Thermovirga lienii DSM 17291 plasmid pTLIE01, complete sequence.
Bacteria; Synergistota; Synergistia; Synergistales; Thermovirgaceae; Thermovirga.
The complete genome of plasmid of Thermovirga lienii DSM 17291
Submitted (26-OCT-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003097.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4085723\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Thermovirga lienii Cas60314, DSM 17291\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Norway\nenvironment :: Oil fields, Fresh water\nnum_replicons :: 2\nref_biomaterial :: DSM 17291, ATCC BAA-1197\nbiotic_relationship :: Free living\ntrophic_level :: Chemoorganotroph\nrel_to_oxygen :: Obligate anaerobe\nisol_growth_condt :: 16825627\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02948\nType Strain :: Yes\nGreengenes ID :: 143575\nFunding Program :: DOE-GEBA 2007\nIsolation Site :: Production water from an oil well, Norway\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 58C\npH :: 6.5 - 7.0\nGram Staining :: Gram-\nDiseases :: None\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 :: 04/24/2023 01:01:54\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) :: 1,967\nCDSs (total) :: 1,907\nGenes (coding) :: 1,885\nCDSs (with protein) :: 1,885\nGenes (RNA) :: 60\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 22\nCDSs (without protein) :: 22\nPseudo Genes (ambiguous residues) :: 0 of 22\nPseudo Genes (frameshifted) :: 11 of 22\nPseudo Genes (incomplete) :: 11 of 22\nPseudo Genes (internal stop) :: 3 of 22\nPseudo Genes (multiple problems) :: 3 of 22\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013810019.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01055
molybdenum cofactor riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005854238.1
GO:0003842 - 1-pyrroline-5-carboxylate dehydrogenase activity [Evidence IEA]
GO:0006562 - proline catabolic process [Evidence IEA]
L-glutamate gamma-semialdehyde dehydrogenase
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF018530.2
COORDINATES: similar to AA sequence:RefSeq:WP_014162180.1
COORDINATES: similar to AA sequence:RefSeq:WP_012158312.1
acetyl-CoA hydrolase/transferase family protein
COORDINATES: protein motif:HMM:TIGR01357.1
GO:0003856 - 3-dehydroquinate synthase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006582854.1
GO:0004107 - chorismate synthase activity [Evidence IEA]
GO:0009073 - aromatic amino acid family biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00507.1
GO:0004764 - shikimate 3-dehydrogenase (NADP+) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006301390.1
GO:0003866 - 3-phosphoshikimate 1-carboxyvinyltransferase activity [Evidence IEA]
3-phosphoshikimate 1-carboxyvinyltransferase
COORDINATES: protein motif:HMM:NF014234.2
GO:0008977 - prephenate dehydrogenase (NAD+) activity [Evidence IEA]; GO:0004665 - prephenate dehydrogenase (NADP+) activity [Evidence IEA]
GO:0006571 - tyrosine biosynthetic process [Evidence IEA]
prephenate dehydrogenase/arogenate dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005660255.1
GO:0003849 - 3-deoxy-7-phosphoheptulonate synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014162178.1
frameshifted; 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_008192590.1
COORDINATES: similar to AA sequence:RefSeq:WP_020533421.1
COORDINATES: similar to AA sequence:RefSeq:WP_006300145.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011697587.1
COORDINATES: similar to AA sequence:RefSeq:WP_012458953.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: similar to AA sequence:RefSeq:WP_012749381.1
GO:0004587 - ornithine-oxo-acid transaminase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016999.2
COORDINATES: similar to AA sequence:RefSeq:WP_010885103.1
tungsten cofactor oxidoreductase radical SAM maturase
COORDINATES: similar to AA sequence:RefSeq:WP_015859520.1
COORDINATES: similar to AA sequence:RefSeq:WP_013467596.1
aldehyde ferredoxin oxidoreductase family protein