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
NZ_CP017458	Legionella pneumophila subsp. fraseri strain Dallas 1E chromosome, complete genome	3 crisprs	cas2,cas1,cas9,RT,cas3,PD-DExK,DinG,DEDDh,WYL,csa3	0	2	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP017458_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP017458_1

200541-201302

TypeII

Consensus_repeat	Method
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CRISPRCasFinder
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CRT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	PILER-CR

10 spacers

cas4,cas2,cas1,cas9

The CRISPR arrays of NZ_CP017458_1

>merge|NZ_CP017458|1|200541-201302|CRISPRCasFinder,CRT,PILER-CR
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGGAAGAAGTCAGGCTACGACCATGAAAACGATGCGACGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTTCTTTAAGCTTTTAAAACGCTTTTCACATACAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCTTTTAGCATTCGAGATTTTGATGATGAAATGGAAGTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTCAAAGAAAGTTAATCCCGTTGAGTGGGTTAGGATGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGATACTTTGTGGGTTTTAGTAGAGGAGCCTTTCTTGTCGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGGTTGAGATCTTTTGAAGTAGTGGAAAAGGGGGATGTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTAAGGATAAACAGACAAGCCTTTTTTGCTGAGAAAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTCAAGAATGCGGGCAATGTGTCAATTGCATTACGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCGGCTGGTATTACAAGGATGCAAGACACATGGATGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTGTAGATGATGGTTTTCAAGTGGCAATTGTTCAAGAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>NZ_CP017458|1|1|200541-201302|CRISPRCasFinder
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGG	AAGAAGTCAGGCTACGACCATGAAAACGATGCGAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTTCTTTAAGCTTTTAAAACGCTTTTCACATACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTTAGCATTCGAGATTTTGATGATGAAATGGAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAAGAAAGTTAATCCCGTTGAGTGGGTTAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATACTTTGTGGGTTTTAGTAGAGGAGCCTTTCTTGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTTGAGATCTTTTGAAGTAGTGGAAAAGGGGGATGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAGGATAAACAGACAAGCCTTTTTTGCTGAGAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAGAATGCGGGCAATGTGTCAATTGCATTAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CGGCTGGTATTACAAGGATGCAAGACACATGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGTAGATGATGGTTTTCAAGTGGCAATTGTTCAAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>NZ_CP017458|1|1|200541-201302|CRT
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGG	AAGAAGTCAGGCTACGACCATGAAAACGATGCGAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTTCTTTAAGCTTTTAAAACGCTTTTCACATACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTTAGCATTCGAGATTTTGATGATGAAATGGAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAAGAAAGTTAATCCCGTTGAGTGGGTTAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATACTTTGTGGGTTTTAGTAGAGGAGCCTTTCTTGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTTGAGATCTTTTGAAGTAGTGGAAAAGGGGGATGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAGGATAAACAGACAAGCCTTTTTTGCTGAGAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAGAATGCGGGCAATGTGTCAATTGCATTAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CGGCTGGTATTACAAGGATGCAAGACACATGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGTAGATGATGGTTTTCAAGTGGCAATTGTTCAAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>NZ_CP017458|1|1|200613-201302|PILER-CR
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTTCTTTAAGCTTTTAAAACGCTTTTCACATACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTTAGCATTCGAGATTTTGATGATGAAATGGAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAAGAAAGTTAATCCCGTTGAGTGGGTTAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATACTTTGTGGGTTTTAGTAGAGGAGCCTTTCTTGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTTGAGATCTTTTGAAGTAGTGGAAAAGGGGGATGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAGGATAAACAGACAAGCCTTTTTTGCTGAGAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTCAAGAATGCGGGCAATGTGTCAATTGCATTAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CGGCTGGTATTACAAGGATGCAAGACACATGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGTAGATGATGGTTTTCAAGTGGCAATTGTTCAAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP017458.1\|WP_027228132.1\|207676_207895_-\|AlpA-family-phage-regulatory-protein	unknown	unknown	gnl\|CDD\|225848
NZ_CP017458.1\|WP_027228120.1\|193644_194040_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027228122.1\|194904_197385_-\|VirB4-family-type-IV-secretion/conjugal-transfer-ATPase	unknown	unknown	gnl\|CDD\|273346
NZ_CP017458.1\|WP_011214455.1\|210268_210475_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_050598121.1\|208355_208688_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027228129.1\|201517_202111_-\|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl\|CDD\|273040
NZ_CP017458.1\|WP_080272190.1\|194036_194183_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027228134.1\|208677_209628_+\|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein	unknown	unknown	gnl\|CDD\|378065
NZ_CP017458.1\|WP_027228124.1\|197662_197953_-\|TrbC/VirB2-family-protein	unknown	unknown	gnl\|CDD\|368210
NZ_CP017458.1\|WP_027228131.1\|203386_207505_-\|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12	cas9	cd09704_cas9_CAS-II-B	gnl\|CDD\|187835
NZ_CP017458.1\|WP_027228125.1\|197949_198153_-\|carbon-storage-regulator	unknown	unknown	gnl\|CDD\|376847
NZ_CP017458.1\|WP_027228123.1\|197371_197653_-\|VirB3-family-type-IV-secretion-system-protein	unknown	unknown	gnl\|CDD\|368285
NZ_CP017458.1\|WP_027228126.1\|198165_198528_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027228127.1\|198493_199363_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_154219812.1\|209860_210028_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_032830294.1\|202091_202391_-\|CRISPR-associated-endonuclease-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|187856
NZ_CP017458.1\|WP_027228135.1\|210423_211629_+\|site-specific-integrase	unknown	unknown	gnl\|CDD\|271189
NZ_CP017458.1\|WP_027228128.1\|199526_200192_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|224885
NZ_CP017458.1\|WP_027228130.1\|202397_203390_-\|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187766
NZ_CP017458.1\|WP_027228121.1\|194197_194908_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|271354

Protein	Function_ID	Function_description	E-value
NZ_CP017458.1\|WP_027228129.1\|201517_202111_-\|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.	4.12817e-15
NZ_CP017458.1\|WP_027228131.1\|203386_207505_-\|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12	gnl\|CDD\|187835	cd09704, Csx12, CRISPR/Cas system-associated protein Cas9. 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; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II.	0
NZ_CP017458.1\|WP_027228134.1\|208677_209628_+\|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.	1.72252e-20
NZ_CP017458.1\|WP_027228124.1\|197662_197953_-\|TrbC/VirB2-family-protein	gnl\|CDD\|368210	pfam04956, TrbC, TrbC/VIRB2 family. Conjugal transfer protein, TrbC has been identified as a subunit of the pilus precursor in bacteria. The protein undergoes three processing steps before gaining its mature cyclic structure. This family also contains several VIRB2 type IV secretion proteins. The virB2 gene encodes a putative type IV secretion system and is known to be a pathogenicity factor in Bartonella species.	3.97251e-12
NZ_CP017458.1\|WP_027228125.1\|197949_198153_-\|carbon-storage-regulator	gnl\|CDD\|376847	pfam02599, CsrA, Global regulator protein family. This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay. In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes. RmsA binds to RmsB regulatory RNA.	3.13961e-15
NZ_CP017458.1\|WP_027228123.1\|197371_197653_-\|VirB3-family-type-IV-secretion-system-protein	gnl\|CDD\|368285	pfam05101, VirB3, Type IV secretory pathway, VirB3-like protein. This family includes the Type IV secretory pathway VirB3 protein, that is found associated with bacterial inner and outer membranes. The family also includes the conjugal transfer protein TrbD family that contains a nucleotide binding motif and may provide energy for the export of DNA or the export of other Trb proteins.	5.20879e-18
NZ_CP017458.1\|WP_027228122.1\|194904_197385_-\|VirB4-family-type-IV-secretion/conjugal-transfer-ATPase	gnl\|CDD\|273346	TIGR00929, CAG_pathogenicity_island_protein_23, type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).	0
NZ_CP017458.1\|WP_032830294.1\|202091_202391_-\|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.	1.31074e-05
NZ_CP017458.1\|WP_027228132.1\|207676_207895_-\|AlpA-family-phage-regulatory-protein	gnl\|CDD\|225848	COG3311, AlpA, Predicted transcriptional regulator [Transcription].	1.23875e-05
NZ_CP017458.1\|WP_027228135.1\|210423_211629_+\|site-specific-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.	3.90026e-37
NZ_CP017458.1\|WP_027228128.1\|199526_200192_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|224885	COG1974, LexA, SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms].	1.51213e-17
NZ_CP017458.1\|WP_027228130.1\|202397_203390_-\|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.	8.09137e-79
NZ_CP017458.1\|WP_027228121.1\|194197_194908_-\|hypothetical-protein	gnl\|CDD\|271354	cd14262, VirB5_like, VirB5 protein family. This family contains VirB5 domains, including TraC, a VirB5 homolog encoded by the pKM101 plasmid, and similar proteins. VirB5 is one of 11 conserved proteins (VirB1-VirB11) in Agrobacterium tumefaciens, the causative agent of crown gall disease, that span the inner and the outer membrane, and is involved in type IV DNA secretion systems (T4SS) which mediate the translocation of virulence factors (proteins and/or DNA) from Gram-negative bacteria into eukaryotic cells. VirB5 assembles extracellular pili by interacting with several essential proteins. VirB2-VirB5 complex formation precedes incorporation into pili; it depends on the inner membrane protein VirB4 to interact directly with and stabilize VirB8 in order for VirB5 to bind to VirB8 and VirB10. Mutagenesis studies show that VirB5 proteins participate in protein-protein interactions important for pilus assembly and function.	6.54808e-18

