Oceanithermus profundus DSM 14977 plasmid pOCEPR01, complete sequence.
Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Oceanithermus.
Complete genome sequence of Oceanithermus profundus type strain (506)
Submitted (23-NOV-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002362.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4086262\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 :: Oceanithermus profundus 506, DSM 14977\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Pacific Ocean\nenvironment :: Deep sea, Hydrothermal vent, Marine\nnum_replicons :: 2\nref_biomaterial :: DSM 14977, VKM B-2274\nbiotic_relationship :: Free living\ntrophic_level :: Chemoorganoheterotroph, Lithoheterotroph,\n Organotroph\nrel_to_oxygen :: Microaerophilic\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02932\nType Strain :: Yes\nGreengenes ID :: 20463\nFunding Program :: DOE-GEBA 2009\nIsolation Site :: Deep-sea hot vent; 13N, East Pacific Rise\nIsolation Comments :: isolated by M. L. Miroshnichenko\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nTemperature Range :: Thermophile\nTemperature Optimum :: 60C\npH :: 7.5\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 :: 05/02/2023 01:29:52\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) :: 2,458\nCDSs (total) :: 2,402\nGenes (coding) :: 2,392\nCDSs (with protein) :: 2,392\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 10\nCDSs (without protein) :: 10\nPseudo Genes (ambiguous residues) :: 0 of 10\nPseudo Genes (frameshifted) :: 2 of 10\nPseudo Genes (incomplete) :: 7 of 10\nPseudo Genes (internal stop) :: 1 of 10\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:TIGR01907.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
type I-E CRISPR-associated protein Cas6/Cse3/CasE
COORDINATES: protein motif:HMM:NF021240.2
type I-E CRISPR-associated protein Cas5/CasD
COORDINATES: protein motif:HMM:NF020902.2
type I-E CRISPR-associated protein Cas7/Cse4/CasC
COORDINATES: protein motif:HMM:NF021034.2
type I-E CRISPR-associated protein Cse2/CasB
COORDINATES: protein motif:HMM:NF021030.2
type I-E CRISPR-associated protein Cse1/CasA
COORDINATES: similar to AA sequence:RefSeq:WP_014630240.1
GO:0008829 - dCTP deaminase activity [Evidence IEA]
GO:0009394 - 2'-deoxyribonucleotide metabolic process [Evidence IEA]
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:NF039653.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF019997.2
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: similar to AA sequence:RefSeq:WP_013458110.1
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
adenosylcobalamin-dependent ribonucleoside-diphosphate reductase
COORDINATES: protein motif:HMM:NF014177.2
COORDINATES: similar to AA sequence:RefSeq:WP_018111164.1
GO:0050797 - thymidylate synthase (FAD) activity [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
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_018314959.1
COORDINATES: similar to AA sequence:RefSeq:WP_003043825.1
COORDINATES: protein motif:HMM:NF024601.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF037202.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
type ISP restriction/modification enzyme
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024158.2
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_013159816.1
COORDINATES: similar to AA sequence:RefSeq:WP_015715984.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF003745.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
ATP-dependent Clp protease ATP-binding subunit ClpX
COORDINATES: similar to AA sequence:RefSeq:WP_011173990.1
GO:0043107 - type IV pilus-dependent motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF024754.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012613.2
S-layer homology domain-containing protein
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:NF013793.2
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: protein motif:HMM:NF014273.2
ParB/Srx family N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: protein motif:HMM:NF040318.1
COORDINATES: similar to AA sequence:RefSeq:WP_013012821.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF025186.2
COORDINATES: protein motif:HMM:NF019575.2
GO:0005886 - plasma membrane [Evidence IEA]
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF012485.2
secretin N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012652.2
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: protein motif:HMM:NF016024.2
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF021503.2
COORDINATES: similar to AA sequence:RefSeq:WP_018462154.1
COORDINATES: similar to AA sequence:RefSeq:WP_014629805.1