Deinococcus peraridilitoris DSM 19664 plasmid pDEIPE02, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Complete sequence of plasmid 2 of Deinococcus peraridilitoris DSM 19664
Submitted (07-MAR-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003384.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087340\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 peraridilitoris DSM 19664\ncollection_date :: 2007\nlat_lon :: -24.60 -69.53\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Chile\nenvironment :: Soil\nnum_replicons :: 3\nref_biomaterial :: DSM 19664, CIP 109416, KR-200, LMG 22246\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: 17625166\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04183\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Arid soil collected from a coastal desert\n north of Antofagasta in Chile\nCell Shape :: Coccus-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nTemperature Optimum :: 30C\npH :: 6.5 - 8.0\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/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 01:25:21\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) :: 4,428\nCDSs (total) :: 4,365\nGenes (coding) :: 4,294\nCDSs (with protein) :: 4,294\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) :: 71\nCDSs (without protein) :: 71\nPseudo Genes (ambiguous residues) :: 0 of 71\nPseudo Genes (frameshifted) :: 27 of 71\nPseudo Genes (incomplete) :: 51 of 71\nPseudo Genes (internal stop) :: 11 of 71\nPseudo Genes (multiple problems) :: 16 of 71\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Arid soil collected from a coastal desert north of Antofagasta in Chile
type strain of Deinococcus peraridilitoris
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012742.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013157178.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013157177.1
COORDINATES: similar to AA sequence:RefSeq:WP_018466416.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015917990.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014629618.1
GO:0004555 - alpha,alpha-trehalase activity [Evidence IEA]
GO:0005991 - trehalose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013646695.1
COORDINATES: similar to AA sequence:RefSeq:WP_013558209.1
COORDINATES: similar to AA sequence:RefSeq:WP_013157826.1
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
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.
nitrilase-related carbon-nitrogen hydrolase
COORDINATES: protein motif:HMM:TIGR01525.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF040326.1
COORDINATES: similar to AA sequence:RefSeq:WP_019010851.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002628428.1
COORDINATES: protein motif:HMM:NF024975.2
COORDINATES: similar to AA sequence:RefSeq:WP_010738846.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF028237.2
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_010889480.1
COORDINATES: similar to AA sequence:RefSeq:WP_011352236.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011550251.1
COORDINATES: similar to AA sequence:RefSeq:WP_020013373.1
COORDINATES: similar to AA sequence:RefSeq:WP_013555253.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015235169.1
COORDINATES: similar to AA sequence:RefSeq:WP_012507828.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_009182217.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF033516.0
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: similar to AA sequence:RefSeq:WP_011530226.1
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_003163686.1
COORDINATES: similar to AA sequence:RefSeq:WP_002731230.1
COORDINATES: similar to AA sequence:RefSeq:WP_015231660.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015231248.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_007921833.1
COORDINATES: similar to AA sequence:RefSeq:WP_012891563.1
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014686401.1
COORDINATES: protein motif:HMM:NF020811.2
COORDINATES: protein motif:HMM:NF012451.2
COORDINATES: protein motif:HMM:NF025056.2
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015231360.1
COORDINATES: protein motif:HMM:NF024423.2
COORDINATES: protein motif:HMM:NF033591.1
COORDINATES: similar to AA sequence:RefSeq:WP_007916766.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF019350.2
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
GAF domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: protein motif:HMM:NF037437.2
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015231509.1