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_003228	Bacteroides fragilis NCTC 9343, complete genome	5 crisprs	DEDDh,RT,cas2,cas6,PrimPol,WYL,cas3,cas1,cas9	2	14	0	0
NC_006873	Bacteroides fragilis NCTC 9343 pBF9343 plasmid complete sequence	0 crisprs	NA	0	0	0	0

1. NC_003228

CRISPR-Cas detection and classification

Crispr_ID: NC_003228_1

• CRISPR_ID: NC_003228_1
• CRISPR_location: 892023-892168
• CRISPR_type: Orphan
• Repeat_type: NA
• Spacer_info: 2 spacers

Consensus repeat of NC_003228_1

Consensus_repeat	Method
GAAATTCCCAATATATTGTGAATTTGA	PILER-CR
ATTCCCAATATATTGTGAATTTGA	CRISPRCasFinder

spacers of NC_003228_1

>1.1|892050|34|NC_003228|PILER-CR
AACAAAAATACTAAGTATTTGTTTGATAAGCAAG
>1.2|892111|34|NC_003228|PILER-CR
GCTTTTTGTGGCTTGAGTTATGTACCTTTATCAT
>1.3|892047|37|NC_003228|CRISPRCasFinder
AACAAAAATACTAAGTATTTGTTTGATAAGCAAGGAA
>1.4|892108|37|NC_003228|CRISPRCasFinder
GCTTTTTGTGGCTTGAGTTATGTACCTTTATCATGAA

CRISPR arrays and Neighbor proteins around NC_003228_1

CRISPR arrays

The CRISPR arrays of NC_003228_1

>merge|NC_003228|1|892023-892168|PILER-CR,CRISPRCasFinder
ATTCCCAATATATTGTGAATTTGAAACAAAAATACTAAGTATTTGTTTGATAAGCAAGGAAATTCCCAATATATTGTGAATTTGAGCTTTTTGTGGCTTGAGTTATGTACCTTTATCATGAAATTCACAATATATTGTGAATTTGA

>NC_003228|1|1|892023-892168|PILER-CR
ATTCCCAATATATTGTGAATTTGAAAC	AAAAATACTAAGTATTTGTTTGATAAGCAAGGAA
ATTCCCAATATATTGTGAATTTGAGCT	TTTTGTGGCTTGAGTTATGTACCTTTATCATGAA
ATTCACAATATATTGTGAATTTGA

>NC_003228|1|1|892023-892168|CRISPRCasFinder
ATTCCCAATATATTGTGAATTTGA	AACAAAAATACTAAGTATTTGTTTGATAAGCAAGGAA
ATTCCCAATATATTGTGAATTTGA	GCTTTTTGTGGCTTGAGTTATGTACCTTTATCATGAA
ATTCACAATATATTGTGAATTTGA

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_003228.3|WP_005818358.1|891809_892022_-|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl|CDD|213767
NC_003228.3|WP_005784912.1|893526_893874_-|hypothetical-protein	unknown	unknown	gnl|CDD|371293
NC_003228.3|WP_005775503.1|889584_890478_+|AraC-family-transcriptional-regulator	unknown	unknown	gnl|CDD|225117
NC_003228.3|WP_077687927.1|890480_891320_-|HipA-domain-containing-protein	unknown	unknown	gnl|CDD|377920
NC_003228.3|WP_077687926.1|894217_894409_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_077687925.1|898330_898951_+|acetyltransferase	unknown	unknown	gnl|CDD|100050
NC_003228.3|WP_010992162.1|895988_897197_+|UDP-N-acetylglucosamine-4,6-dehydratase	unknown	unknown	gnl|CDD|187548
NC_003228.3|WP_010992160.1|892511_893384_-|DUF4373-domain-containing-protein	unknown	unknown	gnl|CDD|379546
NC_003228.3|WP_010992163.1|897216_898350_+|DegT/DnrJ/EryC1/StrS-family-aminotransferase	unknown	unknown	gnl|CDD|99740
NC_003228.3|WP_005784896.1|886458_887286_+|AAA-family-ATPase	unknown	unknown	gnl|CDD|379114
NC_003228.3|WP_010992159.1|888295_889543_+|mechanosensitive-ion-channel-family-protein	unknown	unknown	gnl|CDD|366370
NC_003228.3|WP_008769439.1|893973_894204_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005813291.1|895477_895966_+|transcriptional-regulator	unknown	unknown	gnl|CDD|336454
NC_003228.3|WP_005784914.1|894921_895458_+|capsular-polysaccharide-transcription-antiterminator-UpgY	unknown	unknown	gnl|CDD|193584
NC_003228.3|WP_005784891.1|884333_885425_+|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB	unknown	unknown	gnl|CDD|236515
NC_003228.3|WP_005784907.1|891483_891813_-|phosphatidylinositol-kinase	unknown	unknown	gnl|CDD|274416
NC_003228.3|WP_010992165.1|899011_900067_+|NTP-transferase-domain-containing-protein	unknown	unknown	gnl|CDD|133048
NC_003228.3|WP_005801389.1|885456_886365_-|DMT-family-transporter	unknown	unknown	gnl|CDD|223769
NC_003228.3|WP_005784898.1|887307_888324_+|DUF4435-domain-containing-protein	unknown	unknown	gnl|CDD|373095
NC_003228.3|WP_005796193.1|883236_884325_+|DUF1573-domain-containing-protein	unknown	unknown	gnl|CDD|377880

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_003228.3|WP_005818358.1|891809_892022_-|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].	2.16064e-19
NC_003228.3|WP_005784912.1|893526_893874_-|hypothetical-protein	gnl|CDD|371293	pfam10902, WYL_2, WYL_2, Sm-like SH3 beta-barrel fold. WYL_2 is a family of Sm-like SH3 beta-barrel fold containing domains. WYL is named for three conserved amino acids found in a subset of domains of this superfamily. These residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system.	3.22511e-28
NC_003228.3|WP_005775503.1|889584_890478_+|AraC-family-transcriptional-regulator	gnl|CDD|225117	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription].	1.24557e-30
NC_003228.3|WP_077687927.1|890480_891320_-|HipA-domain-containing-protein	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.	7.7055e-46
NC_003228.3|WP_005813291.1|895477_895966_+|transcriptional-regulator	gnl|CDD|336454	pfam06603, UpxZ, UpxZ family of transcription anti-terminator antagonists. The UpxZ family of proteins acts to inhibit transcription of heterologous capsular polysaccharide loci in Bacteroides species by interfering with the action of the UpxY family of transcription anti-terminators. As antagonists of polysaccharide locus-specific UpxY transcription anti-terminators, the UpxZ proteins exert a hierarchical level of regulation, insuring that only one of the multiple phase-variable capsular polysaccharide loci per cell characteristic of this genus is transcribed at a time.	7.8276e-60
NC_003228.3|WP_077687925.1|898330_898951_+|acetyltransferase	gnl|CDD|100050	cd03360, LbH_AT_putative, Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. A few members are identified as NeuD, a sialic acid (Sia) O-acetyltransferase that is required for Sia synthesis and surface polysaccharide sialylation.	3.45194e-57
NC_003228.3|WP_010992162.1|895988_897197_+|UDP-N-acetylglucosamine-4,6-dehydratase	gnl|CDD|187548	cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was identified in Helicobacter pylori as the hexameric flaA1 gene product (FlaA1). FlaA1 is hexameric, possesses UDP-GlcNAc-inverting 4,6-dehydratase activity, and catalyzes the first step in the creation of a pseudaminic acid derivative in protein glycosylation. Although this subgroup has the NADP-binding motif characteristic of extended SDRs, its members tend to have a Met substituted for the active site Tyr found in most SDR families. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	3.40656e-107
NC_003228.3|WP_010992160.1|892511_893384_-|DUF4373-domain-containing-protein	gnl|CDD|379546	pfam14297, DUF4373, Domain of unknown function (DUF4373). This domain is found in bacteria, eukaryotes and viruses, and is approximately 90 amino acids in length.	6.76132e-31
NC_003228.3|WP_010992163.1|897216_898350_+|DegT/DnrJ/EryC1/StrS-family-aminotransferase	gnl|CDD|99740	cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein encoded by gene pglA, is a galactosyltransferase involved in pilin glycosylation. Additionally, this CD consists of ArnB (PmrH) aminotransferase, a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. This CD also consists of several predicted pyridoxal phosphate-dependent enzymes apparently involved in regulation of cell wall biogenesis. The catalytic lysine which is present in all characterized PLP dependent enzymes is replaced by histidine in some members of this CD.	2.39524e-150
NC_003228.3|WP_005784896.1|886458_887286_+|AAA-family-ATPase	gnl|CDD|379114	pfam13304, AAA_21, AAA domain, putative AbiEii toxin, Type IV TA system. Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.	1.54531e-12
NC_003228.3|WP_010992159.1|888295_889543_+|mechanosensitive-ion-channel-family-protein	gnl|CDD|366370	pfam00924, MS_channel, Mechanosensitive ion channel. Two members of this protein family of M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins.	4.024e-25
NC_003228.3|WP_005784914.1|894921_895458_+|capsular-polysaccharide-transcription-antiterminator-UpgY	gnl|CDD|193584	cd09895, NGN_SP_UpxY, N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY. The N-Utilization Substance G (NusG) proteins are involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS (lipopolysaccharide) biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. UpxY proteins, UpxY proteins, where the x is replaced by the letter designation of the specific polysaccharide (UpaY to UphY), are a family of NusG SP factors that act specifically in transcriptional antitermination of operons from which they are encoded. UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal (NGN) domain is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.	8.4586e-29
NC_003228.3|WP_005784891.1|884333_885425_+|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB	gnl|CDD|236515	PRK09435, PRK09435, methylmalonyl Co-A mutase-associated GTPase MeaB.	0
NC_003228.3|WP_005784907.1|891483_891813_-|phosphatidylinositol-kinase	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.	2.91978e-46
NC_003228.3|WP_010992165.1|899011_900067_+|NTP-transferase-domain-containing-protein	gnl|CDD|133048	cd06426, NTP_transferase_like_2, NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase.	1.14592e-100
NC_003228.3|WP_005801389.1|885456_886365_-|DMT-family-transporter	gnl|CDD|223769	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].	2.55403e-13
NC_003228.3|WP_005784898.1|887307_888324_+|DUF4435-domain-containing-protein	gnl|CDD|373095	pfam14491, DUF4435, Protein of unknown function (DUF4435). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 285 and 362 amino acids in length. This domain is sometimes associated with AAA domains.	3.35851e-66
NC_003228.3|WP_005796193.1|883236_884325_+|DUF1573-domain-containing-protein	gnl|CDD|377880	pfam07610, DUF1573, Protein of unknown function (DUF1573). These hypothetical proteins, from bacteria such as Rhodopirellula baltica, Bacteroides thetaiotaomicron, and Porphyromonas gingivalis, share a region of conserved sequence towards their N-termini.	2.33736e-42

Protein sequences

>NC_003228.3|WP_005818358.1|891809_892022_-|helix-turn-helix-transcriptional-regulator
MKQIGIQIRQRRKMLGINQQTLADLAQISINTITKIENGEININFQKLYAILEVLGLELSLKIKNKEGHL
>NC_003228.3|WP_005784907.1|891483_891813_-|phosphatidylinositol-kinase
MRQGVVYLNKERVGIITELSSNEYKFRYDDEYFNDPSKPSISLTLTKQQQEYTSHYLFPFFANMLSEGHNRIVQARLLQIDEKDDFGILLATAHTDTAGAVTIKPLDYD
>NC_003228.3|WP_077687927.1|890480_891320_-|HipA-domain-containing-protein
MSISGAQQKYSLVVDNGQMRLSLEQEQATLLLKTKLSEYANKEISPANEHLTMQIASQVYNIPTAANGLCFFQNDEPAYITRRFDIAPNGRKFRKEDFASLAGISKGNKGPNYKYDVLSYEEMADIIKQYVSASSVEVLKFFRLVIFNFLFSNGDAHAKNFSLLETPSGDFILAPAYDLLNTRLHIFDDHVFALQRGLFKENTLNGNDGAVTGKEFIEFGIRIGIPPKRVHKELISFCQKAEQVQDLVEKSFLPNQLKKQYLLHYQMRKDSYLSVGIPT
>NC_003228.3|WP_005775503.1|889584_890478_+|AraC-family-transcriptional-regulator
MNALQSNIIREITPLSDKDCFYIAERYKTEFTYPIHNHAEFELNFTEKAAGVRRIVGDSAEVISDYDLVLITGKDLEHVWEQHDCHSKEIREITIQFSSDLFFKSFINKNQFDSIRDMLEKAQKGLCFPMSAILKIYPLLDTLASEKQGFYAVIKFLTILYELSLFNEEARTLSSSSFAKIGIHSDSRRVQKVQEYINAHYQEEIRLNQLADMVGMTPVSFSRFFKLRTGKNLSDYIIDIRLGFAARLLVDSTMSIAEICYECGFNNLSNFNRIFKKKKECSPKEFRENYRKKKKLV
>NC_003228.3|WP_010992159.1|888295_889543_+|mechanosensitive-ion-channel-family-protein
MEQITEKINDLFVSWGFDSSEVGPIMTLVLIIGIAFLADLICRNILLRVVAKLVKKTKATWDDIVFDRKVLIYLSHLVPPIIIYVLIPLAIPNVSALDFIRRICMIYIIAVFLRFISAFLSAVYHVYSEREQFRDRPLKGLLQTAQVILFFIGGIVVISVLIDKSPMVLLTGLGASAAILMLVFKDSIMGFVSGIQLSANNMLKVGDWIAMPKYGADGTVIEVTLNTVKVRNWDNTITTIPPYLLVSDSFQNWRGMQESGGRRVKRSINIDMNSVRFCTSEMLAKYKKIQLLTDYVEQTEQVVKEYNKEHHIDNSILVNGRRQTNLGVFRAYLTNYLKSLPDVNKNLTCMVRYLQPTEQGIPVELYFFSAVKEWVPYEGIQADVFDHLLAIVPEFGLRVFQNPTGEDFREWNRRN
>NC_003228.3|WP_005784898.1|887307_888324_+|DUF4435-domain-containing-protein
MAISLKDNLTSSYFNAAHKLYSKKARRRIVAYVESYDDVAFWRTLLEEFEDEEHYFQVMLPSATSLAKGKKMVLMNTLNTAELGKSLIACVDSDYDFLLQGATATSRKINRNRYIFQTYAYAIENYHCYADSLHEVCVQATLNDRHLIDFNEFMKRYSQIAYPLFLWSVWFYRRHDTYTFTMSEFNACVRLHDVSLRHPERSLEAVRRSVTSKLSELSTRFPQGIEEVDKLSVELKGLGVLPDTTYLFIQGHHIMDNVVMKVLTPVCTALRREREQEIKKLAEHDEQFHNELTCYQNSQVNVEVMLRKNSAYKDLYLYQWLKEDIKEFLYGTDNRKNK
>NC_003228.3|WP_005784896.1|886458_887286_+|AAA-family-ATPase
MELSANYIKRIEIDGLWDRFNIVWDLRPDVNILSGINGVGKTTILNRSVGYLEQLSGEVKSDEKNGVHIFFDNPEATYIPYDVIRSYDRPLIMGDFTARMADKNVKSELDWQLYLLQRRYLDYQVNIGNKMIELLSSNNEEERSKAATLSIAKRRFQDMVDELFSYTRKKIDRRRNDIAFYQDGELLFPYKLSSGEKQMLVILLTVLVQDNAHCVLFMDEPEASLHIEWQQKLISMIRELNPNVQIILTTHSPAVIMEGWLDAVTEVSDIATSYK
>NC_003228.3|WP_005801389.1|885456_886365_-|DMT-family-transporter
MEIDKNLKGHALAFTANMMWGLMSPIGKSALAEFSALSVTTFRMVGAAAAFWILSAFCKQEQVGHRDMVKIFFASLFALVFNQGIFIFGLSLTSPIDASIVTTTSPIITMIVAAIYLKEPVTNKKVLGIFIGAMGALILILSSQAVSAGGGSIWGDLLCMIAQLSFSIYLTVFKGLSQRYSAITINKWMFIYASICYIPFSYQDIASIKWDSISTAAIYQVLYVVLCGSFIAYICIMTAQKLMRPTVVSMYNYVQPIVASIAAILMGIGSFGWEKGVAIALVFLGVYFVTQSKSKADLEGVS
>NC_003228.3|WP_005784891.1|884333_885425_+|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB
MEHPENNEAYKGLVVNAGIEQPSSVNPYLKRKVKKRQLSVSEFVEGIVKGDVTILSQAVTLVESVRPEHQATAQEVIEKCLPYSGNSIRVGISGVPGAGKSTSIDVFGLHVLEKGGKLAVLAIDPSSERSKGSILGDKTRMEQLSVHPKSFIRPSPSAGSLGGVARKTRETIILCEAAGFDKIFVETVGVGQSETAVHSMVDFFLLIQLAGTGDELQGIKRGIMEMADGIVINKADGSNIDKAKLAAAQFRNALHLFPAPDSGWTPRVLTYSGFYNLGVKEIWDMVYEYIDFVKGNGYFEYRRNEQSKYWMYESINEQLRDSFYHNAKIESMLQEKEQQVLRGNLTSFVAAKSLLDTYFEDLK
>NC_003228.3|WP_005796193.1|883236_884325_+|DUF1573-domain-containing-protein
MKRSLLFIFTLLTITLSAVAQPRISSNKETHHFGQIEWKRPVSVEYTITNTGDKPLVLTNVTTSCACSVANWTKTPIAPGEKGTVSATFDAKALGHFNKSIGIYSNAQPSLVYLNFDGEVVQEIKDFTKTHPYAIGQIRIDRTDIDFPDAHSGEKPVITLGVVNLSDRPYEPVLMHLPPYLKMETNPTVLLKGKKGTITLTLDTKQLMDLGLTQSSVYLARFAGDKVGEENEIPVSAVLLPDFSGMTEQDKAVAPVIRLSESKIDLSQVLAKKNKARRDIVITNTGKSPLQISKLQVFNPAVGVALKKTVLQPGESTRLRVTVLKKNLGKKKRHLRILMITNDPVQPKVEIDVKATNNESHN
>NC_003228.3|WP_010992160.1|892511_893384_-|DUF4373-domain-containing-protein
MAIAYDGINYFPVGVNFMEENAMEVIEAKYGIKGSAIVLKLMCKIYKEGYYIRWDEEQCLIFANKAGREVQAEEVQGIIEILFTKGILDRNSYQENGILTSESIQKVWMEATKRRKRELSELPYLMVKPEKENGKADTPPALQEIQQPELFKKEKTPVNPKNVVHHVAVDAKNACNSGQSKVKEKKAEENKEFPPSAPPKGEEEERKGDSAYLPIPGYAFNTMTHNYSGLMDTLKRLSITDTGEVNSILRLSDYGRKGTTVWKLIANTCWSDIGAKGRYLIAALNKTKRR
>NC_003228.3|WP_005784912.1|893526_893874_-|hypothetical-protein
MKKLKSPASQSEAMKLRWKKRIVFEKGYTESCAEWMAERLEALLDHMQYGHATVAYRKQNGSFQLVKATLIYYEAEFRKKYDPTKIEGAVVYWNVDEQRWTTFQVENFMEWRPIV
>NC_003228.3|WP_008769439.1|893973_894204_-|hypothetical-protein
MKHYECLKLLITLYQDGAMGIKKETSQVALARYIDDKKLLGNIRNGIFIPLKFSTILKETNTIWNEMLRDKSIGIK
>NC_003228.3|WP_077687926.1|894217_894409_+|hypothetical-protein
MGFSFFRPLFDLRSLLSEICLLSVLFFLNSFFFFLLFVFVVHNLFNFSDFYLYKMLQRYERKI
>NC_003228.3|WP_005784914.1|894921_895458_+|capsular-polysaccharide-transcription-antiterminator-UpgY
MEVEKETEIWFAMRATYRRETDAMRLLAKENLGCFVPMQYKISIKKGKKVRVLVPIIHNLIFIHACPSEVKRVKSMVAYLQYITDTRSGKKIIIPDNEMQRFIAVAGTYSDHLLYFQPDELNLSKGTKVRITGGDFEGQEGVFLKVKGARDRRVVIAIQGVIAVAMATIHPDLIEVIK
>NC_003228.3|WP_005813291.1|895477_895966_+|transcriptional-regulator
MTLSEEVASLQRAAHDLMYLGMDGSPIYSDDLSRRNNEVYRLTTTLYNSGVQGSTVEEQASVCLALLMGYNASFIDHGEKREHVQKILDRCWDILDTLPASLLKLRLLTACYGEVFDEPLADEARAIIASWDSVSLTTEQQEAINEFQTVVDNPYPWEYVEE
>NC_003228.3|WP_010992162.1|895988_897197_+|UDP-N-acetylglucosamine-4,6-dehydratase
MLNVDNFIGENITFRRSSMFAPDIAANSDRLRQEVEGKSLLVIGGAGSIGSSYIKAILPFKPSKLVVIDLNENGLAELTRDLRSTYGLYIPKEYRTYTLNFADPIFERMFRKEQGFDIVANFSAHKHVRSEKDEYSVQALIENNVIKAKKLLDLLSEFPPRHFFCVSTDKAANPVNIMGASKRIMEDMIMAYSSKFKVTTARFANVAFSNGSLLAGFIDRIMKKQPLAAPNDVKRYFVSPEESGQICMLACVLGNNGEIFFPKLGEEKMITFSSICDRFLRTLGYEKKECATDEEARRYAAEMPDDSKIYPVVYFESDTTGEKGYEEFYVPGEKLNLERFSSLGVIEDASKRPLSELDSFFDELESLFALPDCHKSDIVTALKRFLPNFEHVEKGKNLDQKM
>NC_003228.3|WP_010992163.1|897216_898350_+|DegT/DnrJ/EryC1/StrS-family-aminotransferase
MEYQIPLFQLNFNEDEIQAVADTIRSKWISTGPKCEELENLFIEMMNVKYAVSLSNCTDALHLACLTSGIQPGDEVLCPSLTFAASVNCIRYVGATPVFCDIVGPNHINIDPEDIKRKITSKTKAIIVVHMAGFPAKMDEIMSIAKEYDLKVIEDACHGPLSEYKGKKLGTIGDVATFSFFSNKNISTGEGGMLITNNEKIASKARLLRSHGMTTMSYQRAKGHATAYDIIDLGYNFRMDDIRASIGCVQMRKLQADLEKRVRVRSKYIEELSKIGGLIVPFADNTEFVSNYIMPVVLVNSTKDKRDKIRNRIHASGIQTSNHYPAIHKFSIYKDYGAVLPQTEYVADNEITLPMYADLTDEQIEFVTHTVDVAING
>NC_003228.3|WP_077687925.1|898330_898951_+|acetyltransferase
MLQSMDNKVILVGGFHEIIELCEDNDIEIAGIIDNYLTNDTYWGYPIIGTDDKAKVLFETYKNVPVLITPDVPHVRYKLYHYYKSIGFQVASLISRDASISRSAIIGEGTIIQRGANLSSNIKIGQMVKVNTNANIMHDCLIGNYVTVAPNAVLLGKVEIDDKAYIGANATLLPSVKIGENVTVGAGSVVTKSVRPNTVVKGSPAK
>NC_003228.3|WP_010992165.1|899011_900067_+|NTP-transferase-domain-containing-protein
MLLDKIQNLIIQSDISIFQSMKKMDEEKVKLLFVFRGDCFVGILTIGDIQRAIIKQNDTSMQINNILDQNKVFAYKGESLEIIKNKMIHLRAECMPILDSKGELVDVLFWKDLFIDEVRVDDRKIDLPVVIMAGGKGTRLKPLTNVIPKPLIPIGDKTILEAILDQFESIGCSKFYMSVNYKYDILKFYLAQLDHKYDIRFFKEDKPLGTIGSVSLLKDKISTPFFVSNCDIIIDQDYRDVYDYHINNSNDLTIVTAVKRTRIPYGVIETIENGLMTELIEKPEFTYMINSGVYILQPELINEIPENELFHITHLMEKVKSRGGKIGCFPVSEKSWTDIGEWNEYLKLLGI