>NZ_CP017458.1|WP_027228128.1|199526_200192_+|helix-turn-helix-domain-containing-protein
MNIKKEIGKRILEARKAKGLTLKALGELAGGLKQTRLTNWEQGVRTPGPEEIKSLAQALDVSPAYLMCLSDEKRFKEVQSPSQLVPLLTHYQACEALLHIQTIREQENPNNITLISVSMALLPVLSADAFALKMLDDSMIPEIRINDIQVIDPNAQPNPGDYVAVKVRGKEEAIICVYKKLSYTSSQFELLTLNDNWPDIKVSDIAEVNILGKLVLNIRTY
>NZ_CP017458.1|WP_027228127.1|198493_199363_-|hypothetical-protein
MMDFVINGDELEAMCGLPHIQQLTYLRGIRPYMDVKTRIVGIKRRISHQSISEQLYVEPHQGIKSQSFSRDQIRRAVSGLVRAGLIEVQSEGMHLILKCLLASQHYSVQNKAAINPPQKATIKPRGESLENTGLSEVEAPKADTVEPSKAAIPHKDNYYIYLLSQFEKFWSLYPEKKSKNNAQAVFEELKPNAELFHTIINALNAQINHRDTMKLQGTWVPPWKYPANWLAQRCWEDELSTDALQEKHHAEHTKNTRKRHTTEDLFCPPCDVEERGNNNVIQLQRYLQR
>NZ_CP017458.1|WP_027228126.1|198165_198528_-|hypothetical-protein
MSSSSKDTFNAERRIDLLFSKFAAFYGHVWRSQFKDEVFLKFAKKEWQEALADFTDAVLTKATLNCREFYELPPTLPQMLYCCRQIKKQESFYVVKDVYQPANKAVVSSCLQKCKELLAK
>NZ_CP017458.1|WP_027228125.1|197949_198153_-|carbon-storage-regulator
MLVLTRKAGQQILIGKGLIQMKVLKVDDDIISIGIKAPQHIDIDREEVYLKKLQKEQAESSMQKVAL
>NZ_CP017458.1|WP_027228124.1|197662_197953_-|TrbC/VirB2-family-protein
MSKFNRLSLSISDLYLVAVCTLLPSLSHAQSIESIINRTINYLQGGLARTVGVFCIIIAGYLCLARQKFPKEYFVMILVGMGIIFGGSSLYSTLIG
>NZ_CP017458.1|WP_027228123.1|197371_197653_-|VirB3-family-type-IV-secretion-system-protein
MSDLAISPIFNALTRPAMIAGVTFEYHMLNLIVSMCVFIGLSPLYGLIFIPLHVFGWLVCRYDTHFFTICAKRYLLPEAPNASLWRVRAYEPF
>NZ_CP017458.1|WP_027228122.1|194904_197385_-|VirB4-family-type-IV-secretion/conjugal-transfer-ATPase
MNLSKTLKQVYREAKVSDLFPITHLNTPSVFESQSGFVGSVLKVDGAAFEIEETDTLNHQRFLLHQALVSLDSRFIIYVTTHRQKISCPLIGEFKPGFAKDLDERYQQRFKDKNLYKNTLYITVVLKGDDSSKTGSWLQWAKSLSIQGNSELAEHHREQNIQTLTHAVEQLQANLAPFRASLLGQQDDALGFSELLQFLGLVINAGHPASFKQPVYSPPIANSIPHAFKHETKYPEGHIGQYLSGCQILFGECIQFQGNTQNDCLFGAMLSLKKYPTHTASILLDSLLSLDCEFIATHSFAPIGRDSALDTISKKRSKLLNAEDKALSQTSALTDLEDGIASETLLLGAHHHTVMLLAPSKPLLDAAILEATKRYGAAGIVVVKETLGQEPAFWSQLPCNQHFITRASLITSQNFVDFCPLHNTQTGFSNENFLGGAVTLLETPSKTPVYFNYHARGSKTNPSKGHAAIFGGNNAGKTTLVNFLDAQMGRFGGRSFFIDRDESSKIYVLASGNSSYIKVEPSNPIAMNPLQLPDTAENRSFLKSWFATLVQEEGERVIPSGIAEIINDCIDYNFEQLAPEFRTLSHLSQFLPVDFPRWPHLRRWLKRNDSRIDGEFHWLFDNPNDALNLDFDKVGFDVTYLMDQVQSIIATPVYLYLLHRMRQCLDGRLTSFIIAEAWQLFASPFWEKALREWLPTIRKKNGHFIFDTQSPKTITDSPIKHIVLDNLATLIAFPNPLADRETYMEHLKLTEAQFEAIKENTPESRIFLYKQDHEAFLCKLDLSGLSQYIRVLSANTQSVKLLDDIIQEVGHEPELWLPVFFERSKK
>NZ_CP017458.1|WP_027228121.1|194197_194908_-|hypothetical-protein
MKRTVCFLIAALSLSNVSHADILGVEDAQLILLAMKQLSELQEQYRVLSDTYQTAKNQLDNLNQLKSMNSGHYGFGDFNNSLDSLQSWQSPVSTWQDALQNLSGGNQQRYQALVDAYEKNHPALDEASYSRFTTPANAMRFKEDKAVNRAVMVQTTESYNEINKHMEALHKLSQQIEKTPNTKGAIDLNSRLITEIGFIQLMSLRLQALISQQSAQENLSALQDRAEMAKFNRLPK
>NZ_CP017458.1|WP_080272190.1|194036_194183_-|hypothetical-protein
MKWLLSVLMMVVLSGCSKPPDLDSPCHHFGQYCPQYPINDEPIMELAK
>NZ_CP017458.1|WP_027228120.1|193644_194040_-|hypothetical-protein
MNHLLKSLMVVLIAAVISACQHENPLKTQPAKASVTFLINASANAEKRLHFAIHKDAYGFAYLECMEGKQSPEIRCDALYQGMIAFAKEGHYSGFQKITLADLTDKNLFELLADGYAETAATTWPHLVSGT
>NZ_CP017458.1|WP_027228129.1|201517_202111_-|CRISPR-associated-protein-Cas4
MDTSSYKLPVNMIRQYCFCPRIVYYHMVIGLKVAYPGWVQYGEEYQHKQQILDKRRTLSKFKPISEQAILRQNTMLEHPSYPFYGICDGIIEDELEIIPIELKSFASKISLGQKMQLTAYGMLSELIFEKSCTRGYIITGEKAKAKLIKIDEKSKFKVLEIYAKIKKIFDTETLPYSTANGLQCIQCEFLNHCNDRF
>NZ_CP017458.1|WP_032830294.1|202091_202391_-|CRISPR-associated-endonuclease-Cas2
MQTRLYKEYIVSYDIRDNSIRRTIYERLKDIGLTPVQKSVFWGYLNEPEKRYLTNVLKKELAKQDTAFITPCKLTQEYEVNLINLELDELRKPDGHIIV
>NZ_CP017458.1|WP_027228130.1|202397_203390_-|CRISPR-associated-endonuclease-Cas1
MKHLTLSEQGSSCKLQGERILVFNKDHMVFEGTLNRLKTISIAKQGVTLTSNLLVACAMRGIQIFILDYSGKAVCSLQGGLHRTAKVRENQFKYIYTKEASNMAARFILAKIKNQSAVLKYFAKAKNRPENEKIILHTASQKIAGIVSNITETNWIKLQDWRFTLLGFEGSAAKIYWETVKEVNLVCSDFEGRRPRVNKDITNSMLNYAYSILSSWVWQAITNAGLELYAGILHTSKPGKPSLVLDLMEEFRPWCADRIIFKLRARAQKQNELTPALKKALIDEMANLYAKPLPYHKRRISLESIIQRQVYHLSAVFSGEGKYKGYLFKW
>NZ_CP017458.1|WP_027228131.1|203386_207505_-|type-II-B-CRISPR-associated-RNA-guided-endonuclease-Cas9/Csx12
MESSQLLSPIGIDLGGKFTGVCLSHLESFAELPNHANTKYSVILMDHNNFQLSQAQRRITRHRVRNKKRNQFVKRVALQLFQHMLSRELNVKEEIALCHYLNNRGYTYVDTDLDEYLKDETTVNLLKELLPPESEHNFIDWLLQKMQSSKFREILGSRVEEKKDDKELKNAVKNIKNFITGFEKNSVEGHRHRKVYFENIKSDITNDNQLDGIKKKIPSVCLSNLLGHLSNLQWKNLHRYLAKNPKQFDEQTFGNEFLRMLKNFKHLKGSQESLAVRDLIQQLEQSKDYISILEKTPPEITIPPYEARTNTGMEKDQSLLLNPEKLNNLYPKWRNLIPGIIDAHPFLEKDLEHTKLRDRKRLISPSKQDEKRDSYILQRYLDLNKKIDKFKIKKQLSFLGQGKQLPANLIETHKEMETHFSSSLVSALIQIASAYNKEREDAAQGIWFDNAFSLCELSNINPPRKQKILPLLVGAILSEDFINNKDKWAKFKSFWNTHKIGRTLLKYKCKEIEEARKNSGNAFKIDYEEALNHPEHSNNKALTKIIQTIPDIIQAIQSHLGHNDSQALIYNNPFSLSQLYTILETKRDGFHKNCVAVTCENYWRSQKTEIDPEISYASRLPADSVRPFDGVLARMMQRLAYEIAMAKWEQIKHIPDNSSLLIPIYLEQNRFEFEESFKKIKGISRDKTLEQAIEKQNIRWEEKFQRIINASMNVCPYKGTLIGGQGEIDHIYPRSLSKKHFGTIFNSEANLIYCSSQGNREKKEEHYLLEHLSPIYLKHQFGTDNVSDIKNFISQNVANIKKYISFHLLTPEQQKAARHALFLDYDDEAFKTVTKFLMSQQKARVNGTQKFLGKQIMEFLSTLADSKQLQLEFSIKQINAEEVHNHRELLSKQEPKLAKSQQQSFPSHAIDATLTMGIGLKEFPQFSQELDNSWFINHLMPDEVHLNPVQSKEKYNKPNISSIPLFKDSLYAERFIPVWVKGETFAIGFSEKDLFEIKPSNKEKLFTLLKTYSTKNPGESLQELQAISKAKWLYFPINKTLALEFLHHYFHKETVTPDDTTVCHFINSLRYYTKKESITVKILKESMPVLSVRFESSKKNVLGTFKHTIALPATKDWERLFNHPNFLALKANPNPNPKEFNEFIKKYFLSENNPNSDIPNNDHTIKPQKHKTVRKVFSLPVIPGNAGTMMRIRRKDNKGQPLYQLQTIDDTPSMGIQINEGKLVKQEVLMDAYKTRNLSTIDGINNSERQAYAAFDNWLTLPVSTFKPEIIKLEMKPHSKTRRYIRITQSLADFIKTIDEALMIKPSDSIDDPLNMPNEIVCKNKLFGNELKPRDGKMKIVSTGKTVTYEFESDSTPQWIQKLYVTQLKKHP
>NZ_CP017458.1|WP_027228132.1|207676_207895_-|AlpA-family-phage-regulatory-protein
MTKLPEIGFLRANQIIGDKNANPPIPALIPIGKSTWWAGVKSGRFPKPIKFGSRITVWRVEDIREFIEKASL
>NZ_CP017458.1|WP_050598121.1|208355_208688_+|hypothetical-protein
MASPRQISRCFADLVEMGKLVKIGYGIYAKAYRSEYLNKPVIKGGFSQICKEALTKLGVEWIPGSAEQAYNSGLSTQVPVRTIVQLKSRFRGHLKYGNRQLVVEKGINAR
>NZ_CP017458.1|WP_027228134.1|208677_209628_+|nucleotidyl-transferase-AbiEii/AbiGii-toxin-family-protein
MLGKPLLELITTTGEILELEDLVIEKDYYVAQVINALSKVENDYFRLVFCGGTCLAKAHKVIYRMSEDIDFKIQIKEIDEHLSKTRLLKELKIFRSLIQSKLTHLDLSIGNTVVRNEGQYSRIELDYPSVFPFNSRLRPHILLEFTLSNIRLATSSLPIKTLIEETLENIILFAPCFTHCISVNETAIEKWAGLTRRVVAIERNYHPDDETLIRHVYDLNAIKQASKIDENFFTLAKTIVSNDAKQFKNQHPEYADNPSEEIKQSLSLLKNKLIWKARYQEFIETMVYDNINTIDYETAIANIEHISTKIMGFLSE
>NZ_CP017458.1|WP_154219812.1|209860_210028_-|hypothetical-protein
MENKNALQYGVFTPKAFKFFGQILGTFSKILGTFWVIFEPTENHKRQPYQPENWI
>NZ_CP017458.1|WP_011214455.1|210268_210475_+|hypothetical-protein
MKWVKLKKYCQDSGDTSDAVHAKRKRGIWLDGVQCKLGPDGNIWINLVEVEKWVENGNKATNCSLRAV
>NZ_CP017458.1|WP_027228135.1|210423_211629_+|site-specific-integrase
MGGKRQQGNELQPPRGVSIRQWETGSAIRIIFSYRGVQCRETLKLEPTKANLKYAERLRGEIINAIALGTFNYADYFPDSKRAKLFGHAIIKATTAELLKDYMAIAERTLEASTYNGYRKVCEAHLYPAFGKIPIRELSPVIIRNWITGLNVTVKTVRNILTPLRNMLDQAMNDGIIERNPLDRLVLSKLLNKKASKSDWEVDPFDQDEIKAILDAATGQARNLFQFAFFSGLRTSELIALEWNDIDWLKGTVRVSKAVVLKQEKGTKKKSGVRDVLLLPPAVDALKNQKAFTYLEGSRVFYNPRTNSPWETDGQIRKTCWTHLLKKAGVRYRNPYQTRHTYASMLLSAGENPLWLATQMGHRDTEMIIKHYGRWIPDKSTVAGYQPVSDWNLSMGTTKIG

