Vibrio cortegadensis strain CECT 7227 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach
DOI:10.1007/s00284-021-02725-0 Publication Status: Online-Only
Submitted (05-JAN-2022) 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\nAP025474.1.\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 :: Unicycler v. 0.4.8\nGenome Coverage :: 208x\nSequencing Technology :: Illumina MiSeq; Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/29/2022 11:03:56\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) :: 4,217\nCDSs (total) :: 4,057\nGenes (coding) :: 4,004\nCDSs (with protein) :: 4,004\nGenes (RNA) :: 160\nrRNAs :: 15, 14, 14 (5S, 16S, 23S)\ncomplete rRNAs :: 15, 14, 14 (5S, 16S, 23S)\ntRNAs :: 113\nncRNAs :: 4\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 19 of 53\nPseudo Genes (incomplete) :: 39 of 53\nPseudo Genes (internal stop) :: 8 of 53\nPseudo Genes (multiple problems) :: 10 of 53\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_017420748.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
PhzF family phenazine biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_008223780.1
COORDINATES: similar to AA sequence:RefSeq:WP_017082593.1
COORDINATES: similar to AA sequence:RefSeq:WP_005536335.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016797431.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; 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_000459815.1
COORDINATES: protein motif:HMM:NF008277.0
COORDINATES: similar to AA sequence:RefSeq:WP_011217254.1
GO:0005515 - protein binding [Evidence IEA]; GO:0004856 - xylulokinase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0005997 - xylulose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012128228.1
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_011217244.1
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009045 - xylose isomerase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: protein motif:HMM:NF014026.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
glycoside hydrolase family 3 C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013080.2
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF019349.2
FadR/GntR family transcriptional regulator
COORDINATES: protein motif:HMM:NF020039.2
SMP-30/gluconolactonase/LRE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019427723.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: protein motif:HMM:NF012904.2
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005379703.1
COORDINATES: protein motif:HMM:NF024282.2
COORDINATES: protein motif:HMM:NF021231.2
COORDINATES: protein motif:HMM:NF022461.2
COORDINATES: similar to AA sequence:RefSeq:WP_008216465.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004394048.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004733560.1
COORDINATES: similar to AA sequence:RefSeq:WP_017053113.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017099648.1
COORDINATES: similar to AA sequence:RefSeq:WP_017099649.1
COORDINATES: similar to AA sequence:RefSeq:WP_017053110.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611907.1
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_017098431.1
GO:0003824 - catalytic activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013228.2
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_017098428.1
COORDINATES: similar to AA sequence:RefSeq:WP_011220721.1
COORDINATES: similar to AA sequence:RefSeq:WP_014231405.1
COORDINATES: similar to AA sequence:RefSeq:WP_016792302.1
COORDINATES: similar to AA sequence:RefSeq:WP_017066993.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_009846872.1
COORDINATES: similar to AA sequence:RefSeq:WP_012275304.1
COORDINATES: similar to AA sequence:RefSeq:WP_017051257.1
COORDINATES: similar to AA sequence:RefSeq:WP_012157265.1
COORDINATES: similar to AA sequence:RefSeq:WP_017095787.1
COORDINATES: similar to AA sequence:RefSeq:WP_012601059.1
COORDINATES: similar to AA sequence:RefSeq:WP_004732392.1
GO:0008838 - diaminopropionate ammonia-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008215944.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017065005.1
GO:0003867 - 4-aminobutyrate transaminase activity [Evidence IEA]
GO:0009450 - gamma-aminobutyric acid catabolic process [Evidence IEA]
4-aminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_008081131.1
COORDINATES: similar to AA sequence:RefSeq:WP_006880641.1
GO:0005887 - integral component of plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020335227.1
COORDINATES: similar to AA sequence:RefSeq:WP_014257173.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005471565.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005471596.1
COORDINATES: similar to AA sequence:RefSeq:WP_006880636.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008081144.1
GO:0050498 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014233869.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611746.1
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.
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006958798.1
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_017018434.1
COORDINATES: similar to AA sequence:RefSeq:WP_005376453.1
COORDINATES: similar to AA sequence:RefSeq:WP_004743446.1
COORDINATES: similar to AA sequence:RefSeq:WP_020328397.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017086151.1
NADH:flavin oxidoreductase/NADH oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016798105.1
COORDINATES: similar to AA sequence:RefSeq:WP_005423237.1
COORDINATES: similar to AA sequence:RefSeq:WP_017032185.1
COORDINATES: similar to AA sequence:RefSeq:WP_006070426.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012534954.1
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019820167.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017077033.1
COORDINATES: similar to AA sequence:RefSeq:WP_015728070.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
signal transduction histidine-protein kinase/phosphatase UhpB
COORDINATES: similar to AA sequence:RefSeq:WP_017819640.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016766917.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006069252.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006069253.1