Crispr_ID: NC_003228_2

• CRISPR_ID: NC_003228_2
• CRISPR_location: 2837468-2837633
• CRISPR_type: Orphan
• Repeat_type: NA
• Spacer_info: 1 spacers

Consensus repeat of NC_003228_2

Consensus_repeat	Method
TTTTTCTTTGTCGGGGTAGCGGGATTCGAACCCACGACCCCCAGCTCCCAAAGC	CRISPRCasFinder

spacers of NC_003228_2

>2.1|2837522|58|NC_003228|CRISPRCasFinder
TGGTGCGCTAACCGGACTGCGCTACACCCCGAAACACTTGTAAAAAAAGAGAACTTCC

CRISPR arrays and Neighbor proteins around NC_003228_2

CRISPR arrays

The CRISPR arrays of NC_003228_2

>merge|NC_003228|2|2837468-2837633|CRISPRCasFinder
TTTTTCTTTGTCGGGGTAGCGGGATTCGAACCCACGACCCCCAGCTCCCAAAGCTGGTGCGCTAACCGGACTGCGCTACACCCCGAAACACTTGTAAAAAAAGAGAACTTCCTTTTTCTTTGTCGGGGTAGCGGGATTCGAACCCACGACCCCCTGCTCCCAAAGC

>NC_003228|2|2|2837468-2837633|CRISPRCasFinder
TTTTTCTTTGTCGGGGTAGCGGGATTCGAACCCACGACCCCCAGCTCCCAAAGC	TGGTGCGCTAACCGGACTGCGCTACACCCCGAAACACTTGTAAAAAAAGAGAACTTCC
TTTTTCTTTGTCGGGGTAGCGGGATTCGAACCCACGACCCCCTGCTCCCAAAGC

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_003228.3|WP_010993015.1|2838439_2838781_+|DUF1622-domain-containing-protein	unknown	unknown	gnl|CDD|377914
NC_003228.3|WP_005787747.1|2842030_2843503_+|TolC-family-protein	unknown	unknown	gnl|CDD|224455
NC_003228.3|WP_008768867.1|2823116_2823557_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005806198.1|2836069_2837314_-|tyrosine-recombinase	unknown	unknown	gnl|CDD|271185
NC_003228.3|WP_005787741.1|2837874_2838093_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993014.1|2832050_2832674_+|BACON-domain-containing-protein	unknown	unknown	gnl|CDD|271342
NC_003228.3|WP_005787745.1|2840303_2841668_-|sigma-54-dependent-Fis-family-transcriptional-regulator	unknown	unknown	gnl|CDD|225114
NC_003228.3|WP_032595863.1|2830762_2831956_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005777810.1|2838849_2839023_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005787744.1|2839029_2840307_-|sensor-histidine-kinase	unknown	unknown	gnl|CDD|236901
NC_003228.3|WP_010993012.1|2828397_2830500_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005787749.1|2843541_2844792_+|efflux-RND-transporter-periplasmic-adaptor-subunit	unknown	unknown	gnl|CDD|273776
NC_003228.3|WP_008768868.1|2823569_2824244_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005793807.1|2834558_2834897_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_077687800.1|2841643_2841889_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005793795.1|2847508_2849854_+|FtsX-like-permease-family-protein	unknown	unknown	gnl|CDD|274576
NC_003228.3|WP_010993016.1|2844935_2847359_+|ABC-transporter-permease	unknown	unknown	gnl|CDD|378928
NC_003228.3|WP_008768873.1|2833510_2833945_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_008768871.1|2830544_2830766_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_008770335.1|2832726_2833353_-|BACON-domain-containing-protein	unknown	unknown	gnl|CDD|271342

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_003228.3|WP_010993015.1|2838439_2838781_+|DUF1622-domain-containing-protein	gnl|CDD|377914	pfam07784, DUF1622, Protein of unknown function (DUF1622). This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.	1.80833e-23
NC_003228.3|WP_005787747.1|2842030_2843503_+|TolC-family-protein	gnl|CDD|224455	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].	5.10302e-26
NC_003228.3|WP_008770335.1|2832726_2833353_-|BACON-domain-containing-protein	gnl|CDD|271342	cd14948, BACON, Bacteroidetes-Associated Carbohydrate-binding (putative) Often N-terminal (BACON) domain. The BACON domain is found in diverse domain architectures and accociated with a wide variety of domains, including carbohydrate-active enzymes and proteases. It was named for its suggested function of carbohydrate binding; the latter was inferred from domain architectures, sequence conservation, and phyletic distribution. However, recent experimental data suggest that its primary function in Bacteroides ovatus endo-xyloglucanase BoGH5A is to distance the catalytic module from the cell surface and confer additional mobility to the catalytic domain for attack of the polysaccharide. No evidence for a direct role in carbohydrate binding could be found in that case. The large majority of BACON domains are found in Bacteroidetes.	1.87575e-07
NC_003228.3|WP_005806198.1|2836069_2837314_-|tyrosine-recombinase	gnl|CDD|271185	cd01185, INTN1_C_like, Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain. IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. 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.	1.43542e-20
NC_003228.3|WP_005787744.1|2839029_2840307_-|sensor-histidine-kinase	gnl|CDD|236901	PRK11360, PRK11360, two-component system sensor histidine kinase AtoS.	3.10832e-34
NC_003228.3|WP_005793795.1|2847508_2849854_+|FtsX-like-permease-family-protein	gnl|CDD|274576	TIGR03434, ADOP, Acidobacterial duplicated orphan permease. Members of this protein family are found, so far, only in three species of Acidobacteria, namely Acidobacteria bacterium Ellin345, Acidobacterium capsulatum ATCC 51196, and Solibacter usitatus Ellin6076, where they form large paralogous families. Each protein contains two copies of a domain called the efflux ABC transporter permease protein (pfam02687). However, unlike other members of that family (including LolC, FtsX, and MacB), genes for these proteins are essentially never found fused or adjacent to ABC transporter ATP-binding protein (pfam00005) genes. We name this family ADOP, for Acidobacterial Duplicated Orphan Permease, to reflect the restricted lineage, internal duplication, lack of associated ATP-binding cassette proteins, and permease homology. The function is unknown.	5.91894e-30
NC_003228.3|WP_010993016.1|2844935_2847359_+|ABC-transporter-permease	gnl|CDD|378928	pfam12704, MacB_PCD, MacB-like periplasmic core domain. This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein. Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter.	7.35542e-15
NC_003228.3|WP_005787745.1|2840303_2841668_-|sigma-54-dependent-Fis-family-transcriptional-regulator	gnl|CDD|225114	COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms].	8.70368e-160
NC_003228.3|WP_005787749.1|2843541_2844792_+|efflux-RND-transporter-periplasmic-adaptor-subunit	gnl|CDD|273776	TIGR01730, COG0845:_Membrane-fusion_protein, RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane. [Transport and binding proteins, Unknown substrate].	1.06032e-21
NC_003228.3|WP_010993014.1|2832050_2832674_+|BACON-domain-containing-protein	gnl|CDD|271342	cd14948, BACON, Bacteroidetes-Associated Carbohydrate-binding (putative) Often N-terminal (BACON) domain. The BACON domain is found in diverse domain architectures and accociated with a wide variety of domains, including carbohydrate-active enzymes and proteases. It was named for its suggested function of carbohydrate binding; the latter was inferred from domain architectures, sequence conservation, and phyletic distribution. However, recent experimental data suggest that its primary function in Bacteroides ovatus endo-xyloglucanase BoGH5A is to distance the catalytic module from the cell surface and confer additional mobility to the catalytic domain for attack of the polysaccharide. No evidence for a direct role in carbohydrate binding could be found in that case. The large majority of BACON domains are found in Bacteroidetes.	1.60933e-06

