Mycobacterium dioxanotrophicus strain PH-06 plasmid unnamed2, 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\nCP020811.1.\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: protein motif:HMM:NF017885.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007240526.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003882613.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003882615.1
helix-turn-helix domain containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016893147.1
COORDINATES: protein motif:HMM:NF036523.2
COORDINATES: similar to AA sequence:RefSeq:WP_003882618.1
COORDINATES: similar to AA sequence:RefSeq:WP_003882619.1
COORDINATES: similar to AA sequence:RefSeq:WP_007240717.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase 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_005260983.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_005569446.1
GO:0003824 - catalytic activity [Evidence IEA]
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_014805362.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012835503.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003921369.1
frameshifted; internal stop; 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_006241455.1
COORDINATES: similar to AA sequence:RefSeq:WP_015353969.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005572969.1
COORDINATES: similar to AA sequence:RefSeq:WP_014818398.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF014395.2
COORDINATES: similar to AA sequence:RefSeq:WP_006246388.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243403.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243404.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243406.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243407.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243408.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243409.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF040041.1
COORDINATES: similar to AA sequence:RefSeq:WP_014214333.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020661064.1
COORDINATES: similar to AA sequence:RefSeq:WP_015746935.1
COORDINATES: protein motif:HMM:NF022231.2
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014378922.1
COORDINATES: similar to AA sequence:RefSeq:WP_009977319.1
COORDINATES: similar to AA sequence:RefSeq:WP_007776093.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014942308.1
COORDINATES: similar to AA sequence:RefSeq:WP_008361940.1
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003820652.1
COORDINATES: similar to AA sequence:RefSeq:WP_011210843.1
GO:0097573 - glutathione oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013470231.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243422.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243421.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805563.1
COORDINATES: protein motif:HMM:NF020332.2
COORDINATES: protein motif:HMM:NF024776.2
COORDINATES: similar to AA sequence:RefSeq:WP_020661063.1
COORDINATES: similar to AA sequence:RefSeq:WP_008734493.1
COORDINATES: similar to AA sequence:RefSeq:WP_005477162.1
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_019736443.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831157.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246307.1
COORDINATES: protein motif:HMM:NF014581.2
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:TIGR03922.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: protein motif:HMM:NF022650.2
COORDINATES: protein motif:HMM:TIGR03921.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
type VII secretion-associated serine protease mycosin
COORDINATES: protein motif:HMM:TIGR03920.1
GO:0003674 - molecular_function [Evidence IEA]
type VII secretion integral membrane protein EccD
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF025377.2
COORDINATES: protein motif:HMM:NF017793.2
COORDINATES: protein motif:HMM:NF013021.2
COORDINATES: protein motif:HMM:NF013727.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016964.2
COORDINATES: protein motif:HMM:NF025407.2
COORDINATES: similar to AA sequence:RefSeq:WP_017835891.1
COORDINATES: protein motif:HMM:NF024254.2
helix-turn-helix transcriptional regulator
YbaB/EbfC family nucleoid-associated protein
COORDINATES: protein motif:HMM:NF014616.2
COORDINATES: protein motif:HMM:NF022280.2
COORDINATES: protein motif:HMM:NF013073.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148545.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005148546.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011726768.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805346.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113621.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148620.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243945.1
COORDINATES: similar to AA sequence:RefSeq:WP_015293394.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008710443.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007168486.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805342.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212208.1
COORDINATES: similar to AA sequence:RefSeq:WP_007170682.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_016888815.1