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Crispr_ID: NZ_CP017458_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP017458_2

1745474-1745594

Orphan

Consensus_repeat	Method
CCTGGCAGCAGCGCTGATCAGCATTCCAAAAAGC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP017458_2

>merge|NZ_CP017458|2|1745474-1745594|CRISPRCasFinder
CCTGGCAGCAGCGCTGATCAGCATTCCAAAAAGCGTCACCACGCTTAACTTGAGCGACAATGGCTTTTATCAACTAAGCGCTGATCGCCTGGCAGCAGCGCTGACCAGCATTCCAAAAAGC

>NZ_CP017458|2|2|1745474-1745594|CRISPRCasFinder
CCTGGCAGCAGCGCTGATCAGCATTCCAAAAAGC	GTCACCACGCTTAACTTGAGCGACAATGGCTTTTATCAACTAAGCGCTGATCG
CCTGGCAGCAGCGCTGACCAGCATTCCAAAAAGC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP017458.1\|WP_027227098.1\|1741511_1742168_+\|methyltransferase	unknown	unknown	gnl\|CDD\|226608
NZ_CP017458.1\|WP_027227095.1\|1736847_1737912_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|375919
NZ_CP017458.1\|WP_027227101.1\|1745077_1745263_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227096.1\|1738736_1740161_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227093.1\|1733353_1735372_-\|enoyl-CoA-hydratase/isomerase-family-protein	unknown	unknown	gnl\|CDD\|236864
NZ_CP017458.1\|WP_027227108.1\|1753181_1753709_-\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|366181
NZ_CP017458.1\|WP_027221798.1\|1751095_1752043_-\|MerR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|133381
NZ_CP017458.1\|WP_027227092.1\|1732558_1733293_-\|L,D-transpeptidase-family-protein	unknown	unknown	gnl\|CDD\|182341
NZ_CP017458.1\|WP_027227110.1\|1754665_1756447_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224055
NZ_CP017458.1\|WP_027221790.1\|1740950_1741325_-\|Y4oB-family-protein	unknown	unknown	gnl\|CDD\|378249
NZ_CP017458.1\|WP_027227103.1\|1747795_1748866_-\|glutamate-5-kinase	unknown	unknown	gnl\|CDD\|235460
NZ_CP017458.1\|WP_027227104.1\|1749049_1749475_-\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|379228
NZ_CP017458.1\|WP_027227109.1\|1753705_1754662_-\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|377252
NZ_CP017458.1\|WP_027227107.1\|1752366_1753116_-\|MerR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|133381
NZ_CP017458.1\|WP_027227102.1\|1746533_1747787_-\|glutamate-5-semialdehyde-dehydrogenase	unknown	unknown	gnl\|CDD\|234685
NZ_CP017458.1\|WP_027227097.1\|1740271_1740949_-\|RES-family-NAD+-phosphorylase	unknown	unknown	gnl\|CDD\|378053
NZ_CP017458.1\|WP_027227094.1\|1735364_1736684_-\|acetyl-CoA-C-acetyltransferase	unknown	unknown	gnl\|CDD\|181265
NZ_CP017458.1\|WP_027227111.1\|1756439_1757900_-\|ABC-F-family-ATP-binding-cassette-domain-containing-protein	unknown	unknown	gnl\|CDD\|223562
NZ_CP017458.1\|WP_027227099.1\|1742388_1744704_+\|phosphoenolpyruvate-carboxylase	unknown	unknown	gnl\|CDD\|225227
NZ_CP017458.1\|WP_027227105.1\|1749764_1750745_-\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_CP017458.1\|WP_027227098.1\|1741511_1742168_+\|methyltransferase	gnl\|CDD\|226608	COG4123, COG4123, Predicted O-methyltransferase [General function prediction only].	9.4923e-17
NZ_CP017458.1\|WP_027227095.1\|1736847_1737912_-\|hypothetical-protein	gnl\|CDD\|375919	pfam18493, DUF5617, Domain of unknown function (DUF5617). This is a C-terminal domain of unknown function found in gammaproteobacteria.	0.00124043
NZ_CP017458.1\|WP_027227094.1\|1735364_1736684_-\|acetyl-CoA-C-acetyltransferase	gnl\|CDD\|181265	PRK08170, PRK08170, acetyl-CoA C-acetyltransferase.	0
NZ_CP017458.1\|WP_027227109.1\|1753705_1754662_-\|GNAT-family-N-acetyltransferase	gnl\|CDD\|377252	pfam04229, GrpB, GrpB protein. This family has been suggested to belong to the nucleotidyltransferase superfamily. It occurs at the C-terminus of dephospho-CoA kinase (CoaE) in a number of cases, where it plays a role in the proper folding of the enzyme.	2.95879e-75
NZ_CP017458.1\|WP_027227093.1\|1733353_1735372_-\|enoyl-CoA-hydratase/isomerase-family-protein	gnl\|CDD\|236864	PRK11154, fadJ, fatty acid oxidation complex subunit alpha FadJ.	6.39957e-165
NZ_CP017458.1\|WP_027227108.1\|1753181_1753709_-\|GNAT-family-N-acetyltransferase	gnl\|CDD\|366181	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.	5.74582e-10
NZ_CP017458.1\|WP_027221798.1\|1751095_1752043_-\|MerR-family-transcriptional-regulator	gnl\|CDD\|133381	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.	1.42202e-39
NZ_CP017458.1\|WP_027227092.1\|1732558_1733293_-\|L,D-transpeptidase-family-protein	gnl\|CDD\|182341	PRK10260, PRK10260, L,D-transpeptidase; Provisional.	1.06069e-44
NZ_CP017458.1\|WP_027227110.1\|1754665_1756447_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224055	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].	6.81973e-134
NZ_CP017458.1\|WP_027221790.1\|1740950_1741325_-\|Y4oB-family-protein	gnl\|CDD\|378249	pfam09722, DUF2384, Protein of unknown function (DUF2384). Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. The function is unknown.	1.89824e-05
NZ_CP017458.1\|WP_027227103.1\|1747795_1748866_-\|glutamate-5-kinase	gnl\|CDD\|235460	PRK05429, PRK05429, gamma-glutamyl kinase; Provisional.	4.38624e-128
NZ_CP017458.1\|WP_027227104.1\|1749049_1749475_-\|GNAT-family-N-acetyltransferase	gnl\|CDD\|379228	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions.	7.29365e-12
NZ_CP017458.1\|WP_027227107.1\|1752366_1753116_-\|MerR-family-transcriptional-regulator	gnl\|CDD\|133381	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.	1.23107e-48
NZ_CP017458.1\|WP_027227102.1\|1746533_1747787_-\|glutamate-5-semialdehyde-dehydrogenase	gnl\|CDD\|234685	PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.	0
NZ_CP017458.1\|WP_027227097.1\|1740271_1740949_-\|RES-family-NAD+-phosphorylase	gnl\|CDD\|378053	pfam08808, RES, RES domain. This presumed domain contains 3 highly conserved polar groups that could form an active site. These are an arginine, glutamate and serine, hence the RES domain. The domain is found widely distributed in bacteria. The domain is about 150 residues in length.	1.67994e-28
NZ_CP017458.1\|WP_027227111.1\|1756439_1757900_-\|ABC-F-family-ATP-binding-cassette-domain-containing-protein	gnl\|CDD\|223562	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only].	1.30909e-85
NZ_CP017458.1\|WP_027227099.1\|1742388_1744704_+\|phosphoenolpyruvate-carboxylase	gnl\|CDD\|225227	COG2352, Ppc, Phosphoenolpyruvate carboxylase [Energy production and conversion].	1.9644e-56