Protein sequences

>NC_003228.3|WP_005806198.1|2836069_2837314_-|tyrosine-recombinase
MASIKLYFDKRVNRKDGKFPLKINVTHKRQQALINLGVLLSPDQWDSTKGKVINGPNKSFLNGYISQRVHCAETELLNLRIAGKLDLMTGKQFKEHLQRILLRGKLEEKQEETGCSFVQYYTRFVEGKKNPQTKAVYQYTLDRICRFVDVPDKFRFEDVTYAWLKSFEIHLSETSKVNSISIHMRNIRAVFNDALNTETISCYPFRRFKIKQEATAKRALTPEELVTLRDYPCEEHQKQYVDIFMLIFYLVGINTVDLCRLEKIRNGRIEYRRAKTKKIYNIKVEPEAAEIIERYKGSKYLLNILERYKNYKDYAHRLNENLQEIGSVELVEKVINGKRRRVKKRFPLFPELTVYWARHTWATIAHKIGVSKDVISLALGHEFGCKTTSIYIDYDMEKVDKANRQVLDYLENLK
>NC_003228.3|WP_005793807.1|2834558_2834897_+|hypothetical-protein
MKKVLVALTMVMGMGSAVAFAQEPVKLPAMEQNQQTSQDKFTKITVKELPQVVKSTLSKDYEGTIVKEAFVAEKENGKVYKIIVTAIKEDQSTEEITVLLNEKGEPVNEKDC
>NC_003228.3|WP_008768873.1|2833510_2833945_+|hypothetical-protein
MKLIVYNSRLAKRMLFPGYSTIMLFGIILTKSGKEECPPALIRHEQIHQRQYLECFILPVLPAVLFTPWILTLCPLSFYILYLTEWFISFVRYFWGQGMTDPGRAGHRAYMSSAMEMEAKVKEVETGYLERRKHFAFMRYYDKI
>NC_003228.3|WP_008770335.1|2832726_2833353_-|BACON-domain-containing-protein
MAKASWCNVSPMSGSENGALTISAAAHAGREARSTTVTVTAKNGTKPSASIAVSQAGVGVQLTMDTSKPDLPGEGGSVTINGNSNSPTLKISVPLINLPGVTASAKFNAPGITDKVLAASETVTIPGDPGANGSYAFSIKLEIARNPLPTPLAPNVDVTDSAGKMVRCQFKWAAGASALSVNKSSLSLVNAGTGQTVDVTSNDEWAVS
>NC_003228.3|WP_010993014.1|2832050_2832674_+|BACON-domain-containing-protein
MAKASWCNVSPMSGSKNGTLTISAGVHTGRTARSTTVTVTAANGTKPSATIAVSQAGTGVSTTMDANKPDLPSSGGVVNINGTSNSSKLKWTCTARVMGVDMPIDDNYVKVAVNGGNIGNNVAIPGDPGASGSFNFVATLTFPASMFPVDAVVTFRLTDDTDSAKQCTFTWKAGASSLSVNKSSLSLVNGGTGQTVNVTSNDDWNVS
>NC_003228.3|WP_032595863.1|2830762_2831956_+|hypothetical-protein
MSFEIIRKTGEIAFVANPIAFEVKTSGEAEIEIRLRVGAQEVFSASYVPFGDRIHFDIAEILQPFVTSGPLEDSEDLILPVSGFMAGYTLEVKGQETRTLTGKVICGGISKQAAREMAGRGMDFILNRLRDYSSQFLFTTRTRGKHIAIRETEVSPLIFIHPDKRIQVESEYGNRIKLPEGTAGEIYALNIGRIRREFFHKYNQIVSFIRVLVPAEEAFDISFTPGEVSENGLSFLFRNSLGCYEVIEMPGKMICSLDRGDDENYRTFDEEGGDYITGRPRPDLLQKMKLNTGFKRKTELKFIQDLLSSDDIRLLNGTARRRVLVTCEEYGYEEPMKEPTSLVLDIEVAERESNYTPDMDGENAPPFIELLPGEVEIPSEGGQVRVRVESNIMWEVV
>NC_003228.3|WP_008768871.1|2830544_2830766_+|hypothetical-protein
METKNQNKIVTAPSLENTQELYEIYRQRYGADKTPEDFYRFMTTPGVERRSFLLENTQARPLSINNTIIHKCV
>NC_003228.3|WP_010993012.1|2828397_2830500_+|hypothetical-protein
MALTIQTEKGIFDLPRDFSVEIENTSPIYTDKGSQTIASTLPATGHNLSMVDYIHRPDIRNAPKRDAATVVTDGVYRRTGKLNITSVSTESGIVCNIGFDESLMYEAWKNVSLKELPGLPVIKYPEGVAALARHLEEVMRYQTPADYHVFRIQVASETLEETEYPEFINPIGSDGKTYALLKEARTERVVISGQAVDVRVPAGYGISPFLKVSRILEMIFSAYGFTLVENPFATDYQLSKMVVLNNVADTIVTGEIDYRNLMPDCTVNEFLDALFCRTGAKVYVNAGRKAVIRLLKDSIGATASADWTPLKASEPEINYTPAKQLKLSAGTSFKEAEPAADSFEKFLKPYGGIITEFTGDRDVPDELYITYQPSTGRYYKRDIVNKKKKWISSDFFPWDKATPGVEYLEITGKDECVPMAFKTGLLTPGYLAGAVNINTTLRGVAKEQGEKKQTPLAFCFAMGKTNQIIGAGALVEEYYFGSSLCRGPKGEYFQDPGGNVYRYSLVFRGEDGAFNRFFKEYDAVLRHADHVYAVQMNPDKAGLLKLDASRPVMLHGQRMMVESLKYALPLRKGRPCQVKLRSLKLLQPYDLDKEQELVPMIPQQATWKVFTYFDRDMELRVQELREQPGIIRVDVVAKEVLTKPEEGDFDMYPPPSLQDVADKRKIMYTYKGKLKYRPYPPGLTQEEVVNYRAGVIAVKI
>NC_003228.3|WP_008768868.1|2823569_2824244_+|hypothetical-protein
MENDRVSLEDLTQGQWLELRYQMEPRNFKRLVERARNAGIDVPACVGVKNYAPKIKFSTLSETARYVRSQDIEAVKTFNRRCENWSIFVTAELRSQARMSFPHNPKRSKGATPLSESINGNVRYDKKYKVEVRSLGFSFARHGVMLHYGASSGHGGYIGSKWRDRFGNIRTTNPASFGKMGQGNRKAVHWFNPVLRKHLPTLADIAAEYCMDMSLNLAGLFLEE
>NC_003228.3|WP_008768867.1|2823116_2823557_+|hypothetical-protein
MVDLQQYEEYFRELSQALPGIGSMIPVTYDIDIYEYVQSLRAEDLPVLFVVLPTCESLSRDPDCVVERNFGMCLLLDKTDWQRERGLDAQKRLQPTFEEIKSMMRQEYGRCGIFSRLNLEEMTSSPESGLFKALSGWSLGFTFDSI
>NC_003228.3|WP_005787741.1|2837874_2838093_-|hypothetical-protein
MAKVINRDVPIAEENTTLTGQPATNMYDDWSEEMEDRADNVYDDTKKKSAGNKKSKEKKLKEIDEVVKEDLE
>NC_003228.3|WP_010993015.1|2838439_2838781_+|DUF1622-domain-containing-protein
MLTQFLNLLATIISVISLLIVTYGALIAIISFIINELKRVTGAYTPTNIRKLRAVFGTYLLLGLEFLIASDILKTVLEPTMNELIILGGIVVVRTILSVFLNKEIKELETENN
>NC_003228.3|WP_005777810.1|2838849_2839023_+|hypothetical-protein
MNTEKEKTSSEEQKKAEKVLKDKVPVQQTGTYSEATKKEVRDAVKELNPDMSGLDRG
>NC_003228.3|WP_005787744.1|2839029_2840307_-|sensor-histidine-kinase
MKRYSISVVLHILLLVVLSIGGYLLFCYELWFSTLIVGILLIATGVHLYSIQMKLAGMMRRLTDCIRFNDMTQNFQPPFKSKMMVELADELSQTLRLFRGRLLEEEIKHQYYENLLNKVDTAVVVTDRSGRVEWMNRAAVALVGQESRLPQEWLTTSWNETQVVRIRQQGASVEMAVSCTLFAAQNKERLLVSLKNIHSVLERNEMEAWQKLIRVLTHEIMNSITPIISLSETLSERGIPERLSEKEYGVMLQAMQTIHRRSKGLLGFVENYRRLTRIPTPARTLVAVDELFSDLRKLFPDSFIHFAATHRGATLYIDRAQIEQVLINLIKNAKESCGQNTAPQIEVELEQVPGKVCSLTVRDNGEGILPEVIDKVFVPFFTTKPSGSGIGLSLCKQIMNLHGGTITVSSEIGKGSCFTLMFPGR
>NC_003228.3|WP_005787745.1|2840303_2841668_-|sigma-54-dependent-Fis-family-transcriptional-regulator
MEQLGKILIVDDNEDVLFALNLLLEPYTEKIKVATTPDRIEHFMTTFGPDIILLDMNFSRDAISGQEGFESLEQILKIDPQAIVIFMTAYADTDKAVRAIKAGATDFIPKPWEKEKLLATLSSGMKLRQSRHEVNMLKEQVEVLSGQGGPENEIIGESEAMQEVFSTINKLSETDANILILGENGTGKDVIARLLYRCSPRYGKPFVTIDLGSIPEQLFESELFGYEKGAFTDARKAKAGRMEVATGGTLFLDEIGNLSLPMQSKLLTAIEKRQISRLGSTQSVPIDVRLICATNADIRAMVDEGNFRQDLLYRINTIEIHIPPLRERGNDVILLAEFFLERYARKYKKEMHGLTREAKNKLLKYNWPGNVRELQHTIERAVILGDGSLLKPENFLFHSSVRQKKEEEVLNLELLERQAVEKAMRLSEGNITRAAEYLGITRFALYRKLEKLGL
>NC_003228.3|WP_077687800.1|2841643_2841889_-|hypothetical-protein
MDIICTFALRLKVSEYIRLTLASLHGKIRCTRCITGTRRVVQLVHDEMHNWYTTSCTTGISYPLKESKLARNITWNSLEKY
>NC_003228.3|WP_005787747.1|2842030_2843503_+|TolC-family-protein
MNLKTILIIAGCSYIFPATAQERTMELSLDETVKLAKLQSPDAQTARHSFRSAYWNYKYYRANYLPALSLTSDPNLNRAINKVTLGDGTVKFVEQNMLSTDLTLNLTQNIPWTGGSLFVETAAQRMDIFSDHTTAWQTSPINIGYRQSLFGYNSLKWDRRIEPVRYREAKKSYVETLELVATRATQKFFNLATAQSNYETATTNYANADTLYQYAQGRYNIGTITENEMLQLELNKLTEETNRMNARIEMDNCMQELRSYLGIQSDEELKVKINDHVPDFSVELHEALLLANENSPEIQNMIRRKLESESNVSYARANAGLKADIYLRFGLTQTADKLGSAYKRPLDQQYVSLSVALPILDWGRGKGKVRVARSNRDLVYTQVEQDKTDFELNIRKLVKQFNLQAQRVRIAARTDETAQRRSDVARKLYLLGKSTILDLNASITEKDQARRNYITALYNYWSLYYTLRSLTLFDFEGKTPLTENYDLLID
>NC_003228.3|WP_005787749.1|2843541_2844792_+|efflux-RND-transporter-periplasmic-adaptor-subunit
MDIKIEKKPWYIRYKFYIAGGIAFVAFLVYVIILSAGPRKLRIESENIQIAEVKDDKFMEYVDVEGLIQPILTIKVNTREAGSVERIIAEEGSLLQKGDTILTLSNPDLLRSIEDQRDDWEKQRITYQEKEIEMEQKSLSLKQQTLETNYELARLKKSFTLDKEEFRMGIKSKAQLEVSEDEYNYKVKNAELQREGLRHDSAVTIIRKDLIRTDMERERKKYERATERLGNLVVKAPISGQLSFVKVTPGQQVGSSESIAEIKVLDQYKIHTSLSEYYIDRITTGLPATVNYQGKKYPLRITKVVPEVKDRMFDVDLVFTGEMPDNVRVGKSFRVQIELGQPEQAIVIPRGNFYQATGGQWIYKANASKTKAVRTPITIGRQNPQQYEITGGLEPGDYVVTTGYDTFGEAEELILK
>NC_003228.3|WP_010993016.1|2844935_2847359_+|ABC-transporter-permease
MKTIRLAWKALARFRTYTFINILGLALSLACVLIILRYIHQEVTVNHFCKDLENTYLLYIEYEDGRRTISSNEDRNNDPNFIDPLNDPSVLKSTRWINFPEDRITVGKQIYNVKTVVTDSVFLQILPYPSVSGISSLKSPNDAIITRRLAERLFGKENPIGKTMTYSTGDIVTVTGVIGEPTTKSFLDFDLIISERLQHSWSRLSNSLVQLIPGTDFKKLNVKNEKFMKLRCHMDAPTRLQFFPLKDFYFDKTVRVYNNNIRKGNYNNILVLAVVTIALLIIGLFNFINIYTVMMLKRAREFGVKKVYGAGAKDVFAQIFTENFILTGMALCISWCIIEITGGMMEHVLRIPQTSNTEFSATLSVGILILLPLLTSIYPFIRYNYVSPSVSIRSVNAGGHSIVSRVLFLFVQYIITFVLIIVSLFFTKQVRFMLSADLNYTTKDIIQCQLYAERSSYDINISYEEWERRKQREKSNLAYIKEEMDHSPLFIRWEYGENPNQLDDNYINVRNAQRDEFKQVIYSSLSNKYIELFGFQLKEGRLWNDSVDQWTDYKMIINESAKSLLEIDNIETALIQPERRLWWSLSKSEEMKKNPPYQVIGVIKDFKIGHLSKTTPPLFIVYEDPRGSYRDRLMAQIVPGKKQEAIAFLKRLRDEILGEGEFEYSFLEDEIATMYQEDKRTAEIYSLFSIIAILISCLGLFGLSMFDIRQRYREIALRKVNGATLKEIYPLLLKKYSIILGMAFIISAPLSWYIISKYLEGFANKAPISWWLFAIAAIVTAFISLATLIWQIRKAANINPAKVLKGE
>NC_003228.3|WP_005793795.1|2847508_2849854_+|FtsX-like-permease-family-protein
MIRHYFKIAFRNLLKYKTQSIISIIGLAVGITCFALATLWIRYEMTYDTFHRRADDIYLVRAQLTITDGTLSNSMPYPAIEYLRKNISEIEDICGISPFKTNLRFKDKGGDLLAIEVDSAFIRMFDVRILQGNVNFLKKKSNEIAITEAVAKEWFGNESPLGKEIELGSRPCKVCAVVSGWSQHSNLSYGALLPARHHPSWQSNSEQIFVRILPDTDKSALQKRISSLDASSQEKESTLGKLNFTPITSLRYSDYLQKDEIVISFNYIRYFAMAGVLVIVCSLFNYLTLFVSRLRMRGRELGLRKVCGSTNRSLFALLSVEYLIVLLAGSLLGMAFIEACLPHFIELAQISEATPLYTEVIIYILAVIVLSFGISQIPLYYFRSRTLQSSIRNKKGSPQRGIFRRLGLIAQLIISLGFIFCTTIMMKQLYYLKNTDLGIERHNIGNVAVWMKGDINEWSSKIANLPMVTEALPPHYFPIVPTGPMMYTDINGWDGLNETTDETYSVGLIPSGKEFFDFYGLQLTEGEWLSEKNSPGDVIINETAALTFGWRNPVGKQFYSEYEHNRTYYTVVGVVKDFSYLPPTIAPRPLAFVRTEEQKYLWSRASILFKFTEGSWEACKDTIRKMKEEDFPSSFLRLYNEEEEYNKYLRSESALMTLLGIVSIVCVIISIFGIFSQVTLSCEQRRKEIAIRKVNGATIGSILQMFIKEYFVLLLVAALIAFPASYGMMRVWIESYVRQTSTPFWIYIVLFAGIGIIIVISIFWRVWNAAKQNPAEVVKTE

Crispr_ID: NC_003228_3

• CRISPR_ID: NC_003228_3
• CRISPR_location: 2998004-2998546
• CRISPR_type: Unclear
• Repeat_type: NA
• Spacer_info: 8 spacers
• Cas_protein_info: cas2,cas6

Consensus repeat of NC_003228_3

Consensus_repeat	Method
ATTTCAATTCCATAAGGTACAATTAATAC	CRISPRCasFinder
ATTTCAATTCCATAAGGTACAATTAATAC	CRT
ATTTCAATTCCATAAGGTACAATTAATAC	PILER-CR

spacers of NC_003228_3

>3.1|2998033|37|NC_003228|CRISPRCasFinder,CRT
CAGTGCAGCACATCGTAATATCTTGCATTTTGCACAA
>3.2|2998099|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR
TAACCGGACTTACAGCTGATAATCAGTTAGAGTA
>3.3|2998162|36|NC_003228|CRISPRCasFinder,CRT,PILER-CR
CAATTACACAGATCGTAAAACTTGCCGAGCTATTTA
>3.4|2998227|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR
CGTATTCGCCATCGAACCGAAGACCGGCGTGTAT
>3.5|2998290|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR
AGCAAGGGAAACTGTACGATGTACAAGTACTCGG
>3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR
CTGATGAAGCGATTAAGAAGATCAATGTGATGATTAA
>3.7|2998419|36|NC_003228|CRISPRCasFinder,CRT,PILER-CR
TCAGTTACCCTGACGGCCAATCCTTCCGCCATTTCC
>3.8|2998484|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR
GAAGTCCGCTGAAATCCAGCCCGCCTTTTCGTTC

CRISPR arrays and Neighbor proteins around NC_003228_3

CRISPR arrays

The CRISPR arrays of NC_003228_3

>merge|NC_003228|3|2998004-2998546|CRISPRCasFinder,CRT,PILER-CR
GTCCTAATTCCATAAGGTACAATTAATACCAGTGCAGCACATCGTAATATCTTGCATTTTGCACAAATTTCAATTCCATAAGGTACAATTAATACTAACCGGACTTACAGCTGATAATCAGTTAGAGTAATTTCAATTCCATAAGGTACAATTAATACCAATTACACAGATCGTAAAACTTGCCGAGCTATTTAATTTCAATTCCATAAGGTACAATTAATACCGTATTCGCCATCGAACCGAAGACCGGCGTGTATATTTCAATTCCATAAGGTACAATTAATACAGCAAGGGAAACTGTACGATGTACAAGTACTCGGATTTCAATTCCATAAGGTACAATTAATACCTGATGAAGCGATTAAGAAGATCAATGTGATGATTAAATTTCAATTCCATAAGGTACAATTAATACTCAGTTACCCTGACGGCCAATCCTTCCGCCATTTCCATTTCAATTCCATAAGGTACAATTAATACGAAGTCCGCTGAAATCCAGCCCGCCTTTTCGTTCATTTCAATTCCATAAGGTACAATTAATAC

>NC_003228|3|3|2998004-2998546|CRISPRCasFinder
GTCCTAATTCCATAAGGTACAATTAATAC	CAGTGCAGCACATCGTAATATCTTGCATTTTGCACAA
ATTTCAATTCCATAAGGTACAATTAATAC	TAACCGGACTTACAGCTGATAATCAGTTAGAGTA
ATTTCAATTCCATAAGGTACAATTAATAC	CAATTACACAGATCGTAAAACTTGCCGAGCTATTTA
ATTTCAATTCCATAAGGTACAATTAATAC	CGTATTCGCCATCGAACCGAAGACCGGCGTGTAT
ATTTCAATTCCATAAGGTACAATTAATAC	AGCAAGGGAAACTGTACGATGTACAAGTACTCGG
ATTTCAATTCCATAAGGTACAATTAATAC	CTGATGAAGCGATTAAGAAGATCAATGTGATGATTAA
ATTTCAATTCCATAAGGTACAATTAATAC	TCAGTTACCCTGACGGCCAATCCTTCCGCCATTTCC
ATTTCAATTCCATAAGGTACAATTAATAC	GAAGTCCGCTGAAATCCAGCCCGCCTTTTCGTTC
ATTTCAATTCCATAAGGTACAATTAATAC

>NC_003228|3|1|2998004-2998546|CRT
GTCCTAATTCCATAAGGTACAATTAATAC	CAGTGCAGCACATCGTAATATCTTGCATTTTGCACAA
ATTTCAATTCCATAAGGTACAATTAATAC	TAACCGGACTTACAGCTGATAATCAGTTAGAGTA
ATTTCAATTCCATAAGGTACAATTAATAC	CAATTACACAGATCGTAAAACTTGCCGAGCTATTTA
ATTTCAATTCCATAAGGTACAATTAATAC	CGTATTCGCCATCGAACCGAAGACCGGCGTGTAT
ATTTCAATTCCATAAGGTACAATTAATAC	AGCAAGGGAAACTGTACGATGTACAAGTACTCGG
ATTTCAATTCCATAAGGTACAATTAATAC	CTGATGAAGCGATTAAGAAGATCAATGTGATGATTAA
ATTTCAATTCCATAAGGTACAATTAATAC	TCAGTTACCCTGACGGCCAATCCTTCCGCCATTTCC
ATTTCAATTCCATAAGGTACAATTAATAC	GAAGTCCGCTGAAATCCAGCCCGCCTTTTCGTTC
ATTTCAATTCCATAAGGTACAATTAATAC

>NC_003228|3|2|2998070-2998546|PILER-CR
ATTTCAATTCCATAAGGTACAATTAATAC	TAACCGGACTTACAGCTGATAATCAGTTAGAGTA
ATTTCAATTCCATAAGGTACAATTAATAC	CAATTACACAGATCGTAAAACTTGCCGAGCTATTTA
ATTTCAATTCCATAAGGTACAATTAATAC	CGTATTCGCCATCGAACCGAAGACCGGCGTGTAT
ATTTCAATTCCATAAGGTACAATTAATAC	AGCAAGGGAAACTGTACGATGTACAAGTACTCGG
ATTTCAATTCCATAAGGTACAATTAATAC	CTGATGAAGCGATTAAGAAGATCAATGTGATGATTAA
ATTTCAATTCCATAAGGTACAATTAATAC	TCAGTTACCCTGACGGCCAATCCTTCCGCCATTTCC
ATTTCAATTCCATAAGGTACAATTAATAC	GAAGTCCGCTGAAATCCAGCCCGCCTTTTCGTTC
ATTTCAATTCCATAAGGTACAATTAATAC

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_003228.3|WP_010993064.1|2999648_3000320_-|CRISPR-associated-endoribonuclease-Cas6	cas6	cd09652_cas6_CAS-I:CAS-III	gnl|CDD|273848
NC_003228.3|WP_008660463.1|3001141_3001996_+|type-I-methionyl-aminopeptidase	unknown	unknown	gnl|CDD|238519
NC_003228.3|WP_005788073.1|2996961_2997366_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005788091.1|3008785_3008986_-|winged-helix-turn-helix-domain-containing-protein	unknown	unknown	gnl|CDD|371235
NC_003228.3|WP_005788068.1|2991465_2994186_-|pyruvate,-phosphate-dikinase	unknown	unknown	gnl|CDD|236446
NC_003228.3|WP_005788087.1|3005554_3006733_-|sodium:proton-antiporter	unknown	unknown	gnl|CDD|366411
NC_003228.3|WP_005788089.1|3006878_3008660_-|elongation-factor-4	unknown	unknown	gnl|CDD|235462
NC_003228.3|WP_005788055.1|2987373_2988498_+|2-iminoacetate-synthase-ThiH	unknown	unknown	gnl|CDD|236425
NC_003228.3|WP_005788064.1|2990683_2991253_-|PorT-family-protein	unknown	unknown	gnl|CDD|372635
NC_003228.3|WP_008768963.1|2995875_2996799_+|RluA-family-pseudouridine-synthase	unknown	unknown	gnl|CDD|223638
NC_003228.3|WP_005788062.1|2989969_2990482_-|outer-membrane-beta-barrel-protein	unknown	unknown	gnl|CDD|379226
NC_003228.3|WP_005793479.1|3009132_3009597_-|hypothetical-protein	unknown	unknown	gnl|CDD|378246
NC_003228.3|WP_005788070.1|2994452_2995871_+|23S-rRNA-(uracil(1939)-C(5))-methyltransferase-RlmD	unknown	unknown	gnl|CDD|225174
NC_003228.3|WP_005788060.1|2989283_2989892_+|thiamine-phosphate-synthase	unknown	unknown	gnl|CDD|238317
NC_003228.3|WP_005793495.1|2988520_2989222_+|HesA/MoeB/ThiF-family-protein	unknown	unknown	gnl|CDD|238386
NC_003228.3|WP_041926232.1|3003250_3003997_+|hypothetical-protein	unknown	unknown	gnl|CDD|376845
NC_003228.3|WP_010993066.1|3004196_3005510_-|Na+/H+-antiporter-NhaA	unknown	unknown	gnl|CDD|377746
NC_003228.3|WP_010993063.1|2998758_2999022_-|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl|CDD|187856
NC_003228.3|WP_005793488.1|3001996_3003223_+|DNA-recombination-protein-RmuC	unknown	unknown	gnl|CDD|224241
NC_003228.3|WP_008768964.1|2997388_2997823_-|hypothetical-protein	unknown	unknown	unknown

