Vagococcus carniphilus strain ATCC BAA-640 plasmid p_unnamed2, 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\nCP060722.1.\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: similar to AA sequence:RefSeq:WP_012058465.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016174990.1
COORDINATES: similar to AA sequence:RefSeq:WP_015543863.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF037417.2
COORDINATES: similar to AA sequence:RefSeq:WP_015426465.1
COORDINATES: similar to AA sequence:RefSeq:WP_016173944.1
GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: protein motif:HMM:NF017353.2
COORDINATES: similar to AA sequence:RefSeq:WP_002320668.1
COORDINATES: similar to AA sequence:RefSeq:WP_006532607.1
COORDINATES: similar to AA sequence:RefSeq:WP_002344895.1
COORDINATES: similar to AA sequence:RefSeq:WP_002344896.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002339788.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002396205.1
COORDINATES: similar to AA sequence:RefSeq:WP_002340526.1
COORDINATES: similar to AA sequence:RefSeq:WP_016627749.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000221326.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001032575.1
COORDINATES: similar to AA sequence:RefSeq:WP_001178744.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002316688.1
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_002316687.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002316685.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_002342451.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_002291321.1
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_002297185.1
frameshifted; 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_002291076.1
COORDINATES: similar to AA sequence:RefSeq:WP_002291081.1
COORDINATES: similar to AA sequence:RefSeq:WP_002342352.1
SpaH/EbpB family LPXTG-anchored major pilin
COORDINATES: similar to AA sequence:RefSeq:WP_002291088.1
pilin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002342351.1
SpaA isopeptide-forming pilin-related protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_002337530.1
COORDINATES: similar to AA sequence:RefSeq:WP_002333827.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782321.1
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002300090.1
COORDINATES: similar to AA sequence:RefSeq:WP_002300091.1
COORDINATES: similar to AA sequence:RefSeq:WP_002300092.1
COORDINATES: similar to AA sequence:RefSeq:WP_005237742.1
COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1
IS6-like element IS1216 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_016621817.1
COORDINATES: similar to AA sequence:RefSeq:WP_007207926.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002287843.1
COORDINATES: similar to AA sequence:RefSeq:WP_002399460.1
COORDINATES: similar to AA sequence:RefSeq:WP_014939776.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_016634928.1
Asp23/Gls24 family envelope stress response protein
COORDINATES: similar to AA sequence:RefSeq:WP_016185123.1
COORDINATES: protein motif:HMM:NF033218.1
alkaline shock response membrane anchor protein AmaP