete sequence	13648-13677	8	0.733
NC_005090_1	1.2|1386371|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386371-1386400	30	HQ317390	Colwellia phage 9A, complete genome	42941-42970	8	0.733
NC_005090_1	1.5|1386569|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386569-1386598	30	LR134125	Klebsiella aerogenes strain NCTC10006 genome assembly, plasmid: 5	495066-495095	8	0.733
NC_005090_1	1.6|1386635|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386635-1386664	30	LC081338	Vibrio sp. 04Ya108 plasmid pSEA1 DNA, complete genome	110092-110121	8	0.733
NC_005090_1	1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386305-1386334	30	NZ_CP043831	Bacillus sp. BS98 plasmid unnamed1	84306-84335	9	0.7
NC_005090_1	1.8|1386768|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386768-1386797	30	NZ_CP041045	Paracoccus sp. AK26 plasmid pAK1, complete sequence	200396-200425	9	0.7
NC_005090_1	1.9|1386834|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT	1386834-1386863	30	MT773557	Myoviridae sp. isolate BML_S_1 genomic sequence	132129-132158	9	0.7

1. spacer 1.4|1386503|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP019050 (Klebsiella pneumoniae subsp. pneumoniae strain RJA166 plasmid pRJA166c, complete sequence) position: , mismatch: 6, identity: 0.8

agcttgaggatggtacatataccctcacaa	CRISPR spacer
gttttgaggatggtacatttgccctcacag	Protospacer
. .*************** *.********.

2. spacer 1.4|1386503|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NC_030948 (Ralstonia phage RSP15 DNA, complete genome) position: , mismatch: 6, identity: 0.8

agcttgaggatggtacatataccctcacaa	CRISPR spacer
aagttgcggatggtacatataccctaactt	Protospacer
*. *** ****************** **  

3. spacer 1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NC_010631 (Nostoc punctiforme PCC 73102 plasmid pNPUN01, complete sequence) position: , mismatch: 7, identity: 0.767

tcgccaaagaagttaccaatctaattgagc	CRISPR spacer
ttcacaaagaagttaccaatttaattgctg	Protospacer
*.  ****************.******   

4. spacer 1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP045196 (Acinetobacter indicus strain TQ23 plasmid p23TQ-37k, complete sequence) position: , mismatch: 8, identity: 0.733

tcgccaaagaagttaccaatctaattgagc	CRISPR spacer
acattaaagaagtaaccaatctaattaatg	Protospacer
 *...******** ************.*  

5. spacer 1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP044020 (Acinetobacter indicus strain HY20 plasmid pAI02, complete sequence) position: , mismatch: 8, identity: 0.733

tcgccaaagaagttaccaatctaattgagc	CRISPR spacer
acatgaaagaagtaaccaatctaattaatg	Protospacer
 *.. ******** ************.*  

6. spacer 1.2|1386371|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to HQ317390 (Colwellia phage 9A, complete genome) position: , mismatch: 8, identity: 0.733

aaggttgatcttgttttcattgcaacaagg	CRISPR spacer
atcattgatcttgttttcattccaagcatc	Protospacer
*  .***************** ***  *  

7. spacer 1.5|1386569|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to LR134125 (Klebsiella aerogenes strain NCTC10006 genome assembly, plasmid: 5) position: , mismatch: 8, identity: 0.733

agctacatagcctgcaactgagtcgaaata	CRISPR spacer
ccgtacattgcctgcaactgagtcatatca	Protospacer
   ***** ***************. * .*

8. spacer 1.6|1386635|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to LC081338 (Vibrio sp. 04Ya108 plasmid pSEA1 DNA, complete genome) position: , mismatch: 8, identity: 0.733

aaaagaatggtacaagaagtacgctaacac	CRISPR spacer
tcgtcactgctacaagaagtacgctaacaa	Protospacer
  .  * ** ******************* 

9. spacer 1.1|1386305|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP043831 (Bacillus sp. BS98 plasmid unnamed1) position: , mismatch: 9, identity: 0.7

tcgccaaagaagttaccaatctaattgagc	CRISPR spacer
catggaaaaaagttaccaatctaattatgt	Protospacer
.    ***.*****************. *.

10. spacer 1.8|1386768|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP041045 (Paracoccus sp. AK26 plasmid pAK1, complete sequence) position: , mismatch: 9, identity: 0.7

atttcaggggcaaggaaatagaagctgatg	CRISPR spacer
gcggcaggggcaaggcgatagaagctgcgt	Protospacer
..  *********** .**********   

11. spacer 1.9|1386834|30|NC_005090|PILER-CR,CRISPRCasFinder,CRT matches to MT773557 (Myoviridae sp. isolate BML_S_1 genomic sequence) position: , mismatch: 9, identity: 0.7

catcagtatgctcagagcagacgacaaaga	CRISPR spacer
ggatgttatgctcagagcagacggaaaagg	Protospacer
 . .. *****************. ****.