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_003228.3|WP_010993064.1|2999648_3000320_-|CRISPR-associated-endoribonuclease-Cas6	cas6	cd09652_cas6_CAS-I:CAS-III	6.9e-26	86.5	0.3
NC_003228.3|WP_010993063.1|2998758_2999022_-|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	8.5e-25	81.5	0.0

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_003228.3|WP_010993064.1|2999648_3000320_-|CRISPR-associated-endoribonuclease-Cas6	gnl|CDD|273848	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6.	9.8875e-25
NC_003228.3|WP_008660463.1|3001141_3001996_+|type-I-methionyl-aminopeptidase	gnl|CDD|238519	cd01086, MetAP1, Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.	7.65745e-140
NC_003228.3|WP_005788091.1|3008785_3008986_-|winged-helix-turn-helix-domain-containing-protein	gnl|CDD|371235	pfam10771, DUF2582, Winged helix-turn-helix domain (DUF2582). This family is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold. Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested that these proteins are not very likely to bind to DNA.	1.84664e-24
NC_003228.3|WP_005788068.1|2991465_2994186_-|pyruvate,-phosphate-dikinase	gnl|CDD|236446	PRK09279, PRK09279, pyruvate phosphate dikinase; Provisional.	0
NC_003228.3|WP_005788087.1|3005554_3006733_-|sodium:proton-antiporter	gnl|CDD|366411	pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family. Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family.	0.00100961
NC_003228.3|WP_005788089.1|3006878_3008660_-|elongation-factor-4	gnl|CDD|235462	PRK05433, PRK05433, GTP-binding protein LepA; Provisional.	0
NC_003228.3|WP_005788055.1|2987373_2988498_+|2-iminoacetate-synthase-ThiH	gnl|CDD|236425	PRK09240, thiH, 2-iminoacetate synthase ThiH.	0
NC_003228.3|WP_005788064.1|2990683_2991253_-|PorT-family-protein	gnl|CDD|372635	pfam13568, OMP_b-brl_2, Outer membrane protein beta-barrel domain. This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.	6.71541e-13
NC_003228.3|WP_008768963.1|2995875_2996799_+|RluA-family-pseudouridine-synthase	gnl|CDD|223638	COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis].	4.55498e-67
NC_003228.3|WP_005788062.1|2989969_2990482_-|outer-membrane-beta-barrel-protein	gnl|CDD|379226	pfam13505, OMP_b-brl, Outer membrane protein beta-barrel domain. This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.	5.42949e-05
NC_003228.3|WP_005793479.1|3009132_3009597_-|hypothetical-protein	gnl|CDD|378246	pfam09719, C_GCAxxG_C_C, Putative redox-active protein (C_GCAxxG_C_C). This entry represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters.	1.20542e-38
NC_003228.3|WP_005788070.1|2994452_2995871_+|23S-rRNA-(uracil(1939)-C(5))-methyltransferase-RlmD	gnl|CDD|225174	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis].	4.2194e-124
NC_003228.3|WP_005788060.1|2989283_2989892_+|thiamine-phosphate-synthase	gnl|CDD|238317	cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.	6.53903e-31
NC_003228.3|WP_005793495.1|2988520_2989222_+|HesA/MoeB/ThiF-family-protein	gnl|CDD|238386	cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1). .	1.04156e-112
NC_003228.3|WP_041926232.1|3003250_3003997_+|hypothetical-protein	gnl|CDD|376845	pfam02596, DUF169, Uncharacterized ArCR, COG2043.	2.71454e-26
NC_003228.3|WP_010993066.1|3004196_3005510_-|Na+/H+-antiporter-NhaA	gnl|CDD|377746	pfam06965, Na_H_antiport_1, Na+/H+ antiporter 1. This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyze the exchange of H+ for Na+ in a manner that is highly dependent on the pH.	3.45767e-165
NC_003228.3|WP_010993063.1|2998758_2999022_-|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.	2.97832e-27
NC_003228.3|WP_005793488.1|3001996_3003223_+|DNA-recombination-protein-RmuC	gnl|CDD|224241	COG1322, COG1322, Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].	4.76227e-92

Protein sequences

>NC_003228.3|WP_008768964.1|2997388_2997823_-|hypothetical-protein
MKTLNFMKTLFLLVAIVGLSSCGDKYYSDDYLRNSNAKLCGKTWVNDSEKNDVDEWVRHTLKFDDNGRLAETYAYYHVNESQPYRTETNNLTWSWIDDTMEGIVFDYGVNGVTYFDNVWVREHNMSGKLNGKVVVFVDSKYNRN
>NC_003228.3|WP_005788073.1|2996961_2997366_-|hypothetical-protein
MKGYWKILLILMLAVGFASCEDDQGEIEYVITGRAWTGDVGMNAHNGEPLFSTFEFGNDGFGVETQFYASDGLLYDQFRFQWYWEDSYNRNLVLNYGKNGISYMDDVRIYGDRITGAFYLSDDARGFNFELRME
>NC_003228.3|WP_008768963.1|2995875_2996799_+|RluA-family-pseudouridine-synthase
MNMKRIKRTPAEKARAQYTGYLVKEPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIYVVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTLYVSSSSYDDGGSKSITHYRTIKRANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGIDGGPNPLGRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKLFLKK
>NC_003228.3|WP_005788070.1|2994452_2995871_+|23S-rRNA-(uracil(1939)-C(5))-methyltransferase-RlmD
MARKKKELPLLEKVTITDVAAEGKAIAKVDDLVVFVPYVVPGDVVDLQVKRKKNKYAEAEAVKFHELSPVRAVPFCQHYGVCGGCKWQVLPYAEQIKYKQKQVEDNLRRIGKIELPEISPILGSAKTEFYRNKLEFTFSNKRWLTAEEVKQDVKYDQMNAVGFHIPGAFDKVLAIEKCWLQDDISNRIRNTIRDYAYEHNYSFINLRSQEGMLRNMIVRTSSTGELMVILICKITEEHEMDLFKQLLQYVADQFPEITSLLYIINNKCNDTINDLDVHVFRGNDHIFEEMEGLRFKVGPKSFYQTNSEQAYNLYKVARDFAGLTGDELVYDLYTGTGTIANFVSRQARKVIGIEYVPEAIEDAKVNAEINGIENTLFFAGDMKDILTQDFINQYGRPDVIITDPPRAGMHQDVVDVILFAEPKRIVYVSCNPATQARDLQLLDVKYRVKAVQPVDMFPHTHHVENVVLLELK
>NC_003228.3|WP_005788068.1|2991465_2994186_-|pyruvate,-phosphate-dikinase
MDKKRVYTFGNGLAEGKAGMRNLLGGKGANLAEMNLIGVPVPPGFTITTDVCTEYYEMGQEKVVSLLKEEVEKAIANIENLMRSKFGDVENPLLVSVRSGARASMPGMMDTILNLGLNDEVVEGLTRKTGNARFAWDSYRRFVQMYGDVVLGMKPVNKEDQDPFEAIIEEVKHAKGVKLDNELEVEDLKELVKKFKAAVKAQTGKDFPTCAYEQLWGAICAVFNSWMNERAILYRKMEGIPDEWGTAVSVQAMVFGNMGDTSATGVCFSRDAATGEDLFNGEYLINAQGEDVVAGIRTPQQITKIGSQRWAQLAGVSEEERASKYPSMEEAMPEIYKQLDELQTKLENHYKDMQDMEFTVQEGKLWFLQTRNGKRTGAAMVKIAMDLFRQGMIDEKTALMRVEPNKLDELLHPVFDKSALKQAKVLTRGLPASPGAATGQIVFFADDAAEWHAAGKRVVMVRIETSPEDLAGMAVAEGILTARGGMTSHAAVVARGMGKCCVSGAGALNIDYKARTVEVDGVLLKEGDFISLNGSTGEVYQGKVETKAAELSGDFADLMKLADKYTRLQVRTNADTPHDAEVARNFGAVGIGLCRTEHMFFEGEKIKAMREMILAENAEGRRKALAKILPYQQADFKGIFKAMAGCPVTVRLLDPPLHEFVPHDLKGQQEMADTMGVSLQYIQQRVESLCEHNPMLGHRGCRLGNTYPEITQMQTRAILGAALELKKEGIETHPEIMVPLTGILYEFQQQESVIRAEADKLFEEVGDRIDFKVGTMIEIPRAALTADRIASSAEFFSFGTNDLTQMTFGYSRDDIASFLPVYLEKKILKVDPFQVLDQNGVGQLVRMATEKGRAIRPDLKCGICGEHGGEPSSVKFCHKVGLNYVSCSPFRVPIARLAAAQAAIEE
>NC_003228.3|WP_005788064.1|2990683_2991253_-|PorT-family-protein
MKRNLVFVLFALVSVVGFSQVSWNAKVGMNISNFTGDFDMNAKVGFKIGGGMEYGFNEIWSLQPSLFVSSKGAKKDELSVNAVYLELPVMAAARFKVADNTNIVLSAGPYFACGIAGNSKVDLGKGRLEVDTFGDDGLLKRGDVGLGIGVAAEFGKIIAGLDGQFGFVDVMDNVNGKNLNLSISVGYKF
>NC_003228.3|WP_005788062.1|2989969_2990482_-|outer-membrane-beta-barrel-protein
MKKIVLFLFVAIATLSVKAQDLYMGGTVGLWRNDDANTTSFKLAPEIGYNLSEQWALGVELQFNHEYKEHISTNTFAIAPYARFSYYENKIVRLFVDGGFGFATTKVKDGGDAVNGFEIGLKPGIAIKLNQHFSLVAKCGFLGYKDDYMGNGFGFSASSEDLTFGFHYEF
>NC_003228.3|WP_005788060.1|2989283_2989892_+|thiamine-phosphate-synthase
MKLIVVTTPTFFVEEDKIITALFEEGLDILHLRKPETPAMYSERLLTLIPEKYHKRIVTHEHFYLKEEFNLMGIHLNARNPKEPHDYSGHISCSCHSVEEVKNKKHFYDYVFMSPVYDSISKEGYNSPYTAEELRLAAKDKIIDNKVMALGGITPDNILEVKDFGFGGAVVLGDLWGKFDACSDQDYLAVIEHFKKLKRMAD
>NC_003228.3|WP_005793495.1|2988520_2989222_+|HesA/MoeB/ThiF-family-protein
MERYSRQTMLPEIGEAGQLKLKAAKVLIVGVGGLGSPIALYLAGAGVGTIGLADDDEVSLSNLQRQILYTEEEVGDLKAICASMRISALNREIKVNACPGRLSKENARDLIGQYDIIVDGCDNFATRYLLSDVCSELGKPYVYGAICGFEGQVSVFNYGEGTQRKTYRDLYPDEEGMLHMPPPPKGVVGVTPAVTGSVEACEVLKIICGFGEVLAGKLWTIDLRTLQSNIFSL
>NC_003228.3|WP_005788055.1|2987373_2988498_+|2-iminoacetate-synthase-ThiH
MFSDELEKISWEETTKAIYSKTDADVRRALSKEHCDVNDFMALISPAAAPYLETMARLSRKYTMERFGKTISMFVPLYITNSCTNSCVYCGFNHNNPMKRTILTEEEMVNEYKAIKKLAPFENLLLVTGENPAKAGVDYIERALLLAKPYFANLQIEVMPLKAEEYERLTHAGLNGVICFQETYNKANYNIYHPRGMKSKFEWRVNGFDRMGQAGVHKIGMGVLIGLEEWRTDITMMAYHLRYLQKHYWKTKYSVNFPRMRPSENGGFQPNVVMNDRELAQVTFAMRIFDHDVDISYSTRESAAFRNHMATLGVTTMSAESKTEPGGYFTYPQALEQFHVSDERKAVEVDAALRSLGRIPVYKDWDTALTLPQC
>NC_003228.3|WP_010993063.1|2998758_2999022_-|CRISPR-associated-endonuclease-Cas2
MYVIFVYDFGEKRVSKMLRLCRRYLNWIQNSVFEGELSEVRLKELLLLAKGVMNPEEDCIIIFKGATQCSLEKEIVGKELANIDNFL
>NC_003228.3|WP_010993064.1|2999648_3000320_-|CRISPR-associated-endoribonuclease-Cas6
MRIRIKTTSNEKILPFDYQGKLIGVIHKWLGNNELHDKISLYSFSWLLGGVMVDKKGYVFPNGAELLISFHEDQHLKKIIDSILLDSEIFYGLCVKDITIVGSPVFTEEPQRFFLASPIFIKRRIEEIMGYKYYFYDDQESNQLMTETLKHKMREAGLPEDDTLRVEFDISYSKKKKKMVTIHGIKSIANMCPVIIHGTQTSKRFAWVVGLGNGTGSGYGALI
>NC_003228.3|WP_008660463.1|3001141_3001996_+|type-I-methionyl-aminopeptidase
MKKFIKGVRFTPSNYPDEIEDKIQKYRKQGYKLPPRKVLRTPEQIEGIRESAKINTALLNHIAENIREGMSTEEIDRLVYDFTTSHGAIPAPLNYEGFPKSVCTSINDVVCHGIPSSTEILKSGDIINVDVSTIYNGYFSDASRMFMIGEVSPEKQRLVQVTKECMEIGIAAAQPWARLGDVGAAIQEHAEKNGYSVVRDLCGHGVGIKFHEEPDVEHFGRRGTGMLILPGMTFTIEPMINMGTYEVFVDSADDWTVCTDDGLPSAQWENMILINETGNEILTY
>NC_003228.3|WP_005793488.1|3001996_3003223_+|DNA-recombination-protein-RmuC
MELTLLLIIAALLVALLALTLTRNNRAQSEEMQRALRQQMQENREELNRSIRELRMEMTQTLNQGLQQLQDAMHKNMMTTGELQRQKFDAMARQQETLIQSTEKRLDDMRVMVEEKLQKTLNERIGQSFEIVRSQLENVQKGLGEMKSLAQDVGGLKKVLSNVKMRGTFGEVQLGALLEQMMSPEQYEANVKTKKSGTEFVEFAIKLPGKDDANSTVYLPIDAKFPKDVYEQYYDAFEAGDAALMESCGRQLETTIKKMAKDIHDKYVDPPFTTDFAILFLPFESIYAEVIRRTSLVETLQKDYKIVVTGPTTLGAILNSLQMGFRTLAIQKRTGEVWTVLGAVKTEFGKFGGLLEKVQKNLQSAGDQLEEVMGKRTRAIERKLRQVEELPHEESRRILPIDDGGEDD
>NC_003228.3|WP_041926232.1|3003250_3003997_+|hypothetical-protein
MEITLKNQFITLWNTYFPQAGLPITFQYSADTQNLPIVEAPKGHRCIIAQLTQVQRGKTLCIQADSVGCRGGKRYTNFTDKMFPGFECFLSHNEQGEGERYKQTPELAAAALAQLPALPVKGENLIFKRWDKLEAEDMPEVVIFFVSADILSGLFTLACFDNVAPDAVIAPFGASCASIIYHPYREQLDGTNRAVLGSFDPSARKCMKPDLLSFAIPFNKFKSMVSQMEESFLKTATWDVIKKRMGSS
>NC_003228.3|WP_010993066.1|3004196_3005510_-|Na+/H+-antiporter-NhaA
MTVLRSMKDFSSMNITASILLFVTAIAAAVIANSPAASVYQEFLSHELHFRIGGFNLLSHAGHNLTMIEFINDGLMTIFFLMVGLEIKRELLVGELSSFRKAALPFIAACGGMVVPVVIYSMVCAPGTEGGQGLAIPMATDIAFSLGVLSLLGKRVPLSLKIFLTAFAVVDDIGGILVIAIFYSSHVAYEYLLWAALLYVLLYFIGKKGATNKIFFLVVGVVIWYLFLQSGIHSTISGVILAFVIPAKPQLNVGTYIERIRRIISTFPEMGANNIVLTNQQIAKLKEVESASDRVISPLQSLEDNLHGAVNYLVLPLFAFVNAGVMFSGEGEVIGGVTLAVALGLLAGKFLGIYSFTWLAVKSGLTPMPLGMNWKNISGVALLGGIGFTVSLFIANLSFGSAHPVLLNQAKLGVLSGTVMAGILGYLVLHWVLPKRR
>NC_003228.3|WP_005788087.1|3005554_3006733_-|sodium:proton-antiporter
MRKVLSFSAFLIIGLLLSQYLPLLAGEGYATVKIVSNILLYICLSFIMINVGREFEVDKTRWRSYAGDYFIAMATAAMPWFLIAIYYVFVLLPPEFWNSWEAWKENLLLSRFAAPTSAGILFTMLAAIGLKSSWIYKKIQVLAIFDDLDTILLMIPLQIMMIGLRWQLIVVVFIVFLLLSLGWKQLGRYNWRQDWKAIMGYSVLVFVATQAVYYFSKQLYGEEGSIHIEVLLPAFVLGMIMKHKEIDTPVEHKVSTGVSFLFMFLVGMSMPHFIGVNFAETHAGTHSVTGSQEMMSWGMIALHVLIVSLLSNIGKLFPVFFYRDRKFSERLALSIGMFTRGEVGAGVIFIALGYNLGGPALVISVLTIVLNLILTGIFVLWVKKLALRSYTT
>NC_003228.3|WP_005788089.1|3006878_3008660_-|elongation-factor-4
MDKIRNFCIIAHIDHGKSTLADRLLEFTNTIQVTEGQMLDDMDLEKERGITIKSHAIQMEYTYKGEKYILNLIDTPGHVDFSYEVSRSIAACEGALLIVDASQGVQAQTISNLYMAIEHDLEIIPIINKCDMASAMPEEVEDEIVELLGCKRDEIIRASGKTGMGVEEILAAVIERIPHPQGDESAPLQALIFDSVFNSFRGIIAYFKITNGVIRAGDKVKFFNTGKEYVADEIGVLKMEMVPRKELRTGDVGYIISGIKTSKEVKVGDTITHVARPCDKAIAGFEEVKPMVFAGVYPIEAEEFEDLRASLEKLQLNDASLTFQPESSLALGFGFRCGFLGLLHMEIVQERLDREFDMNVITTVPNVSYHIYDKQGNMTEVHNPGGMPDPTMIDHIEEPYIKASIITTTDYIGPIMTLCLGKRGELLKQEYISGNRVELFYNMPLGEIVIDFYDRLKSISKGYASFDYHPDGFRPSKLVKLDILLNGESVDALSTLTHFDNAYDMGRRMCEKLKELIPRQQFEIAIQAAIGAKIIARETIKAVRKDVTAKCYGGDISRKRKLLEKQKKGKKRMKQIGNVEVPQKAFLAVLKLD
>NC_003228.3|WP_005788091.1|3008785_3008986_-|winged-helix-turn-helix-domain-containing-protein
MLKEKAGEIAGKIWNALNGTEGLTAKQIKKATKLVDKDLFLGLGWLLREDKISTQEIEGELFVTLN
>NC_003228.3|WP_005793479.1|3009132_3009597_-|hypothetical-protein
MTKEERISRATELFKSGYNCSQSVVAAFADMYGFTEEQALRMAASFGGGIGRMRETCGAACGMFLLAGLEKGAIDGADREGKAANYALVQELAAEFKKRNGSLNCGELLGLKKKAPVSSEPEARTEQYYAKRPCSKMVEEAARIWAEYLEKEKK

