Mycolicibacterium rufum strain JCM 16372 plasmid unnamed2, 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
REFSEQ INFORMATION: The reference sequence is identical to\nCP103313.1.\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 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: similar to AA sequence:RefSeq:WP_011780238.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011767776.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006246245.1
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_013470137.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896342.1
COORDINATES: similar to AA sequence:RefSeq:WP_011727590.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011729574.1
COORDINATES: similar to AA sequence:RefSeq:WP_005142312.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470385.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011855201.1
GO:0018578 - protocatechuate 3,4-dioxygenase activity [Evidence IEA]
GO:0046278 - 3,4-dihydroxybenzoate metabolic process [Evidence IEA]
protocatechuate 3,4-dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011559101.1
protocatechuate 3,4-dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_003929145.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891525.1
GO:0047575 - 4-carboxymuconolactone decarboxylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011559104.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011777851.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891522.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777780.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891560.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891555.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013470353.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011559054.1
SCP2 sterol-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012398.2
COORDINATES: similar to AA sequence:RefSeq:WP_011767840.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211472.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011562958.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0044237 - cellular metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011559073.1
GO:0019439 - aromatic compound catabolic process [Evidence IEA]; GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011559074.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767844.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013470371.1
COORDINATES: protein motif:HMM:NF013920.2
COORDINATES: similar to AA sequence:RefSeq:WP_011562964.1
MaoC family dehydratase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006897055.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562966.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_011767849.1
GO:0008695 - 3-phenylpropionate dioxygenase activity [Evidence IEA]
GO:0019380 - 3-phenylpropionate catabolic process [Evidence IEA]
3-phenylpropionate/cinnamic acid dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011562968.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562969.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011562970.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211492.1
class II aldolase/adducin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011562972.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562973.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767817.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211487.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777834.1
COORDINATES: similar to AA sequence:RefSeq:WP_003907833.1
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_011562978.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011562979.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_011562980.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011562981.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562982.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612273.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562986.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562987.1
COORDINATES: similar to AA sequence:RefSeq:WP_003937103.1
GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors [Evidence IEA]
2-oxoacid:acceptor oxidoreductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011779162.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024966.2
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611796.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611204.1
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: protein motif:HMM:NF033543.1
COORDINATES: similar to AA sequence:RefSeq:WP_012836485.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_013470254.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007732099.1
COORDINATES: similar to AA sequence:RefSeq:WP_011892095.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878443.1
COORDINATES: similar to AA sequence:RefSeq:WP_012803697.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: similar to AA sequence:RefSeq:WP_006215290.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003943400.1
COORDINATES: protein motif:HMM:NF025878.2
COORDINATES: similar to AA sequence:RefSeq:WP_006141792.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562689.1
COORDINATES: protein motif:HMM:NF012401.2
COORDINATES: similar to AA sequence:RefSeq:WP_017555472.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF039499.1
COORDINATES: similar to AA sequence:RefSeq:WP_017555459.1
COORDINATES: similar to AA sequence:RefSeq:WP_005149413.1
COORDINATES: similar to AA sequence:RefSeq:WP_015288385.1
COORDINATES: similar to AA sequence:RefSeq:WP_007172373.1