Desulfohalobium retbaense DSM 5692 plasmid pDRET01, complete sequence.
Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfohalobiaceae; Desulfohalobium.
Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
The complete plasmid of Desulfohalobium retbaense DSM 5692
Submitted (08-SEP-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001735.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082992\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\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##Metadata-START##\nOrganism Display Name :: Desulfohalobium retbaense DSM 5692\nCulture Collection ID :: DSM 5692\nGOLD Stamp ID :: Gi02246\nGreengenes ID :: 10400\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: GeneMark\nIsolation Site :: Saline sediment from Retba Lake in Senegal\n Africa\nIsolation Country :: Senegal\nLatitude :: 14.833333\nLongitude :: -17.233333\nOxygen Requirement :: Anaerobe\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 35C\nSalinity :: Halophile\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nPhenotypes :: Sulfate reducer\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/22/2023 00:46:46\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) :: 2,547\nCDSs (total) :: 2,487\nGenes (coding) :: 2,472\nCDSs (with protein) :: 2,472\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 15\nCDSs (without protein) :: 15\nPseudo Genes (ambiguous residues) :: 0 of 15\nPseudo Genes (frameshifted) :: 3 of 15\nPseudo Genes (incomplete) :: 13 of 15\nPseudo Genes (internal stop) :: 4 of 15\nPseudo Genes (multiple problems) :: 3 of 15\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Desulfohalobium retbaense
COORDINATES: similar to AA sequence:RefSeq:WP_006924212.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012813882.1
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: similar to AA sequence:RefSeq:WP_015752780.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015752319.1
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_005994224.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: similar to AA sequence:RefSeq:WP_017158739.1
COORDINATES: similar to AA sequence:RefSeq:WP_012813873.1
COORDINATES: protein motif:HMM:NF027470.2
COORDINATES: similar to AA sequence:RefSeq:WP_015752054.1
COORDINATES: similar to AA sequence:RefSeq:WP_015750832.1
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:NF024908.2
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ISKra4-like element ISDere1 family transposase
COORDINATES: protein motif:HMM:NF012372.2
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018999759.1
COORDINATES: similar to AA sequence:RefSeq:WP_007946713.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008173657.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
frameshifted; 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.
COORDINATES: protein motif:HMM:NF024183.2
COORDINATES: protein motif:HMM:NF033559.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_018126032.1
COORDINATES: protein motif:HMM:NF025637.2
GO:0004519 - endonuclease activity [Evidence IEA]
HNH endonuclease signature motif containing protein
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0042578 - phosphoric ester hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025001.2