Treponema succinifaciens DSM 2489 plasmid pTRESU01, complete sequence.
Bacteria; Spirochaetota; Spirochaetia; Spirochaetales; Treponemataceae; Treponema.
The complete genome of plasmid of Treponema succinifaciens DSM 2489
Submitted (01-APR-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002632.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089450\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 :: Treponema succinifaciens DSM 2489\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Host\nnum_replicons :: 2\nref_biomaterial :: DSM 2489\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 :: Gi05836\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: colon of swine\nCell Shape :: Helical-shaped\nMotility :: Motile\nTemperature Range :: Mesophile\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 :: 05/02/2023 01:48:38\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,837\nCDSs (total) :: 2,772\nGenes (coding) :: 2,754\nCDSs (with protein) :: 2,754\nGenes (RNA) :: 65\nrRNAs :: 5, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 4, 4 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 18\nCDSs (without protein) :: 18\nPseudo Genes (ambiguous residues) :: 0 of 18\nPseudo Genes (frameshifted) :: 1 of 18\nPseudo Genes (incomplete) :: 15 of 18\nPseudo Genes (internal stop) :: 4 of 18\nPseudo Genes (multiple problems) :: 2 of 18\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: similar to AA sequence:RefSeq:WP_018527166.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016736.2
COORDINATES: similar to AA sequence:RefSeq:WP_020614518.1
COORDINATES: similar to AA sequence:RefSeq:WP_020614517.1
COORDINATES: protein motif:HMM:NF018565.2
COORDINATES: protein motif:HMM:NF021220.2
COORDINATES: similar to AA sequence:RefSeq:WP_013702739.1
COORDINATES: protein motif:HMM:NF013700.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019844.2
GO:0070064 - proline-rich region binding [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016595.2
COORDINATES: protein motif:HMM:NF033516.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF012708.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF016845.2
phage tail sheath subtilisin-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020614508.1
COORDINATES: similar to AA sequence:RefSeq:WP_020614507.1
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013700536.1
contractile injection system protein, VgrG/Pvc8 family
COORDINATES: protein motif:HMM:NF025611.2
COORDINATES: similar to AA sequence:RefSeq:WP_013702721.1
prealbumin-like fold domain-containing protein
COORDINATES: protein motif:HMM:NF023120.2
COORDINATES: similar to AA sequence:RefSeq:WP_013702735.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700549.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700537.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700538.1
COORDINATES: similar to AA sequence:RefSeq:WP_013702731.1
COORDINATES: protein motif:HMM:NF026945.2
polymorphic toxin type 44 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013702724.1
COORDINATES: similar to AA sequence:RefSeq:WP_013702719.1
COORDINATES: protein motif:HMM:NF024747.2
4Fe-4S cluster-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018527184.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013702684.1
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013702752.1
COORDINATES: similar to AA sequence:RefSeq:WP_013702750.1
COORDINATES: protein motif:HMM:NF024704.2
COORDINATES: protein motif:HMM:NF022657.2
COORDINATES: protein motif:HMM:NF024986.2
COORDINATES: similar to AA sequence:RefSeq:WP_013700390.1
COORDINATES: protein motif:HMM:NF025078.2
COORDINATES: protein motif:HMM:NF026870.2
polymorphic toxin type 30 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013701932.1
COORDINATES: similar to AA sequence:RefSeq:WP_013701933.1
COORDINATES: similar to AA sequence:RefSeq:WP_013701934.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: similar to AA sequence:RefSeq:WP_006443297.1
COORDINATES: similar to AA sequence:RefSeq:WP_006443296.1
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: similar to AA sequence:RefSeq:WP_009538362.1
COORDINATES: similar to AA sequence:RefSeq:WP_002761671.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF025019.2
COORDINATES: similar to AA sequence:RefSeq:WP_013701925.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013701922.1
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF033564.0
COORDINATES: similar to AA sequence:RefSeq:WP_013701920.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013701919.1
COORDINATES: similar to AA sequence:RefSeq:WP_002705581.1
COORDINATES: similar to AA sequence:RefSeq:WP_013701900.1
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_009106835.1
COORDINATES: similar to AA sequence:RefSeq:WP_009106831.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013260.2
COORDINATES: protein motif:HMM:NF037422.2
COORDINATES: protein motif:HMM:NF019997.2
ArdC-like ssDNA-binding domain-containing protein