Vibrio cholerae strain RFB16 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Genome sequence of Vibrio cholerae strains RFB05 and RFB16 isolated from North Park Lake in Allegheny County Pennsylvania
Submitted (28-AUG-2019) Microbiology and Molecular Genetics, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15219, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP043555.1.\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 2.4.1 v. 2.4.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 555x\nSequencing Technology :: PacBio Sequel II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/09/2022 22:49:35\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) :: 3,839\nCDSs (total) :: 3,702\nGenes (coding) :: 3,644\nCDSs (with protein) :: 3,644\nGenes (RNA) :: 137\nrRNAs :: 11, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 10, 10 (5S, 16S, 23S)\ntRNAs :: 102\nncRNAs :: 4\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 23 of 58\nPseudo Genes (incomplete) :: 33 of 58\nPseudo Genes (internal stop) :: 16 of 58\nPseudo Genes (multiple problems) :: 10 of 58\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: protein motif:HMM:NF013793.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_019281300.1
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: similar to AA sequence:RefSeq:WP_019281290.1
COORDINATES: similar to AA sequence:RefSeq:WP_014708273.1
COORDINATES: similar to AA sequence:RefSeq:WP_019281283.1
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_019281277.1
COORDINATES: protein motif:HMM:NF039183.1
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_003799880.1
COORDINATES: protein motif:HMM:NF037735.2
COORDINATES: similar to AA sequence:RefSeq:WP_020406883.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019281328.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF024108.2
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019281326.1
COORDINATES: similar to AA sequence:RefSeq:WP_008500008.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: similar to AA sequence:RefSeq:WP_019281323.1
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:TIGR02761.1
type IV conjugative transfer system protein TraE
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_019281318.1
COORDINATES: similar to AA sequence:RefSeq:WP_019281317.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_019281315.1
COORDINATES: similar to AA sequence:RefSeq:WP_019281314.1
type-F conjugative transfer system protein TraW
COORDINATES: protein motif:HMM:NF010297.0
conjugal transfer pilus assembly protein TraU
COORDINATES: protein motif:HMM:TIGR02742.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_019281310.1
COORDINATES: similar to AA sequence:RefSeq:WP_019281309.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR00608.1