Paraclostridium bifermentans strain DSM 14991 plasmid unnamed1, complete sequence.
Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae; Paraclostridium.
Complete genome sequence of Paraclostridium bifermentans DSM 14991
Submitted (14-JUL-2021) Biodiscovery Institute, School of Life Sciences, Heap Lab University of Nottingham, Biodiscovery Institute, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP079738.1.\nBacteria and source DNA available from DSMZ 14991.\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 :: JUL-2021\nAssembly Method :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/31/2022 04:11:43\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;\n repeat_region\nGenes (total) :: 3,530\nCDSs (total) :: 3,376\nGenes (coding) :: 3,356\nCDSs (with protein) :: 3,356\nGenes (RNA) :: 154\nrRNAs :: 16, 16, 16 (5S, 16S, 23S)\ncomplete rRNAs :: 16, 16, 16 (5S, 16S, 23S)\ntRNAs :: 102\nncRNAs :: 4\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 2 of 20\nPseudo Genes (incomplete) :: 13 of 20\nPseudo Genes (internal stop) :: 5 of 20\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003427882.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018590252.1
COORDINATES: protein motif:HMM:NF014566.2
type II CAAX endopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003703826.1
ABC transporter ATP-binding protein/permease
COORDINATES: similar to AA sequence:RefSeq:WP_003359868.1
COORDINATES: similar to AA sequence:RefSeq:WP_003493121.1
COORDINATES: similar to AA sequence:RefSeq:WP_010292852.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0031179 - peptide modification [Evidence IEA]
radical SAM/SPASM domain Clo7bot peptide maturase
COORDINATES: protein motif:HMM:TIGR04333.1
COORDINATES: similar to AA sequence:RefSeq:WP_010292855.1
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: similar to AA sequence:RefSeq:WP_000777410.1
COORDINATES: protein motif:HMM:NF024741.2
COORDINATES: similar to AA sequence:RefSeq:WP_000994771.1
COORDINATES: protein motif:HMM:NF015983.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003426457.1
COORDINATES: protein motif:HMM:NF016526.2
accessory gene regulator B family protein
COORDINATES: protein motif:HMM:NF025854.2
COORDINATES: protein motif:HMM:NF012301.2
LytTR family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014968100.1
COORDINATES: similar to AA sequence:RefSeq:WP_012704673.1
COORDINATES: similar to AA sequence:RefSeq:WP_010073702.1
COORDINATES: protein motif:HMM:NF016763.2
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_003355866.1
GO:0004815 - aspartate-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0006422 - aspartyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00230
T-box leader; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_018590115.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000282277.1
COORDINATES: similar to AA sequence:RefSeq:WP_018590113.1
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family glutamic-type intramembrane protease
COORDINATES: similar to AA sequence:RefSeq:WP_008680049.1
COORDINATES: protein motif:HMM:NF024881.2
COORDINATES: similar to AA sequence:RefSeq:WP_017561583.1
COORDINATES: similar to AA sequence:RefSeq:WP_006309043.1
COORDINATES: similar to AA sequence:RefSeq:WP_003361850.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF022641.2
COORDINATES: similar to AA sequence:RefSeq:WP_004460303.1
COORDINATES: similar to AA sequence:RefSeq:WP_003444750.1
COORDINATES: protein motif:HMM:NF024212.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007287509.1
COORDINATES: protein motif:HMM:NF038403.1
permease prefix domain 1-containing protein
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF025054.2
COORDINATES: similar to AA sequence:RefSeq:WP_007084167.1
COORDINATES: similar to AA sequence:RefSeq:WP_003229650.1
COORDINATES: similar to AA sequence:RefSeq:WP_004611327.1
COORDINATES: similar to AA sequence:RefSeq:WP_000556078.1
COORDINATES: protein motif:HMM:NF025159.2
COORDINATES: similar to AA sequence:RefSeq:WP_018589585.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_016208112.1
COORDINATES: similar to AA sequence:RefSeq:WP_008698118.1
COORDINATES: similar to AA sequence:RefSeq:WP_003477213.1
COORDINATES: similar to AA sequence:RefSeq:WP_004454415.1
