Clostridium baratii strain CDC51267 plasmid pNPD11_1, complete sequence.
Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
Submitted (28-FEB-2017) BioScience B11, Los Alamos National Laboratory, PO Box 1663 M888, Los Alamos, NM 87545, USA
Submitted (22-JAN-2016) BioScience B11, Los Alamos National Laboratory, PO Box 1663 M888, Los Alamos, NM 87545, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP014203.1.\nSource DNA available from Shannon Johnson.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Velvet v. 1.2.08; HGAP v. 3; Phrap v. 4.24\nGenome Coverage :: 342x; 357x\nSequencing Technology :: Illumina; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 08:30:12\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) :: 3,112\nCDSs (total) :: 2,995\nGenes (coding) :: 2,990\nCDSs (with protein) :: 2,990\nGenes (RNA) :: 117\nrRNAs :: 11, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 10, 10 (5S, 16S, 23S)\ntRNAs :: 82\nncRNAs :: 4\nPseudo Genes (total) :: 5\nCDSs (without protein) :: 5\nPseudo Genes (ambiguous residues) :: 0 of 5\nPseudo Genes (frameshifted) :: 0 of 5\nPseudo Genes (incomplete) :: 4 of 5\nPseudo Genes (internal stop) :: 1 of 5\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_095889389.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003372331.1
GO:0005576 - extracellular region [Evidence IEA]
GO:0004222 - metalloendopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003409822.1
neurotoxin-associated TULIP family protein P47
COORDINATES: similar to AA sequence:RefSeq:WP_011987706.1
COORDINATES: similar to AA sequence:RefSeq:WP_012703709.1
COORDINATES: similar to AA sequence:RefSeq:WP_012720205.1
COORDINATES: similar to AA sequence:RefSeq:WP_003374241.1
COORDINATES: protein motif:HMM:NF016432.2
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_007493676.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003451037.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422164.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF004046.0
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015390614.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF024487.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF016159.2
RepB family plasmid replication initiator protein
COORDINATES: protein motif:HMM:NF014786.2
COORDINATES: protein motif:HMM:NF024367.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003896 - DNA primase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
CHC2 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004460194.1
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR02937.1
COORDINATES: protein motif:HMM:NF039493.1
COORDINATES: protein motif:HMM:NF024078.2
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF013073.2
COORDINATES: protein motif:HMM:NF012415.2
COORDINATES: protein motif:HMM:NF037639.2
SpaA isopeptide-forming pilin-related protein
COORDINATES: protein motif:HMM:TIGR01076.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:NF024787.2
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019612.2
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013500.2
COORDINATES: similar to AA sequence:RefSeq:WP_004456622.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF040570.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF015102.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003899 - DNA-directed 5'-3' RNA polymerase activity [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]
DNA-directed RNA polymerase subunit alpha C-terminal domain-containing protein