>NZ_CP017458.1|WP_027227101.1|1745077_1745263_-|hypothetical-protein
MMFTLLLCLDTHDLQDLAQRLMHKKRLPYATSHAEKRLHLGLKNNGLLMYNQRFREGKRQE
>NZ_CP017458.1|WP_027227099.1|1742388_1744704_+|phosphoenolpyruvate-carboxylase
MKQDVSHLPRELSRMVFWSLTRLKKAIAEVYGKETYERIEQIRLSMQDTIGSESFALGKVLHNLQMELSKLDKKQLYQIAHGFSLMMELINTCENAYRIFRINQRKEQIYSDFPQGIHYVLTAHPTEARTNEFLKLFKEIRDYLVEVLKSPYLMNESHLDQMLKISLQINISYHEKPSVEDEAQYIYQYALHPLNIKLYHSFLEKGVPIQLRTWVGGDKDGHSGVNEKIMLKSLELSRSFFIAYIQECLKEVLGIIKLSTALNKNKFLADQIDQLVKKANGLKKIQPKDHEKVSAFKKELTAIQSNTLKFLNFEPEQFSIISSIFHLYPALVMPIELREDSAIVKESLTSIKKTTITKMLEQVHSITHGTDPKNYIRGFILSMVESAEDIKNGINLVKQVFKSYALPVVPLFENQLALTNADTILNDSITEDIRQKHLRQWDGNYEVMLGYSDSSKENGVLPSRLMIAKSLKNIQSTLENKNLRPIFFHGSGGSIERGGGDIKEQTASWSKEMMSNYKVTVQGEMVARLFGSSSILKSQIDKFLDIYSQKGKSNDNDYPEELSLFSTRVSQKYKTLIQSDWFWQIVEQASPYHFLKELKIGSRPTKRKSGPDQRKLRAIPWILCWTQTRLLFPTWWGIGSTWSELNGIEKNRLKALYKENALFAAFVKQLGVTLSKVYLPIWEQYLYQLTGSNEYLKPFQSELESTVLFFYQITGEKDFCFHQPWLGESIQLRSTLIHPLNLIQIEAMKRKDLPLLRKTVTGISCGMLTTG
>NZ_CP017458.1|WP_027227098.1|1741511_1742168_+|methyltransferase
MIDAVQNEPNIHFTYNYKQPDEYHFSLDSIHLAKFVAKQLKPYRDLGSLRVLDLCAGCGVIGIELSWHLQAIRQIDFIEIQDIYTEYFYQNIANVNRPELQLRWHLLNYDELHEKKWEGTFDLIISNPPYFQPGHGMLSPSKFKNRCRFYLDSSFQHYIRALENSLANKGRAYFLLRPLQQHGLDLFSDIQKVLQETSVTAKKISHIRGSDIILLEKR
>NZ_CP017458.1|WP_027221790.1|1740950_1741325_-|Y4oB-family-protein
MQTNTSSLQNIPDDVVWKSLTNLVERFDLKESEARILMGDMPRSTYTSHKAKLNRDQKERVSYLLGIYKSLRILFEDGEQARTWINRKNNLPPFNGLTPKEYMLEGGIVRLADVRKFLDFWRGY
>NZ_CP017458.1|WP_027227097.1|1740271_1740949_-|RES-family-NAD+-phosphorylase
MYSYIDFSEKVHRLIPSKFPPVTLFDWADSAEELEQIALLEGLTNERILAELGKINLIDKEDWIGGPGSTPIMAAFTHTGFESRFSDGSFGVYYAASSLETAIKETCFHRARFYSASNEKPCSISMREYVATIKKPLIDIRDKRYKELFNPDPAYYGKSQEFGKKVHEKKEWGLLYPSVRNLNGLCMAVLRPPALTLPRQGCHLRYIWDGEKISDVYKESKIANV
>NZ_CP017458.1|WP_027227096.1|1738736_1740161_+|hypothetical-protein
MIVIFVHGWSVTHTNTYGELPQWLENQSKQGKLDIQVGNVYLGRYISFDDTVTVDDIARAFDQALRDEIADKLRDGERFACITHSTGGPIVRKWMDLYFKNNLAKCPLSHFIMLAPANHGSALAQLGKSRLARIKSFFEGVEPGKYVLDWLELGSNMSWQLNESWLDYDCTANGIYCFVLTGQKIDRQLYDALNSYTGEAGSDGVVRVAATNMNYSLLKLHQEGDNGESLVVAKMTRTQPMAFGVLPGLSHSGKNIGIIRSITIANAATHPTAIWVLRCLQVKSRDSYNTLVQELDKITKETQKNEHTEFVKTLVFKREYITNRYSMIIFRLIDDRGNHLVDYDLYLTAGPQYSEQALPAGFFIDRQRNLNNRGKLTYFLDYDIMEGGINTPKMQGNLGFRVKAYPESSDQALAYYRLLDFHSSLADIHKILHPNETVMVEIMLQRRVDRTVFRITNNLAPAKISVKTTGKKVD
>NZ_CP017458.1|WP_027227095.1|1736847_1737912_-|hypothetical-protein
MWYDILLEYLGEKICPSNKEKARLLISQLLKLLKEDPDFGENFEPEFIFGVMVALYDYSTNHGNQNVSLDEFGKYCIGLIMVFSKISDDLSIYCSDFTYILSDKTILQELKIEGELATIRKDYLKKKRTNPEVTPFVDQKDVANPFEIYKKIGELAKIDLLKDLENRTLAYLNFSVKIQTEKIADMLNDLLNRVQNQQVIVSELYQYLLPYKGKDDLFDALIFSLKRELKKLSHNNFSPKTQPSSISKINLVLVPSLKIDQLPRHNPEIVNICEKLENYVFKGSSKKGSFFSAKNYCNHTKEVNEIVQKILKGDLLTIEAILDELAKINIENRKDELILLIKELQNERGCIRKL
>NZ_CP017458.1|WP_027227094.1|1735364_1736684_-|acetyl-CoA-C-acetyltransferase
MKHQSNLSGRNVYVVDGSRTPFLKAKGVGPFSGSDLAVAAGTTLLNRQPFSPDELDEVIIGSAMPGPDEANIARVIALRLGCGDKVPAFTVMRNCASGMQALDNAAIQIATGRSNLVLAGGTDAMSHAPLLFNEKMASWLANWFAAKSMGQKLALITKFKPSYLAPVIALLRGLTDPIVGLNMGQTAEKVAYRFGITREQMDEFATQSHLRIAKAYAENRMSEVAPIIDYKGCIYPQDDGIRADSTVEKLSKLKPFFDKKYGMVTPGNSSQITDGACLLLLASAEAVKKYALPVLGRIVDSQWAALDPSQMGLGPVHAATPILERHNLKPQDLDCWEINEAFAAQVLGCLAAWDDEEYCKTQLGLKEAIGAPSLERLNRDGGAIALGHPIGASGARIVLHVLKSLEQRNESRGMAAICIGGGQGGAMYLERVTEVKGHE
>NZ_CP017458.1|WP_027227093.1|1733353_1735372_-|enoyl-CoA-hydratase/isomerase-family-protein
MNNYKHWDLQRDKDAILWLGLNRRDAAVNSINEEVLDELNSLLHEISHDKKAMGLIIYSLKEKGFIAGADVNAFSQFESSSQAVDFLQKGQAVFARLQALSIPSVAMIDGFCMGGGYELALACTYRIATDDKDTRIGLPEVMLGIHPGWGGTVRLPQLIGGFKALSQVILTGSAIPSVKAKSLGMIDEVVPVRQLRRAAVYFIKNKPPRHRPSFIESLTNSSLLRKPIAYLLRYNVAKRVRKEHYPAPYAVIDLWEKEGGVGERAYLKEADSIEKLVSQSDTAKNLIRAFLLRERLKGFAKDSQFKAVHVHVIGAGVMGGDIAAWCALRGLQVTLQDKSYEQIAPAIGRAHKLYSKKLRKPRLIQAAMDRLIADPEGHGVKRADVIIEAVFENLAVKQEIMKTVEKNAKKDAIIATNTSSIPLDEISSVMSKPERLVGIHFFNPVAKMDLVEIVSSSSTAKKIQQNSCAFVNQIGKLPLPVKSSPGFLINRVLMPYLMECVQLLDEGYSAETIDEAALQFGMFMGPVELADTVGMDVCLAVAENLTSHFGGTIPQRLRDLVKEGKLGRKTGEGFYKYKNGKAIKKKAPAHVDKTIADRLILRMVNESAACIRERVVEDSDLLDAGMIFATGFAPFRGGPMNYAKDFGKDKLETLFKTFESKYGERFKVDTSL
>NZ_CP017458.1|WP_027227092.1|1732558_1733293_-|L,D-transpeptidase-family-protein
MEQKSKSIIRVWYLILLLSQYSFANVYVLPESGNTVGEIQVAFSEFGETIDEVGRRFNVGYYEMVRANPGVNARYPLAANTKLIIPSRFVLPNVPRKGIVINLAAYRLYYFPPDDNVVITYPVGIGKKGWETPLGLSKITSKEINPTWRPTVKLQKAAESIGAPIPSEFPPGPYNPLGQYVLRLGWPTILIHGSNRVDGIGAKVSAGCIRMLPEDIEHLYGLVAIGTPVRIINDSLQRPAALNQ