COORDINATES: similar to AA sequence:RefSeq:WP_009888684.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]; GO:0030973 - molybdate ion binding [Evidence IEA]
GO:0015689 - molybdate ion transport [Evidence IEA]
molybdate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006188167.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00442
guanidine-I (ykkC/yxkD leader) riboswitch; Guanidine-I riboswitches control genes whose products are involved in modification or pumping out guanidine as a toxic compound from bacteria; This is class of guanidine riboswitches is based on the ykkC/yxkD leader; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_000118520.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
quaternary ammonium compound efflux SMR transporter SugE
COORDINATES: similar to AA sequence:RefSeq:WP_012058930.1
COORDINATES: similar to AA sequence:RefSeq:WP_004454608.1
COORDINATES: protein motif:HMM:NF024088.2
COORDINATES: similar to AA sequence:RefSeq:WP_013897851.1
COORDINATES: similar to AA sequence:RefSeq:WP_010277852.1
COORDINATES: similar to AA sequence:RefSeq:WP_003415588.1
COORDINATES: similar to AA sequence:RefSeq:WP_003456965.1
COORDINATES: similar to AA sequence:RefSeq:WP_016174881.1
COORDINATES: protein motif:HMM:NF019468.2
COORDINATES: similar to AA sequence:RefSeq:WP_009895104.1
COORDINATES: similar to AA sequence:RefSeq:WP_003426701.1
GO:0004821 - histidine-tRNA ligase activity [Evidence IEA]
GO:0006427 - histidyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011987610.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010293403.1
COORDINATES: similar to AA sequence:RefSeq:WP_012059922.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_003230776.1
COORDINATES: similar to AA sequence:RefSeq:WP_010295132.1
COORDINATES: similar to AA sequence:RefSeq:WP_019156629.1
COORDINATES: similar to AA sequence:RefSeq:WP_016178411.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018590733.1
COORDINATES: similar to AA sequence:RefSeq:WP_014519109.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_018591410.1
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_018592254.1
COORDINATES: protein motif:HMM:NF024698.2
COORDINATES: protein motif:HMM:NF016296.2
COORDINATES: protein motif:HMM:NF024812.2
COORDINATES: similar to AA sequence:RefSeq:WP_009170295.1
COORDINATES: similar to AA sequence:RefSeq:WP_003411643.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0016002 - sulfite reductase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
anaerobic sulfite reductase subunit AsrA
COORDINATES: similar to AA sequence:RefSeq:WP_003414985.1
anaerobic sulfite reductase subunit AsrB
COORDINATES: similar to AA sequence:RefSeq:WP_003449786.1
GO:0016002 - sulfite reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003420866.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011590494.1
COORDINATES: similar to AA sequence:RefSeq:WP_009897164.1
COORDINATES: similar to AA sequence:RefSeq:WP_012059909.1
COORDINATES: similar to AA sequence:RefSeq:WP_018590272.1
COORDINATES: similar to AA sequence:RefSeq:WP_018592723.1
formate/nitrite transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018592722.1
COORDINATES: similar to AA sequence:RefSeq:WP_003423354.1
COORDINATES: similar to AA sequence:RefSeq:WP_018592720.1
COORDINATES: similar to AA sequence:RefSeq:WP_018112794.1
COORDINATES: similar to AA sequence:RefSeq:WP_010073599.1
COORDINATES: protein motif:HMM:NF012503.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_018589577.1
COORDINATES: similar to AA sequence:RefSeq:WP_018589576.1
COORDINATES: similar to AA sequence:RefSeq:WP_004460591.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016695 - oxidoreductase activity, acting on hydrogen as donor [Evidence IEA]
COORDINATES: protein motif:HMM:NF024116.2
COORDINATES: similar to AA sequence:RefSeq:WP_007789797.1
COORDINATES: protein motif:HMM:NF027890.2
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003373553.1
COORDINATES: similar to AA sequence:RefSeq:WP_009894335.1
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: protein motif:HMM:TIGR00057.1
GO:0061710 - L-threonylcarbamoyladenylate synthase [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014793475.1
COORDINATES: protein motif:HMM:NF024917.2
COORDINATES: similar to AA sequence:RefSeq:WP_018590529.1