Crispr_ID: NC_003228_4

• CRISPR_ID: NC_003228_4
• CRISPR_location: 4661170-4663207
• CRISPR_type: TypeII
• Repeat_type: NA
• Spacer_info: 26 spacers
• Cas_protein_info: cas2,cas1,cas9

Consensus repeat of NC_003228_4

Consensus_repeat	Method
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	PILER-CR
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CRISPRCasFinder

spacers of NC_003228_4

>4.1|4661217|30|NC_003228|PILER-CR,CRISPRCasFinder
GATTCGAAGATATGCAAATGTAGCAAGTAT
>4.2|4661294|29|NC_003228|PILER-CR,CRISPRCasFinder
TGATTTGGCATCTGCTATTTGATCAATCA
>4.3|4661370|30|NC_003228|PILER-CR,CRISPRCasFinder
GCAATTACCCCAATCCTTCATGCCCTGAGA
>4.4|4661447|30|NC_003228|PILER-CR,CRISPRCasFinder
TTTGCCGGATACCTTAGTAGTGGTAGTCAC
>4.5|4661524|30|NC_003228|PILER-CR,CRISPRCasFinder
GATAGCGGCGGGGGAGCGAACGGCAACGAA
>4.6|4661601|29|NC_003228|PILER-CR,CRISPRCasFinder
AGAACCATCACGAATCAGATTCCAATACT
>4.7|4661677|30|NC_003228|PILER-CR,CRISPRCasFinder
ATCCTGCGAAATTTCGACCTTATCGCCGGG
>4.8|4661754|29|NC_003228|PILER-CR,CRISPRCasFinder
GTTATTGTAAGAGTCATAAAAGCGTGTAC
>4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder
TTAAATACCTCGTCAAAAGCGGATTCCGCA
>4.10|4661907|30|NC_003228|PILER-CR,CRISPRCasFinder
GTCTTGGGAATCTGTACGATTGTTGCAGAA
>4.11|4661984|30|NC_003228|PILER-CR,CRISPRCasFinder
TCTTAACAATGCGCTGCATCTCTCGAATAA
>4.12|4662061|30|NC_003228|PILER-CR,CRISPRCasFinder
CCACAAATCTTTATTCCAGTTGGCGTACCG
>4.13|4662138|30|NC_003228|PILER-CR,CRISPRCasFinder
AAACCATTCAAATATCTGCGCAATTGGGTA
>4.14|4662215|29|NC_003228|PILER-CR,CRISPRCasFinder
ACTGTTGAACTTTTTACTCGTAATCCTAA
>4.15|4662291|30|NC_003228|PILER-CR,CRISPRCasFinder
TCAATTGACCCGAAAGTGCAACGGTCAGGT
>4.16|4662368|29|NC_003228|PILER-CR,CRISPRCasFinder
TAAGGATAGGAATATTCAATCTTATACAG
>4.17|4662444|29|NC_003228|PILER-CR,CRISPRCasFinder
GCATAAAGAACTGGCATATTACCACTGAC
>4.18|4662520|29|NC_003228|PILER-CR,CRISPRCasFinder
AACAGAACTATCAGACACTATCTCTGAGT
>4.19|4662596|30|NC_003228|PILER-CR,CRISPRCasFinder
CGAATGGTCAAAACTATGCTGCTCAGGTTA
>4.20|4662673|30|NC_003228|PILER-CR,CRISPRCasFinder
CTCCAACTCTCGAAGAGCAGCAACAATATC
>4.21|4662750|30|NC_003228|PILER-CR,CRISPRCasFinder
TTCTTGCGGTTTAAACACTTCATTAAAAGC
>4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder
AAACTTAGTAACAGAACCGACAATATTAGA
>4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder
TCTTTTAACCTTTTATTAGCATTTCTCAA
>4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder
TGCTTAGTTATAACGCAGAATATGCACAT
>4.25|4663056|29|NC_003228|PILER-CR,CRISPRCasFinder
AGTGTCTTAAAGAGGTGATTAATGAAATG
>4.26|4663132|29|NC_003228|PILER-CR,CRISPRCasFinder
AGACTTAGCCATTTGTGTGGCATTCACCA

CRISPR arrays and Neighbor proteins around NC_003228_4

CRISPR arrays

The CRISPR arrays of NC_003228_4

>merge|NC_003228|4|4661170-4663207|PILER-CR,CRISPRCasFinder
GTTATGATTTACTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGATTCGAAGATATGCAAATGTAGCAAGTATGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTGATTTGGCATCTGCTATTTGATCAATCAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGCAATTACCCCAATCCTTCATGCCCTGAGAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTTTGCCGGATACCTTAGTAGTGGTAGTCACGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGATAGCGGCGGGGGAGCGAACGGCAACGAAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAGAACCATCACGAATCAGATTCCAATACTGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCATCCTGCGAAATTTCGACCTTATCGCCGGGGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGTTATTGTAAGAGTCATAAAAGCGTGTACGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTTAAATACCTCGTCAAAAGCGGATTCCGCAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGTCTTGGGAATCTGTACGATTGTTGCAGAAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTCTTAACAATGCGCTGCATCTCTCGAATAAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCCCACAAATCTTTATTCCAGTTGGCGTACCGGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAAACCATTCAAATATCTGCGCAATTGGGTAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCACTGTTGAACTTTTTACTCGTAATCCTAAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTCAATTGACCCGAAAGTGCAACGGTCAGGTGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTAAGGATAGGAATATTCAATCTTATACAGGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCGCATAAAGAACTGGCATATTACCACTGACGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAACAGAACTATCAGACACTATCTCTGAGTGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCCGAATGGTCAAAACTATGCTGCTCAGGTTAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCCTCCAACTCTCGAAGAGCAGCAACAATATCGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTTCTTGCGGTTTAAACACTTCATTAAAAGCGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAAACTTAGTAACAGAACCGACAATATTAGAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTCTTTTAACCTTTTATTAGCATTTCTCAAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCTGCTTAGTTATAACGCAGAATATGCACATGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAGTGTCTTAAAGAGGTGATTAATGAAATGGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGCAGACTTAGCCATTTGTGTGGCATTCACCAGTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC

>NC_003228|4|3|4661170-4663207|PILER-CR
GTTATGATTTACTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GATTCGAAGATATGCAAATGTAGCAAGTAT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TGATTTGGCATCTGCTATTTGATCAATCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GCAATTACCCCAATCCTTCATGCCCTGAGA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTTGCCGGATACCTTAGTAGTGGTAGTCAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GATAGCGGCGGGGGAGCGAACGGCAACGAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGAACCATCACGAATCAGATTCCAATACT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	ATCCTGCGAAATTTCGACCTTATCGCCGGG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GTTATTGTAAGAGTCATAAAAGCGTGTAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTAAATACCTCGTCAAAAGCGGATTCCGCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GTCTTGGGAATCTGTACGATTGTTGCAGAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCTTAACAATGCGCTGCATCTCTCGAATAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CCACAAATCTTTATTCCAGTTGGCGTACCG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AAACCATTCAAATATCTGCGCAATTGGGTA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	ACTGTTGAACTTTTTACTCGTAATCCTAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCAATTGACCCGAAAGTGCAACGGTCAGGT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TAAGGATAGGAATATTCAATCTTATACAG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GCATAAAGAACTGGCATATTACCACTGAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AACAGAACTATCAGACACTATCTCTGAGT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CGAATGGTCAAAACTATGCTGCTCAGGTTA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CTCCAACTCTCGAAGAGCAGCAACAATATC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTCTTGCGGTTTAAACACTTCATTAAAAGC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AAACTTAGTAACAGAACCGACAATATTAGA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCTTTTAACCTTTTATTAGCATTTCTCAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TGCTTAGTTATAACGCAGAATATGCACAT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGTGTCTTAAAGAGGTGATTAATGAAATG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGACTTAGCCATTTGTGTGGCATTCACCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC

>NC_003228|4|4|4661170-4663207|CRISPRCasFinder
GTTATGATTTACTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GATTCGAAGATATGCAAATGTAGCAAGTAT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TGATTTGGCATCTGCTATTTGATCAATCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GCAATTACCCCAATCCTTCATGCCCTGAGA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTTGCCGGATACCTTAGTAGTGGTAGTCAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GATAGCGGCGGGGGAGCGAACGGCAACGAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGAACCATCACGAATCAGATTCCAATACT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	ATCCTGCGAAATTTCGACCTTATCGCCGGG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GTTATTGTAAGAGTCATAAAAGCGTGTAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTAAATACCTCGTCAAAAGCGGATTCCGCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GTCTTGGGAATCTGTACGATTGTTGCAGAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCTTAACAATGCGCTGCATCTCTCGAATAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CCACAAATCTTTATTCCAGTTGGCGTACCG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AAACCATTCAAATATCTGCGCAATTGGGTA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	ACTGTTGAACTTTTTACTCGTAATCCTAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCAATTGACCCGAAAGTGCAACGGTCAGGT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TAAGGATAGGAATATTCAATCTTATACAG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	GCATAAAGAACTGGCATATTACCACTGAC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AACAGAACTATCAGACACTATCTCTGAGT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CGAATGGTCAAAACTATGCTGCTCAGGTTA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	CTCCAACTCTCGAAGAGCAGCAACAATATC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TTCTTGCGGTTTAAACACTTCATTAAAAGC
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AAACTTAGTAACAGAACCGACAATATTAGA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TCTTTTAACCTTTTATTAGCATTTCTCAA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	TGCTTAGTTATAACGCAGAATATGCACAT
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGTGTCTTAAAGAGGTGATTAATGAAATG
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC	AGACTTAGCCATTTGTGTGGCATTCACCA
GTTGTGATTTGCTTTCAAATTAGTATCTTTGAACCATTGGAAACAGC

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_003228.3|WP_009293009.1|4665078_4665603_-|hypothetical-protein	unknown	unknown	gnl|CDD|379118
NC_003228.3|WP_077687812.1|4672359_4673289_-|lipase	unknown	unknown	gnl|CDD|238863
NC_003228.3|WP_005791999.1|4649700_4650648_-|phosphate-ABC-transporter-substrate-binding-protein	unknown	unknown	gnl|CDD|378974
NC_003228.3|WP_005791614.1|4670551_4670812_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993657.1|4648247_4649681_-|tetratricopeptide-repeat-protein	unknown	unknown	gnl|CDD|274350
NC_003228.3|WP_005791995.1|4647081_4647942_-|ATP-binding-cassette-domain-containing-protein	unknown	unknown	gnl|CDD|213197
NC_003228.3|WP_008770318.1|4653743_4654187_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005792004.1|4652158_4652764_-|biopolymer-transporter-ExbD	unknown	unknown	gnl|CDD|376792
NC_003228.3|WP_010993659.1|4663315_4663648_-|CRISPR-associated-endonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|226043
NC_003228.3|WP_009293010.1|4665618_4669929_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	cd09643_cas9_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|375967
NC_003228.3|WP_005791625.1|4664703_4664940_-|hypothetical-protein	unknown	unknown	gnl|CDD|379118
NC_003228.3|WP_005792006.1|4652791_4653604_-|MotA/TolQ/ExbB-proton-channel-family-protein	unknown	unknown	gnl|CDD|376576
NC_003228.3|WP_005791628.1|4663651_4664584_-|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	gnl|CDD|274694
NC_003228.3|WP_010993660.1|4670327_4670540_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_077687810.1|4670006_4670387_-|hypothetical-protein	unknown	unknown	gnl|CDD|376574
NC_003228.3|WP_041926262.1|4660048_4660276_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_041926344.1|4670885_4672373_-|MBOAT-family-protein	unknown	unknown	gnl|CDD|224610
NC_003228.3|WP_005792001.1|4650650_4651466_-|energy-transducer-TonB	unknown	unknown	gnl|CDD|367555
NC_003228.3|WP_050443496.1|4654385_4654685_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005792003.1|4651495_4652146_-|biopolymer-transporter-ExbD	unknown	unknown	gnl|CDD|376792

HMMScan for Signature genes

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_003228.3|WP_005791628.1|4663651_4664584_-|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	2.9e-87	287.0	0.0
NC_003228.3|WP_009293010.1|4665618_4669929_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	cd09643_cas9_CAS-II-A:CAS-II-B:CAS-II-C	8.3e-70	230.9	46.8
NC_003228.3|WP_010993659.1|4663315_4663648_-|CRISPR-associated-endonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	2e-31	103.3	0.1

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_003228.3|WP_077687812.1|4672359_4673289_-|lipase	gnl|CDD|238863	cd01825, SGNH_hydrolase_peri1, SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.	4.36549e-67
NC_003228.3|WP_005791999.1|4649700_4650648_-|phosphate-ABC-transporter-substrate-binding-protein	gnl|CDD|378974	pfam12849, PBP_like_2, PBP superfamily domain. This domain belongs to the periplasmic binding protein superfamily.	6.26613e-37
NC_003228.3|WP_010993657.1|4648247_4649681_-|tetratricopeptide-repeat-protein	gnl|CDD|274350	TIGR02917, TPR_domain_protein, putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.	1.11106e-06
NC_003228.3|WP_005791995.1|4647081_4647942_-|ATP-binding-cassette-domain-containing-protein	gnl|CDD|213197	cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A. This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.	1.74028e-49
NC_003228.3|WP_005791628.1|4663651_4664584_-|type-II-CRISPR-associated-endonuclease-Cas1	gnl|CDD|274694	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system.	1.84378e-135
NC_003228.3|WP_005792004.1|4652158_4652764_-|biopolymer-transporter-ExbD	gnl|CDD|376792	pfam02472, ExbD, Biopolymer transport protein ExbD/TolR. This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria. The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins.	1.15551e-12
NC_003228.3|WP_010993659.1|4663315_4663648_-|CRISPR-associated-endonuclease-Cas2	gnl|CDD|226043	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms].	1.3546e-26
NC_003228.3|WP_009293010.1|4665618_4669929_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9	gnl|CDD|375967	pfam18541, RuvC_III, RuvC endonuclease subdomain 3. Cas9 proteins are abundant across the bacterial kingdom, but vary widely in both sequence and size. All known Cas9 enzymes contain an HNH domain that cleaves the DNA strand complementary to the guide RNA sequence (target strand), and a RuvC nuclease domain required for cleaving the noncomplementary strand (non-target strand), yielding double-strand DNA breaks (DSBs). The crystal structures of type II-A and II-C Cas9 proteins highlight the features in Cas9 enzymes that support their function as RNA-guided endonucleases. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. The RuvC domain forms the structural core of the nuclease lobe, a six-stranded beta sheet surrounded by four alpha helices, with all three conserved subdomains (I, II, III) contributing catalytic residues to the active site.	4.40484e-47
NC_003228.3|WP_005791625.1|4664703_4664940_-|hypothetical-protein	gnl|CDD|379118	pfam13310, Virulence_RhuM, Virulence protein RhuM family. There are currently no experimental data for members of this group or their homologs. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium.	5.84606e-24
NC_003228.3|WP_009293009.1|4665078_4665603_-|hypothetical-protein	gnl|CDD|379118	pfam13310, Virulence_RhuM, Virulence protein RhuM family. There are currently no experimental data for members of this group or their homologs. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium.	9.71926e-63
NC_003228.3|WP_077687810.1|4670006_4670387_-|hypothetical-protein	gnl|CDD|376574	pfam01610, DDE_Tnp_ISL3, Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165.	2.67899e-08
NC_003228.3|WP_041926344.1|4670885_4672373_-|MBOAT-family-protein	gnl|CDD|224610	COG1696, DltB, Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane].	7.94887e-86
NC_003228.3|WP_005792001.1|4650650_4651466_-|energy-transducer-TonB	gnl|CDD|367555	pfam03544, TonB_C, Gram-negative bacterial TonB protein C-terminal. The TonB_C domain is the well-characterized C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane. TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance.	9.40269e-21
NC_003228.3|WP_005792006.1|4652791_4653604_-|MotA/TolQ/ExbB-proton-channel-family-protein	gnl|CDD|376576	pfam01618, MotA_ExbB, MotA/TolQ/ExbB proton channel family. This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane.	1.71919e-31
NC_003228.3|WP_005792003.1|4651495_4652146_-|biopolymer-transporter-ExbD	gnl|CDD|376792	pfam02472, ExbD, Biopolymer transport protein ExbD/TolR. This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria. The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins.	1.68278e-20

