Clostridium tagluense strain CM022 plasmid pCM022-180, complete sequence.
Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
Clostridia strains as spoilage organisms
Submitted (28-OCT-2021) Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nCP086157.1.\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 Date :: OCT-2021\nAssembly Method :: unicycler v. 1\nAssembly Name :: CM022\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 150x\nSequencing Technology :: Nanopore/Illumina miniseq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/08/2022 11:54:01\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\nGenes (total) :: 5,122\nCDSs (total) :: 4,979\nGenes (coding) :: 4,890\nCDSs (with protein) :: 4,890\nGenes (RNA) :: 143\nrRNAs :: 15, 15, 14 (5S, 16S, 23S)\ncomplete rRNAs :: 15, 15, 14 (5S, 16S, 23S)\ntRNAs :: 94\nncRNAs :: 5\nPseudo Genes (total) :: 89\nCDSs (without protein) :: 89\nPseudo Genes (ambiguous residues) :: 0 of 89\nPseudo Genes (frameshifted) :: 23 of 89\nPseudo Genes (incomplete) :: 72 of 89\nPseudo Genes (internal stop) :: 16 of 89\nPseudo Genes (multiple problems) :: 20 of 89\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: protein motif:HMM:NF014717.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011590398.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_003364778.1
COORDINATES: similar to AA sequence:RefSeq:WP_011860970.1
Catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
phosphoribosylaminoimidazolecarboxamide formyltransferase
COORDINATES: nucleotide motif:Rfam:14.4:RF01750
ZMP/ZTP riboswitches appear to regulate genes involved in one-carbon metabolism; Derived by automated computational analysis using gene prediction method: cmsearch.
5-aminoimidazole-4-carboxamide ribonucleotide (ZMP)/ 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-triphosphate (ZMT)
COORDINATES: protein motif:HMM:NF012711.2
GO:0004314 - [acyl-carrier-protein] S-malonyltransferase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: protein motif:HMM:NF013166.2
beta-ketoacyl synthase N-terminal-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014606813.1
ATP-dependent Clp protease proteolytic subunit
COORDINATES: protein motif:HMM:NF013786.2
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: protein motif:HMM:NF012584.2
COORDINATES: protein motif:HMM:NF014054.2
chorismate pyruvate-lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011968069.1
GO:0004803 - transposase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010964210.1
GO:0003849 - 3-deoxy-7-phosphoheptulonate synthase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007931067.1
4Fe-4S double cluster binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017210351.1
COORDINATES: similar to AA sequence:RefSeq:WP_003399097.1
COORDINATES: similar to AA sequence:RefSeq:WP_007062254.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_007062255.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007062256.1
COORDINATES: similar to AA sequence:RefSeq:WP_007062257.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518283.1
metal-dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004618901.1
COORDINATES: similar to AA sequence:RefSeq:WP_003520743.1
GO:0015093 - ferrous iron transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011987542.1
COORDINATES: similar to AA sequence:RefSeq:WP_007785668.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF019170.2
COORDINATES: similar to AA sequence:RefSeq:WP_011969134.1
COORDINATES: similar to AA sequence:RefSeq:WP_017211038.1
rRNA adenine N-6-methyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009888452.1
COORDINATES: similar to AA sequence:RefSeq:WP_013758003.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
TfoX/Sxy family DNA transformation protein
COORDINATES: similar to AA sequence:RefSeq:WP_015592364.1
COORDINATES: protein motif:HMM:NF024854.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF025633.2
COORDINATES: similar to AA sequence:RefSeq:WP_006353365.1
COORDINATES: protein motif:HMM:NF037406.2
COORDINATES: similar to AA sequence:RefSeq:WP_010235146.1
COORDINATES: similar to AA sequence:RefSeq:WP_014968609.1
COORDINATES: protein motif:HMM:NF014660.2
GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_010234566.1
COORDINATES: similar to AA sequence:RefSeq:WP_019279115.1
TipAS antibiotic-recognition domain-containing protein
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:NF025054.2
COORDINATES: similar to AA sequence:RefSeq:WP_006718408.1
COORDINATES: similar to AA sequence:RefSeq:WP_011987317.1
GO:0016740 - transferase activity [Evidence IEA]
Vat family streptogramin A O-acetyltransferase
COORDINATES: protein motif:HMM:NF012307.2
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019392528.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_007782531.1
COORDINATES: protein motif:HMM:NF019984.2
group II intron maturase-specific domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017211905.1
COORDINATES: protein motif:HMM:NF013625.2
peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF022413.2
COORDINATES: protein motif:HMM:NF033592.1
COORDINATES: similar to AA sequence:RefSeq:WP_012858454.1
GO:0004478 - methionine adenosyltransferase activity [Evidence IEA]
GO:0006556 - S-adenosylmethionine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013078.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012869.2
COORDINATES: protein motif:HMM:NF012879.2
COORDINATES: similar to AA sequence:RefSeq:WP_002601091.1
COORDINATES: protein motif:HMM:NF015983.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016571.2
COORDINATES: similar to AA sequence:RefSeq:WP_002205086.1
COORDINATES: similar to AA sequence:RefSeq:WP_014277677.1
COORDINATES: similar to AA sequence:RefSeq:WP_015043757.1
COORDINATES: similar to AA sequence:RefSeq:WP_005585568.1
COORDINATES: protein motif:HMM:TIGR00350.1
COORDINATES: similar to AA sequence:RefSeq:WP_019420768.1
COORDINATES: similar to AA sequence:RefSeq:WP_017895125.1
COORDINATES: similar to AA sequence:RefSeq:WP_007059922.1
COORDINATES: protein motif:HMM:NF013672.2
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017751464.1
COORDINATES: similar to AA sequence:RefSeq:WP_012058402.1
COORDINATES: protein motif:HMM:NF019844.2
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: protein motif:HMM:NF012245.2
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011967633.1
COORDINATES: protein motif:HMM:NF022373.2
COORDINATES: similar to AA sequence:RefSeq:WP_013726328.1
COORDINATES: similar to AA sequence:RefSeq:WP_003376628.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02937.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF024803.2
COORDINATES: similar to AA sequence:RefSeq:WP_006097091.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017413390.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988274.1
COORDINATES: similar to AA sequence:RefSeq:WP_007064307.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890861.1
COORDINATES: protein motif:HMM:NF022077.2
COORDINATES: similar to AA sequence:RefSeq:WP_017825063.1
COORDINATES: protein motif:HMM:NF024711.2
COORDINATES: similar to AA sequence:RefSeq:WP_017895001.1
COORDINATES: similar to AA sequence:RefSeq:WP_014826644.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]
GO:0046500 - S-adenosylmethionine metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_011722215.1
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032592430.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012446723.1
COORDINATES: similar to AA sequence:RefSeq:WP_007062556.1
COORDINATES: similar to AA sequence:RefSeq:WP_003375459.1
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: protein motif:HMM:NF013421.2
COORDINATES: similar to AA sequence:RefSeq:WP_002157862.1
COORDINATES: similar to AA sequence:RefSeq:WP_012343258.1
COORDINATES: similar to AA sequence:RefSeq:WP_012424406.1
COORDINATES: protein motif:HMM:NF014826.2
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010075185.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011722898.1
COORDINATES: similar to AA sequence:RefSeq:WP_014520644.1
lantibiotic immunity ABC transporter MutG family permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011949125.1
lantibiotic immunity ABC transporter MutE/EpiE family permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007060638.1
lantibiotic protection ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003426711.1
COORDINATES: protein motif:HMM:NF015368.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008827383.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015614995.1