Pseudonocardia dioxanivorans CB1190 plasmid pPSED03, complete sequence.
Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae; Pseudonocardia.
Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190
Submitted (16-MAR-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002598.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083663\nSource DNA and organism available from Shaily Mahendra\n(mahendra@seas.ucla.edu)\nContacts: Shaily Mahendra (mahendra@seas.ucla.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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 :: Pseudonocardia dioxanivorans CB1190\ncollection_date :: Missing\nlat_lon :: 34.299366 -79.876714\ndepth :: Missing\nalt_elev :: Missing\ncountry :: USA\nenvironment :: Sludge, Fresh water\nnum_replicons :: 4\nref_biomaterial :: ATCC 55486, DSM 44775\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 :: Gi02043\nType Strain :: Yes\nGreengenes ID :: 91804\nIsolation Site :: Industrial sludge contaminated with\n 1,4-dioxane\nIsolation Comments :: isolated by RE Parales, JA Romesser, for\n Celgene Corporation\nTemperature Range :: Mesophile\nTemperature Optimum :: 30CC\nGram Staining :: Gram+\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: 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 :: 12/08/2022 11:21:14\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,057\nCDSs (total) :: 6,998\nGenes (coding) :: 6,859\nCDSs (with protein) :: 6,859\nGenes (RNA) :: 59\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 139\nCDSs (without protein) :: 139\nPseudo Genes (ambiguous residues) :: 0 of 139\nPseudo Genes (frameshifted) :: 36 of 139\nPseudo Genes (incomplete) :: 114 of 139\nPseudo Genes (internal stop) :: 5 of 139\nPseudo Genes (multiple problems) :: 15 of 139\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
industrial sludge contaminated with 1,4-dioxane
type strain of Pseudonocardia dioxanivorans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:TIGR01613.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: protein motif:HMM:NF022388.2