>NZ_CP017458.1|WP_027227102.1|1746533_1747787_-|glutamate-5-semialdehyde-dehydrogenase
MNTHVVNQLRAAKKATTDLSLIQSDTRTEVLKTLAANLEKHLENIIQENQKDLSLMPEQDPRYDRLLLSKERILSLANDVRKVADLPNPLGVNLLEKSMPSGLSIKKITVPLGVIAVIYESRPNVTIDIFSLCFKSGNVSILKGGKEAYFTNSYLVLLIKNTLKNFNINTDLVCLLPPERALMTQLLNATGFVDLCIPRGSQNLINFVRDNAKIPVIETGAGIVHTYFDKSGDLEKGKKIINNAKTRRVSVCNALDTLIIHTDRLKDLPELVEALSKNNVIIYADKEAYQALDKSYPEQLLMRAKPQDFGHEFLDYKLAIKTVPNIQAAIDHIQQFSSHHSEAIIAEEESAIDKFLIEVDAAAVYANASTAFTDGGEFGLGAEIGISTQKVHARGPMGLDALTSYKWVIRGTGQIRN
>NZ_CP017458.1|WP_027227103.1|1747795_1748866_-|glutamate-5-kinase
MKIIIKVGTQSILSADGSPIYSVLNNLVNQIIYLKNLGHQVILVSSGAVGSGRKIAKNSLGKTYGDTVGEKQLLASIGQPELMNLYSNLFKNENILVSQLLLTKQDFHTRQHYLNIARLLTELLKHQNIIPIVNENDSVAIEELMFTDNDELAGLIAAQINADYLILLTNVDGVFTSHPNDPGAKLINRIDPNLAWPNVSAVKSKLGRGGMVSKLDTARKMAGLGINTAIANVNVESIVLKILDREAVGTIILASKRKSSIKRWIAFSHRTCLPSIVINDNLIALLRNGNRVMSILPIGIEDFRGECKKGDLIDILNSNNEKIGVGIARYDFLRLKDYLRLQNKPAFIHYDHLHIL
>NZ_CP017458.1|WP_027227104.1|1749049_1749475_-|GNAT-family-N-acetyltransferase
MNYQFELVVDTKLLEQQDKMIRDGIVNFNAPFTGSKPERYSIYVKDNENNIVGGAIVYAHKSSIYVDVLWVSEKYRGQGIGAELLRSVETEAVKRGILESTLDTFSFQAEGFYLKQGYKHLGTIKNYLEGHDRIYLRKKLK
>NZ_CP017458.1|WP_027227105.1|1749764_1750745_-|hypothetical-protein
MQLKSETKSTFHGKYSKSSPVVGARVKELELIYTHKEIFANYQKVVYDQQKLNVIPLAFKEKADEISKEIYAAYIKKYSDHGLTIENSVDWNNVGFTRTYLSDLENEWNTWSVDPLVATPNDKSHIEGQMYRPAYICALHELMHVEEMTPGILKGQYARFKSVVEVLTVTKTIILMDEVYKKTLNLPMDIEVDYENSFKLFGKTIKQGEFANFYRTLEAKYPSLAEALVSKQSLTFLNQTNVEPMNINMQVLGGFLAVVGYAAVALAFLLNNASFGTVGLVVTGLGVASIFGGVGLFANGIYKNERTTDNEILDASACLVRNTNSP
>NZ_CP017458.1|WP_027221798.1|1751095_1752043_-|MerR-family-transcriptional-regulator
MTQWFVKDLSQLTGVSVQTLHHYDRIGLLKPSLRLANGYRVYSEKDLLKLQQIIALKFFGFELSQIKTLLAEESNALSHFNSQARLLEQKASTLLEGAKTLRRIIDTVDKNQSIPWETIIQLIEVYKMTEHLEHGWVKEIFTPDELKQYVEFEKEMKANATPEQKAAMENNWSQLVNEVKNNLKQDPDSKTGVYLGKKIMDWVNGVYGKKYAHLRTKKFEQGFGEGKGLDEVGLTPEIVSWMDKAMDAYWRDRIYGILEQVGKTSSSIVLNLWNEMLVDMYGEETSRKNAIYEIALNDDKVSPEAKAWLRNILNS
>NZ_CP017458.1|WP_027227107.1|1752366_1753116_-|MerR-family-transcriptional-regulator
MAYTVKQLAKISNVSVRTLHWYDEIGLLKPAYQGANGYRYYEEKQCLKLQQILFFRELGFPLNDIQKLLMQNDFDHIKALRAHKQILERDINRKNQLIATIDKTIQHLRGKHKMSNEELYYGFDSQRQKQYERELVKEGVVSQDWMDKYKKKINQWAQADKDRFIQEGKEINQLLISAINNQLKPSSPEVQAIIHRHHAWVGWNPTKEGYIGLSQRYLTPEFRKFYEQQHPALLEFIIEGMLFYANKNL
>NZ_CP017458.1|WP_027227108.1|1753181_1753709_-|GNAT-family-N-acetyltransferase
MTQIEIVIKTQELSDIPVLVDAFQKANWQKPASLFEAYYQEQRKSLRIVWLAYSRDQIAGYATLKWISQYQPFAHQQIPEIMDLNVLPSFRKQGVGTALMQAAEEKAAGESDVVGIGVGLYGGHDGGYGQAQRLYVNRGYIPDGLGVTYGYKPTVPGQTYPLDDDLILWFTKKLR
>NZ_CP017458.1|WP_027227109.1|1753705_1754662_-|GNAT-family-N-acetyltransferase
MSVKQEQHLIKVVPYDSSWSMQFEQEAEQIKKALGNNCIDIHHIGSTSVPGLAAKPVIDMIPVILDLSKVDSANTAMRTLGYEAKGEYGIPFRRYFQKGDNQRTHHAHVFELGNSEIERHLKFRDWMRSHPEDREAYARLKQELARQYSDDITAYCLGKEDFIAIIDKKAGFNGLRMVKALTPREWDKVRHFRQFYFFDKAGLSDPYTWTFEHDAHVHFVLFQGSEIIGYTHLQLWPHNRAALRIIVIDELKRNHQYGNRFLTLCEKWLKSQGYQSLHVESSPDALRFYRNNGYIDMSFDDPDGYEGDPRDTAVGKIL
>NZ_CP017458.1|WP_027227110.1|1754665_1756447_-|ABC-transporter-ATP-binding-protein
MTNRLPNHLGSFVWHFLKPYRNIVMLFILFALLAGFWGPFNSLLVKSFINTLAAKASKDLSSLYWIAGLLVLNFIVFDNITWRTLGYLNYKYEAVIKNQIISQTFEYVLGGSTQFFQDNLSGRIADQITTLADNLEIILHRVSVDFLRGASLLVVSFITAYFVNVLFFYILFLWFIAFASFSIWMSARLVQLSDNHASSESQLSGQLVDSLANQSNIRIFSRKIYEVERMNAFFRMVQRAFQRKELFIVLLCCAQGGMIAVMMGFASITLIHLYGKGLVSIGDFALILGLSMELGHMMWYTMYQVDQFNQALGKAKQSLNALVIPHEIKDKGNASQLVVTQGQIEFSRVKFHYQGGYSLFQNKSVTIKAGQKVGLVGYSGSGKSTFVNLILRLYEVVEGQILIDGQNLSEVTQESLRQAIAMIPQDPTLFHRSLMDNIRYGRTDATDEEVILASRKAHAHEFISLLPEGYKTLVGERGVKLSGGQRQRIAIARAILKNAPILMLDEATSQLDSITESNIQESLWELMQGKTTLVIAHRLSTLLHMDRILVFDKGHIVEDGNHDELLKRGGLYKTLWNAQVGGFLPDQQNEKGE
>NZ_CP017458.1|WP_027227111.1|1756439_1757900_-|ABC-F-family-ATP-binding-cassette-domain-containing-protein
MNHKPIQFKDISLNFSHKSCFQNFSGEIHFGDRIALIGRNGSGKSMLLKMLCGLSLAPAGEIKVPRDVRFGHLPQVIEDYPDLSGGQRLNQVLSKILSDKPNVLLLDEPTNHLDSRNRRSLMRMLKYYPGTLIIASHDTEFINTVTDILWHIDLGQVTVFRGAYFDYQQMLEDKKASIKQGLSRIAQQKKESHLALMKEQERNKRARVQGEKKIAQRKWPTIRSHTKLGSAITTGNKRLSHINYKKQQLIEELSSLNLTEVIQPKFKLKGLEHHKLLIRIQDASIAYESGVILKDIYFHLSGCERVALHGNNASGKSTFVKAILGDSQIKRTGEWAVPNCNTIGYLDQHYQHLNLNETVLDLMSSKMPHATYAEIRAHLNDFLFRKNEEVEIKVKSLSGGEKARLSLALIAAQPPKLLILDEITNNVDLETRTHIIEVLSEFPGAMLVISHDHDFLESIHIETKYQIHQGKLYGFNDAYLEVIHHD

