Vibrio rumoiensis strain FERM P-14531 plasmid 2, 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\nAP018688.1.\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_001901413.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017218262.1
COORDINATES: similar to AA sequence:RefSeq:WP_001048895.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000369162.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_076611500.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; 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_010320052.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020820691.1
COORDINATES: similar to AA sequence:RefSeq:WP_007293166.1
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013625.2
peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF023166.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019280871.1
COORDINATES: similar to AA sequence:RefSeq:WP_004394065.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:TIGR04416.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_003029810.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006118530.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005229637.1
IS110-like element IS5075 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
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.
Tn3-like element ISPa38 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001097412.1
GO:0020037 - heme binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
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_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_001293886.1
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011809177.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100856.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100853.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
COORDINATES: similar to AA sequence:RefSeq:WP_001452736.1
COORDINATES: similar to AA sequence:RefSeq:WP_006991878.1
Tn3-like element ISShfr9 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_017017030.1
COORDINATES: similar to AA sequence:RefSeq:WP_004393986.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138014.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787758.1
COORDINATES: similar to AA sequence:RefSeq:WP_001963166.1
COORDINATES: similar to AA sequence:RefSeq:WP_017820257.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
dihydroxyacetone kinase operon transcriptional regulator DhaR
COORDINATES: similar to AA sequence:RefSeq:WP_017820258.1
GO:0008965 - phosphoenolpyruvate-protein phosphotransferase activity [Evidence IEA]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [Evidence IEA]; GO:0006808 - regulation of nitrogen utilization [Evidence IEA]
phosphoenolpyruvate--protein phosphotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_005379705.1
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005379704.1
COORDINATES: similar to AA sequence:RefSeq:WP_005379703.1
COORDINATES: protein motif:HMM:TIGR01386.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011715680.1
internal stop; 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_076612151.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009841415.1
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009841416.1
COORDINATES: similar to AA sequence:RefSeq:WP_004733414.1
COORDINATES: similar to AA sequence:RefSeq:WP_008910655.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076612081.1
COORDINATES: similar to AA sequence:RefSeq:WP_005716609.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019840070.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611433.1
IS4-like element ISPrst1 family transposase
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011848115.1
COORDINATES: similar to AA sequence:RefSeq:WP_005524776.1
GO:0004456 - phosphogluconate dehydratase activity [Evidence IEA]
GO:0009255 - Entner-Doudoroff pathway through 6-phosphogluconate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015878876.1
bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
COORDINATES: similar to AA sequence:RefSeq:WP_004413661.1
COORDINATES: protein motif:HMM:NF022590.2
COORDINATES: similar to AA sequence:RefSeq:WP_011070739.1
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_017015871.1
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_004798229.1
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009848319.1
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_019824395.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006713543.1
COORDINATES: similar to AA sequence:RefSeq:WP_019830223.1
COORDINATES: similar to AA sequence:RefSeq:WP_005419177.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005536335.1
COORDINATES: similar to AA sequence:RefSeq:WP_020977920.1
COORDINATES: similar to AA sequence:RefSeq:WP_018404802.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016915975.1
COORDINATES: similar to AA sequence:RefSeq:WP_006248253.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564931.1
COORDINATES: similar to AA sequence:RefSeq:WP_016800055.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006958798.1