Rhodothermus marinus DSM 4252 plasmid pRMAR01, complete sequence.
Bacteria; Rhodothermota; Rhodothermia; Rhodothermales; Rhodothermaceae; Rhodothermus.
Complete genome sequence of Rhodothermus marinus type strain (R-10)
The complete plasmid of Rhodothermus marinus DSM 4252
Submitted (27-OCT-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001808.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083220\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 :: Rhodothermus marinus R-10, DSM 4252\nCulture Collection ID :: DSM 4252, ATCC 43812\nGOLD Stamp ID :: Gi02303\nFunding Program :: DOE-GEBA 2007\nAssembly Method :: Newbler version 1.1.02.15, Phrap\nSequencing Depth :: 8.8x Sanger; 23.8x 454\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Submarine alkaline hot spring at Reykjanes\n in Iceland\nCollection Date :: 1988\nIsolation Country :: Iceland\nLatitude :: 63.88\nLongitude :: -22.5\nDepth :: 2-3 meters\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 65C\nSalinity :: Halophile\npH :: 7\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Hot spring, Marine\nEnergy Source :: Heterotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/16/2023 14:30:16\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) :: 2,974\nCDSs (total) :: 2,923\nGenes (coding) :: 2,910\nCDSs (with protein) :: 2,910\nGenes (RNA) :: 51\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 13\nCDSs (without protein) :: 13\nPseudo Genes (ambiguous residues) :: 0 of 13\nPseudo Genes (frameshifted) :: 0 of 13\nPseudo Genes (incomplete) :: 12 of 13\nPseudo Genes (internal stop) :: 1 of 13\nCRISPR Arrays :: 9\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:TIGR02621.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
type I-U CRISPR-associated helicase/endonuclease Cas3
COORDINATES: protein motif:HMM:TIGR02165.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02570.1
type I-U CRISPR-associated RAMP protein Csb1/Cas7u
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF024748.2
COORDINATES: protein motif:HMM:NF013661.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0042834 - peptidoglycan binding [Evidence IEA]
peptidoglycan recognition family protein
COORDINATES: protein motif:HMM:NF033709.1
COORDINATES: protein motif:HMM:NF026255.2
COORDINATES: protein motif:HMM:TIGR04183.1
COORDINATES: protein motif:HMM:NF013776.2
COORDINATES: similar to AA sequence:RefSeq:WP_014072535.1
type III-A CRISPR-associated RAMP protein Csm5
COORDINATES: similar to AA sequence:RefSeq:WP_014072536.1
type III-A CRISPR-associated RAMP protein Csm4
COORDINATES: similar to AA sequence:RefSeq:WP_014072537.1
type III-A CRISPR-associated RAMP protein Csm3
COORDINATES: similar to AA sequence:RefSeq:WP_014072538.1
type III-A CRISPR-associated protein Csm2
COORDINATES: similar to AA sequence:RefSeq:WP_012845303.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072540.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845305.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072541.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845307.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072543.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845309.1
TIGR02221 family CRISPR-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_012845310.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072544.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845312.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845313.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845314.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072545.1
CRISPR system precrRNA processing endoribonuclease RAMP protein Cas6
COORDINATES: similar to AA sequence:RefSeq:WP_014072546.1
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014072547.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014072548.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016246.2
COORDINATES: similar to AA sequence:RefSeq:WP_012845322.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072550.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072551.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845325.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072553.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845327.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845328.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845329.1
TIGR02710 family CRISPR-associated CARF protein
COORDINATES: similar to AA sequence:RefSeq:WP_014072558.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845332.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845333.1
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012844128.1
ribonuclease H-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014072560.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014072561.1
COORDINATES: similar to AA sequence:RefSeq:WP_012843691.1
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_012845339.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012845340.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF025469.2
COORDINATES: similar to AA sequence:RefSeq:WP_014072564.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012845343.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845344.1
COORDINATES: similar to AA sequence:RefSeq:WP_012844121.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012845346.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845347.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845348.1
COORDINATES: protein motif:HMM:NF025124.2
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF024954.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012845352.1
COORDINATES: protein motif:HMM:NF016330.2
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012845353.1
COORDINATES: similar to AA sequence:RefSeq:WP_014066970.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_012845356.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014072504.1
COORDINATES: similar to AA sequence:RefSeq:WP_014066972.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072506.1
COORDINATES: similar to AA sequence:RefSeq:WP_017293525.1
EcoRV family type II restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_017293524.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
Dam family site-specific DNA-(adenine-N6)-methyltransferase
COORDINATES: protein motif:HMM:NF037510.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF025625.2
COORDINATES: protein motif:HMM:NF033590.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014630471.1
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_014072518.1
type II toxin-antitoxin system prevent-host-death family antitoxin
AVAST type 2 anti-phage system protein Avs2
COORDINATES: similar to AA sequence:RefSeq:WP_014101551.1
COORDINATES: similar to AA sequence:RefSeq:WP_004361669.1