Vescimonas fastidiosa strain MM35 plasmid pMM35_02.
Bacteria; Firmicutes; Clostridia; Eubacteriales; Oscillospiraceae; Vescimonas.
Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces
Int. J. Syst. Evol. Microbiol. 71 (2021) In press
Submitted (03-SEP-2020) Contact:Yuko Shigeno RIKEN, Center for Brain Science; 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP023417.1.\nAnnotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).\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 :: Flye v. 2.6\nGenome Coverage :: 3121X\nSequencing Technology :: Oxford Nanopore Technologies MinION;\n Illumina Miseq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/16/2022 03:47:11\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) :: 2,427\nCDSs (total) :: 2,360\nGenes (coding) :: 2,298\nCDSs (with protein) :: 2,298\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 62\nCDSs (without protein) :: 62\nPseudo Genes (ambiguous residues) :: 0 of 62\nPseudo Genes (frameshifted) :: 30 of 62\nPseudo Genes (incomplete) :: 30 of 62\nPseudo Genes (internal stop) :: 5 of 62\nPseudo Genes (multiple problems) :: 3 of 62\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_015537354.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014116204.1
GO:0003747 - translation release factor activity [Evidence IEA]
GO:0006415 - translational termination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008977012.1
COORDINATES: similar to AA sequence:RefSeq:WP_015513727.1
sulfurtransferase-like selenium metabolism protein YedF
COORDINATES: similar to AA sequence:RefSeq:WP_004077665.1
GO:0004756 - selenide, water dikinase activity [Evidence IEA]
GO:0001887 - selenium compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012697.2
COORDINATES: similar to AA sequence:RefSeq:WP_008982303.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF015378.2
COORDINATES: similar to AA sequence:RefSeq:WP_005347114.1
COORDINATES: similar to AA sequence:RefSeq:WP_007590845.1
COORDINATES: protein motif:HMM:TIGR00545.1
GO:0017118 - lipoyltransferase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009535313.1
COORDINATES: similar to AA sequence:RefSeq:WP_009213592.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016992 - lipoate synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009107 - lipoate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005539012.1
COORDINATES: protein motif:HMM:NF033504.1
GO:0050043 - lactate racemase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012382.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013486106.1
COORDINATES: similar to AA sequence:RefSeq:WP_008754388.1
amino acid ABC transporter ATP-binding protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020839.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF012686.2
COORDINATES: protein motif:HMM:NF014476.2
COORDINATES: similar to AA sequence:RefSeq:WP_014119568.1
GO:0004019 - adenylosuccinate synthase activity [Evidence IEA]; GO:0005525 - GTP binding [Evidence IEA]
GO:0006164 - purine nucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014119570.1
GO:0004018 - N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006573824.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004065360.1
COORDINATES: similar to AA sequence:RefSeq:WP_007712699.1
COORDINATES: similar to AA sequence:RefSeq:WP_009298623.1
COORDINATES: similar to AA sequence:RefSeq:WP_007712704.1
COORDINATES: similar to AA sequence:RefSeq:WP_003499611.1
COORDINATES: similar to AA sequence:RefSeq:WP_009298617.1
COORDINATES: protein motif:HMM:NF039505.1
COORDINATES: similar to AA sequence:RefSeq:WP_006873396.1
COORDINATES: similar to AA sequence:RefSeq:WP_006873397.1
COORDINATES: similar to AA sequence:RefSeq:WP_016296073.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009298610.1
GO:0003676 - nucleic acid binding [Evidence IEA]
S1 RNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF019941.2
SpaA isopeptide-forming pilin-related protein
COORDINATES: protein motif:HMM:NF033902.0
SpaH/EbpB family LPXTG-anchored major pilin
COORDINATES: protein motif:HMM:NF033745.1
COORDINATES: similar to AA sequence:RefSeq:WP_008982246.1
COORDINATES: similar to AA sequence:RefSeq:WP_006873416.1
COORDINATES: protein motif:HMM:TIGR02937.1
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007712846.1
COORDINATES: similar to AA sequence:RefSeq:WP_009298587.1
COORDINATES: protein motif:HMM:NF019265.2
COORDINATES: similar to AA sequence:RefSeq:WP_009298583.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019239060.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501968.1
COORDINATES: similar to AA sequence:RefSeq:WP_005946396.1
COORDINATES: similar to AA sequence:RefSeq:WP_015553421.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005946400.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005946402.1
COORDINATES: similar to AA sequence:RefSeq:WP_005946404.1
COORDINATES: similar to AA sequence:RefSeq:WP_019679741.1
ferredoxin thioredoxin reductase catalytic beta chain
COORDINATES: similar to AA sequence:RefSeq:WP_005426676.1
COORDINATES: similar to AA sequence:RefSeq:WP_003864624.1
COORDINATES: similar to AA sequence:RefSeq:WP_005921786.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010965865.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024934.2
COORDINATES: protein motif:HMM:NF016430.2
COORDINATES: protein motif:HMM:NF025643.2
COORDINATES: similar to AA sequence:RefSeq:WP_012739118.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF027746.2
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF037417.2
dockerin type I repeat-containing protein
COORDINATES: protein motif:HMM:NF013156.2
GO:0030246 - carbohydrate binding [Evidence IEA]
GO:0000272 - polysaccharide catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021028.2
COORDINATES: protein motif:HMM:NF012622.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
dockerin type I domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005600924.1
COORDINATES: protein motif:HMM:NF013998.2
COORDINATES: protein motif:HMM:NF013961.2
transglutaminase-like domain-containing protein
COORDINATES: protein motif:HMM:NF024753.2
COORDINATES: similar to AA sequence:RefSeq:WP_009429484.1
COORDINATES: similar to AA sequence:RefSeq:WP_015553424.1
COORDINATES: similar to AA sequence:RefSeq:WP_005921781.1
COORDINATES: similar to AA sequence:RefSeq:WP_005921779.1
COORDINATES: similar to AA sequence:RefSeq:WP_005921775.1
COORDINATES: similar to AA sequence:RefSeq:WP_015536764.1
COORDINATES: similar to AA sequence:RefSeq:WP_013852041.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
ClbS/DfsB family four-helix bundle protein
COORDINATES: similar to AA sequence:RefSeq:WP_015514854.1
GO:0004791 - thioredoxin-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005344679.1
COORDINATES: similar to AA sequence:RefSeq:WP_002605420.1
COORDINATES: similar to AA sequence:RefSeq:WP_015565303.1
COORDINATES: similar to AA sequence:RefSeq:WP_015557300.1
COORDINATES: protein motif:HMM:NF023184.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004221190.1
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_016323186.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007037895.1
COORDINATES: similar to AA sequence:RefSeq:WP_006573637.1
COORDINATES: similar to AA sequence:RefSeq:WP_009257977.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003911 - DNA ligase (NAD+) activity [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013271820.1
COORDINATES: protein motif:HMM:NF025642.2
COORDINATES: similar to AA sequence:RefSeq:WP_009257971.1
COORDINATES: similar to AA sequence:RefSeq:WP_006771595.1
COORDINATES: similar to AA sequence:RefSeq:WP_009298703.1
COORDINATES: protein motif:HMM:TIGR01448.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006771599.1
COORDINATES: similar to AA sequence:RefSeq:WP_006573485.1
COORDINATES: similar to AA sequence:RefSeq:WP_009323456.1
COORDINATES: similar to AA sequence:RefSeq:WP_006573483.1
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_014795375.1
COORDINATES: similar to AA sequence:RefSeq:WP_015708944.1
COORDINATES: protein motif:HMM:NF013315.2
GO:0008168 - methyltransferase activity [Evidence IEA]