Protein sequences

>NC_003228.3|WP_041926262.1|4660048_4660276_-|hypothetical-protein
MPYFCIRFPRDGQHLILTCCNGVGRALQNNKNNFLFIWIIIIKVVIFAVRFAERGPLAVFSFPFAQRGLEIKGGH
>NC_003228.3|WP_050443496.1|4654385_4654685_+|hypothetical-protein
MEKVLLTSPPIKQIIQSSETSYIKPIHSLESPLLQGSVPPRDAEIPTSSNNRYIGQEKAIGFPIAISIKKVLSGGQPGAPFPSPLYKTSHPLRSFDRRG
>NC_003228.3|WP_008770318.1|4653743_4654187_-|hypothetical-protein
MRTSVKFILMFVLLMLSFSISGNALNITECSHKSVNSCQVSASSLDTNYSYRYGSDITGFDKSQTLSVSDVELGFKPVSETYSSNNLRLRRILEDSDLFKDTMRKWCLVRENLLVLDQSKSYYSDKDPHYASISCHYYIFALRRILI
>NC_003228.3|WP_005792006.1|4652791_4653604_-|MotA/TolQ/ExbB-proton-channel-family-protein
METTQKKSTKIVGIKNAGLVIICCFIIAVCIYHFILGNPTNFMNNDPNNHPLPGNFMGTIYKGGVIVPVIQTLLLTVLALSIERYFALRSAFGRGSLVKFVSNIKEALSVGDLRKAQEICDKQRGSVANVVTSTLRKYEEMENESSLSKDQKLLAIQKELEEATALELPMMEQNLPIIGTITTLGTLMGLLGTVIGMIRSFAALAAGGSADSMALSQGISEALINTAFGILTGALAVISYNYYTNKIDKLTYSLDEVGFSIVQTFAATHK
>NC_003228.3|WP_005792004.1|4652158_4652764_-|biopolymer-transporter-ExbD
MGRAKIKKKSTFIDMTAMSDVTVLLLTFFMLTSTFVKKEPVQVTTPASVSEIKIPEKNILQILVDPNGKIFMSMDKQSDLKAVLESMGQEYGVTFTPEQEKKFMLASTFGVPMKNMKTYLDLPTDKQDAVLKNEGIPCDSLDNQFKSWVRNARAVNSDLRIAIKADADTPYSVIKNVMNSLQDLRENRYNLITSLKTTSEN
>NC_003228.3|WP_005792003.1|4651495_4652146_-|biopolymer-transporter-ExbD
MSAEVQESGKKKGNSKQKKMTVRVDFTPMVDMNMLLITFFMLCTSLSKPQTMEISMPSNDKNITEEQQSKVKASQAITLLLGPDDKLYYYEGEPNYKDYTSLKETTYKPDGLRGILLKKNATAVRQVNDLKQKKLELKISEDEFTKQLSEIKSGKNTPTVIIKAMDNASYKNLIDALDEMQICNIGKYVITNIAEADEFLVKNFESKGELSQNIAD
>NC_003228.3|WP_005792001.1|4650650_4651466_-|energy-transducer-TonB
MAKIDLTSFEWCELIFKGKNKAYGAYKMRADSPKRHNVAMVIVLIIALVGFSLPTLIKMATPKQKEVMTEVTTLSQLEEPEVKQEEMKRVEPVAPPPPALKSSIKFTAPVIKKDEEVHEDDEIKSQEELTQTKVAISIADVKGNDEANGKDIADLKQVVTQAEPAEEQVFDMVEQMPTFPGGTTELMKYIGEHLKYPPIAAENGTQGKVICRFVIGKDGQVRDVTIARSLDPYCDKEAIRVIKSMPKWIPGKQNGKAVAVNFTVPIVFKLQ
>NC_003228.3|WP_005791999.1|4649700_4650648_-|phosphate-ABC-transporter-substrate-binding-protein
MTKKQFWLIGAWSLIALSACSSKPKDGLTDTYTSGVIAITADESFQPIVQEEIDVFEGLFPLAGIVPRYTTEVDAINQLLKDSVRLAITTRTLTPEEMNSFHSRKFFPREIKLATDGLALIVNRQNADSLISVRDIRRILTGQVQKWKELYPASGLGDIQLVFDNKNSSTVRFAVDSICKGAPLSDKDVKALKTNQQVIDYVAHTPDAIGVIGVNWLGNRSDTTNLSFRDEIRVMSVSADDVATVENSYKPYQAYLYYGNYPLARPIYVLLNDPRNALPWGFASFLTSDRGQRIILKSGLVPATQPVRIVDVKDE
>NC_003228.3|WP_010993657.1|4648247_4649681_-|tetratricopeptide-repeat-protein
MKRFQLFLVGAFVAAGPLFAQSADADWHSEVAKVKELIQANPAQASEEAAQLLKGKNKKNTDLLIAIGQAYLEAGKVNEAEAYAALGQKANSKSAAVSVLQGDIAVAKKDAGKACQLYEQAIYFDPNYKEAYLKFADVYKGASPQLAIEKLEQLKNLDPSCVAADKKLAEVYYLNNKFDKAAEAYAHFINTPEATEDDLTKYSFALFLNHDFEKSLQIALMGLQKNPRDAAFNRLAMYNYTDLKRYDEAMKAADAFFKESDKADFSYLDYMYFGHLLNAVKKYDQAVEAYMKAITLDPAKTDLWREVSSSYELNNEFAKAIEAYKKYSESLSADKRTPDVQFQIGKLYYEKGTQSDTLTVSLDERKAALVSADSIFTEIAKVAPDSYLGNFWRARTNSALDPETTQGLAKPYYEEVAAFLIDKNDPRYNSALIECYSYLGYYYLVANKLPESKEYWNKILAIDPANATAKRALDGIK
>NC_003228.3|WP_005791995.1|4647081_4647942_-|ATP-binding-cassette-domain-containing-protein
MKMITVENLSFLYRKSKRAVLHDFSLSLEKGRVYGLLGKNGAGKSTLLYLMSGLLTPKSGKVVYHDVDVRRRLPITLQDMFLVPEEFDLPPVSLISYIELNSPFYPRFSKEDMVKYLHYFEMDINIDLGALSMGQKKKVFMSFALATNTSLLLMDEPTNGLDIPGKSQFRKFIASGMTDDKTILISTHQVRDIDKVLDHVLIMDNSRVLLNESTMSICDKLFFTESENRELLQSSLFSTPSIQGNFLLLPNESGEDSEINLELLFNATLAVPERISALFHSKQIEL
>NC_003228.3|WP_010993659.1|4663315_4663648_-|CRISPR-associated-endonuclease-Cas2
MDRFNEYRIMWVLVLFDLPTETKKEKKAYADFRKNLQKDGFTMFQFSIYVRHCGSSENAAVHIKRVKSFLPEFGHVGIMCITDKQFGDIELFYGKKVQDVNTPGQQLELF
>NC_003228.3|WP_005791628.1|4663651_4664584_-|type-II-CRISPR-associated-endonuclease-Cas1
MIKKTLYFGNPVYLSLRNAQLVIKLPDVEKATVLPETLKKQAEVTKPIEDIGIVVLDNKQITITSGVLEALLENNCSVITCDSRSMPVGLMLPLYGNTTQNERFRKQLDTSLPLKKQLWQQTIQAKINNQASVLKDCMDEEVKCMRIWATNVRSGDPDNLEARAAAYYWKSLFSDVDSFTREREGIPPNNLLNYGYAILRAVVARGLVISGLLPTLGIHHHNRYNAYCLADDIMEPYRPYVDELVFSLIQEYGKNAELTKEMKTRLLTVPTLEVIIGGKRSPLMVAVGQTTASLYKCFNGELRRISYPER
>NC_003228.3|WP_005791625.1|4664703_4664940_-|hypothetical-protein
MALTTWKNAPNGMIRNPDVSIAKNYLNEMEMDDLNRIVSMYLDYAERQAKKRTSDVHERLGEKVGRIFAVQRISRPTT
>NC_003228.3|WP_009293009.1|4665078_4665603_-|hypothetical-protein
MDKNNNNPPIPSDFFLYKNSNGEVKVEIYIFNETVWLPQDKIAQLFGVDRSIVTEHLKNVYKSGELSKGVTCAIFAQVQIEGTGQVTRQIEFYNLDAILSVGYRVNSIQATQFGIWANSVLKEYLIKGGAMNDERLKNPQMLFGKDYFEEQLARIRDIRGNEQRFYQKITDIYS
>NC_003228.3|WP_009293010.1|4665618_4669929_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9
MKRILGLDLGTNSIGWALVNEAENKDERSSIVKLGVRVNPLTVDELTNFEKGKSITTNADRTLKRGMRRNLQRYKLRRETLTEVLKEHKLITEDTILSENGNRTTFETYRLRAKAVTEEISLEEFARVLLMINKKRGYKSSRKAKGVEEGTLIDGMDIARELYNNNLTPGELCLQLLDAGKKFLPDFYRSDLQNELDRIWEKQKEYYPEILTDVLKEELRGKKRDAVWAICAKYFVWKENYTEWNKEKGKTEQQEREHKLEGIYSKRKRDEAKRENLQWRVNGLKEKLSLEQLVIVFQEMNTQINNSSGYLGAISDRSKELYFNKQTVGQYQMEMLDKNPNASLRNMVFYRQDYLDEFNMLWEKQAVYHKELTEELKKEIRDIIIFYQRRLKSQKGLIGFCEFESRQIEVDIDGKKKIKTVGNRVISRSSPLFQEFKIWQILNNIEVTVVGKKRKRRKLKENYSALFEELNDAEQLELNGSRRLCQEEKELLAQELFIRDKMTKSEVLKLLFDNPQELDLNFKTIDGNKTGYALFQAYSKMIEMSGHEPVDFKKPVEKVVEYIKAVFDLLNWNTDILGFNSNEELDNQPYYKLWHLLYSFEGDNTPTGNGRLIQKMTELYGFEKEYATILANVSFQDDYGSLSAKAIHKILPHLKEGNRYDVACVYAGYRHSESSLTREEIANKVLKDRLMLLPKNSLHNPVVEKILNQMVNVINVIIDIYGKPDEIRVELARELKKNAKEREELTKSIAQTTKAHEEYKTLLQTEFGLTNVSRTDILRYKLYKELESCGYKTLYSNTYISREKLFSKEFDIEHIIPQARLFDDSFSNKTLEARSVNIEKGNKTAYDFVKEKFGESGADNSLEHYLNNIEDLFKSGKISKTKYNKLKMAEQDIPDGFIERDLRNTQYIAKKALSMLNEISHRVVATSGSVTDKLREDWQLIDVMKELNWEKYKALGLVEYFEDRDGRQIGRIKDWTKRNDHRHHAMDALTVAFTKDVFIQYFNNKNASLDPNANEHAIKNKYFQNGRAIAPMPLREFRAEAKKHLENTLISIKAKNKVITGNINKTRKKGGVNKNMQQTPRGQLHLETIYGSGKQYLTKEEKVNASFDMRKIGTVSKSAYRDALLKRLYENDNDPKKAFAGKNSLDKQPIWLDKEQMRKVPEKVKIVTLEAIYTIRKEISPDLKVDKVIDVGVRKILIDRLNEYGNDAKKAFSNLDKNPIWLNKEKGISIKRVTISGISNAQSLHVKKDKDGKPILDENGRNIPVDFVNTGNNHHVAVYYRPVIDKRGQLVVDEAGNPKYELEEVVVSFFEAVTRANLGLPIIDKDYKTTEGWQFLFSMKQNEYFVFPNEKTGFNPKEIDLLDVENYGLISPNLFRVQKFSLKNYVFRHHLETTIKDTSSILRGITWIDFRSSKGLDTIVKVRVNHIGQIVSVGEY
>NC_003228.3|WP_077687810.1|4670006_4670387_-|hypothetical-protein
MDKVALSRGELSILSNKASHGGKGSIVAIIRGMDIYMVSSVLFRLSRRRYQVRDIKLDMTPNMEQIVRSCFPTAKRVIDRFHKKLAYEAVLETLVAQKRTRQMPHPKCFHNGIVLIVICFKLVTQR
>NC_003228.3|WP_010993660.1|4670327_4670540_+|hypothetical-protein
MGSLVAEYGEFTARKGNFINTDVSTDILFKKQLILCMGKLIPVKITTNDCGITASEEHRQRYTKSSITYN
>NC_003228.3|WP_005791614.1|4670551_4670812_-|hypothetical-protein
MLLFILNRRMLFLSNILDGKPATRDSMILSLFKISLFAVKKTLNIRCRHRILKQSNQYINRNWRMVAEGIRMAQYLFCVFFIKELY
>NC_003228.3|WP_041926344.1|4670885_4672373_-|MBOAT-family-protein
MFPIDIDFSRLLEAFKYNPDAPMIFSSGIFLWLFAAFMVIYTLLQHRNTARILFVALFSYYFYYKSSGTYFFLLAIVTVTDFVIAWLMDRTDVRWKRKFCVVLSVSVNLGLLCYFKYTNFLGGVIASLMGGEFTALDIFLPVGISFFTFQSLSYTIDVYREEIKPLTSLLDYAFYVSFFPQLVAGPIVRARDFIPQIRKPLYVSQEMFGRGIFLIVAGLFKKAVISDYISINFVERIFDNPTLYSGVENLMGLYGYALQIYCDFSGYSDMAIGIALLLGFHFNLNFNSPYKSASITEFWRRWHISLSSWLRDYLYISLGGNRHGKFRQYLNLIITMFLGGLWHGASWNFVLWGTFHGVALALHKAWMSIIGRKKGETSHGIRRVLGVIITFHFVCFCWIFFRNADFHNSMDMLNQIFTAFRPQLFPQLIEGYWRVFALMAVGFLLHFAPDSWENAVCRGVIKLPFLGKAIVMVAMIYLVIQMKSSEIQPFIYFQF
>NC_003228.3|WP_077687812.1|4672359_4673289_-|lipase
MEKNSMKGERPMRLNRWLGVLILLLSGVWSVRAQDLLPACPQVDKGTKACKPMREPGSLGDTVSVKIVFPVAFKGVGRNEVVDSLGILAPVLEHLRLVQNGSSEDTVRIVHIGDSHIRGHIFPRTTGARLTETFGAISYTDMGVNGATCLTFTHPDRIAAIAALKPELLILSFGTNESHNRKYNSNVHYRQMEELLELLHDSLPDVPILMTTPPGSYESFRQRRRRRTYAINPRTVTAVNTIHDFARRHKLVVWDMYNVVGGSLRACKNWSDAQLMRPDHVHYLPEGYTLQGELLYEAIIKAYNEYVSH

Crispr_ID: NC_003228_5

• CRISPR_ID: NC_003228_5
• CRISPR_location: 4822242-4822341
• CRISPR_type: Orphan
• Repeat_type: NA
• Spacer_info: 1 spacers

Consensus repeat of NC_003228_5

Consensus_repeat	Method
GACGAAGGTAATGGTACATCAACAAGACTAC	CRISPRCasFinder

spacers of NC_003228_5

>5.1|4822273|38|NC_003228|CRISPRCasFinder
TACAATCCCTAAAAGCAGAAACTCCAATACTAACTAAG

CRISPR arrays and Neighbor proteins around NC_003228_5

CRISPR arrays

The CRISPR arrays of NC_003228_5

>merge|NC_003228|5|4822242-4822341|CRISPRCasFinder
GACGAAGGTAATGGTACATCAACAAGACTACTACAATCCCTAAAAGCAGAAACTCCAATACTAACTAAGGACGAAGGTAATGGTACATCAGCAAGACTAC

>NC_003228|5|5|4822242-4822341|CRISPRCasFinder
GACGAAGGTAATGGTACATCAACAAGACTAC	TACAATCCCTAAAAGCAGAAACTCCAATACTAACTAAG
GACGAAGGTAATGGTACATCAGCAAGACTAC

Neighbor Proteins Overview

Protein	Signature genes	Signature genes Name	Protein_function
NC_003228.3|WP_005804070.1|4826693_4827707_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993702.1|4830310_4830529_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993696.1|4816004_4818539_-|prolyl-oligopeptidase-family-serine-peptidase	unknown	unknown	gnl|CDD|238865
NC_003228.3|WP_010993697.1|4819984_4820857_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005804079.1|4818796_4819960_-|hypothetical-protein	unknown	unknown	gnl|CDD|227604
NC_003228.3|WP_077687829.1|4835158_4837456_+|TonB-dependent-receptor	unknown	unknown	gnl|CDD|378104
NC_003228.3|WP_005804072.1|4825680_4826661_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993693.1|4808502_4810926_-|hypothetical-protein	unknown	unknown	gnl|CDD|224117
NC_003228.3|WP_077687815.1|4815792_4815966_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005804068.1|4831469_4832225_+|response-regulator-transcription-factor	unknown	unknown	gnl|CDD|225818
NC_003228.3|WP_010993706.1|4832248_4833754_+|4Fe-4S-dicluster-domain-containing-protein	unknown	unknown	gnl|CDD|319895
NC_003228.3|WP_010993695.1|4814836_4815508_-|hypothetical-protein	unknown	unknown	gnl|CDD|372421
NC_003228.3|WP_010993700.1|4827723_4828932_-|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_005797599.1|4811371_4812304_-|site-specific-integrase	unknown	unknown	gnl|CDD|271185
NC_003228.3|WP_009293026.1|4833776_4835159_+|aldo/keto-reductase	unknown	unknown	gnl|CDD|224370
NC_003228.3|WP_010993701.1|4829608_4830166_+|NUDIX-hydrolase	unknown	unknown	gnl|CDD|239516
NC_003228.3|WP_041926276.1|4823028_4825644_-|hypothetical-protein	unknown	unknown	gnl|CDD|365830
NC_003228.3|WP_005791467.1|4810974_4811145_+|hypothetical-protein	unknown	unknown	unknown
NC_003228.3|WP_010993692.1|4806837_4807413_-|DUF4369-domain-containing-protein	unknown	unknown	gnl|CDD|379543
NC_003228.3|WP_010993694.1|4812479_4814618_+|DUF2961-domain-containing-protein	unknown	unknown	gnl|CDD|378582

rpsblast for functional proteins

Protein	Function_ID	Function_description	E-value
NC_003228.3|WP_010993696.1|4816004_4818539_-|prolyl-oligopeptidase-family-serine-peptidase	gnl|CDD|238865	cd01827, sialate_O-acetylesterase_like1, sialate O-acetylesterase_like family of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.	1.08151e-111
NC_003228.3|WP_005804079.1|4818796_4819960_-|hypothetical-protein	gnl|CDD|227604	COG5279, CYK3, Uncharacterized protein involved in cytokinesis, contains TGc (transglutaminase/protease-like) domain [Cell division and chromosome partitioning].	1.61652e-17
NC_003228.3|WP_077687829.1|4835158_4837456_+|TonB-dependent-receptor	gnl|CDD|378104	pfam08973, TM1506, Domain of unknown function (DUF1893). A member of the deaminase fold that binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate. Contextual analysis suggests that the domain is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase.	3.3452e-67
NC_003228.3|WP_010993693.1|4808502_4810926_-|hypothetical-protein	gnl|CDD|224117	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning].	8.38445e-08
NC_003228.3|WP_005804068.1|4831469_4832225_+|response-regulator-transcription-factor	gnl|CDD|225818	COG3279, LytT, Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms].	6.74742e-42
NC_003228.3|WP_010993706.1|4832248_4833754_+|4Fe-4S-dicluster-domain-containing-protein	gnl|CDD|319895	cd16373, DMSOR_beta_like, uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.	1.5986e-46
NC_003228.3|WP_010993695.1|4814836_4815508_-|hypothetical-protein	gnl|CDD|372421	pfam12990, DUF3874, Domain of unknonw function from B. Theta Gene description (DUF3874). Based on Bacteroides thetaiotaomicron gene BT_4228, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture.	2.02566e-26
NC_003228.3|WP_005797599.1|4811371_4812304_-|site-specific-integrase	gnl|CDD|271185	cd01185, INTN1_C_like, Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain. IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. 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.	1.89179e-24
NC_003228.3|WP_010993701.1|4829608_4830166_+|NUDIX-hydrolase	gnl|CDD|239516	cd03424, ADPRase_NUDT5, ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer.	6.21276e-45
NC_003228.3|WP_041926276.1|4823028_4825644_-|hypothetical-protein	gnl|CDD|365830	pfam00041, fn3, Fibronectin type III domain.	0.000138092
NC_003228.3|WP_009293026.1|4833776_4835159_+|aldo/keto-reductase	gnl|CDD|224370	COG1453, COG1453, Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only].	2.38031e-105
NC_003228.3|WP_010993692.1|4806837_4807413_-|DUF4369-domain-containing-protein	gnl|CDD|379543	pfam14289, DUF4369, Domain of unknown function (DUF4369). This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam00578.	8.95177e-15
NC_003228.3|WP_010993694.1|4812479_4814618_+|DUF2961-domain-containing-protein	gnl|CDD|378582	pfam11175, DUF2961, Protein of unknown function (DUF2961). This family of proteins has no known function.	5.90472e-73