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Crispr_ID: NZ_CP017458_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP017458_3

2682126-2682298

Orphan

Consensus_repeat	Method
TCGAATAAATTTACCGCCATAACAGTAATTT	CRISPRCasFinder

2 spacers

The CRISPR arrays of NZ_CP017458_3

>merge|NZ_CP017458|3|2682126-2682298|CRISPRCasFinder
TCGAATAAATTTACCGCCATAACAGTAATTTTATAAATTTAACATAAATAAATACACAGAAAATTAGAAAATCGAGTAAATTTACCGCCATAACAGTAATTTATGGTGAATTAATGCAAAAAAATGCAATAATAAATTTATTTTAATCATTTTTACTGCTATAACAGTAATAT

>NZ_CP017458|3|3|2682126-2682298|CRISPRCasFinder
TCGAATAAATTTACCGCCATAACAGTAATTT	TATAAATTTAACATAAATAAATACACAGAAAATTAGAAAA
TCGAGTAAATTTACCGCCATAACAGTAATTT	ATGGTGAATTAATGCAAAAAAATGCAATAATAAATTTATT
TTAATCATTTTTACTGCTATAACAGTAATAT

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP017458.1\|WP_027227414.1\|2680961_2681879_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176109
NZ_CP017458.1\|WP_031301595.1\|2679743_2679992_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|180883
NZ_CP017458.1\|WP_027227409.1\|2676896_2677802_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176114
NZ_CP017458.1\|WP_027227424.1\|2690287_2691742_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_032830191.1\|2675245_2676466_+\|type-II-toxin-antitoxin-system-HipA-family-toxin	unknown	unknown	gnl\|CDD\|341492
NZ_CP017458.1\|WP_011214444.1\|2686547_2686715_-\|DUF3309-domain-containing-protein	unknown	unknown	gnl\|CDD\|378708
NZ_CP017458.1\|WP_027227407.1\|2675031_2675259_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|213767
NZ_CP017458.1\|WP_027227417.1\|2682848_2683787_+\|lpg2370-family-Dot/Icm-T4SS-effector	unknown	unknown	gnl\|CDD\|377920
NZ_CP017458.1\|WP_027227419.1\|2685235_2686423_-\|fatty-acid-desaturase	unknown	unknown	gnl\|CDD\|224316
NZ_CP017458.1\|WP_027227416.1\|2682543_2682852_+\|HipA-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|274416
NZ_CP017458.1\|WP_027227406.1\|2673513_2674536_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227415.1\|2682319_2682547_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|213767
NZ_CP017458.1\|WP_027227408.1\|2676500_2676857_-\|preprotein-translocase	unknown	unknown	gnl\|CDD\|271182
NZ_CP017458.1\|WP_027227422.1\|2688038_2688680_-\|RsmD-family-RNA-methyltransferase	unknown	unknown	gnl\|CDD\|370496
NZ_CP017458.1\|WP_027227413.1\|2680298_2680772_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227418.1\|2684080_2685244_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_063720028.1\|2687313_2687670_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227410.1\|2677892_2678753_+\|DUF2608-domain-containing-protein	unknown	unknown	gnl\|CDD\|378542
NZ_CP017458.1\|WP_027227423.1\|2689223_2690126_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP017458.1\|WP_027227411.1\|2679416_2679728_-\|cupin	unknown	unknown	gnl\|CDD\|380355

Protein	Function_ID	Function_description	E-value
NZ_CP017458.1\|WP_027227414.1\|2680961_2681879_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176109	cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	2.49817e-54
NZ_CP017458.1\|WP_031301595.1\|2679743_2679992_-\|hypothetical-protein	gnl\|CDD\|180883	PRK07206, PRK07206, hypothetical protein; Provisional.	4.2641e-28
NZ_CP017458.1\|WP_027227409.1\|2676896_2677802_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176114	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	7.11546e-52
NZ_CP017458.1\|WP_032830191.1\|2675245_2676466_+\|type-II-toxin-antitoxin-system-HipA-family-toxin	gnl\|CDD\|341492	cd17793, HipA, type II toxin-antitoxin sytem toxin HipA and similar proteins. This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Escherichia coli and Shewanella oneidensis HipA, which is a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. Structures of HipAB:DNA complexes from both Escherichia coli and Shewanella oneidensis reveal distinct complex assembly.	1.05604e-164
NZ_CP017458.1\|WP_011214444.1\|2686547_2686715_-\|DUF3309-domain-containing-protein	gnl\|CDD\|378708	pfam11752, DUF3309, Protein of unknown function (DUF3309). This family is conserved in bacteria but its function is not known.	1.02464e-06
NZ_CP017458.1\|WP_027227407.1\|2675031_2675259_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|213767	TIGR03070, couple_hipB, transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions].	2.73488e-18
NZ_CP017458.1\|WP_027227417.1\|2682848_2683787_+\|lpg2370-family-Dot/Icm-T4SS-effector	gnl\|CDD\|377920	pfam07804, HipA_C, HipA-like C-terminal domain. The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species. This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products.	1.15502e-59
NZ_CP017458.1\|WP_027227419.1\|2685235_2686423_-\|fatty-acid-desaturase	gnl\|CDD\|224316	COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].	9.99483e-86
NZ_CP017458.1\|WP_027227415.1\|2682319_2682547_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|213767	TIGR03070, couple_hipB, transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions].	3.72777e-23
NZ_CP017458.1\|WP_027227408.1\|2676500_2676857_-\|preprotein-translocase	gnl\|CDD\|271182	cd00801, INT_P4_C, Bacteriophage P4 integrase, C-terminal catalytic domain. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This 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.	2.84214e-13
NZ_CP017458.1\|WP_027227416.1\|2682543_2682852_+\|HipA-N-terminal-domain-containing-protein	gnl\|CDD\|274416	TIGR03071, couple_hipA, HipA N-terminal domain. Although Pfam models pfam07805 and pfam07804 currently are called HipA-like N-terminal domain and HipA-like C-terminal domain, respectively, those models hit the central and C-terminal regions of E. coli HipA but not the N-terminal region. This model hits the N-terminal region of HipA and its homologs, and also identifies proteins that lack match regions for pfam07804 and pfam07805.	2.48908e-43
NZ_CP017458.1\|WP_027227422.1\|2688038_2688680_-\|RsmD-family-RNA-methyltransferase	gnl\|CDD\|370496	pfam09445, Methyltransf_15, RNA cap guanine-N2 methyltransferase. RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyze methylation of the exocyclic N2 amine of 7-methylguanosine.	4.41586e-28
NZ_CP017458.1\|WP_027227410.1\|2677892_2678753_+\|DUF2608-domain-containing-protein	gnl\|CDD\|378542	pfam11019, DUF2608, Protein of unknown function (DUF2608). This family is conserved in Bacteria. The function is not known.	2.08218e-66
NZ_CP017458.1\|WP_027227411.1\|2679416_2679728_-\|cupin	gnl\|CDD\|380355	cd02226, cupin_YdbB-like, Bacillus subtilis YdbB and related proteins, cupin domain. This family includes bacterial proteins homologous to YdbB, a Bacillus subtilis protein of unknown function. It also includes protein Nmb1881 From Neisseria meningitidis, also of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.	1.62088e-10

