Thermobacillus composti KWC4 plasmid pTHECO01, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Thermobacillus.
Complete sequence of plasmid of Thermobacillus composti KWC4
Submitted (10-JAN-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003256.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089799\nSource DNA and organism available from Iain Anderson\n(IJAnderson@lbl.gov)\nContacts: Iain Anderson (IJAnderson@lbl.gov)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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 :: Thermobacillus composti KWC4\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Missing\nnum_replicons :: 2\nref_biomaterial :: DSM 18247, JCM 13945\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: 17625178\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04510\nType Strain :: Yes\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: composting reactor\nCell Shape :: Rod-shaped\nSporulation :: Sporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 50C\nSalinity :: Halotolerant\npH :: 5.6 - 10.1\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 :: 12/29/2022 01:33:36\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,098\nCDSs (total) :: 4,020\nGenes (coding) :: 3,904\nCDSs (with protein) :: 3,904\nGenes (RNA) :: 78\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 4\nPseudo Genes (total) :: 116\nCDSs (without protein) :: 116\nPseudo Genes (ambiguous residues) :: 0 of 116\nPseudo Genes (frameshifted) :: 48 of 116\nPseudo Genes (incomplete) :: 70 of 116\nPseudo Genes (internal stop) :: 11 of 116\nPseudo Genes (multiple problems) :: 12 of 116\nCRISPR Arrays :: 9\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013235.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF023069.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017727436.1
aspartyl-phosphate phosphatase Spo0E family protein
COORDINATES: protein motif:HMM:NF037909.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008786574.1
COORDINATES: protein motif:HMM:NF037035.2
COORDINATES: similar to AA sequence:RefSeq:WP_003542057.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: protein motif:HMM:TIGR00608.1
COORDINATES: protein motif:HMM:TIGR03831.1
COORDINATES: protein motif:HMM:NF025442.2
COORDINATES: protein motif:HMM:NF013954.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF024062.2
TcpE family conjugal transfer membrane protein
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: protein motif:HMM:NF025186.2
COORDINATES: protein motif:HMM:NF024108.2
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015256761.1
COORDINATES: similar to AA sequence:RefSeq:WP_015253877.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF020250.2
COORDINATES: similar to AA sequence:RefSeq:WP_018977651.1
Flp pilus assembly complex ATPase component TadA
COORDINATES: similar to AA sequence:RefSeq:WP_010345943.1
COORDINATES: similar to AA sequence:RefSeq:WP_009596008.1
COORDINATES: similar to AA sequence:RefSeq:WP_019007344.1
COORDINATES: protein motif:HMM:NF012613.2
S-layer homology domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005544129.1
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF012271.2
GO:0005515 - protein binding [Evidence IEA]
fibronectin type III domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015844920.1
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: similar to AA sequence:RefSeq:WP_015253876.1
COORDINATES: similar to AA sequence:RefSeq:WP_006446171.1
COORDINATES: protein motif:HMM:TIGR01439.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF020438.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010349896.1
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_011012468.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015253687.1
COORDINATES: similar to AA sequence:RefSeq:WP_008409492.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008881890.1
COORDINATES: similar to AA sequence:RefSeq:WP_007061545.1
winged helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:TIGR03558.1
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:NF012422.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015615797.1
COORDINATES: similar to AA sequence:RefSeq:WP_007127197.1
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: similar to AA sequence:RefSeq:WP_013919215.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_006675361.1
COORDINATES: similar to AA sequence:RefSeq:WP_015253349.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
ISNCY-like element ISTco5 family transposase
COORDINATES: protein motif:HMM:NF014516.2
COORDINATES: protein motif:HMM:NF013736.2
COORDINATES: protein motif:HMM:NF039653.1
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007781077.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_015253338.1
COORDINATES: protein motif:HMM:NF014177.2
COORDINATES: similar to AA sequence:RefSeq:WP_013921588.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024367.2