Protein sequences

>NC_003228.3|WP_010993697.1|4819984_4820857_-|hypothetical-protein
MMIMKKFCLFTMLFSVLMFADVAAQEIQVKSFQKLERDLTARTRPRLDLNDNPCALIKIETTGRDFEFEGNVIGAPLYRKGEVQVYVTQGCRRLTLKHEKYGVLRYEFPEKIEKQVVYELSIKLVEDKNNKIRTLVMPVFSYGSFEQTSYGLMVGVVKKTGGYLKVKTDFGSVSSDLDPVDKASGWYTGGEQQSRFAITAGVLQRVFQRDWKTLYLYAGVGYGSRNYAKEVDGEVDGIQNPYVKINSDCYKGVEAELGAVARFGGVAVSLGVQTNQFKQVEANIGIGIMF
>NC_003228.3|WP_005804079.1|4818796_4819960_-|hypothetical-protein
MKLKRFWFLSLMAICMPFYGEAQPSSNRYARVDAAILSIPDEYTKKVDTFAEYINRKFKGDEAKMRAIYVWMTHRMAYNVFTTFTSRNEVYSEEKEVQETLSTRKGVCRQFALLFKTLAGKVGIKAYLIDGYGKSGNVVLPEVHEWCVAQVNGEWYFFDPTYDTGYIEDYRFVSAPDDVYFKQLPERFIQTHMPFDPLWQFLKRPYSYSEFEKGVLESGRNVPFFCWQDSLKVYDRQSWVEQLEAARSRILANGKGNDLVDYFLQLNQANTQVGKDSEAIDVYAAATDLQNRAVDSINVFIRYRKAGFRPRKAEAQVRRMIEVSEELTLRADSLINSVHTISPQYKQALLNLRESIMDLAMQIYKHKLFLERYYATKPSLRGNLLRR
>NC_003228.3|WP_010993696.1|4816004_4818539_-|prolyl-oligopeptidase-family-serine-peptidase
MKNAIISLLLLLMVTQYVTAQKKVIKIACIGNSITYGVGTRNPAKDSYPAVLGQMLGDGYEVRNFGVSARTMLMKGDHPYMKEERYRQALAYNPDIVTIKLGTNDTKPQNWRYKSDFKKDMETMIRTIRALPSKPEIYLCYPIPAYAVQWGINDSTIVHGVMPVIDQLAAKYRLKVIDLHTPLTGMKECFADHVHPNEKAAARIARVIYRQLTGKEAPEHVSQPFPGHKSKWQGFDQYTFTYQDRQAIVVCPERAAAGNPWIWRPAFFGAFASVDEALLKRGFHVAYYDLTHLYGSPRARKSGTDFYWNMVQMYGLSPRVTLEGFSRGGLFAYNWAADHPDKVACIYVDAPVCDVFSWPGRSSGNAGLWKGMLDEWGLTEVRMNTFPGNPIDRLKPLADARIPVICVCGDSDRVVPFSENSAVVRQRYTAMGAPFELILKPGVDHHPHSLENPTPVVDFIVRHQAGYEAGQCYTLRGNYQNSYRKFEKERVGTVAFLGGSITEMKGWRDMICEDLKQRFPYTKFTFVAAGIPSTGSTPGAFRLTDDVLSKGKVDLLFVEAAVNDDTNGFSAIEQVRGMEGIVRHALVSNPSMDIMMLHFIYDPFIPKLDKGQMPDVILNHERVANHYLLPSVNLASEIAARMRSGEFTWEQFGGTHPNPLGHAYYAATINKVLDEMYAPCATAKDAAKPHALPAVPLDAYSYTNGRLVDIRQAHIGKGWQLVAPWTPRLAAETRPGFVDVPMLETNRPGAKLTLDFEGTAVGIFCVSGPAAGILEYSVDGAPFKKLDTFTAWSGGLYIPWVYMFDTELPMGKHRLTLRMSKDHHPQSKGTSCQIRQFVVNDSCE
>NC_003228.3|WP_077687815.1|4815792_4815966_+|hypothetical-protein
MLIEERYKDEDTGSGGVNSLPKLELSYSAGVCFFLLKQAKRTIINLKIKKERIYHQI
>NC_003228.3|WP_010993695.1|4814836_4815508_-|hypothetical-protein
MSKRKLTTKFEEEPLNFGTGMWNVGLTPNVCRCTLLLPTSCMTCLVGTGRTASGRWPATYVPFDESAISELKRYASFIAISNHSDLLSDPSGSRRFICINITGRIRNGVAINYLQPYAQAVQELREGECFYFSPEEEAVLMENNQEFELQTPVGHLFQQYFRSADEGEKCETLLAVDILGRIQKKSGFKLSATKIVHLGRILRKLGVPCKKMKNGNFYCVVEL
>NC_003228.3|WP_010993694.1|4812479_4814618_+|DUF2961-domain-containing-protein
MNTKSKRPLLSFPKPKFTTGMIRLSITLLFSTLCIGSFGQKKSPITVETLLEEMTSYDKMTRYPALPYRSMQQSSYDRRSVSPDRPGWFANDDGEGFIRLEEHDGRKEKVLFEDEGPGAITRIWLTTFGSIHTILRFYFDGKDEPGWVVPSYDLQKFGVRGLKKGLIEPDDKWIRGSLIYLPVTYADGCKVTMEELTPERTNRHFLFNYRKYPTGTPVETFSRKVAERIPQSVEKTSATLYRNIDKGVDPQARYGKGALIHRQNLSLNKGEKQQLNLHKGKRAISLLQFNVKTDPDLKPGTDDFARLMRSLIISISFDGQQTVWAPLSDFAGSGMGAFASRSFFFYSDGKGIVCSKWLMPYRQNCEISVLNLSPYKTDVHIDIVSQPYKWDNRSLYFHTAWKQERGLPVVTWMEHEKCMDWNFTTISGRGVYRGDLLSLFNHTTEWYGEGDEKITVDHEAFPSHFGTGTEDYYSFDGYFKSQTPFAGQPRQDMKDFYGYNSFFRVRCLDGIPFNQQLKFDFELLGWENGTVDYSSTVFWYGDLNSQAAGSSGIEEIEAGLLPTPTQSPVCSIANAIDFCQIQPTSKSERLRYDRQRLSGHPGKWNLKDHLVCHGGKKGDYIEFEFSGFEDREYSLNLFCTKAADYGNIKFYVNRQENGKQLDCYSQEVEATGAINLGMHKPIDGKFILRIELTGQNALSTGTLFGLDCIRIE
>NC_003228.3|WP_005797599.1|4811371_4812304_-|site-specific-integrase
MKEKDLIRFMDRMIEERKAEYALGTAHIYQASRNALSAFLKAHDIPFKRVRPELLKQFERFLRRRGNSWNTVSTYMRVLRAVYNRAVDRRLAPHVPHLFKAVYTGTQADIKRALKAEEMGQLLDTKCTRKQSELLQKTHHLFVLMFLLRGLPFVDLAYIQKKDLNGNILTYHRRKTGRQITITVTKDAMNIIREYMDTTTESPYLFPILSAEGGEDTIYREYQQALRIFNYQLTKLGELLGLTTELTSYTARHTWATLAYYLEVHPGIIREAMGHSSIKVTETYLKPFNIKKLDETNLSIIGYAKRSFEG
>NC_003228.3|WP_005791467.1|4810974_4811145_+|hypothetical-protein
MFSLADDGLASILCNTSIYSYFVGNPKQTIEGCKWRFAKRNSSKRESLFIIRYKKE
>NC_003228.3|WP_010993693.1|4808502_4810926_-|hypothetical-protein
MRKWTYLVAALLVGGATTTFTGCIDNDEPAGIEQLRGAKAEFIKAKAAFEDALTQIQLVKVEREQVALEADKVALDLQKLNLEKEQASTAWLKDSLQARQDTLAASLKEQLLAIQKKEADTNADLQASLAALEVAMVTAKDEAFGEAIKDVKEALAGITEGESHTYGALDYLKNSNARLLKAKSDLLDFLSDNKYLEDKLNAGIDEAKAALATQEKVLEDMKTFAATPTSEWNTKLAEISKQIAAVNADVVAKSEAIAKQTAEIQPVLADIERENAKLDTKDKSFTIPVVDAALQNDLAGFVQESNVLTSDEFNKVFKQDGATGEYTMIADLNLSGLSLNNYYEATSVVSYIRYTYSSSSSQNVGYIQLFNNAYNSVFSIYRNNTQPTDAEIAKAKGELARMAIDKADKYAIFQKDSTAWMDSYLAYMTALTNYKNYQQTTTWDAIAAKVNTYKALAPAEQTKDKANALLADLKAYGQLRDAVDGATGKIYNVDNKEIRLYNVTIVDDSETPTGNQVTLSNFNSTIQSNAAWILGSQQLATSFYNSTLSDFDGAIQRLILASNTLFGKGGQLTDIIEPKKVGDKYYLPEDVEAGNHTCSYYLYTTAMKDVAIFTNIEKWIALDNSLTADLEKFDDAKKTIADNVATLQAGIADKQDAIWKAELERQLLDCNQSLSSGNPYSVSNPSACQIQALNSLMTTIKNAITNGGQVTYVTYDPVNHKFERVEGTIEKLISDQESKIATAKDAVATAEGKLEAYQTLGKDDKSRFESDLQVAITNAEQEVAFIQAEVDRLNATLKKLLDAYAAE
>NC_003228.3|WP_010993692.1|4806837_4807413_-|DUF4369-domain-containing-protein
MKRNLTGVLLMGLIMGACNHTPKEGAYHLRGVVTNEKLEGRTIYLRDAIEGVVRYDSTTVSEGRFVFNGKVTAPQVRELFIQETDSDRFPVTLPVVLEPGEINAKIGDIVLVEGTGLNEEMMQTLMALDEFRGRDFTGKEINEIKEAFGGFVLEQIVKHAGSPVGNYLYEAYQNKLSENQQTEARKTLGIG
>NC_003228.3|WP_041926276.1|4823028_4825644_-|hypothetical-protein
MKKIWNWLNVIVFVVLGACSSDDRDNSVFKPEFDNGEIEHNNVGRSEVVLRGRIVIPDGLGSFECGFMYSTASTVPTKDAIRVSATPDTGGLCEVALTNLEPDTKYYYCMYASNGSAIIRSAPIKEFRTLSNSAPELEEPLAIGIGENSLTIECKIKDSGSSKLQQFGIAYKVKGEVGEPTRKATSKFKDGTNDTFEITIEGLSAETTYEIYAYAINTKDEGKSSVIYQATSSQEAARLTTQEISEVGANWVTLMAVIEDPGKGEMIEKGFYLSEKNSPDKETTYKVEEKSDDNIYSYKVSGLVPNTTYSVRAYAKNRVGSEVTKLAFGGRKEFTTQSLKAPVVSEPTYDMDVDKMTLTVSARIMDTGNGTISRAGFYYSTTHQTPDQEDTHLEGKVEGDVFTAVIKELAKNQVYYIRPFAVNDAEQIGFGEVLKVTSVPVSVPALGEITSSTQGKEMKLSSKVTDAGGGTVSERGFYWSTASVSGYPETDIPKMNKVVAEGTDATFSALVKDIKANTVYYVYAYAVNEGGKGYSYYYSFEPTKAVVPVAGKLSYTWDKATPDVLTLSSSVVSAGNVEISEKGFYWGTGWNDDINSMTKVPGTDTENGFTASITIKPNTVYHLRAYVVNSGNMTGYSDTETFGGDQWVINDPVLSQVTTSVVNGIMTLKAKVTNTGYGSLARKGFYYSTTGEPSASSVFLEGTGGDDGFTATIQLEVGVTYRVRAFAQSQFMDNGCFGSVTELTPWMKPTLRNDINFSSTGSSITASTYINNNGTNAVGESGKGTISDQGFCYSTSSQEPVVTTESNAEGGSVTAAAGNEIKTTISGLKLGTTYYIRAYAKNEHGLSYGPVKQYSTKRAPEPGDIDNPSKN
>NC_003228.3|WP_005804072.1|4825680_4826661_-|hypothetical-protein
MKTIQIKFILLIAFLQLSVFAKAQYATDFHLTDMDNANLKEAVQVNITNLLTEINSAYVEKRLPDFSKISMAMEVQNSIRMLWENTPFRCAETEVIERCLNMNGTYQVRNIPLFLSQPDGSKDEYQEGVIGFDSQAKITDFHLAISTNLYTKVLVAGKEVADFRYRQLILDYVEQFRTAYNTKDLIFLNQIFSDDALIITGKVIRSVPSEMNHFVASEKVVYNKQSKKEYLSRLKTIFGANKRIHVIFDEINVVKHPAKEGFYGVTLKQGYTSDSYHDEGYLFLLWDFTNEDAPKIHVRTWQPEMLNATTKLPEEEIFTCDDFEVE
>NC_003228.3|WP_005804070.1|4826693_4827707_-|hypothetical-protein
MVRGITLFLAMGLVPLLVYSQGITVSQDSLREKVRDIKLSEKYVYAEATTPVGMSEAQQYSLDLLHVHVIGIFSQRFKMDPKDVEEIWDVIEDKCQNVVIKNGDLFRVCTYILKDAFAFHKNPGKALEKWKRAEAERVQQDSLKQDNAESELKLTADDTRKVGGIVSLLNQVGVETEDGSVVNKPEQVVADTVPTLYSSAPTTVVMTTPEAPSKVITPATTTGKTSSVESPIEIEELPSAVESLPDTDRLLVTNLLALNSFDEVLSFLEKGQREGKLIYGNVKTIKNPQASYLVIIKDKRLITVLNKGAKERTNLKTNTADALKNYKGHGVIWFQVF
>NC_003228.3|WP_010993700.1|4827723_4828932_-|hypothetical-protein
MKLALFVLNLNWKTHMYGSIDKKQMTCRISWVILFCFCDITFLLSQEQGKFVSKKLENIAFQLSSQYQADCSVKQRILLKPLCPDKQIIVTTDLYRTVNHIGFELFDRTVMEQNPSPVYTFVERYLLELLLTDNDEGMRHLLEESKVMVRLGQNNRLLTHARLLSVLREMNSAHSFIITTDNSRYTMVWYHDKEMLFSLRFPIQYELIWGMNKVEAENLFYMNLENYRLGRRPSPACIPQSLKALNDSCYVTGEDFYGIEAISSSQYYKKGTDGKFTPILDIHSPVESISNLFTISADERCKVQVTQCMYGNRKNSFELPLCELVDYCKNSGCDVYVGMERSVGNHFWGIAFMVNRSLGYNHLLYFDTDIRILLYPDRYKMNMQLYGFVPIHNLRNLFGGQN
>NC_003228.3|WP_010993701.1|4829608_4830166_+|NUDIX-hydrolase
MEKKDEIWQVVSSKYLFRRPWLTVRCDDMLLPNGNHIPEYYILEYPDWVNTIAITKEGKFVFVRQFRPGIGKQLYELCAGVCEKEDASPLVSAQRELLEETGYGKGNWKEYMVISANPSTHTNLTHCFLATDVEQIDTQHLEDTEALTVHLLSLEEVKELLENGQIMQSLHAAPLWKYMAEHKQI
>NC_003228.3|WP_010993702.1|4830310_4830529_-|hypothetical-protein
MQAILGYMMKTALIRLTSGRFRDIYLSKESMMLFFLTAKKSKIMIPYFVMSCQNEKRSIKAKLFHFFSINTI
>NC_003228.3|WP_005804068.1|4831469_4832225_+|response-regulator-transcription-factor
MKVLIVEDETAAYENLTDILTEITPDIRIMANTESVTQTVGWLQSNPAPDLIFMDIHLSDGSAFAIFDRIELETPIIFTTAYDRYAIEAFKVNSIDYLLKPVKVEDVEHALEKYSKLTRQDLLQYLSQLTLLKPAPRYKDKLLIAHKDKLLPVNIKNISYFYATGKNTYVCLKDGNRYPYSKTLEQIASSLNPEDFIRANKQFIVARDSVTDITIWFDNRLLITLDTEVPERIYVSKNKASEFKTWLVNDK
>NC_003228.3|WP_010993706.1|4832248_4833754_+|4Fe-4S-dicluster-domain-containing-protein
MLRKIRLTCGIICLTLITLLFLDFTGTLHGWFGWLAKIQFLPAVLALNVGVVVLLIILTGVFGRIYCSVICPLGVFQDVAAWIGKKRKKLPYSYSPALSLLRYGALAIFIITLVAGVSFIATLFAPYSAYGRIANNLFQPIWLWGNNLFAHLAERAGSYAFYEVDIWIKSLPTFIVAAATFVILILLAWRNGRTYCNTICPVGTVLGFLSRYSLFRITIDTEKCNKCGLCARHCKATCINAKEHTIDYSRCVVCMDCLGKCKQKALSYQLRTTKARPAKAEENAHAASSKEVNEARRNFLTVTAMAATASALKAQEKKVDGGLAAIEDKKIPNRQTPITPPGSLSARNMAAHCTACQLCVSACSNQVLRPSTNLMNLMQPEISYERGYCRPECNDCSQVCPTGAIHPITTADKSSTQIGHAVWIKANCVSLTDGVKCDNCARHCPTGAIQMIVAEPEKETSPQIPAINTERCIGCGACENLCPARPFSAIYVEGHERHRII
>NC_003228.3|WP_009293026.1|4833776_4835159_+|aldo/keto-reductase
MEKQNNHIDRRGFLKIVGISAATTTAALYGCGSGTKSSQGRNASSPVPTDQMTYRSVGGIKDKVSLLGYGCMRWPTVPSPEGKGDLINQEAVNELVDYAIAHGVNYFDTSPVYVQGWSEKATGIALKRHPREKLYIATKLSNFSNFSRENSLAMYHQSFKDMQVEYFDYYLLHAIGGGGMKVFNERYIDNGMLDFLLKEREAGRIRHLGWSFHGDVEVFDQVLAMHDTVKWDFVQIQLNYVDWRHATGNNVNAEYLYGELAKRNIAAVIMEPLLGGRLSNVPEHIVGRLKQRRPEDSVASWAFRFAGSPELVLTVLSGMTYMEHLQDNIRTYSPLVPLTDDDKEYLEETAQLMMQYPTIPCNDCKYCMPCPYGIDIPAILVHYNKCVNEGNIPQSQTSENYKEARRAFLVGYDRSVPKLRQASHCIGCNQCTPHCPQSIHIPEELHRIDRFVEQLKQGTL
>NC_003228.3|WP_077687829.1|4835158_4837456_+|TonB-dependent-receptor
MEKIIDLLHSGGYSCVIGNGTEIRTFTQRGVADLYDLFRQDPSFMKGACIADKVIGKAAAGLMVLGGIRQVYADVISQPALALLHNANIEVSYVRLVPFIENRDKSGWCPLETACYGIESIQEIFRIIENFLSKIRMKKNLLGILLVCAFLSSSLQAQVRKDTTQAGHNYEIDGVVVTGTRNETDIRHLPMTISVVNRETIRQRSEPSLLPTLTEQVPGLFTTSRGVMGYGVSNGAAGGISLRGIGGSPTTGLLVLIDGHPQYMGLMGHPIADAYQSMLAEKVEVVRGPASVLYGSNAMGGVINIVTRRQREDGVRTGVRLGYGSYDTWMTEATNQVKKGRFNSIITGSYNRTNGHRPNMEFEQYGGYTRLGYELDHSWNVSADLNLTHFNASNPGTVSTPVFDNDSRITRGMTSFALENRYERTSGALKFFYNWGKHHINDGYGTGEEPLDYRFNSKDRMMGISWYQSASLFSGNRLTAGIDYMQFGGEAWNRFIADKHKEGISDKSENEIAGYLDFRQAIGSYLTMDAGLRIDHHTVTGTEWIPQVGLSVQLPQDASLKAMASKGFRNPTIRELYMFRPANPDLLPERLWNYELSYSQRLLKGTFYYGVNLFYINGDNMIQTIRTDGRPLNVNTGKVENWGAEADIAYHIHPMWRLTANYSWLHMEHPLIAAPEHKLYTGIDFTQKKWSFSTGIQYVTGLYTAVVPQEKKENFLLWNLRGSYRICSIADLFVKGENLLAQRYEINAGYPMPKATCMGGININF

