Deinococcus geothermalis DSM 11300 plasmid pDGEO02, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Complete sequence of Plasmid2 pDGEO02 of Deinococcus geothermalis DSM 11300
Submitted (11-OCT-2007) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000856.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 3634504\nSource DNA available from Michael J Daly (mdaly@usuhs.mil)\nBacteria available from DSMZ: DSM 11300\nContacts: Michael J Daly (mdaly@usuhs.mil)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\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##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/28/2022 01:46:19\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) :: 3,167\nCDSs (total) :: 3,104\nGenes (coding) :: 3,046\nCDSs (with protein) :: 3,046\nGenes (RNA) :: 63\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 14 of 58\nPseudo Genes (incomplete) :: 47 of 58\nPseudo Genes (internal stop) :: 11 of 58\nPseudo Genes (multiple problems) :: 9 of 58\nCRISPR Arrays :: 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012173261.1
incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008274353.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010477003.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011525746.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS4-like element ISDge11 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012695021.1
GO:0004803 - transposase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS6-like element ISDge13 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011531399.1
COORDINATES: similar to AA sequence:RefSeq:WP_018467724.1
COORDINATES: similar to AA sequence:RefSeq:WP_013159573.1
COORDINATES: similar to AA sequence:RefSeq:WP_013159572.1
COORDINATES: similar to AA sequence:RefSeq:WP_013159571.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012742.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011688311.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011609.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: protein motif:HMM:NF024487.2
COORDINATES: similar to AA sequence:RefSeq:WP_011530228.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612299.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS1-like element ISDge2 family transposase
COORDINATES: protein motif:HMM:NF024685.2
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_008872600.1
COORDINATES: protein motif:HMM:NF019334.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF040318.1
COORDINATES: similar to AA sequence:RefSeq:WP_015235802.1
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]
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF013884.2
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF020387.2
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:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_019009593.1
COORDINATES: similar to AA sequence:RefSeq:WP_019010866.1
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683995.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525687.1
COORDINATES: protein motif:HMM:NF014477.2
COORDINATES: protein motif:HMM:NF013918.2
ferric reductase-like transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013859736.1
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_013012334.1
COORDINATES: protein motif:HMM:NF024245.2
helix-hairpin-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012493.2
C-terminal helicase domain-containing protein
COORDINATES: protein motif:HMM:NF025052.2
COORDINATES: protein motif:HMM:NF040138.1
COORDINATES: protein motif:HMM:NF016736.2
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173303.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011531391.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011531389.1
COORDINATES: protein motif:HMM:NF018933.2
NUMOD3 domain-containing DNA-binding protein
COORDINATES: protein motif:HMM:NF017673.2
phage terminase large subunit family protein
COORDINATES: protein motif:HMM:NF014786.2
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024952.2
COORDINATES: protein motif:HMM:NF012403.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173259.1
IS701-like element ISDge14 family transposase
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: protein motif:HMM:NF020811.2
COORDINATES: protein motif:HMM:NF017009.2
COORDINATES: protein motif:HMM:NF037660.2
COORDINATES: similar to AA sequence:RefSeq:WP_011525616.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014432429.1
COORDINATES: similar to AA sequence:RefSeq:WP_013159718.1
COORDINATES: similar to AA sequence:RefSeq:WP_020009774.1
COORDINATES: similar to AA sequence:RefSeq:WP_013159720.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012452254.1
COORDINATES: similar to AA sequence:RefSeq:WP_015744870.1
COORDINATES: similar to AA sequence:RefSeq:WP_006410415.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020886764.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_011479396.1
COORDINATES: protein motif:HMM:NF013752.2