Thermovibrio ammonificans HB-1 plasmid pTHEAM01, complete sequence.
Bacteria; Aquificota; Aquificae; Desulfurobacteriales; Desulfurobacteriaceae; Thermovibrio.
Complete sequence of plasmid of Thermovibrio ammonificans HB-1
Submitted (03-JAN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002445.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087345\nSource DNA and organism available from Costantino Vetriani\n(vetriani@marine.rutgers.edu)\nContacts: Costantino Vetriani (vetriani@marine.rutgers.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 :: Thermovibrio ammonificans HB-1, DSM 15698\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Deep sea, Fresh water, Hydrothermal vent,\n Marine\nnum_replicons :: 2\nref_biomaterial :: DSM 15698, JCM 12110\nbiotic_relationship :: Free living\ntrophic_level :: Chemolithoautotroph\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02061\nType Strain :: Yes\nGreengenes ID :: 83837\nIsolation Site :: Walls of an active deep-sea hydrothermal\n vent chimney on the East Pacific Rise at 9\n degrees 50'N\nCell Shape :: Rod-shaped\nMotility :: Motile\nTemperature Range :: Thermophile\nTemperature Optimum :: 60 - 80C\npH :: 5 - 7\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 :: 12/28/2022 01:09:20\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) :: 1,887\nCDSs (total) :: 1,829\nGenes (coding) :: 1,826\nCDSs (with protein) :: 1,826\nGenes (RNA) :: 58\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 3\nPseudo Genes (total) :: 3\nCDSs (without protein) :: 3\nPseudo Genes (ambiguous residues) :: 0 of 3\nPseudo Genes (frameshifted) :: 0 of 3\nPseudo Genes (incomplete) :: 3 of 3\nPseudo Genes (internal stop) :: 0 of 3\nCRISPR Arrays :: 8\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9 degrees 50' N
type strain of Thermovibrio ammonificans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF040179.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013633.2
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF013180.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF024108.2
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:TIGR01051.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF014244.2
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF019146.2
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021634.2
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF012485.2
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
secretin N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF015380.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF019934.2
COORDINATES: protein motif:HMM:TIGR02532.1
COORDINATES: protein motif:HMM:NF019575.2
COORDINATES: protein motif:HMM:NF024498.2
thioredoxin fold domain-containing protein
COORDINATES: protein motif:HMM:NF033788.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_010999604.1
COORDINATES: protein motif:HMM:NF016024.2
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]