Mycobacterium dioxanotrophicus strain PH-06 plasmid unnamed4, al1l pseudoknot.
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\nCP020813.1.\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: similar to AA sequence:RefSeq:WP_011896300.1
incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_019175580.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012359884.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006246582.1
COORDINATES: similar to AA sequence:RefSeq:WP_005882715.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246580.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006947554.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246577.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008720624.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011896298.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896297.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896296.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011896294.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896293.1
COORDINATES: similar to AA sequence:RefSeq:WP_020661064.1
COORDINATES: protein motif:HMM:NF024776.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033832.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896291.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896290.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113706.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896289.1
COORDINATES: protein motif:HMM:TIGR00665.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
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_011896287.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896286.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896285.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896284.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896283.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243963.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896281.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896280.1
COORDINATES: similar to AA sequence:RefSeq:WP_005115661.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011896278.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896277.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896276.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896275.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113689.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896274.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896273.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896272.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896271.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896270.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896269.1
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: similar to AA sequence:RefSeq:WP_011896266.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896264.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896262.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767790.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767791.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244133.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244132.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896257.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011726768.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611735.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_014211372.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: similar to AA sequence:RefSeq:WP_011777794.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777793.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_008256165.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211308.1
COORDINATES: protein motif:HMM:NF014068.2
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014211310.1
COORDINATES: similar to AA sequence:RefSeq:WP_005461384.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019205 - nucleobase-containing compound kinase activity [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012392389.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211313.1
incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.