Rhodococcus ruber strain C1 plasmid unnamed1, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; Rhodococcus.
Biodegradation of phenol by a highly tolerant Rhodococcus ruber C1: Biochemical characterization and comparative genomic analysis
Submitted (22-SEP-2019) School of Chemistry and Chemical Engineering, Chongqing University of Technology, 69 Hong Guang Road, Chongqing 400054, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP044212.1.\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 :: HGAP v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 295.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 16:56:15\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) :: 5,254\nCDSs (total) :: 5,185\nGenes (coding) :: 5,121\nCDSs (with protein) :: 5,121\nGenes (RNA) :: 69\nrRNAs :: 5, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 4, 4 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 64\nCDSs (without protein) :: 64\nPseudo Genes (ambiguous residues) :: 0 of 64\nPseudo Genes (frameshifted) :: 36 of 64\nPseudo Genes (incomplete) :: 29 of 64\nPseudo Genes (internal stop) :: 4 of 64\nPseudo Genes (multiple problems) :: 5 of 64\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF019913.2
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: protein motif:HMM:NF041196.1
ScbR family autoregulator-binding transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007170719.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554640.1
COORDINATES: similar to AA sequence:RefSeq:WP_006946692.1
COORDINATES: similar to AA sequence:RefSeq:WP_017682289.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596691.1
COORDINATES: similar to AA sequence:RefSeq:WP_017682291.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596689.1
COORDINATES: similar to AA sequence:RefSeq:WP_006937375.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006937373.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011331217.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331216.1
COORDINATES: similar to AA sequence:RefSeq:WP_006937367.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011331214.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006937363.1
COORDINATES: similar to AA sequence:RefSeq:WP_006937361.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005141495.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005248951.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006553261.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681821.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939272.1
COORDINATES: similar to AA sequence:RefSeq:WP_003944619.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006942279.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939275.1
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcsB
polyprenol phosphate mannosyl transferase 2
COORDINATES: similar to AA sequence:RefSeq:WP_006934825.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596786.1
COORDINATES: similar to AA sequence:RefSeq:WP_006934828.1
COORDINATES: protein motif:HMM:NF025378.2
COORDINATES: similar to AA sequence:RefSeq:WP_003939280.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010596789.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596790.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939283.1
COORDINATES: similar to AA sequence:RefSeq:WP_006934835.1
vitamin K epoxide reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003939285.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939286.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596795.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010596796.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553268.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010596798.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596799.1
COORDINATES: similar to AA sequence:RefSeq:WP_007296042.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008720941.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939294.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331645.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010596924.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939297.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596926.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596929.1
internal stop; 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_012834389.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_010596927.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939301.1
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_012834392.1
COORDINATES: similar to AA sequence:RefSeq:WP_009476869.1
COORDINATES: protein motif:HMM:NF015216.2
GO:0018836 - alkylmercury lyase activity [Evidence IEA]
GO:0046413 - organomercury catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003934317.1
COORDINATES: similar to AA sequence:RefSeq:WP_005264946.1
COORDINATES: similar to AA sequence:RefSeq:WP_003934808.1
COORDINATES: similar to AA sequence:RefSeq:WP_003934807.1
COORDINATES: protein motif:HMM:NF025637.2
COORDINATES: similar to AA sequence:RefSeq:WP_005483587.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018895858.1
COORDINATES: similar to AA sequence:RefSeq:WP_006936872.1
COORDINATES: similar to AA sequence:RefSeq:WP_003934805.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681395.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553233.1
COORDINATES: similar to AA sequence:RefSeq:WP_003935893.1
GO:0008703 - 5-amino-6-(5-phosphoribosylamino)uracil reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003936299.1
COORDINATES: similar to AA sequence:RefSeq:WP_006933570.1
COORDINATES: similar to AA sequence:RefSeq:WP_006933567.1
COORDINATES: similar to AA sequence:RefSeq:WP_006933565.1
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_006933563.1
COORDINATES: similar to AA sequence:RefSeq:WP_003936297.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017681390.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681389.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596730.1
COORDINATES: similar to AA sequence:RefSeq:WP_006934611.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553223.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596727.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331185.1
COORDINATES: similar to AA sequence:RefSeq:WP_006934618.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596724.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553218.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681381.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596721.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681379.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010596719.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681377.1
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006934642.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554221.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554220.1
COORDINATES: similar to AA sequence:RefSeq:WP_006934646.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596714.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553203.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553202.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553201.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553200.1
COORDINATES: similar to AA sequence:RefSeq:WP_005574668.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553198.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212400.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554624.1
COORDINATES: similar to AA sequence:RefSeq:WP_004018622.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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_006554626.1
COORDINATES: similar to AA sequence:RefSeq:WP_018799625.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554628.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554629.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554630.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554631.1
COORDINATES: similar to AA sequence:RefSeq:WP_005438381.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554633.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005203167.1
COORDINATES: similar to AA sequence:RefSeq:WP_006554635.1
GO:0018942 - organometal metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014351103.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014351101.1
COORDINATES: similar to AA sequence:RefSeq:WP_018555354.1
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_019044389.1
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity [Evidence IEA]
GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011212244.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179560.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179563.1
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005179567.1
COORDINATES: similar to AA sequence:RefSeq:WP_006902503.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179570.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212238.1
COORDINATES: similar to AA sequence:RefSeq:WP_012687035.1
COORDINATES: similar to AA sequence:RefSeq:WP_006931032.1
COORDINATES: similar to AA sequence:RefSeq:WP_017682318.1
COORDINATES: protein motif:HMM:NF016724.2