Phocaeicola salanitronis DSM 18170 plasmid pBACSA01, complete sequence.
Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Phocaeicola.
The complete sequence of plasmid1 of Bacteroides salanitronis DSM 18170
Submitted (17-FEB-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002531.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087335\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 :: Bacteroides salanitronis BL78, DSM 18170\ncollection_date :: isolated by P. T. N. Lan\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Japan\nenvironment :: Host\nnum_replicons :: 4\nref_biomaterial :: DSM 18170, CCUG 54637, JCM 13657\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: 17158987\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04003\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: caecum of chicken\nHost Name :: caecum of healthy chicken\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 37CC\nGram Staining :: Gram-\nDiseases :: None\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 09:37:47\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) :: 3,770\nCDSs (total) :: 3,668\nGenes (coding) :: 3,594\nCDSs (with protein) :: 3,594\nGenes (RNA) :: 102\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 82\nncRNAs :: 2\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 13 of 74\nPseudo Genes (incomplete) :: 58 of 74\nPseudo Genes (internal stop) :: 11 of 74\nPseudo Genes (multiple problems) :: 7 of 74\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_007559113.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008765224.1
COORDINATES: similar to AA sequence:RefSeq:WP_007856468.1
COORDINATES: similar to AA sequence:RefSeq:WP_008675930.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199143.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199144.1
COORDINATES: similar to AA sequence:RefSeq:WP_008671657.1
COORDINATES: similar to AA sequence:RefSeq:WP_008765218.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008765216.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199149.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647321.1
COORDINATES: similar to AA sequence:RefSeq:WP_007559134.1
COORDINATES: similar to AA sequence:RefSeq:WP_008675920.1
COORDINATES: similar to AA sequence:RefSeq:WP_005799219.1
COORDINATES: similar to AA sequence:RefSeq:WP_013063035.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647331.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647332.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647334.1
COORDINATES: protein motif:HMM:NF024745.2
COORDINATES: similar to AA sequence:RefSeq:WP_007559152.1
COORDINATES: similar to AA sequence:RefSeq:WP_004295336.1
COORDINATES: protein motif:HMM:NF015648.2
COORDINATES: similar to AA sequence:RefSeq:WP_011199162.1
COORDINATES: similar to AA sequence:RefSeq:WP_008671625.1
topoisomerase C-terminal repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004295339.1
COORDINATES: similar to AA sequence:RefSeq:WP_004295340.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647355.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004295346.1
COORDINATES: protein motif:HMM:NF015935.2
COORDINATES: similar to AA sequence:RefSeq:WP_008779785.1
COORDINATES: similar to AA sequence:RefSeq:WP_005942704.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011264142.1
COORDINATES: similar to AA sequence:RefSeq:WP_007660158.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004295357.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_004295359.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_008765230.1
COORDINATES: similar to AA sequence:RefSeq:WP_008765225.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF037081.2
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_005799260.1
COORDINATES: similar to AA sequence:RefSeq:WP_008782593.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007562419.1
COORDINATES: similar to AA sequence:RefSeq:WP_005868776.1
COORDINATES: similar to AA sequence:RefSeq:WP_007757018.1
COORDINATES: similar to AA sequence:RefSeq:WP_004295368.1