Clostridium tyrobutyricum strain KCTC 5387 plasmid pCTK01, complete sequence.
Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses
Submitted (20-JAN-2016) Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehakro, Yuseong, Daejeon 34141, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP014171.1.\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##Genome-Assembly-Data-START##\nAssembly Method :: CLC Genomics Workbench v. 5.5.2\nReference-guided Assembly :: GCF_000429805.1, GCA_000392375.2,\n GCA_000974305.1\nGenome Coverage :: 224x\nSequencing Technology :: Ion Torrent\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 22:05:24\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) :: 3,156\nCDSs (total) :: 3,069\nGenes (coding) :: 3,020\nCDSs (with protein) :: 3,020\nGenes (RNA) :: 87\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 63\nncRNAs :: 5\nPseudo Genes (total) :: 49\nCDSs (without protein) :: 49\nPseudo Genes (ambiguous residues) :: 0 of 49\nPseudo Genes (frameshifted) :: 19 of 49\nPseudo Genes (incomplete) :: 34 of 49\nPseudo Genes (internal stop) :: 10 of 49\nPseudo Genes (multiple problems) :: 11 of 49\nCRISPR Arrays :: 2\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_003415108.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003414651.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004455436.1
COORDINATES: similar to AA sequence:RefSeq:WP_012961264.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017895193.1
type II toxin-antitoxin system Phd/YefM family antitoxin
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: similar to AA sequence:RefSeq:WP_015614996.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015614997.1
COORDINATES: similar to AA sequence:RefSeq:WP_017210183.1
COORDINATES: similar to AA sequence:RefSeq:WP_010234476.1
GO:0003796 - lysozyme activity [Evidence IEA]
GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA]; GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003441394.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_010890810.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890809.1
COORDINATES: similar to AA sequence:RefSeq:WP_006211846.1
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: similar to AA sequence:RefSeq:WP_003359749.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010782375.1
CagC family type IV secretion system protein
COORDINATES: protein motif:HMM:NF041427.1
TrsD/TraD family conjugative transfer protein
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF025081.2
COORDINATES: similar to AA sequence:RefSeq:WP_003242300.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:TIGR04540.1
COORDINATES: similar to AA sequence:RefSeq:WP_012102358.1
COORDINATES: protein motif:HMM:NF019149.2
COORDINATES: protein motif:HMM:NF012451.2
COORDINATES: similar to AA sequence:RefSeq:WP_015614845.1
COORDINATES: similar to AA sequence:RefSeq:WP_003374297.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_011948467.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_012704811.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015446 - ATPase-coupled arsenite transmembrane transporter activity [Evidence IEA]
GO:0071722 - detoxification of arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017752922.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025156.2
COORDINATES: similar to AA sequence:RefSeq:WP_012102877.1
COORDINATES: similar to AA sequence:RefSeq:WP_010233415.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009440487.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005336015.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF024685.2
anti-phage defense-associated sirtuin Dsr2
COORDINATES: similar to AA sequence:RefSeq:WP_010233454.1
COORDINATES: similar to AA sequence:RefSeq:WP_009173002.1
COORDINATES: similar to AA sequence:RefSeq:WP_010241105.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013624052.1
ATP-binding cassette domain-containing protein