Prevotella dentalis DSM 3688 plasmid pPREDE02, complete sequence.
Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella.
Complete sequence of plasmid 2 of Prevotella dentalis DSM 3688
Submitted (29-FEB-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003371.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089468\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 :: Prevotella dentalis DSM 3688\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Host, Human oral microflora\nnum_replicons :: 4\nref_biomaterial :: ATCC 49559, CCUG 48288, DSM 3688, JCM 13448,\n NCTC 12043\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05356\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Human dental root canal\nHost Name :: Homo sapiens\nBody Sample Site :: Oral\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 37C\nGram Staining :: Gram-\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 :: 10/05/2022 10:04:35\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) :: 2,657\nCDSs (total) :: 2,579\nGenes (coding) :: 2,516\nCDSs (with protein) :: 2,516\nGenes (RNA) :: 78\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 2\nPseudo Genes (total) :: 63\nCDSs (without protein) :: 63\nPseudo Genes (ambiguous residues) :: 0 of 63\nPseudo Genes (frameshifted) :: 21 of 63\nPseudo Genes (incomplete) :: 38 of 63\nPseudo Genes (internal stop) :: 17 of 63\nPseudo Genes (multiple problems) :: 10 of 63\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_019236263.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF015839.2
COORDINATES: protein motif:HMM:NF015397.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002449121.1
MobC family plasmid mobilization relaxosome protein
COORDINATES: similar to AA sequence:RefSeq:WP_015365429.1
replication initiation factor domain-containing protein