Mycobacterium dioxanotrophicus strain PH-06 plasmid unnamed3, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycobacterium.
Whole Genome Sequence of 1,4-Dioxane Degrading Bacterium Mycobacterium dioxanotrophicus PH-06
Submitted (11-APR-2017) Civil and Environmental Engineering, Rice University, Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Ms-519, Houston, TX 77005, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP020812.1.\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 :: RS_HGAP Assembly of SMRT Analysis v. 2.3.0\nGenome Coverage :: 100x\nSequencing Technology :: Illumina Hiseq; PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/30/2022 05:07:05\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,873\nCDSs (total) :: 7,778\nGenes (coding) :: 7,523\nCDSs (with protein) :: 7,523\nGenes (RNA) :: 95\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 82\nncRNAs :: 4\nPseudo Genes (total) :: 255\nCDSs (without protein) :: 255\nPseudo Genes (ambiguous residues) :: 0 of 255\nPseudo Genes (frameshifted) :: 135 of 255\nPseudo Genes (incomplete) :: 145 of 255\nPseudo Genes (internal stop) :: 11 of 255\nPseudo Genes (multiple problems) :: 32 of 255\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Mycobacterium dioxanotrophicus
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF019984.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
group II intron maturase-specific domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011726646.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; 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_076611736.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [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_006247209.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:NP_218155.1
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_011777794.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777793.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011777792.1
COORDINATES: similar to AA sequence:RefSeq:WP_003887996.1
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_076611260.1
COORDINATES: similar to AA sequence:RefSeq:WP_020109886.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006245909.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_012392133.1
aromatic/alkene/methane monooxygenase hydroxylase/oxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_006947302.1
aromatic/alkene monooxygenase hydroxylase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_014805364.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805363.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006947312.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611735.1
COORDINATES: similar to AA sequence:RefSeq:NP_215563.1
COORDINATES: similar to AA sequence:RefSeq:WP_007172192.1
COORDINATES: similar to AA sequence:RefSeq:WP_007298228.1
COORDINATES: similar to AA sequence:RefSeq:WP_011729601.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558018.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211329.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011726768.1
COORDINATES: similar to AA sequence:RefSeq:WP_003936224.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211332.1
COORDINATES: similar to AA sequence:RefSeq:WP_011730775.1
COORDINATES: similar to AA sequence:RefSeq:WP_009475183.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805772.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211336.1
COORDINATES: protein motif:HMM:NF013753.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003920877.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211338.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014211339.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211340.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211341.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211342.1
COORDINATES: similar to AA sequence:RefSeq:WP_018332348.1
GO:0050661 - NADP binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GO:0046170 - methanol catabolic process [Evidence IEA]
This methanol dehydrogenase is considered a nicotinoprotein, since its NADP cofactor remains is not dissociable, but instead remains permanently bound. A member of this family has been shown to act as a formaldehyde dismutase, able to convert two molecules of formaldehyde (plus one water molecule) into one of methanol and one of formate, with no net change in its redox state. More recently, it was shown in Mycobacterium smegmatis that this enzyme is critical to ethanol utilization, for which the biosynthesis of the cofactor-like electron carrier mycofactocin is also required; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805763.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007236615.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211346.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211347.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211348.1
COORDINATES: protein motif:HMM:NF024881.2
COORDINATES: similar to AA sequence:RefSeq:WP_014211353.1
methane monooxygenase/ammonia monooxygenase subunit C
COORDINATES: similar to AA sequence:RefSeq:WP_014211354.1
methane monooxygenase/ammonia monooxygenase subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_014211355.1
methane monooxygenase/ammonia monooxygenase subunit B
COORDINATES: similar to AA sequence:RefSeq:WP_014805747.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211371.1
COORDINATES: similar to AA sequence:RefSeq:WP_011778565.1
GO:0140604 - mycofactocin biosynthetic process [Evidence IEA]
Members of this protein family, MftF, are glycosyltransferases, members of PF00535 (glycosyl transferase family 2). The encoding gene is found as part of the mycofactocin cassette, in Mycobacterium tuberculosis, many other Actinobacteria, and occasional members of other lineages. Mycofactocin itself, a putative redox carrier, is a heavily modified derivative of the C-terminal Val-Tyr dipeptide of the mycofactocin precursor MftA (TIGR03969).; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
mycofactocin biosynthesis glycosyltransferase MftF
COORDINATES: similar to AA sequence:RefSeq:WP_003934896.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896234.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896233.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896231.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896230.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896229.1
COORDINATES: similar to AA sequence:RefSeq:WP_005061889.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896227.1
COORDINATES: similar to AA sequence:RefSeq:WP_003881398.1
COORDINATES: similar to AA sequence:RefSeq:WP_003933635.1
COORDINATES: similar to AA sequence:RefSeq:WP_014209973.1
COORDINATES: similar to AA sequence:RefSeq:WP_003896509.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896226.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011896225.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896224.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896223.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896218.1
GO:0005615 - extracellular space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011896217.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896216.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896215.1
COORDINATES: similar to AA sequence:RefSeq:WP_016888204.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896209.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896208.1
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: similar to AA sequence:RefSeq:WP_011896206.1
COORDINATES: similar to AA sequence:RefSeq:WP_013493917.1
COORDINATES: similar to AA sequence:RefSeq:WP_020661064.1
COORDINATES: similar to AA sequence:RefSeq:WP_020661063.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896205.1
COORDINATES: similar to AA sequence:RefSeq:WP_005115616.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124930.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246577.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554629.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246580.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246582.1
COORDINATES: similar to AA sequence:RefSeq:WP_012359884.1
frameshifted; incomplete; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.