Vibrio penaeicida strain IFO 15640T plasmid pIFO15640, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Genome sequencing of 5 strains of Vibrio penaeicida
Submitted (08-SEP-2021) Contact:Hidehiro Kondo Tokyo University of Marine Science and Technology, Laboratory of Genome Science; Konan 4-5-7, Minato, Tokyo 108-8477, Japan URL :http://www2.kaiyodai.ac.jp/~h-kondo/genome/index.html
REFSEQ INFORMATION: The reference sequence is identical to\nAP025146.1.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Flye v. 2.7; Hypo v. 1.0.3\nGenome Coverage :: 225x\nSequencing Technology :: Illumina Miseq; ONT GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/16/2022 02:20:52\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 6,035\nCDSs (total) :: 5,891\nGenes (coding) :: 5,812\nCDSs (with protein) :: 5,812\nGenes (RNA) :: 144\nrRNAs :: 11, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 10, 10 (5S, 16S, 23S)\ntRNAs :: 108\nncRNAs :: 5\nPseudo Genes (total) :: 79\nCDSs (without protein) :: 79\nPseudo Genes (ambiguous residues) :: 0 of 79\nPseudo Genes (frameshifted) :: 30 of 79\nPseudo Genes (incomplete) :: 48 of 79\nPseudo Genes (internal stop) :: 12 of 79\nPseudo Genes (multiple problems) :: 9 of 79\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013793.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF022728.2
COORDINATES: protein motif:HMM:NF012915.2
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:NF013427.2
COORDINATES: similar to AA sequence:RefSeq:WP_011399149.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF012894.2
phosphate ABC transporter substrate-binding/OmpA family protein
COORDINATES: protein motif:HMM:NF017617.2
COORDINATES: similar to AA sequence:RefSeq:WP_011399143.1
putative urea ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013947960.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF023254.2
COORDINATES: similar to AA sequence:RefSeq:WP_000411105.1
COORDINATES: similar to AA sequence:RefSeq:WP_005500335.1
COORDINATES: similar to AA sequence:RefSeq:WP_017110838.1
COORDINATES: protein motif:HMM:NF037735.2
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: similar to AA sequence:RefSeq:WP_016800228.1
COORDINATES: similar to AA sequence:RefSeq:WP_016800229.1
COORDINATES: protein motif:HMM:NF013704.2
COORDINATES: protein motif:HMM:NF012318.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001339197.1
IS4-like element ISVsa5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000275181.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000428546.1
tetracyline resistance-associated transcriptional repressor TetC
COORDINATES: similar to AA sequence:RefSeq:WP_001089064.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
tetracycline efflux MFS transporter Tet(B)
COORDINATES: similar to AA sequence:RefSeq:WP_000088605.1
tetracycline resistance transcriptional repressor TetR(B)
COORDINATES: similar to AA sequence:RefSeq:WP_001284954.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000460649.1
COORDINATES: similar to AA sequence:RefSeq:WP_000562370.1
COORDINATES: similar to AA sequence:RefSeq:WP_000599530.1
GO:0015501 - glutamate:sodium symporter activity [Evidence IEA]
GO:0015813 - L-glutamate transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005227464.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016790684.1
COORDINATES: similar to AA sequence:RefSeq:WP_005372765.1
COORDINATES: similar to AA sequence:RefSeq:WP_017086526.1
COORDINATES: similar to AA sequence:RefSeq:WP_020194363.1
COORDINATES: similar to AA sequence:RefSeq:WP_017015673.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF014668.2
GO:0006282 - regulation of DNA repair [Evidence IEA]
COORDINATES: protein motif:HMM:NF020305.2
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014234839.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: similar to AA sequence:RefSeq:WP_014234837.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019820388.1
COORDINATES: similar to AA sequence:RefSeq:WP_005535640.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017031016.1
COORDINATES: similar to AA sequence:RefSeq:WP_017064054.1
COORDINATES: similar to AA sequence:RefSeq:WP_019820371.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017045322.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
type I-F CRISPR-associated endoribonuclease Cas6/Csy4
COORDINATES: similar to AA sequence:RefSeq:WP_016786788.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017024409.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_017085618.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017632242.1
COORDINATES: similar to AA sequence:RefSeq:WP_020328739.1
COORDINATES: similar to AA sequence:RefSeq:WP_005437097.1
COORDINATES: similar to AA sequence:RefSeq:WP_017069961.1
GO:0008773 - [protein-PII] uridylyltransferase activity [Evidence IEA]
DUF294 nucleotidyltransferase-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017076728.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005437108.1
COORDINATES: similar to AA sequence:RefSeq:WP_017634230.1
GO:0015297 - antiporter activity [Evidence IEA]; GO:0042910 - xenobiotic transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017028300.1
COORDINATES: similar to AA sequence:RefSeq:WP_017032101.1
COORDINATES: similar to AA sequence:RefSeq:WP_017634227.1
COORDINATES: similar to AA sequence:RefSeq:WP_017821221.1
COORDINATES: similar to AA sequence:RefSeq:WP_017095873.1
COORDINATES: similar to AA sequence:RefSeq:WP_017076737.1
COORDINATES: similar to AA sequence:RefSeq:WP_005388516.1
COORDINATES: similar to AA sequence:RefSeq:WP_017033914.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_017028320.1
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017033912.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017028322.1
COORDINATES: similar to AA sequence:RefSeq:WP_017821223.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017821224.1
COORDINATES: similar to AA sequence:RefSeq:WP_005450851.1
COORDINATES: similar to AA sequence:RefSeq:WP_017188220.1
COORDINATES: similar to AA sequence:RefSeq:WP_005388506.1
bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
COORDINATES: similar to AA sequence:RefSeq:WP_005388501.1
COORDINATES: similar to AA sequence:RefSeq:WP_005438998.1
COORDINATES: similar to AA sequence:RefSeq:WP_001171117.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005388499.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006069127.1
COORDINATES: similar to AA sequence:RefSeq:WP_010649632.1
COORDINATES: similar to AA sequence:RefSeq:WP_014074800.1
COORDINATES: protein motif:HMM:NF013122.2
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013324.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF024498.2
thioredoxin fold domain-containing protein
COORDINATES: protein motif:HMM:NF012339.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:TIGR00595.1
GO:0005658 - alpha DNA polymerase:primase complex [Evidence IEA]
GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0003688 - DNA replication origin binding [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
hybrid sensor histidine kinase/response regulator
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF019348.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF019153.2
COORDINATES: protein motif:HMM:TIGR03743.1
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF021981.2
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF019265.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF024254.2
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: protein motif:HMM:NF019335.2
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF022224.2
COORDINATES: similar to AA sequence:RefSeq:WP_010436982.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025438.2
COORDINATES: protein motif:HMM:NF040322.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: protein motif:HMM:NF024703.2
COORDINATES: similar to AA sequence:RefSeq:WP_013654781.1
COORDINATES: similar to AA sequence:RefSeq:WP_006230232.1
COORDINATES: similar to AA sequence:RefSeq:WP_008218079.1
COORDINATES: similar to AA sequence:RefSeq:WP_011840016.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019823948.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_017045306.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008218099.1
COORDINATES: similar to AA sequence:RefSeq:WP_017449159.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_017089030.1
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_004741672.1