Vibrio rumoiensis strain FERM P-14531 plasmid 1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Submitted (18-MAY-2018) Contact:Tomoo Sawabe Hokkaido University, Faculty of Fisheries Sciences; 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018687.1.\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 :: Canu v. 1.6; Pilon v. 1.22\nGenome Coverage :: 658x\nSequencing Technology :: Illumina MiSeq; ONT MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 02:55:55\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,845\nCDSs (total) :: 3,725\nGenes (coding) :: 3,628\nCDSs (with protein) :: 3,628\nGenes (RNA) :: 120\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 91\nncRNAs :: 4\nPseudo Genes (total) :: 97\nCDSs (without protein) :: 97\nPseudo Genes (ambiguous residues) :: 0 of 97\nPseudo Genes (frameshifted) :: 47 of 97\nPseudo Genes (incomplete) :: 59 of 97\nPseudo Genes (internal stop) :: 16 of 97\nPseudo Genes (multiple problems) :: 20 of 97\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013141690.1
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: similar to AA sequence:RefSeq:WP_013141686.1
COORDINATES: similar to AA sequence:RefSeq:WP_001258027.1
COORDINATES: similar to AA sequence:RefSeq:WP_000268394.1
COORDINATES: similar to AA sequence:RefSeq:WP_001256128.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220991.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220990.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220989.1
COORDINATES: similar to AA sequence:RefSeq:WP_000225028.1
COORDINATES: similar to AA sequence:RefSeq:WP_000757530.1
COORDINATES: similar to AA sequence:RefSeq:WP_000018404.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220983.1
COORDINATES: similar to AA sequence:RefSeq:WP_000409412.1
COORDINATES: similar to AA sequence:RefSeq:WP_015994302.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220978.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220977.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220976.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220975.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220972.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:YP_005220971.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220970.1
COORDINATES: similar to AA sequence:RefSeq:WP_016535194.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220968.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220966.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220965.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220964.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220963.1
Fe3+-siderophore ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_013141674.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220961.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220960.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220959.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005220958.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220957.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220956.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220955.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220954.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220953.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220951.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:YP_005220950.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221100.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221099.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221098.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221097.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221096.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221095.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221094.1
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221093.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221092.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221091.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221090.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221089.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221088.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221087.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221086.1
COORDINATES: similar to AA sequence:RefSeq:WP_000101263.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221085.1
COORDINATES: similar to AA sequence:RefSeq:WP_011112884.1
frameshifted; 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_011000070.1
GO:0004803 - transposase activity [Evidence IEA]
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_018715399.1
COORDINATES: similar to AA sequence:RefSeq:WP_003076107.1
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_015866014.1
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_011787830.1
COORDINATES: similar to AA sequence:RefSeq:WP_011918375.1
COORDINATES: similar to AA sequence:RefSeq:WP_011638898.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011787804.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612056.1
ISL3-like element ISPpu12 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013504665.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014702287.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001219642.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011787803.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011787802.1
COORDINATES: similar to AA sequence:RefSeq:WP_011918924.1
COORDINATES: similar to AA sequence:RefSeq:WP_003121549.1
COORDINATES: similar to AA sequence:RefSeq:WP_012248032.1
COORDINATES: similar to AA sequence:RefSeq:WP_020229288.1
COORDINATES: similar to AA sequence:RefSeq:WP_016973624.1
COORDINATES: similar to AA sequence:RefSeq:WP_007837906.1
COORDINATES: similar to AA sequence:RefSeq:WP_004636773.1
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141614.1
