Thermus oshimai JL-2 plasmid pTHEOS02, complete sequence.
Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus.
Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin
Submitted (06-JAN-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003251.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4090416\nSource DNA and organism available from Brian Hedlund\n(brian.hedland@unlv.edu)\nContacts: Brian Hedlund (brian.hedland@unlv.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Thermus oshimai JL-2\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Marine\nnum_replicons :: 3\nref_biomaterial :: Missing\nbiotic_relationship :: Free living\ntrophic_level :: Heterotroph\nrel_to_oxygen :: Missing\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi06476\nType Strain :: No\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nTemperature Range :: Thermophile\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/23/2023 08:49:52\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) :: 2,567\nCDSs (total) :: 2,507\nGenes (coding) :: 2,481\nCDSs (with protein) :: 2,481\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 26\nCDSs (without protein) :: 26\nPseudo Genes (ambiguous residues) :: 0 of 26\nPseudo Genes (frameshifted) :: 5 of 26\nPseudo Genes (incomplete) :: 20 of 26\nPseudo Genes (internal stop) :: 5 of 26\nPseudo Genes (multiple problems) :: 4 of 26\nCRISPR Arrays :: 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003049277.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003048834.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049272.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049270.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632313.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065452.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015065453.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632204.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632205.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_003049741.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632207.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016041133.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632212.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632213.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632214.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065464.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065465.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632217.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632218.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632219.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632220.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014632221.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632222.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632223.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065466.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049657.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049659.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
cysteine peptidase family C39 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003049660.1
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_018461947.1
COORDINATES: similar to AA sequence:RefSeq:WP_013157653.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003049670.1
COORDINATES: similar to AA sequence:RefSeq:WP_015716386.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049681.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049683.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049650.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049652.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049653.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049655.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632233.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632244.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632243.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065478.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632241.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065480.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632239.1
COORDINATES: similar to AA sequence:RefSeq:WP_015716433.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065483.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511356.1
COORDINATES: similar to AA sequence:RefSeq:WP_015717530.1
COORDINATES: similar to AA sequence:RefSeq:WP_003049296.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632261.1
COORDINATES: similar to AA sequence:RefSeq:WP_003048176.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
IS200/IS605 family accessory protein TnpB-related protein
COORDINATES: protein motif:HMM:TIGR03831.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632264.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511348.1
COORDINATES: similar to AA sequence:RefSeq:WP_014632266.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003048933.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003048940.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174478.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF019291.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013159907.1
phospholipase D-like domain-containing protein