Rhodococcus fascians D188 plasmid unnamed2, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; Rhodococcus.
Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for Rhodococcus Isolates PBTS 1 and PBTS 2
Submitted (14-APR-2016) EPPWS, New Mexico State Universtiy, 945 College Ave Skeen Hall, Las Cruces, NM 88003, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP015237.1.\nSource bacteria available from Danny Vereecke, Ghent University,\nDepartment of Applied Biosciences, Valentyn Vaerwyckweg 1,\nSchoonmeersen 9000 Ghent, Belgium.\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 v. 2\nGenome Coverage :: 148X\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/13/2022 02:46:57\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,180\nCDSs (total) :: 5,118\nGenes (coding) :: 5,058\nCDSs (with protein) :: 5,058\nGenes (RNA) :: 62\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 23 of 60\nPseudo Genes (incomplete) :: 34 of 60\nPseudo Genes (internal stop) :: 5 of 60\nPseudo Genes (multiple problems) :: 2 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019664613.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017836506.1
COORDINATES: similar to AA sequence:RefSeq:WP_006947275.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019664614.1
COORDINATES: similar to AA sequence:RefSeq:WP_008709946.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212366.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720321.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720322.1
COORDINATES: similar to AA sequence:RefSeq:WP_007618209.1
COORDINATES: similar to AA sequence:RefSeq:WP_013798165.1
COORDINATES: similar to AA sequence:RefSeq:WP_020460235.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helicase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611781.1
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_006082846.1
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_012691911.1
COORDINATES: similar to AA sequence:RefSeq:WP_003934208.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_008720748.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720465.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005513497.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: protein motif:HMM:NF013594.2
COORDINATES: similar to AA sequence:RefSeq:WP_008720468.1
COORDINATES: similar to AA sequence:RefSeq:WP_008719718.1
COORDINATES: protein motif:HMM:NF025378.2
COORDINATES: similar to AA sequence:RefSeq:WP_007296014.1
COORDINATES: similar to AA sequence:RefSeq:WP_012686887.1
COORDINATES: similar to AA sequence:RefSeq:WP_012835883.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720478.1
COORDINATES: protein motif:HMM:NF016149.2
COORDINATES: similar to AA sequence:RefSeq:WP_005240299.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008720974.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596797.1
COORDINATES: similar to AA sequence:RefSeq:WP_006553267.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596387.1
COORDINATES: similar to AA sequence:RefSeq:WP_019746373.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008720941.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720077.1
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_006942498.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003882927.1
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
COORDINATES: similar to AA sequence:RefSeq:WP_008720127.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720128.1
vitamin K epoxide reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008720130.1
COORDINATES: similar to AA sequence:RefSeq:WP_007735280.1
COORDINATES: similar to AA sequence:RefSeq:WP_003944619.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008720147.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005245488.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720458.1
COORDINATES: similar to AA sequence:RefSeq:WP_011598763.1
iron ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011598764.1
COORDINATES: similar to AA sequence:RefSeq:WP_003944587.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720462.1
COORDINATES: similar to AA sequence:RefSeq:WP_010596927.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720464.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_015453099.1
COORDINATES: protein motif:HMM:NF024803.2
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_019749804.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019750063.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720413.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612020.1
COORDINATES: similar to AA sequence:RefSeq:WP_003937320.1
BtrH N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005560919.1
COORDINATES: similar to AA sequence:RefSeq:WP_006901466.1
transglutaminase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008720359.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003942426.1
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_005086615.1
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_003942428.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008720452.1
COORDINATES: similar to AA sequence:RefSeq:WP_006898167.1
COORDINATES: similar to AA sequence:RefSeq:WP_019160232.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720419.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_019749855.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720911.1
COORDINATES: protein motif:HMM:NF023805.2
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007301084.1
COORDINATES: protein motif:HMM:TIGR02779.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007389172.1
COORDINATES: similar to AA sequence:RefSeq:WP_020546169.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008720030.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878317.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008720028.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008720026.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720024.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331634.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720905.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720903.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720166.1
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008719970.1
COORDINATES: similar to AA sequence:RefSeq:WP_016885128.1
COORDINATES: similar to AA sequence:RefSeq:WP_008719965.1
DnaB-like helicase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008719963.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805852.1
COORDINATES: protein motif:HMM:NF020332.2
COORDINATES: protein motif:HMM:NF019371.2
COORDINATES: similar to AA sequence:RefSeq:WP_020729196.1
COORDINATES: protein motif:HMM:NF027484.2
COORDINATES: protein motif:HMM:NF022355.2
COORDINATES: protein motif:HMM:NF021897.2
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006947292.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939310.1
COORDINATES: protein motif:HMM:NF024798.2