DNA replication terminus site-binding protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221073.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221072.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221071.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221070.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221069.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221068.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221067.1
COORDINATES: similar to AA sequence:RefSeq:WP_016139426.1
COORDINATES: similar to AA sequence:RefSeq:WP_014254777.1
COORDINATES: similar to AA sequence:RefSeq:WP_000121288.1
COORDINATES: similar to AA sequence:RefSeq:WP_000243483.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221065.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221066.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221064.1
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014777740.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221062.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221061.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221060.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221059.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221058.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221057.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221056.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221054.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221053.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141585.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141584.1
COORDINATES: similar to AA sequence:RefSeq:WP_000071869.1
GO:0002953 - 5'-deoxynucleotidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000050847.1
COORDINATES: similar to AA sequence:RefSeq:WP_001187970.1
phosphoadenosine phosphosulfate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_000042274.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141579.1
COORDINATES: similar to AA sequence:RefSeq:WP_001093867.1
COORDINATES: similar to AA sequence:RefSeq:WP_011899375.1
COORDINATES: similar to AA sequence:RefSeq:WP_000201432.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000410925.1
COORDINATES: similar to AA sequence:RefSeq:WP_000209075.1
COORDINATES: similar to AA sequence:RefSeq:WP_000994741.1
COORDINATES: similar to AA sequence:RefSeq:WP_000651508.1
COORDINATES: similar to AA sequence:RefSeq:WP_000340223.1
COORDINATES: similar to AA sequence:RefSeq:WP_001176699.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141572.1
COORDINATES: similar to AA sequence:RefSeq:WP_001102699.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
class I ribonucleotide reductase maintenance protein YfaE
COORDINATES: similar to AA sequence:RefSeq:WP_000477209.1
COORDINATES: similar to AA sequence:RefSeq:WP_000793770.1
COORDINATES: similar to AA sequence:RefSeq:WP_000018871.1
COORDINATES: similar to AA sequence:RefSeq:WP_001447572.1
COORDINATES: similar to AA sequence:RefSeq:WP_000039317.1
COORDINATES: similar to AA sequence:RefSeq:WP_000170086.1
COORDINATES: similar to AA sequence:RefSeq:WP_000706865.1
COORDINATES: similar to AA sequence:RefSeq:WP_001282585.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000739140.1
COORDINATES: similar to AA sequence:RefSeq:WP_000085161.1
CbbQ/NirQ/NorQ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001186917.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141561.1
COORDINATES: similar to AA sequence:RefSeq:WP_000796664.1
COORDINATES: similar to AA sequence:RefSeq:WP_000709517.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141558.1
conjugal transfer mating pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_005507569.1
COORDINATES: similar to AA sequence:RefSeq:WP_001337754.1
COORDINATES: similar to AA sequence:RefSeq:WP_001447719.1
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_001010738.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184404.1
COORDINATES: similar to AA sequence:RefSeq:WP_000637386.1
COORDINATES: similar to AA sequence:RefSeq:WP_001259344.1
COORDINATES: similar to AA sequence:RefSeq:WP_000606833.1
COORDINATES: similar to AA sequence:RefSeq:WP_000993344.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010845916.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_000647304.1
COORDINATES: similar to AA sequence:RefSeq:WP_000794249.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_001049717.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_000433889.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_001052531.1
COORDINATES: similar to AA sequence:RefSeq:WP_001275801.1
COORDINATES: similar to AA sequence:RefSeq:WP_001231465.1
COORDINATES: similar to AA sequence:RefSeq:WP_000869261.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184411.1
COORDINATES: similar to AA sequence:RefSeq:WP_000743450.1
COORDINATES: similar to AA sequence:RefSeq:WP_000332868.1
COORDINATES: similar to AA sequence:RefSeq:WP_000178858.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_001337757.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184413.1
COORDINATES: similar to AA sequence:RefSeq:WP_010845927.1
COORDINATES: similar to AA sequence:RefSeq:WP_000366824.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013141535.1
COORDINATES: similar to AA sequence:RefSeq:WP_014386427.1
COORDINATES: similar to AA sequence:RefSeq:WP_000895693.1
COORDINATES: protein motif:HMM:NF012372.2
COORDINATES: similar to AA sequence:RefSeq:WP_000647188.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221048.1
COORDINATES: similar to AA sequence:RefSeq:WP_015058947.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221046.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221044.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221043.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221042.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221041.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221040.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017086524.1