Vagococcus carniphilus strain ATCC BAA-640 plasmid p_unnamed1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Vagococcus.
Genome sequence of Vagococcus carniphilus ATCC BAA-640T
Submitted (26-AUG-2020) Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP060721.1.\nBacteria and source DNA available from ATCC BAA-640.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 330.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 04:53:38\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,059\nCDSs (total) :: 2,951\nGenes (coding) :: 2,907\nCDSs (with protein) :: 2,907\nGenes (RNA) :: 108\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 83\nncRNAs :: 4\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 25 of 44\nPseudo Genes (incomplete) :: 20 of 44\nPseudo Genes (internal stop) :: 8 of 44\nPseudo Genes (multiple problems) :: 9 of 44\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+.
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF014581.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF027718.2
COORDINATES: similar to AA sequence:RefSeq:WP_010734662.1
COORDINATES: protein motif:HMM:NF016119.2
GO:0004197 - cysteine-type endopeptidase activity [Evidence IEA]
GO:0045184 - establishment of protein localization [Evidence IEA]; GO:0016485 - protein processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF037639.2
SpaA isopeptide-forming pilin-related protein
COORDINATES: protein motif:HMM:TIGR00261.1
COORDINATES: protein motif:HMM:NF020291.2
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002287942.1
COORDINATES: similar to AA sequence:RefSeq:WP_002404829.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01653.1
COORDINATES: similar to AA sequence:RefSeq:WP_016176069.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
putative bacteriocin export ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_016176068.1
COORDINATES: protein motif:HMM:NF014717.2
COORDINATES: similar to AA sequence:RefSeq:WP_010782399.1
COORDINATES: protein motif:HMM:NF037096.2
COORDINATES: similar to AA sequence:RefSeq:WP_001032575.1
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_064305258.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS1216 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001226076.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003725292.1
quaternary ammonium compound efflux SMR transporter BcrC
COORDINATES: similar to AA sequence:RefSeq:WP_003725293.1
quaternary ammonium compound efflux SMR transporter BcrB
COORDINATES: similar to AA sequence:RefSeq:WP_003725294.1
efflux transporter transcriptional regulator BcrA
COORDINATES: similar to AA sequence:RefSeq:WP_000120518.1
COORDINATES: similar to AA sequence:RefSeq:WP_017370594.1
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_013710761.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024554.2
COORDINATES: protein motif:HMM:NF037847.2