Singulisphaera acidiphila DSM 18658 plasmid pSINAC01, complete sequence.
Bacteria; Planctomycetota; Planctomycetia; Isosphaerales; Isosphaeraceae; Singulisphaera.
Complete sequence of plasmid 1 of Singulisphaera acidiphila DSM 18658
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\nCP003365.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089469\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 :: Singulisphaera acidiphila DSM 18658\ncollection_date :: 2008\nlat_lon :: 58.233 36.2\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Russia\nenvironment :: Acidic wetlands\nnum_replicons :: 4\nref_biomaterial :: DSM 18658, ATCC BAA-1392, VKM B-2454\nbiotic_relationship :: Missing\ntrophic_level :: Missing\nrel_to_oxygen :: Microaerophilic\nisol_growth_condt :: 18450711\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05834\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Sphagnum peat sampled from the bog\n Obukhovskoe (acidic wetland)\nCell Shape :: Sphere-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nTemperature Optimum :: 20-26C\npH :: 5 - 6.2\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 :: 09/25/2022 10:35:52\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) :: 7,336\nCDSs (total) :: 7,237\nGenes (coding) :: 7,158\nCDSs (with protein) :: 7,158\nGenes (RNA) :: 99\nrRNAs :: 8, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 8, 8 (5S, 16S, 23S)\ntRNAs :: 71\nncRNAs :: 4\nPseudo Genes (total) :: 79\nCDSs (without protein) :: 79\nPseudo Genes (ambiguous residues) :: 0 of 79\nPseudo Genes (frameshifted) :: 23 of 79\nPseudo Genes (incomplete) :: 58 of 79\nPseudo Genes (internal stop) :: 11 of 79\nPseudo Genes (multiple problems) :: 12 of 79\nCRISPR Arrays :: 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
sphagnum peat from the bog Obukhovskoe (acidic wetland)
type strain of Singulisphaera acidiphila
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_015250666.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015245556.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015250668.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250669.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_015250670.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250672.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_015250673.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250674.1
COORDINATES: similar to AA sequence:RefSeq:WP_002653617.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_015250676.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998883.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250678.1
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015250679.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250680.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250681.1
PSD1 and planctomycete cytochrome C domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015250682.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250683.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250684.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250685.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250686.1
COORDINATES: similar to AA sequence:RefSeq:WP_018617263.1
COORDINATES: protein motif:HMM:NF025011.2
helicase-associated domain-containing protein
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_015244204.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250690.1
COORDINATES: similar to AA sequence:RefSeq:WP_015250691.1