Deinococcus proteolyticus MRP plasmid pDEIPR02, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T))
Submitted (18-FEB-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002538.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087341\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 :: Deinococcus proteolyticus MRP, DSM 20540\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Soil\nnum_replicons :: 5\nref_biomaterial :: DSM 20540, ATCC 35074, CCM 2703\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04185\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Faeces of Lama glama\nIsolation Comments :: isolated by M. Kobatake MRP\nHost Name :: Lama glama\nCell Shape :: Coccus-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nGram Staining :: Gram+\nPhenotypes :: Radiation resistant\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-Titanium, Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 02:11:33\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) :: 2,790\nCDSs (total) :: 2,732\nGenes (coding) :: 2,688\nCDSs (with protein) :: 2,688\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) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 17 of 44\nPseudo Genes (incomplete) :: 28 of 44\nPseudo Genes (internal stop) :: 4 of 44\nPseudo Genes (multiple problems) :: 4 of 44\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Deinococcus proteolyticus
COORDINATES: similar to AA sequence:RefSeq:WP_020717333.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
class I SAM-dependent DNA methyltransferase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF021190.2
COORDINATES: similar to AA sequence:RefSeq:WP_014682832.1
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_007427511.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [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: similar to AA sequence:RefSeq:WP_013554998.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013614160.1
COORDINATES: similar to AA sequence:RefSeq:WP_017664687.1
COORDINATES: protein motif:HMM:NF015377.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF025278.2
COORDINATES: protein motif:HMM:NF012610.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_014682864.1
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017569.2
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: similar to AA sequence:RefSeq:WP_027480237.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01448.1
GO:0004386 - helicase activity [Evidence IEA]
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:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_014682720.1
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615842.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615839.1
COORDINATES: protein motif:HMM:NF037081.2
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013159910.1
COORDINATES: similar to AA sequence:RefSeq:WP_018461885.1
GO:0004803 - transposase activity [Evidence IEA]
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_014682735.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018314959.1
COORDINATES: protein motif:HMM:NF012686.2
COORDINATES: protein motif:HMM:NF037233.2
COORDINATES: protein motif:HMM:NF014643.2
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615904.1
COORDINATES: protein motif:HMM:NF024980.2
winged helix-turn-helix domain-containing protein
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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:NF024975.2
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: similar to AA sequence:RefSeq:WP_010889332.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016107.2
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019009334.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013615355.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_019009310.1
COORDINATES: similar to AA sequence:RefSeq:WP_010889330.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_004095157.1
COORDINATES: similar to AA sequence:RefSeq:WP_019008660.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612299.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019587824.1
COORDINATES: similar to AA sequence:RefSeq:WP_019585218.1
COORDINATES: similar to AA sequence:RefSeq:WP_017362369.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009321.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000014 - single-stranded DNA endodeoxyribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019011229.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF037088.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: protein motif:HMM:NF021503.2
DUF2227 family putative metal-binding protein
COORDINATES: protein motif:HMM:NF012652.2
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01420.1
GO:0043107 - type IV pilus-dependent motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF016253.2
GO:0043683 - type IV pilus assembly [Evidence IEA]; GO:0043107 - type IV pilus-dependent motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF012485.2
type II and III secretion system protein
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF019575.2
COORDINATES: protein motif:HMM:NF012415.2
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013616066.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615998.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615997.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615993.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615989.1
COORDINATES: protein motif:HMM:NF020811.2
COORDINATES: protein motif:HMM:NF020302.2
DNA-directed RNA polymerase sigma-70 factor
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013616011.1
COORDINATES: protein motif:HMM:NF015736.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013555558.1
COORDINATES: similar to AA sequence:RefSeq:WP_015234965.1
COORDINATES: similar to AA sequence:RefSeq:WP_015234964.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014682753.1