Defluviicoccus vanus strain Ben 114 plasmid unnamed, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Defluviicoccus.
Complete closed genome sequence of Defluviicoccus vanus
Submitted (27-MAY-2020) Integrative Analysis Unit, Singapore Centre for Environmental Life Sciences Engineering, 28 Medical Drive, Singapore 117456, Singapore
REFSEQ INFORMATION: The reference sequence is identical to\nCP053924.1.\nBacteria and source DNA available from National Collection of\nIndustrial, Food and Marine Bacteria, Aberdeen, UK.\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 Date :: 24-JUL-2019\nAssembly Method :: Unicycler v. 0.4.7\nGenome Representation :: Full\nExpected Final Version :: No\nReference-guided Assembly :: align-xgenus: made from MEGAN-LR using\n NR\nGenome Coverage :: 100.0x\nSequencing Technology :: Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/12/2022 05:35:08\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) :: 3,849\nCDSs (total) :: 3,792\nGenes (coding) :: 3,414\nCDSs (with protein) :: 3,414\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 378\nCDSs (without protein) :: 378\nPseudo Genes (ambiguous residues) :: 0 of 378\nPseudo Genes (frameshifted) :: 169 of 378\nPseudo Genes (incomplete) :: 239 of 378\nPseudo Genes (internal stop) :: 13 of 378\nPseudo Genes (multiple problems) :: 42 of 378\nCRISPR Arrays :: 4\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:NF024515.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014385.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF027890.2
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012566035.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012115378.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_003494050.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650493.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017364873.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219839.1
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: protein motif:HMM:NF019128.2
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF015118.2
type IV secretion system VirB4 family; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013641202.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013641303.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012477434.1
COORDINATES: similar to AA sequence:RefSeq:WP_007967576.1
COORDINATES: similar to AA sequence:RefSeq:WP_006966982.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013984772.1
COORDINATES: similar to AA sequence:RefSeq:WP_012218065.1
COORDINATES: protein motif:HMM:NF012264.2
COORDINATES: similar to AA sequence:RefSeq:WP_008452460.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_020403957.1
COORDINATES: similar to AA sequence:RefSeq:WP_009209125.1
GO:0005887 - integral component of plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001067793.1
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_019197529.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0050380 - undecaprenyl-diphosphatase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007406331.1
COORDINATES: protein motif:HMM:TIGR00077.1
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008098670.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_016855514.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]; GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_003584576.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132723.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015272183.1
COORDINATES: similar to AA sequence:RefSeq:WP_011504718.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654593.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020820000.1
COORDINATES: similar to AA sequence:RefSeq:WP_004541786.1
COORDINATES: similar to AA sequence:RefSeq:WP_014761918.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092676.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436621.1
COORDINATES: protein motif:HMM:NF023390.2