Desulfovibrio ferrophilus strain IS5 plasmid pDFE, complete sequence.
Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio.
Multi-heme cytochromes provide a pathway for survival in energy-limited environments
DOI:10.1126/sciadv.aao5682 Publication Status: Online-Only
Submitted (04-MAR-2016) Contact:Xiao Deng the University of Tokyo, Department of Engineering; Hongo 7-3-1, Tokyo 113-8654, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP017379.1.\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 :: Velvet v. 2.0\nGenome Coverage :: 60x\nSequencing Technology :: 454 GS FLX; ABI 3730\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 13:23:19\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) :: 3,425\nCDSs (total) :: 3,351\nGenes (coding) :: 3,341\nCDSs (with protein) :: 3,341\nGenes (RNA) :: 74\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 4\nPseudo Genes (total) :: 10\nCDSs (without protein) :: 10\nPseudo Genes (ambiguous residues) :: 0 of 10\nPseudo Genes (frameshifted) :: 7 of 10\nPseudo Genes (incomplete) :: 3 of 10\nPseudo Genes (internal stop) :: 1 of 10\nPseudo Genes (multiple problems) :: 1 of 10\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:NF016820.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015836768.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006798361.1
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF013561.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:TIGR01056.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012652.2
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:NF019608.2