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_003228_3	3.5|2998290|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR	2998290-2998323	34	NC_003228.3	1747401-1747434	0	1.0
NC_003228_3	3.8|2998484|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR	2998484-2998517	34	NC_003228.3	1747187-1747220	1	0.971

1. spacer 3.5|2998290|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR matches to position: 1747401-1747434, mismatch: 0, identity: 1.0

agcaagggaaactgtacgatgtacaagtactcgg	CRISPR spacer
agcaagggaaactgtacgatgtacaagtactcgg	Protospacer
**********************************

2. spacer 3.8|2998484|34|NC_003228|CRISPRCasFinder,CRT,PILER-CR matches to position: 1747187-1747220, mismatch: 1, identity: 0.971

gaagtccgctgaaatccagcccgccttttcgttc	CRISPR spacer
gaagtccgcggaaatccagcccgccttttcgttc	Protospacer
********* ************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_003228_3	3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR	2998353-2998389	37	NZ_CP043609	Bacteroides fragilis strain GUT04 plasmid unnamed1, complete sequence	75133-75169	1	0.973
NC_003228_3	3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR	2998353-2998389	37	NZ_CP036540	Bacteroides fragilis strain DCMOUH0017B plasmid pBFO17_1, complete sequence	32928-32964	1	0.973
NC_003228_3	3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR	2998353-2998389	37	NZ_CP036547	Bacteroides fragilis strain DCMSKEJBY0001B plasmid pBFS01_1, complete sequence	49999-50035	1	0.973
NC_003228_4	4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder	4662980-4663008	29	MT630433	Bacteroides phage vB_BfrS_23, complete genome	20890-20918	1	0.966
NC_003228_4	4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder	4662980-4663008	29	NC_016770	Bacteroides phage B124-14, complete genome	20222-20250	2	0.931
NC_003228_4	4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder	4662980-4663008	29	HE608841	Bacteroides phage B124-14 complete genome	20222-20250	2	0.931
NC_003228_4	4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder	4662980-4663008	29	MN078104	Bacteroides phage Barc2635, complete genome	45866-45894	2	0.931
NC_003228_4	4.18|4662520|29|NC_003228|PILER-CR,CRISPRCasFinder	4662520-4662548	29	HG322870	Sulfolobus monocaudavirus SMV1 complete genome	29496-29524	4	0.862
NC_003228_4	4.1|4661217|30|NC_003228|PILER-CR,CRISPRCasFinder	4661217-4661246	30	MN694251	Marine virus AFVG_250M445, complete genome	2134-2163	6	0.8
NC_003228_4	4.2|4661294|29|NC_003228|PILER-CR,CRISPRCasFinder	4661294-4661322	29	CP011075	Brevibacillus laterosporus strain B9 plasmid unnamed1, complete sequence	516998-517026	6	0.793
NC_003228_4	4.20|4662673|30|NC_003228|PILER-CR,CRISPRCasFinder	4662673-4662702	30	NC_010733	Vibrio nigripulchritudo plasmid pSFn1, complete sequence	10818-10847	6	0.8
NC_003228_4	4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder	4662827-4662856	30	CP029293	Lactococcus lactis subsp. lactis KLDS 4.0325 plasmid unnamed6	48340-48369	6	0.8
NC_003228_4	4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder	4662827-4662856	30	NC_017963	Enterococcus faecium DO plasmid 3, complete sequence	72740-72769	6	0.8
NC_003228_4	4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder	4662827-4662856	30	NZ_LR135255	Enterococcus faecium isolate E7098 plasmid 2	186403-186432	6	0.8
NC_003228_4	4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder	4662904-4662932	29	MK554696	Fusobacterium phage Fnu1, complete genome	109000-109028	6	0.793
NC_003228_4	4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder	4662904-4662932	29	NZ_CP009064	Borreliella afzelii K78 plasmid lp28-3, complete sequence	22748-22776	6	0.793
NC_003228_4	4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder	4662904-4662932	29	NC_017233	Borreliella afzelii PKo plasmid lp28-3, complete sequence	1088-1116	6	0.793
NC_003228_4	4.5|4661524|30|NC_003228|PILER-CR,CRISPRCasFinder	4661524-4661553	30	NC_010878	Thermus sp. 4C plasmid pL4C, complete sequence	8312-8341	7	0.767
NC_003228_4	4.16|4662368|29|NC_003228|PILER-CR,CRISPRCasFinder	4662368-4662396	29	MT446420	UNVERIFIED: Escherichia virus TH54, complete genome	140122-140150	7	0.759
NC_003228_4	4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder	4662827-4662856	30	MH830363	Enterococcus faecalis plasmid p1, complete sequence	32490-32519	7	0.767
NC_003228_4	4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder	4662827-4662856	30	MH617247	Microviridae sp. isolate ctbb942, complete genome	3333-3362	7	0.767
NC_003228_4	4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder	4662904-4662932	29	NZ_CP015884	Enterococcus faecalis strain sorialis plasmid Efsorialis-p1, complete sequence	52672-52700	7	0.759
NC_003228_4	4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder	4662904-4662932	29	NZ_AP019825	Leptotrichia hofstadii strain JCM16775 plasmid pJCM16775-2, complete sequence	8657-8685	7	0.759
NC_003228_4	4.10|4661907|30|NC_003228|PILER-CR,CRISPRCasFinder	4661907-4661936	30	MH884511	Exiguobacterium phage vB_EalM-132, complete genome	51164-51193	8	0.733
NC_003228_4	4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder	4661830-4661859	30	MF495478	Aeromonas salmonicida plasmid pS121-1b, complete sequence	22398-22427	9	0.7
NC_003228_4	4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder	4661830-4661859	30	NZ_CP038450	Aeromonas media strain R50-22 plasmid pAeme6, complete sequence	118982-119011	9	0.7
NC_003228_4	4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder	4661830-4661859	30	NZ_CP022170	Aeromonas salmonicida strain S121 plasmid pS121-1a, complete sequence	22376-22405	9	0.7
NC_003228_4	4.19|4662596|30|NC_003228|PILER-CR,CRISPRCasFinder	4662596-4662625	30	MN694017	Marine virus AFVG_250M1107, complete genome	22943-22972	9	0.7
NC_003228_1	1.1|892050|34|NC_003228|PILER-CR	892050-892083	34	NC_023559	Oenococcus phage phi9805, complete genome	36716-36749	12	0.647

1. spacer 3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP043609 (Bacteroides fragilis strain GUT04 plasmid unnamed1, complete sequence) position: , mismatch: 1, identity: 0.973

ctgatgaagcgattaagaagatcaatgtgatgattaa	CRISPR spacer
ctgatgaagcgattaagaaaatcaatgtgatgattaa	Protospacer
*******************.*****************

2. spacer 3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP036540 (Bacteroides fragilis strain DCMOUH0017B plasmid pBFO17_1, complete sequence) position: , mismatch: 1, identity: 0.973

ctgatgaagcgattaagaagatcaatgtgatgattaa	CRISPR spacer
ctgatgaagcgattaagaaaatcaatgtgatgattaa	Protospacer
*******************.*****************

3. spacer 3.6|2998353|37|NC_003228|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP036547 (Bacteroides fragilis strain DCMSKEJBY0001B plasmid pBFS01_1, complete sequence) position: , mismatch: 1, identity: 0.973

ctgatgaagcgattaagaagatcaatgtgatgattaa	CRISPR spacer
ctgatgaagcgattaagaaaatcaatgtgatgattaa	Protospacer
*******************.*****************

4. spacer 4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder matches to MT630433 (Bacteroides phage vB_BfrS_23, complete genome) position: , mismatch: 1, identity: 0.966

tgcttagttataacgcagaatatgcacat	CRISPR spacer
tgcttagttatcacgcagaatatgcacat	Protospacer
*********** *****************

5. spacer 4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder matches to NC_016770 (Bacteroides phage B124-14, complete genome) position: , mismatch: 2, identity: 0.931

tgcttagttataacgcagaatatgcacat	CRISPR spacer
tgcttggttatcacgcagaatatgcacat	Protospacer
*****.***** *****************

6. spacer 4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder matches to HE608841 (Bacteroides phage B124-14 complete genome) position: , mismatch: 2, identity: 0.931

tgcttagttataacgcagaatatgcacat	CRISPR spacer
tgcttggttatcacgcagaatatgcacat	Protospacer
*****.***** *****************

7. spacer 4.24|4662980|29|NC_003228|PILER-CR,CRISPRCasFinder matches to MN078104 (Bacteroides phage Barc2635, complete genome) position: , mismatch: 2, identity: 0.931

tgcttagttataacgcagaatatgcacat	CRISPR spacer
tgcttggttatcacgcagaatatgcacat	Protospacer
*****.***** *****************

8. spacer 4.18|4662520|29|NC_003228|PILER-CR,CRISPRCasFinder matches to HG322870 (Sulfolobus monocaudavirus SMV1 complete genome) position: , mismatch: 4, identity: 0.862

aacagaactatcagacactatctctgagt	CRISPR spacer
aacagaactaacagacactatctttgaaa	Protospacer
********** ************.***. 

9. spacer 4.1|4661217|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MN694251 (Marine virus AFVG_250M445, complete genome) position: , mismatch: 6, identity: 0.8

gattcgaagatatgcaaatgtagcaagtat	CRISPR spacer
aattgacagataagcaaatggagcaagtat	Protospacer
.*** . ***** ******* *********

10. spacer 4.2|4661294|29|NC_003228|PILER-CR,CRISPRCasFinder matches to CP011075 (Brevibacillus laterosporus strain B9 plasmid unnamed1, complete sequence) position: , mismatch: 6, identity: 0.793

tgatttggcatctgctatttgatcaatca	CRISPR spacer
taagctttcatcggctatttgatcaatca	Protospacer
*.* .*  **** ****************

11. spacer 4.20|4662673|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NC_010733 (Vibrio nigripulchritudo plasmid pSFn1, complete sequence) position: , mismatch: 6, identity: 0.8

ctccaactctcgaagagcagcaacaatatc	CRISPR spacer
tcccgcctctcgatgagcagcagcaatatc	Protospacer
..**. ******* ********.*******

12. spacer 4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder matches to CP029293 (Lactococcus lactis subsp. lactis KLDS 4.0325 plasmid unnamed6) position: , mismatch: 6, identity: 0.8

aaacttagtaacagaaccgacaatattaga	CRISPR spacer
aaactttgcaacagaaccgacaataccact	Protospacer
****** *.****************..*  

13. spacer 4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NC_017963 (Enterococcus faecium DO plasmid 3, complete sequence) position: , mismatch: 6, identity: 0.8

aaacttagtaacagaaccgacaatattaga	CRISPR spacer
aaactttgcaacagaaccgacaaaaccaaa	Protospacer
****** *.************** *..*.*

14. spacer 4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_LR135255 (Enterococcus faecium isolate E7098 plasmid 2) position: , mismatch: 6, identity: 0.8

aaacttagtaacagaaccgacaatattaga	CRISPR spacer
aaactttgcaacagaaccgacaaaaccaaa	Protospacer
****** *.************** *..*.*

15. spacer 4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder matches to MK554696 (Fusobacterium phage Fnu1, complete genome) position: , mismatch: 6, identity: 0.793

tcttttaaccttttattagcatttctcaa	CRISPR spacer
tattttaaaattttattagcatttcttgg	Protospacer
* ******  ****************...

16. spacer 4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_CP009064 (Borreliella afzelii K78 plasmid lp28-3, complete sequence) position: , mismatch: 6, identity: 0.793

tcttttaaccttttattagcatttctcaa	CRISPR spacer
tcttttaaccttttattggccttatcaaa	Protospacer
*****************.** ** .. **

17. spacer 4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder matches to NC_017233 (Borreliella afzelii PKo plasmid lp28-3, complete sequence) position: , mismatch: 6, identity: 0.793

tcttttaaccttttattagcatttctcaa	CRISPR spacer
tcttttaaccttttattggccttatcaaa	Protospacer
*****************.** ** .. **

18. spacer 4.5|4661524|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NC_010878 (Thermus sp. 4C plasmid pL4C, complete sequence) position: , mismatch: 7, identity: 0.767

gatagcggcgggggagcgaacggcaacgaa	CRISPR spacer
aagggcggcgggggaacgaactgcaacgcc	Protospacer
.* .***********.***** ******  

19. spacer 4.16|4662368|29|NC_003228|PILER-CR,CRISPRCasFinder matches to MT446420 (UNVERIFIED: Escherichia virus TH54, complete genome) position: , mismatch: 7, identity: 0.759

taaggataggaatattcaatcttatacag	CRISPR spacer
gcttaatacgaatattcaaccttatacag	Protospacer
    .*** **********.*********

20. spacer 4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MH830363 (Enterococcus faecalis plasmid p1, complete sequence) position: , mismatch: 7, identity: 0.767

aaacttagtaacagaaccgacaatattaga	CRISPR spacer
aaactttgcaacagaaccgacaagactgat	Protospacer
****** *.************** *.*.. 

21. spacer 4.22|4662827|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MH617247 (Microviridae sp. isolate ctbb942, complete genome) position: , mismatch: 7, identity: 0.767

---aaacttagtaacagaaccgacaatattaga	CRISPR spacer
atcaaa---agtaacagaaccaacaatattgtt	Protospacer
   ***   ************.********.  

22. spacer 4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_CP015884 (Enterococcus faecalis strain sorialis plasmid Efsorialis-p1, complete sequence) position: , mismatch: 7, identity: 0.759

tcttttaaccttttattagcatttctcaa	CRISPR spacer
ctttttaaacttttattagcattaaaaaa	Protospacer
..****** **************    **

23. spacer 4.23|4662904|29|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_AP019825 (Leptotrichia hofstadii strain JCM16775 plasmid pJCM16775-2, complete sequence) position: , mismatch: 7, identity: 0.759

tcttttaaccttttattagcatttctcaa	CRISPR spacer
tattttcaccttttattagcattctgaac	Protospacer
* **** ****************..  * 

24. spacer 4.10|4661907|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MH884511 (Exiguobacterium phage vB_EalM-132, complete genome) position: , mismatch: 8, identity: 0.733

gtcttgggaatctgtacgattgttgcagaa	CRISPR spacer
gtcttgggactatgtacgattgtttatact	Protospacer
********* * ************   .  

25. spacer 4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MF495478 (Aeromonas salmonicida plasmid pS121-1b, complete sequence) position: , mismatch: 9, identity: 0.7

ttaaatacctcgtcaaaagcggattccgca	CRISPR spacer
gaaaatacctcatcaaaagcggaattgctc	Protospacer
  *********.*********** *.  . 

26. spacer 4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_CP038450 (Aeromonas media strain R50-22 plasmid pAeme6, complete sequence) position: , mismatch: 9, identity: 0.7

ttaaatacctcgtcaaaagcggattccgca	CRISPR spacer
gaaaatacctcatcaaaagcggaattgctc	Protospacer
  *********.*********** *.  . 

27. spacer 4.9|4661830|30|NC_003228|PILER-CR,CRISPRCasFinder matches to NZ_CP022170 (Aeromonas salmonicida strain S121 plasmid pS121-1a, complete sequence) position: , mismatch: 9, identity: 0.7

ttaaatacctcgtcaaaagcggattccgca	CRISPR spacer
gaaaatacctcatcaaaagcggaattgctc	Protospacer
  *********.*********** *.  . 

28. spacer 4.19|4662596|30|NC_003228|PILER-CR,CRISPRCasFinder matches to MN694017 (Marine virus AFVG_250M1107, complete genome) position: , mismatch: 9, identity: 0.7

cgaatggtcaaaactatgctgctcaggtta	CRISPR spacer
ttgtcgctcaaaactatgctactcaggtac	Protospacer
. . .* *************.*******  

29. spacer 1.1|892050|34|NC_003228|PILER-CR matches to NC_023559 (Oenococcus phage phi9805, complete genome) position: , mismatch: 12, identity: 0.647

aacaaaaatactaagtatttgtttgataagcaag	CRISPR spacer
tttaaaattattaagtatttgtttgatttctctc	Protospacer
  .**** **.****************   .