Vibrio taketomensis strain C4III291 plasmid pVtak1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Vibrio taketomensis sp. nov. by genome taxonomy
DOI:10.1016/j.syapm.2019.126048 Publication Status: Online-Only
Submitted (24-APR-2019) 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\nAP019653.1.\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. 0.4.7\nGenome Coverage :: 43.1x\nSequencing Technology :: Illumina MiSeq; ONT MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/27/2022 03:07:48\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) :: 4,100\nCDSs (total) :: 3,937\nGenes (coding) :: 3,636\nCDSs (with protein) :: 3,636\nGenes (RNA) :: 163\nrRNAs :: 13, 12, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 13, 12, 12 (5S, 16S, 23S)\ntRNAs :: 122\nncRNAs :: 4\nPseudo Genes (total) :: 301\nCDSs (without protein) :: 301\nPseudo Genes (ambiguous residues) :: 0 of 301\nPseudo Genes (frameshifted) :: 274 of 301\nPseudo Genes (incomplete) :: 33 of 301\nPseudo Genes (internal stop) :: 29 of 301\nPseudo Genes (multiple problems) :: 33 of 301\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019282033.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001227124.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]
pilus (MSHA type) biogenesis protein MshL
COORDINATES: similar to AA sequence:RefSeq:WP_019826973.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000117850.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006711944.1
COORDINATES: similar to AA sequence:RefSeq:WP_000190450.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017043826.1
COORDINATES: similar to AA sequence:RefSeq:WP_006711948.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019575.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016955131.1
COORDINATES: similar to AA sequence:RefSeq:WP_020433220.1
GO:0008360 - regulation of cell shape [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000952872.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011261173.1
COORDINATES: protein motif:HMM:NF021653.2
COORDINATES: similar to AA sequence:RefSeq:WP_017041098.1
COORDINATES: similar to AA sequence:RefSeq:WP_017038231.1
carbon-nitrogen hydrolase family protein
COORDINATES: protein motif:HMM:NF013673.2
COORDINATES: protein motif:HMM:NF040244.1
COORDINATES: protein motif:HMM:NF039907.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011151227.1
GO:0016990 - arginine deiminase activity [Evidence IEA]
GO:0006527 - arginine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000019333.1
COORDINATES: similar to AA sequence:RefSeq:WP_005441995.1
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_004747238.1
COORDINATES: similar to AA sequence:RefSeq:WP_017820275.1
COORDINATES: similar to AA sequence:RefSeq:WP_017046665.1
COORDINATES: similar to AA sequence:RefSeq:WP_005531005.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_001246635.1
COORDINATES: similar to AA sequence:RefSeq:WP_012126909.1
GO:0030060 - L-malate dehydrogenase activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004415725.1
COORDINATES: similar to AA sequence:RefSeq:WP_000345930.1
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015960603.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000311 - plastid large ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000940598.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009847831.1
GO:0042254 - ribosome biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004409957.1
threonine/serine exporter family protein