>NZ_CP017458.1|WP_027227414.1|2680961_2681879_+|LysR-family-transcriptional-regulator
MDKLNLNLLRALYALLTCRHLTLASKKMGISQSSMSIYLKQLREHFHDDLLVRGQGSIMQLTPLANSLIGKARQALSLIETLFNTIETFNPLISERSFSIGMTDLMSILLTPSLIKRLEQEAPGVKLNIKHPSYLNTVEVFESGDIDLMIGMFERVPESLKQQKLFQDEAVIVGGSNHPGIQKGKICIEELFKYPLIQFSLRETPFYNYFDRYLRQLGHDKRVSISLGQGIMPLFVLTDSHYLTLSIRKVAEKLSHLIPLSIASVPFEVDSFNCYQYWHQKDDADPGHRWLREMVLSIAKKSHLK
>NZ_CP017458.1|WP_027227413.1|2680298_2680772_+|hypothetical-protein
MRSRTEKLSSKRSIINHDHLITDEVCMIGIYREGGDLSIYAESPEGIEHFSINRGNNLDMVILPHTLVGTWRHHQLLRTVEQAAQIRTLRIRSHDYIEQSVTRTELEQFKEVFMLACKEEISNQPEIEDYLQTALGKLHGEAEMTYKPKFTEQCSIL
>NZ_CP017458.1|WP_031301595.1|2679743_2679992_-|hypothetical-protein
MLDEHQNLEYIKKLISFVTLKLNVRPGKYLKKTVDLFSMPGLLILSHESKEQVESDYNLVRKLEQKGLFVLAASQESKTTKI
>NZ_CP017458.1|WP_027227411.1|2679416_2679728_-|cupin
MQIIKSSLFTGDFTWQALDIAQISDASIRLHWADQPYIWHKNDGDEVFVVLSGKVIMHYREGGVENQKELNSGDICYLKEGCEHVAYPKGAARILVIEKAGSI
>NZ_CP017458.1|WP_027227410.1|2677892_2678753_+|DUF2608-domain-containing-protein
MRFIIIFIYLLLLNPVFAEVIHYQTDTFAKIAAQYKKLGTDPKTTLMVFDLDDTLITMTQPLGSVGWWDWQHELQKQGGGSDKLFTKDYQQLVRVQNILFQLVKMEVTDEYVLPFLKDAANQGTTLMGLTARGKEHLSATLMQLKDNQFTIDDKLLFRKKGLKLNNNKTSVAGNFHCPQFSREVIYQQGIMFLDGEDKGEALLCILANTKQDIKTILFVDDAKRNIVSMDNAFANRDEFLVLNVFYTKENAKELEIQTNPHLQAQVFEQWNFIKENLNNVIIRSNF
>NZ_CP017458.1|WP_027227409.1|2676896_2677802_-|LysR-family-transcriptional-regulator
MINNSLNLNDLAIFALVVKKRSFTQAALEAGISKAWVSQKISQLEGKLDIKLLNRTTRSLSLTLGGEILFEHCQTMLKEVIHAENHLREYAKAPSGKLVITCPEISGLDLFPTLLHQFKLLYPQIKIRLIITDQFVDLTQQGIDFAFRTGKLTDSGLVSRYIGAVPRCLVASPEYLSNNSPIKNPADLFNHQLLKHSSLPDWLLKKEEEVFKIHVKNPVIESNSLIFLHKISCLHHGIAFLPYYLCSDALKHKTLVKVLPDWLNVDNEYYMVYHKEKSVLYIHQLFKDFILQSDLNKMISN
>NZ_CP017458.1|WP_027227408.1|2676500_2676857_-|preprotein-translocase
MSDFVCVLMERRGRNKTSEFVFPDESRTGYIYEPQKAVNRVVELYGVPFTKHDFRRTFVTIADSLDLPADALKRLVNHKMNNDVTAGYIMKDVERLRKPMQQVANFILEHMMETAELS
>NZ_CP017458.1|WP_032830191.1|2675245_2676466_+|type-II-toxin-antitoxin-system-HipA-family-toxin
MKNHKLDIYLNQTLAGQLRIDTHGEMSFVYDEGYLENNKNLPLSHSLPLQQAPYSTKQCRPFFSGLLPEAHMRTAIARQLGISEKNDFALLAAIGGECAGAVMILPQDTSITQLKPDYKIIKKQDVLEILQTMHQRPMIVGEDGIRLSLAGAQDKLPVAIIEGNLAIPMNGAPSTHILKPINRDFPSLIENESFCLNLAQKIGLNAVDASIHYADGTPYLLVKRYDRVETKQGIQRLHQEDFCQAMGISPEMKYQREGGPQISECFGLIREISSLPVLDIKELLQGILFNVIIGNNDAHSKNFSLLYHGSKVRLAPFYDLISTVYYPNLASKMAMKVGSKYDFDGLFPRHFIQMAEEARLSGALVRKEVLNLISKIQKNITASPFTSIILQRADKLFQKFQKASTG
>NZ_CP017458.1|WP_027227407.1|2675031_2675259_+|helix-turn-helix-transcriptional-regulator
MIQSPENIGRYIRKVRKELNVTQKDLALTAGTGLRFIIDLENGKPTCQIGKMLQVLQVLGIQLNLSHTDFENEKS
>NZ_CP017458.1|WP_027227406.1|2673513_2674536_-|hypothetical-protein
MFRIRKKYNQNLITISEEEAAILKETSEKLRLALSFERNFEYLIQNYLDYENTIAQKSIGQLVNGPQSIDEFDSHITDVTIKLLNLLSTTKAYIDKSPSILKKLMGEADLFKIECSLQYDTNFSYRFIDSLRNYAQHNNDPLSSLILGGEWVENENLKYYTNPLIDTKALRANKKFRKSVLPEYDVKFHLSYCIRRYIESLSLIHKKMSSSFKADLDTLCDKSKKILSEKDFKLEEEFIFLYENGEYQSICLKMDKYLKFNKKHSRLSNISNQCVSTCVKNQEKKVIKDLDKIPFNSTEAEKKYFISMRSNHGETIASDLELNTLPEDCKNYFKSLINNY
>NZ_CP017458.1|WP_027227415.1|2682319_2682547_+|helix-turn-helix-transcriptional-regulator
MRTHEIANLVHYYRKQSGLSQQELARLAGVGKTVIYDIEKGKESVRLNTLLKVLDVLNIQMKFETPFPQTTDNNS
>NZ_CP017458.1|WP_027227416.1|2682543_2682852_+|HipA-N-terminal-domain-containing-protein
MRKAYVSVNGIKAGTLEELQGGKYQFTYFDDYQGAPVSLTMPLTNKVYYFDVFPPFFEGLLPEGIMLEALLRKYKIDRNDYFGQLVIVGQDVVGAVTIEELR
>NZ_CP017458.1|WP_027227417.1|2682848_2683787_+|lpg2370-family-Dot/Icm-T4SS-effector
MKRCPITYERISDQENYSQRGLHLLSPQLKNLSPLDLSADEQRQEAIARVGKMSIQGVQKKLSAKLKIKEGCFEIVDQNGHYILKPQSDIYPELPENEAITMTLAKTIGLEVPVHGLVYSKDNSLTYFIKRFDRIGHNRKLALEDFAQLSGEDRHTKYKSSMEKVIAVVEQFCTFPKIEFVKLFKLTLFNFLVGNEDMHLKNFSLITKDRKISISPAYDLLNSTIAQKNTKEEIALSLKGKKNNLTKSDFLKYFAIEKLGLNQKVIDGIVQEFHQIIPEWRKLVGFSFLSQQMQEKYLQLLEQRCKRLNFFD
>NZ_CP017458.1|WP_027227418.1|2684080_2685244_+|hypothetical-protein
MYSLPLKSKSLRFFNLVFIALVLSFYLLANANAAGIKRYDFGEMSSKVTKAWDQDVALYVARRFAAENGFDEKEITVKKLEAGATNHFIYLMFINNQLKFVLKGLGTEKEAEALFALQNYSKIPDIQNNPQAATVTLSKTINSYEVKNDRKTYYFAILEAAQGKELFKIMTYELLQHKDINTLKDVFYRIGQQTSELHKTIIGHDQFITPRDLVTVIHDDFHPENTFYNLETNVFSLIDNESMGDSITNPLPIIRELYGFYEVPIIRWPSEKITVDLLKDADPHDIASIYYDFVLGMASVYHDSQDAKRVLIAAIIDLNNMAIAFLKDRYSEPWMLNPSDKNEAHIVWGKLAKVADNPQLAELYINKLAIINTDLQSLSGLWLQQLH
>NZ_CP017458.1|WP_027227419.1|2685235_2686423_-|fatty-acid-desaturase
MFFGILNLTLWGYVLATFVLTQITIAAVTLYLHRYQTHRALTMHPIVSHFFRFWIWLTTGMVTRVWVAIHRKHHAMTDVEGDPHSPQIFSIKKVFWQVPELYREAAKDKDMIEKYSHGTPNDWIERKLYSRYSSKGILLMFLIDLLLFGFPGITIWAIQMIWIPLSAGVVNGLGHYWGYRNFECPDRSTNVFPLGILIGGEELHNNHHTYASSAKFSVKWWEFDLGWFYIRCLSFLGLAKVKKLPPKLAREDTKQCVDLNTVKAIISNRFQIMSDYYKRVTIPILKNEKRNCNYIKNRKEWHLFKEAKRLLRQETTKANAHLQVLLNRFEQLQLVYNYRQSLQQIWLKKVSSQKELIESLNQWCKKAEQSGLDVLHQFSLRLKSYVLIGTDGSSV
>NZ_CP017458.1|WP_011214444.1|2686547_2686715_-|DUF3309-domain-containing-protein
MLGTILLILLILLLLGSVPRWGYSRSWGYTPMGLIGLILVIYLILVLLGKVPIGF
>NZ_CP017458.1|WP_063720028.1|2687313_2687670_+|hypothetical-protein
MNLSVFSASELFAGADPEKVIQELTMVSKSYGSAISYHRLPAGSTKDLSEHSKYYLNLIDKAIEDVNLSLDDNSKATYSLRFALLQPLLVNLVAAAEVLKNEKTQEQEQKSSHSVRFM
>NZ_CP017458.1|WP_027227422.1|2688038_2688680_-|RsmD-family-RNA-methyltransferase
MKSSEICPFGPKLQQYWDKRYDYFHRFDEGIQTDSEGLHTVMPEEAALTQAKLFNNEKIVVDGFCGIGGSAIALARTGKKVIAIEMDSVRLAMAKNNARVYGVEHLITFVHGDFFDVAAEIKADAVLIDPPWGWPRYRKIEEFHLQHFNPNGSKLISYVLDHFNKIVLRAPKTFITSELDQFNVNYEIHSDKLHHSIISISVCITNHSKRKPG
>NZ_CP017458.1|WP_027227423.1|2689223_2690126_-|hypothetical-protein
MFPPLQDPWSELEKLGFNPDYLERLKKRAATSIELTKNIEMLAGYYERFKAAGFTDRDLARIVSLVSFTSDNRLSNIGSRMMLTLVCGGLDLLKAPLNFNSHNLTNMMVSLNGLEKLRQLVKINQSYMIPFKNQAEFKAVFEKKCKKYPMLRVVWCYSDKEELYLENRRQDAIYKDWLSEEELHQLFRLRRVSKSQDLYYWERDKLRPAFLSDNYYSREDLGQTREEFEKALDNADAVESWCDSWANPFDQNPIPKLAKILVPSNQKNTSKIPFFTAVDNNEKSSVIDERYSKYFSNCSK
>NZ_CP017458.1|WP_027227424.1|2690287_2691742_+|hypothetical-protein
MKNKTRALNFLNRIERCIVPQSNPQIMKQLLSALGLDNINTGNEEYKFFIQTIKRKAIDLNPLINKIKSDILKNKSLCTLLAYIEENELIDDAEIENASSTIQLQINLLCLLEAITITMANSNDFAHDIYNHMMKQRGGGATGNPFYNFLFGIPSRATLFERLKLISIDPGLTSIIFHRQMGANPETQADLNDFVSQNRLSGWNADIELANFDVASTSTLPAMGVNILEAVWEDSTGHNKNTSGIPNAQAGLGLIAIMEEKEYTTSFKLAETTLPQGTKLDSDLGYSLIPELKVDNSPKKVSQFHIDEQWMNLYNSWNLCFVIANIDPVFVPLKLLIPSVFSAEPSNYKETRVLTLFLVANLFLNQQTLNNPLFSNKFSFQNGAAILKKWGEINRNHASELMQQCSPKTGKEPEALYNRVLGKHAHLNFGLKLLSYFQDSHQFRLTKKAKQSALNDHSFFSGTAASADNSDQLNLASQPSLNKV

