Desulfovibrio sulfodismutans DSM 3696 plasmid p1, complete sequence.
Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfovibrionaceae; Desulfolutivibrio.
Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov
Submitted (22-OCT-2019) Bioinformatics, Leibniz Institute DSMZ, Inhoffenstr. 7B, Braunschweig 38124, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP045505.1.\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 Date :: 22-AUG-2019\nAssembly Method :: HGAP v. 3\nAssembly Name :: Desulfovibrio_DSM_3696_BM_3smrt_allein_re\n peat_korr\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 206.0x\nSequencing Technology :: PacBio RSII; Illumina NextSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/30/2023 10:39:14\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) :: 4,063\nCDSs (total) :: 3,993\nGenes (coding) :: 3,958\nCDSs (with protein) :: 3,958\nGenes (RNA) :: 70\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 14\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 12 of 35\nPseudo Genes (incomplete) :: 25 of 35\nPseudo Genes (internal stop) :: 1 of 35\nPseudo Genes (multiple problems) :: 3 of 35\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Desulfovibrio sulfodismutans
COORDINATES: similar to AA sequence:RefSeq:WP_012750659.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024600.2
GO:0005509 - calcium ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005992893.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003952 - NAD+ synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012745.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013530.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008869546.1
GO:0047343 - glucose-1-phosphate cytidylyltransferase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
glucose-1-phosphate cytidylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007852243.1
GO:0047733 - CDP-glucose 4,6-dehydratase activity [Evidence IEA]
GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012175377.1
dTDP-4-dehydrorhamnose 3,5-epimerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014414440.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013451281.1
COORDINATES: similar to AA sequence:RefSeq:WP_009849033.1
COORDINATES: similar to AA sequence:RefSeq:WP_007528858.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
cephalosporin hydroxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015723092.1
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF027890.2
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005618062.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013245.2
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_011368646.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024860.2
COORDINATES: protein motif:HMM:NF025665.2
glycoside hydrolase family 99-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001549957.1
COORDINATES: protein motif:HMM:NF013227.2
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: protein motif:HMM:NF012888.2
GO:0050656 - 3'-phosphoadenosine 5'-phosphosulfate binding [Evidence IEA]; GO:0008146 - sulfotransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF020463.2
COORDINATES: protein motif:HMM:NF033581.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008684539.1
GO:0015628 - protein secretion by the type II secretion system [Evidence IEA]
twin-arginine translocase TatA/TatE family subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006922031.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009107076.1
COORDINATES: similar to AA sequence:RefSeq:WP_012749860.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009181506.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020706513.1
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_014266362.1
COORDINATES: similar to AA sequence:RefSeq:WP_015863177.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin