Mycolicibacterium rufum strain JCM 16372 plasmid unnamed, complete sequence.
Mycolicibacterium rufum (Mycobacterium rufum)
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Complete Genome Sequences of 14 Nontuberculous Mycobacteria Type Strains
Microbiol Resour Announc 12 (2), e0121422 (2023)
Submitted (22-AUG-2022) Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
Nucleotide sequence updated by submitter
Submitted (16-FEB-2022) Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nCP092428.2.\n\nOn Oct 6, 2022 this sequence version replaced NZ_CP092428.1.\nBacteria and source DNA available from Japan Collection of\nMicroorganisms (JCM).\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. 2.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 120x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/25/2023 10:39:32\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,907\nCDSs (total) :: 5,851\nGenes (coding) :: 5,752\nCDSs (with protein) :: 5,752\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 99\nCDSs (without protein) :: 99\nPseudo Genes (ambiguous residues) :: 0 of 99\nPseudo Genes (frameshifted) :: 38 of 99\nPseudo Genes (incomplete) :: 70 of 99\nPseudo Genes (internal stop) :: 1 of 99\nPseudo Genes (multiple problems) :: 10 of 99\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_020188485.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805377.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247300.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015354561.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011780905.1
COORDINATES: protein motif:HMM:NF033542.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805584.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:NP_217159.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
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_014212708.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805587.1
low molecular weight phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005112740.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003925109.1
COORDINATES: protein motif:HMM:NF037830.2
COORDINATES: similar to AA sequence:RefSeq:WP_005072193.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008610 - lipid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612273.1
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_011893676.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011780898.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893679.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893680.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896120.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767814.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893683.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893684.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780893.1
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
type II CAAX endopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011896117.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896147.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893689.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767859.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893692.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893693.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780887.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767863.1
COORDINATES: similar to AA sequence:RefSeq:WP_014711801.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011893697.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003928730.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011893699.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893700.1
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcsB
COORDINATES: similar to AA sequence:RefSeq:WP_011767869.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767870.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011780879.1
GO:0009190 - cyclic nucleotide biosynthetic process [Evidence IEA]; GO:0035556 - intracellular signal transduction [Evidence IEA]
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011896131.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896111.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011767878.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893708.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893709.1
COORDINATES: similar to AA sequence:RefSeq:WP_006945647.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893711.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893712.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893713.1
COORDINATES: similar to AA sequence:RefSeq:WP_016889499.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006897775.1
COORDINATES: similar to AA sequence:RefSeq:WP_013473248.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893717.1
COORDINATES: similar to AA sequence:RefSeq:WP_011856861.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011780843.1
NlpC/P60 family peptidoglycan endopeptidase RipA
COORDINATES: similar to AA sequence:RefSeq:WP_011893720.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558852.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891803.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767914.1
NlpC/P60 family peptidoglycan endopeptidase RipB
COORDINATES: similar to AA sequence:RefSeq:WP_011767915.1
COORDINATES: similar to AA sequence:RefSeq:WP_013473242.1
GO:0016787 - hydrolase activity [Evidence IEA]
frameshifted; 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_011891812.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013473240.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893729.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013473238.1
COORDINATES: similar to AA sequence:RefSeq:WP_011856766.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011856844.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805656.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805609.1
GO:0005615 - extracellular space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011856784.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_011893735.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767939.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014213993.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011559381.1
iron ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011893739.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893741.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019311198.1
frameshifted; 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_011767931.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016719387.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003944602.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805599.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780447.1
COORDINATES: similar to AA sequence:RefSeq:WP_019045659.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007633606.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780445.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878317.1
COORDINATES: similar to AA sequence:RefSeq:WP_011856778.1
COORDINATES: similar to AA sequence:RefSeq:WP_018603393.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805566.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011891810.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891809.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767888.1
COORDINATES: similar to AA sequence:RefSeq:WP_005628350.1
COORDINATES: similar to AA sequence:RefSeq:WP_014941477.1
COORDINATES: similar to AA sequence:RefSeq:WP_009155040.1
maleylpyruvate isomerase family mycothiol-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_011562950.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611786.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020099921.1
GO:0008963 - phospho-N-acetylmuramoyl-pentapeptide-transferase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
phospho-N-acetylmuramoyl-pentapeptide- transferase
COORDINATES: similar to AA sequence:RefSeq:WP_013115454.1
COORDINATES: similar to AA sequence:RefSeq:WP_003945505.1
COORDINATES: protein motif:HMM:NF012514.2
COORDINATES: similar to AA sequence:RefSeq:WP_011740221.1
COORDINATES: protein motif:HMM:NF024698.2
COORDINATES: similar to AA sequence:RefSeq:WP_014805532.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298218.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_007768457.1
COORDINATES: protein motif:HMM:NF012708.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF025398.2
COORDINATES: similar to AA sequence:RefSeq:WP_003890979.1
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013021.2
COORDINATES: similar to AA sequence:RefSeq:WP_014805518.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805517.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805516.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005566945.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767790.1
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: similar to AA sequence:RefSeq:WP_011767793.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805339.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148516.1
YbaB/EbfC family nucleoid-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_005148510.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148509.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148507.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148441.1
COORDINATES: similar to AA sequence:RefSeq:WP_009953186.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780469.1
frameshifted; 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.
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148425.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148424.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148423.1
GO:0009986 - cell surface [Evidence IEA]; GO:0005576 - extracellular region [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148421.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148419.1
COORDINATES: protein motif:HMM:NF025377.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148416.1
type VII secretion integral membrane protein EccD
COORDINATES: similar to AA sequence:RefSeq:WP_005148415.1
type VII secretion-associated serine protease mycosin
COORDINATES: protein motif:HMM:TIGR03923.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148411.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011562908.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246302.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148408.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148407.1
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148401.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148400.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005148396.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805914.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611796.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148395.1
COORDINATES: similar to AA sequence:RefSeq:WP_005477162.1
COORDINATES: similar to AA sequence:RefSeq:WP_005247438.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011689697.1
COORDINATES: similar to AA sequence:RefSeq:WP_007732099.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805429.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144158.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805431.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247671.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805433.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805434.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470231.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297890.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144166.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805435.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144169.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805437.1
COORDINATES: similar to AA sequence:RefSeq:WP_006940556.1
COORDINATES: similar to AA sequence:RefSeq:WP_014212622.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243301.1
COORDINATES: similar to AA sequence:RefSeq:WP_013425092.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006243304.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243305.1
COORDINATES: protein motif:HMM:NF013718.2
COORDINATES: similar to AA sequence:RefSeq:WP_006243309.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_006243310.1
COORDINATES: similar to AA sequence:RefSeq:WP_020645876.1
COORDINATES: similar to AA sequence:RefSeq:WP_018161759.1
COORDINATES: similar to AA sequence:RefSeq:WP_020646521.1
GO:0050380 - undecaprenyl-diphosphatase activity [Evidence IEA]
GO:0016311 - dephosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005249436.1
COORDINATES: similar to AA sequence:RefSeq:WP_005102100.1
COORDINATES: similar to AA sequence:RefSeq:WP_007298807.1
COORDINATES: similar to AA sequence:RefSeq:WP_019514499.1
GO:1903425 - fluoride transmembrane transporter activity [Evidence IEA]
GO:1903424 - fluoride transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019514500.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_016887900.1
COORDINATES: similar to AA sequence:RefSeq:WP_010310951.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_005144173.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805342.1