Desulfovibrio vulgaris DP4 plasmid pDVUL01, complete sequence.
Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio.
Complete sequence of plasmid pDVUL01 of Desulfovibrio vulgaris subsp. vulgaris DP4
Submitted (19-DEC-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000528.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4001787\nSource DNA and bacteria available from Christopher Walker\n(cbwalkdr@u.washington.edu)\nContacts: Christopher Walker (cbwalkdr@u.washington.edu)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LLNL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/12/2022 01:20:46\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) :: 3,169\nCDSs (total) :: 3,080\nGenes (coding) :: 3,069\nCDSs (with protein) :: 3,069\nGenes (RNA) :: 89\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 11\nCDSs (without protein) :: 11\nPseudo Genes (ambiguous residues) :: 0 of 11\nPseudo Genes (frameshifted) :: 5 of 11\nPseudo Genes (incomplete) :: 9 of 11\nPseudo Genes (internal stop) :: 2 of 11\nPseudo Genes (multiple problems) :: 4 of 11\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011176581.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011176580.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176729.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011176728.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011176727.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176726.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524695.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176724.1
ABC transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176723.1
CesT family type III secretion system chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_014524694.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787414.1
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011787412.1
autotransporter domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176715.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
7TM diverse intracellular signaling domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176714.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176713.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787408.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176711.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
GO:0051607 - defense response to virus [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-C CRISPR-associated endonuclease Cas1c
COORDINATES: similar to AA sequence:RefSeq:WP_011787406.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004299430.1
GO:0003674 - molecular_function [Evidence IEA]
type I-C CRISPR-associated protein Cas7/Csd2
COORDINATES: similar to AA sequence:RefSeq:WP_011176708.1
GO:0005575 - cellular_component [Evidence IEA]
type I-C CRISPR-associated protein Cas8c/Csd1
COORDINATES: similar to AA sequence:RefSeq:WP_011787403.1
type I-C CRISPR-associated protein Cas5c
COORDINATES: similar to AA sequence:RefSeq:WP_011787402.1
CRISPR-associated helicase/endonuclease Cas3
COORDINATES: similar to AA sequence:RefSeq:WP_014524689.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176704.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176703.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176702.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176701.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176700.1
GO:0030257 - type III protein secretion system complex [Evidence IEA]
GO:0030254 - protein secretion by the type III secretion system [Evidence IEA]
type III secretion system export apparatus subunit SctR
COORDINATES: similar to AA sequence:RefSeq:WP_011176699.1
type III secretion system cytoplasmic ring protein SctQ
COORDINATES: similar to AA sequence:RefSeq:WP_014524688.1
type III secretion system needle length determinant
COORDINATES: similar to AA sequence:RefSeq:WP_014524687.1
YscO family type III secretion system apparatus protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176697.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787394.1
HrpE/YscL family type III secretion apparatus protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176730.1
SctK family type III secretion system sorting platform protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176695.1
type III secretion inner membrane ring lipoprotein SctJ
COORDINATES: similar to AA sequence:RefSeq:WP_014524686.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176694.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176693.1
EscF/YscF/HrpA family type III secretion system needle major subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011176692.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176691.1
type III secretion system inner membrane ring subunit SctD
COORDINATES: similar to AA sequence:RefSeq:WP_014524685.1
type III secretion system outer membrane ring subunit SctC
COORDINATES: similar to AA sequence:RefSeq:WP_011176731.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787387.1
type III secretion system translocon subunit SctB
COORDINATES: similar to AA sequence:RefSeq:WP_011787386.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176687.1
SycD/LcrH family type III secretion system chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_011787384.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787383.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176684.1
GO:0009986 - cell surface [Evidence IEA]
GO:0050709 - negative regulation of protein secretion [Evidence IEA]; GO:0030254 - protein secretion by the type III secretion system [Evidence IEA]
type III secretion system gatekeeper subunit SctW
COORDINATES: similar to AA sequence:RefSeq:WP_011176683.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787381.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787380.1
COORDINATES: similar to AA sequence:RefSeq:WP_011105897.1
GO:0009306 - protein secretion [Evidence IEA]
type III secretion system export apparatus subunit SctV
COORDINATES: similar to AA sequence:RefSeq:WP_011176681.1
type III secretion system export apparatus subunit SctS
COORDINATES: similar to AA sequence:RefSeq:WP_011176680.1
type III secretion system export apparatus subunit SctT
COORDINATES: similar to AA sequence:RefSeq:WP_011787378.1
type III secretion system export apparatus subunit SctU
COORDINATES: similar to AA sequence:RefSeq:WP_011176678.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787376.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524679.1
GO:0016791 - phosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176676.1
iron-containing alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176675.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176670.1
COORDINATES: similar to AA sequence:RefSeq:WP_015862061.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176668.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176667.1
COORDINATES: similar to AA sequence:RefSeq:WP_007523536.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524674.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787366.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176664.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787364.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011787362.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176659.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176658.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176657.1
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176655.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787359.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787358.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176652.1
sulfotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176651.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: similar to AA sequence:RefSeq:WP_011787356.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176649.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787354.1
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_011787352.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176645.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176644.1
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011787349.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014524668.1
phenylacetate--CoA ligase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014524667.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524666.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176640.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176639.1
heparan-alpha-glucosaminide N-acetyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176638.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176637.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524664.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176635.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011176634.1
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176633.1
GO:0004197 - cysteine-type endopeptidase activity [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176632.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787337.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524661.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176629.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787334.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176627.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176626.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787331.1
sugar-transfer associated ATP-grasp domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176624.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176623.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_011787328.1
FemAB family PEP-CTERM system-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176621.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176620.1
TIGR03016 family PEP-CTERM system-associated outer membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176619.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176618.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787326.1
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011787325.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787324.1
TIGR03013 family PEP-CTERM/XrtA system glycosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014524658.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787322.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176612.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176610.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787320.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787319.1
PEP-CTERM proteins occur, often in large numbers, in the proteomes of bacteria that also encode an exosortase, a predicted intramembrane cysteine proteinase. The presence of a PEP-CTERM domain at a protein's C-terminus predicts cleavage within the sorting domain, followed by covalent anchoring to some some component of the (usually Gram-negative) cell surface. Many PEP-CTERM proteins exhibit an unusual sequence composition that includes large numbers of potential glycosylation sites. Expression of one such protein has been shown restore the ability of a bacterium to form floc, a type of biofilm; Derived by automated computational analysis using gene prediction method: Protein Homology.
PEP-CTERM sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011787317.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176606.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524655.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011176601.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176600.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787314.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014524654.1
COORDINATES: similar to AA sequence:RefSeq:WP_014524652.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787310.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176593.1
GO:0016611 - iron-iron nitrogenase complex [Evidence IEA]; GO:0016612 - molybdenum-iron nitrogenase complex [Evidence IEA]; GO:0016613 - vanadium-iron nitrogenase complex [Evidence IEA]
GO:0016163 - nitrogenase activity [Evidence IEA]
GO:0009399 - nitrogen fixation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011176592.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176591.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176590.1
GO:0016612 - molybdenum-iron nitrogenase complex [Evidence IEA]
nitrogenase molybdenum-iron protein alpha chain
COORDINATES: similar to AA sequence:RefSeq:WP_011176589.1
nitrogenase molybdenum-iron protein subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011787307.1
(2Fe-2S) ferredoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011176587.1
nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
COORDINATES: similar to AA sequence:RefSeq:WP_011176586.1
COORDINATES: similar to AA sequence:RefSeq:WP_011176585.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012307.2
COORDINATES: similar to AA sequence:RefSeq:WP_010937781.1
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_011176584.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011787300.1
COORDINATES: similar to AA sequence:RefSeq:WP_011787299.1