Desulfosarcina ovata subsp. sediminis strain 28bB2T plasmid Do28_1, complete sequence.
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae; Desulfosarcina.
Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay
DOI:10.1016/j.syapm.2020.126109 Publication Status: Online-Only
Submitted (07-NOV-2019) Contact:Miho Watanabe Akita Prefectural University, Faculty of Bioresource Sciences, Department of Biological Environment; 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita 010-0195, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP021877.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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 :: Unicycler ver 0.4.7\nGenome Coverage :: 620x\nSequencing Technology :: Illumina NextSeq; Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/23/2022 03:54:04\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) :: 7,352\nCDSs (total) :: 7,290\nGenes (coding) :: 7,215\nCDSs (with protein) :: 7,215\nGenes (RNA) :: 62\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 10 of 75\nPseudo Genes (incomplete) :: 65 of 75\nPseudo Genes (internal stop) :: 10 of 75\nPseudo Genes (multiple problems) :: 9 of 75\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Desulfosarcina ovata subsp. sediminis
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF025819.2
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018753654.1
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: similar to AA sequence:RefSeq:WP_006509966.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024907.2
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF013676.2
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015257607.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_014028382.1
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012176288.1
COORDINATES: similar to AA sequence:RefSeq:WP_020877461.1
COORDINATES: protein motif:HMM:NF013936.2
COORDINATES: similar to AA sequence:RefSeq:WP_010526654.1
COORDINATES: similar to AA sequence:RefSeq:WP_020735947.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
nitric oxide reductase transcriptional regulator NorR
COORDINATES: similar to AA sequence:RefSeq:WP_020876443.1
COORDINATES: similar to AA sequence:RefSeq:WP_015947329.1
COORDINATES: similar to AA sequence:RefSeq:WP_006967941.1
COORDINATES: protein motif:HMM:NF019958.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020161651.1
Members of this family of hydrolases with an active site Cys residue belong to MEROPS family C26; Derived by automated computational analysis using gene prediction method: Protein Homology.
gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012662460.1
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF014582.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03980.1
COORDINATES: similar to AA sequence:RefSeq:WP_012174817.1
COORDINATES: similar to AA sequence:RefSeq:WP_020876361.1
COORDINATES: similar to AA sequence:RefSeq:WP_020876360.1
COORDINATES: similar to AA sequence:RefSeq:WP_006424365.1
COORDINATES: similar to AA sequence:RefSeq:WP_010939296.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0016661 - oxidoreductase activity, acting on other nitrogenous compounds as donors [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF013069.2
COORDINATES: protein motif:HMM:NF014296.2
GO:0004489 - methylenetetrahydrofolate reductase (NAD(P)H) activity [Evidence IEA]
GO:0006555 - methionine metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011711650.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220837.1
COORDINATES: similar to AA sequence:RefSeq:WP_006746770.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008869160.1
COORDINATES: protein motif:HMM:NF014062.2
COORDINATES: similar to AA sequence:RefSeq:WP_011367816.1
COORDINATES: similar to AA sequence:RefSeq:WP_011367815.1
COORDINATES: similar to AA sequence:RefSeq:WP_008479013.1
COORDINATES: similar to AA sequence:RefSeq:WP_012173666.1
COORDINATES: protein motif:HMM:NF013015.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173664.1
COORDINATES: similar to AA sequence:RefSeq:WP_020876793.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006282 - regulation of DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012083247.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
topoisomerase DNA-binding C4 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_043768368.1
COORDINATES: similar to AA sequence:RefSeq:WP_012502752.1
COORDINATES: protein motif:HMM:TIGR02768.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_005671594.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF015205.2
COORDINATES: similar to AA sequence:RefSeq:WP_015904808.1
COORDINATES: protein motif:HMM:TIGR00621.2
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022077.2
COORDINATES: protein motif:HMM:NF028103.2
DNA-primase RepB domain-containing protein
COORDINATES: protein motif:HMM:NF028126.2
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF023713.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: protein motif:HMM:NF022835.2
COORDINATES: protein motif:HMM:NF021897.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF022441.2
COORDINATES: similar to AA sequence:RefSeq:WP_004071424.1
COORDINATES: similar to AA sequence:RefSeq:WP_004072278.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004072279.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012173928.1
GO:0004807 - triose-phosphate isomerase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012173929.1
GO:0006094 - gluconeogenesis [Evidence IEA]; GO:0019682 - glyceraldehyde-3-phosphate metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type I glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_015904644.1
COORDINATES: protein motif:HMM:NF015620.2
COORDINATES: similar to AA sequence:RefSeq:WP_020589820.1
COORDINATES: protein motif:HMM:NF013122.2
COORDINATES: similar to AA sequence:RefSeq:WP_010910911.1
COORDINATES: similar to AA sequence:RefSeq:WP_015743205.1
COORDINATES: similar to AA sequence:RefSeq:WP_015722315.1
internal stop; 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.
hybrid sensor histidine kinase/response regulator
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
formylglycine-generating enzyme family protein