Planctopirus limnophila DSM 3776 plasmid pPLIM01, complete sequence.
Bacteria; Planctomycetota; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctopirus.
Complete genome sequence of Planctomyces limnophilus type strain (Mu 290)
The complete plasmid of Planctomyces limnophilus DSM 3776
Submitted (09-SEP-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001745.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083246\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 :: Planctomyces limnophilus DSM 3776\nCulture Collection ID :: DSM 3776, ATCC 43296, IFAM 1008\nGOLD Stamp ID :: Gi02301\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: GeneMark\nIsolation Site :: Surface water\nOxygen Requirement :: Aerobe\nCell Shape :: Sphere-shaped\nMotility :: Motile\nTemperature Range :: Mesophile\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Fresh water, Marine\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/25/2022 09:45:08\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;\n repeat_region\nGenes (total) :: 4,109\nCDSs (total) :: 4,035\nGenes (coding) :: 4,015\nCDSs (with protein) :: 4,015\nGenes (RNA) :: 74\nrRNAs :: 1, 2, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 2, 1 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 0 of 20\nPseudo Genes (incomplete) :: 20 of 20\nPseudo Genes (internal stop) :: 2 of 20\nPseudo Genes (multiple problems) :: 2 of 20\nCRISPR Arrays :: 1\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:NF013964.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
HNH endonuclease signature motif containing protein
COORDINATES: protein motif:HMM:NF015321.2
COORDINATES: protein motif:HMM:TIGR01537.1
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF012783.2
COORDINATES: protein motif:HMM:TIGR01554.2
COORDINATES: protein motif:HMM:TIGR02215.1
GO:0016032 - viral process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01563.1
COORDINATES: protein motif:HMM:NF027776.2
COORDINATES: protein motif:HMM:NF040129.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF014177.2
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0032775 - DNA methylation on adenine [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_004806691.1
COORDINATES: similar to AA sequence:RefSeq:WP_020402232.1
COORDINATES: similar to AA sequence:RefSeq:WP_017483405.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF019000.2
host-nuclease inhibitor Gam family protein