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Click the colored protein region to show detailed information

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
NZ_CP017458_3	3.2\|2682228\|40\|NZ_CP017458\|CRISPRCasFinder	2682228-2682267	40	NZ_LR134418	Legionella adelaidensis strain NCTC12735 genome assembly, plasmid: 9	257659-257698	1	0.975
NZ_CP017458_1	1.9\|201159\|34\|NZ_CP017458\|CRISPRCasFinder,CRT,PILER-CR	201159-201192	34	NZ_CP016745	Lactococcus lactis subsp. cremoris strain JM2 plasmid pMPJM2, complete sequence	102474-102507	10	0.706
NZ_CP017458_1	1.9\|201159\|34\|NZ_CP017458\|CRISPRCasFinder,CRT,PILER-CR	201159-201192	34	NZ_CP016746	Lactococcus lactis subsp. cremoris strain JM1 plasmid pMPJM1, complete sequence	172093-172126	10	0.706

1. spacer 3.2|2682228|40|NZ_CP017458|CRISPRCasFinder matches to NZ_LR134418 (Legionella adelaidensis strain NCTC12735 genome assembly, plasmid: 9) position: , mismatch: 1, identity: 0.975

atggtgaattaatgcaaaaaaatgcaataataaatttatt	CRISPR spacer
atggtgaattaatgcaaataaatgcaataataaatttatt	Protospacer
****************** *********************

2. spacer 1.9|201159|34|NZ_CP017458|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP016745 (Lactococcus lactis subsp. cremoris strain JM2 plasmid pMPJM2, complete sequence) position: , mismatch: 10, identity: 0.706

cggctggtattacaaggatgcaagacacatggat	CRISPR spacer
caaaaataattacaaggaggcaagagacatggct	Protospacer
*..  .  ********** ****** ****** *

3. spacer 1.9|201159|34|NZ_CP017458|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP016746 (Lactococcus lactis subsp. cremoris strain JM1 plasmid pMPJM1, complete sequence) position: , mismatch: 10, identity: 0.706

cggctggtattacaaggatgcaagacacatggat	CRISPR spacer
caaaaataattacaaggaggcaagagacatggct	Protospacer
*..  .  ********** ****** ****** *

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1039604 : 1046488

Acinetobacter_phage(42.86%)

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_027227549.1\|1039604_1040381_-	indole-3-glycerol phosphate synthase TrpC	A0A0P0IR83	Acinetobacter_phage	2.3e-58	49.0
WP_027227550.1\|1040373_1041408_-	anthranilate phosphoribosyltransferase	A0A0N7IRD9	Acinetobacter_phage	1.4e-76	48.2
WP_027227551.1\|1041385_1041964_-	aminodeoxychorismate/anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	8.6e-55	52.6
WP_027221199.1\|1041997_1042723_-	LPS export ABC transporter ATP-binding protein	A0A2H4PQG7	Staphylococcus_phage	8.1e-18	25.1
WP_027227552.1\|1042719_1043229_-	lipopolysaccharide transport periplasmic protein LptA	NA	NA	NA	NA
WP_027227553.1\|1043209_1043779_-	LPS export ABC transporter periplasmic protein LptC	NA	NA	NA	NA
WP_027227554.1\|1043775_1044303_-	3-deoxy-manno-octulosonate-8-phosphatase KdsC	A0A140XBD6	Dickeya_phage	2.4e-27	47.7
WP_027227555.1\|1044316_1045279_-	KpsF/GutQ family sugar-phosphate isomerase	A0A2P0VNK5	Tetraselmis_virus	4.2e-38	32.3
WP_027227556.1\|1045690_1046488_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	1.7e-21	33.8

DBSCAN-SWA_2

1295248 : 1304744

Staphylococcus_phage(42.86%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_027227755.1\|1295248_1296577_+	sigma-54-dependent Fis family transcriptional regulator	W8CYM9	Bacillus_phage	1.7e-08	26.8
WP_011213531.1\|1296751_1296997_+	hypothetical protein	NA	NA	NA	NA
WP_027227756.1\|1297307_1298744_-	M48 family metallopeptidase	NA	NA	NA	NA
WP_027227757.1\|1298806_1299880_+	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A2H4PQS8	Staphylococcus_phage	1.8e-29	26.9
WP_027227758.1\|1299864_1300479_+	riboflavin synthase	A0A2I2L4R9	Orpheovirus	4.6e-22	38.4
WP_027227759.1\|1300475_1301684_+	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	5.9e-98	48.7
WP_050598205.1\|1301691_1302159_+	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	7.0e-23	49.1
WP_027227761.1\|1302285_1303923_+	CTP synthase	A0A1J0FA14	Only_Syngen_Nebraska_virus	8.5e-156	52.7
WP_027227762.1\|1303919_1304744_+	3-deoxy-8-phosphooctulonate synthase	E3T537	Cafeteria_roenbergensis_virus	2.1e-54	44.3

DBSCAN-SWA_3

2253586 : 2263702

Bacillus_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_027229217.1\|2253586_2255269_-	S8 family serine peptidase	A0A1B0T6A2	Bacillus_phage	6.1e-16	30.4
WP_027229218.1\|2255405_2256410_-	AraC family transcriptional regulator	NA	NA	NA	NA
WP_027229219.1\|2256534_2257860_-	adenosylhomocysteinase	S4VPF6	Pandoravirus	8.1e-48	31.4
WP_027229220.1\|2257878_2259027_-	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	1.7e-126	58.2
WP_027229221.1\|2259229_2260342_-	glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit	R4TGJ8	Halovirus	4.7e-49	34.4
WP_027229222.1\|2260440_2261580_-	molecular chaperone DnaJ	A0A1V0SBY2	Catovirus	1.6e-23	26.7
WP_027229223.1\|2261767_2263702_-	molecular chaperone DnaK	G8DDB7	Micromonas_pusilla_virus	1.3e-147	49.6

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. NZ_CP017458

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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

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection