Rhodococcus opacus PD630 plasmid pRoPD630_2, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; Rhodococcus.
Submitted (07-AUG-2021) Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio, 42, Bologna 40126, Italy
REFSEQ INFORMATION: The reference sequence is identical to\nCP080956.1.\nBacteria and source DNA available from culture collection\nidentifier: DSMZ 44193.\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 :: canu v. 2.2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 438.9x\nSequencing Technology :: Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/29/2022 07:59:14\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;\n repeat_region\nGenes (total) :: 8,336\nCDSs (total) :: 8,270\nGenes (coding) :: 8,070\nCDSs (with protein) :: 8,070\nGenes (RNA) :: 66\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 200\nCDSs (without protein) :: 200\nPseudo Genes (ambiguous residues) :: 0 of 200\nPseudo Genes (frameshifted) :: 118 of 200\nPseudo Genes (incomplete) :: 123 of 200\nPseudo Genes (internal stop) :: 14 of 200\nPseudo Genes (multiple problems) :: 48 of 200\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Germany: gas-works plant 10 km north of Gottingen
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009156943.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: protein motif:HMM:NF024965.2
COORDINATES: similar to AA sequence:RefSeq:WP_005253035.1
COORDINATES: protein motif:HMM:NF013003.2
COORDINATES: similar to AA sequence:RefSeq:WP_005253054.1
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_005571162.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249415.1
DnaB-like helicase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005249416.1
GO:0097573 - glutathione oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005567559.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005249418.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249419.1
COORDINATES: similar to AA sequence:RefSeq:WP_007299965.1
COORDINATES: similar to AA sequence:RefSeq:WP_005261573.1
COORDINATES: similar to AA sequence:RefSeq:WP_016881510.1
COORDINATES: similar to AA sequence:RefSeq:WP_006930917.1
COORDINATES: similar to AA sequence:RefSeq:WP_005261580.1
GO:0004357 - glutamate-cysteine ligase activity [Evidence IEA]
GO:0042398 - cellular modified amino acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009476409.1
COORDINATES: similar to AA sequence:RefSeq:WP_005263389.1
COORDINATES: similar to AA sequence:RefSeq:WP_007299314.1
ScbR family autoregulator-binding transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007297248.1
COORDINATES: similar to AA sequence:RefSeq:WP_012689811.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016693990.1
COORDINATES: similar to AA sequence:RefSeq:WP_005253181.1
COORDINATES: similar to AA sequence:RefSeq:WP_005568917.1
COORDINATES: similar to AA sequence:RefSeq:WP_006931753.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249437.1
COORDINATES: similar to AA sequence:RefSeq:WP_007298014.1
COORDINATES: similar to AA sequence:RefSeq:WP_005573129.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599299.1
COORDINATES: similar to AA sequence:RefSeq:WP_016882006.1
COORDINATES: similar to AA sequence:RefSeq:WP_011595655.1
COORDINATES: similar to AA sequence:RefSeq:WP_003944240.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016882033.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567510.1
COORDINATES: similar to AA sequence:RefSeq:WP_005569569.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567513.1
COORDINATES: similar to AA sequence:RefSeq:WP_005257667.1
COORDINATES: similar to AA sequence:RefSeq:WP_005253425.1
COORDINATES: similar to AA sequence:RefSeq:WP_011598706.1
COORDINATES: similar to AA sequence:RefSeq:WP_018105030.1
COORDINATES: similar to AA sequence:RefSeq:WP_020017168.1
COORDINATES: similar to AA sequence:RefSeq:WP_020017167.1
COORDINATES: similar to AA sequence:RefSeq:WP_012690829.1
COORDINATES: similar to AA sequence:RefSeq:WP_009380501.1
COORDINATES: similar to AA sequence:RefSeq:WP_020516744.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005261579.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939434.1
COORDINATES: similar to AA sequence:RefSeq:WP_011598705.1
COORDINATES: similar to AA sequence:RefSeq:WP_003934347.1
COORDINATES: similar to AA sequence:RefSeq:WP_009480190.1
COORDINATES: similar to AA sequence:RefSeq:WP_011598704.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0051049 - regulation of transport [Evidence IEA]
phosphate signaling complex protein PhoU
COORDINATES: similar to AA sequence:RefSeq:WP_007731048.1
COORDINATES: similar to AA sequence:RefSeq:WP_005574021.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016777.2
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: similar to AA sequence:RefSeq:WP_005560887.1
GO:0003934 - GTP cyclohydrolase I activity [Evidence IEA]
GO:0042559 - pteridine-containing compound biosynthetic process [Evidence IEA]; GO:0046654 - tetrahydrofolate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005567187.1
COORDINATES: similar to AA sequence:RefSeq:WP_005071515.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567191.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567192.1
GO:0061710 - L-threonylcarbamoyladenylate synthase [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005249475.1
COORDINATES: similar to AA sequence:RefSeq:WP_014993036.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567198.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567200.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005567314.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005567316.1
class I adenylate-forming enzyme family protein
COORDINATES: protein motif:HMM:NF024883.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016881598.1
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005572766.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009478858.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_008720342.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005249488.1
COORDINATES: similar to AA sequence:RefSeq:WP_005245777.1
FAD-binding and (Fe-S)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016884634.1
mycofactocin-coupled SDR family oxidoreductase
COORDINATES: protein motif:HMM:NF005559.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249494.1
COORDINATES: similar to AA sequence:RefSeq:WP_013677927.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF012544.2
COORDINATES: similar to AA sequence:RefSeq:WP_005245785.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005245855.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_004021918.1
COORDINATES: similar to AA sequence:RefSeq:WP_006372493.1
COORDINATES: protein motif:HMM:NF013119.2
3,4-dihydroxy-2-butanone-4-phosphate synthase
COORDINATES: similar to AA sequence:RefSeq:WP_011775218.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008312289.1
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.
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012688726.1
COORDINATES: similar to AA sequence:RefSeq:WP_005570148.1
COORDINATES: similar to AA sequence:RefSeq:WP_005567159.1
COORDINATES: similar to AA sequence:RefSeq:WP_007616266.1
COORDINATES: similar to AA sequence:RefSeq:WP_005241514.1
COORDINATES: similar to AA sequence:RefSeq:WP_007299993.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599498.1
GO:0004540 - ribonuclease activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005566945.1
COORDINATES: similar to AA sequence:RefSeq:WP_005566943.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_005249353.1
COORDINATES: similar to AA sequence:RefSeq:WP_005257970.1
COORDINATES: similar to AA sequence:RefSeq:WP_005571579.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249356.1
COORDINATES: similar to AA sequence:RefSeq:WP_007299709.1
COORDINATES: similar to AA sequence:RefSeq:WP_005513177.1
COORDINATES: similar to AA sequence:RefSeq:WP_010149308.1
COORDINATES: similar to AA sequence:RefSeq:WP_011593885.1
COORDINATES: similar to AA sequence:RefSeq:WP_005513116.1
COORDINATES: similar to AA sequence:RefSeq:WP_008264012.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005262973.1
COORDINATES: similar to AA sequence:RefSeq:WP_005262975.1
COORDINATES: protein motif:HMM:NF013618.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011210014.1
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_005262979.1
COORDINATES: similar to AA sequence:RefSeq:WP_005262981.1
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_005262983.1
COORDINATES: similar to AA sequence:RefSeq:WP_005262986.1
COORDINATES: similar to AA sequence:RefSeq:WP_005262988.1
COORDINATES: similar to AA sequence:RefSeq:WP_005262989.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005262991.1
COORDINATES: similar to AA sequence:RefSeq:WP_007516241.1
COORDINATES: similar to AA sequence:RefSeq:WP_005260842.1
COORDINATES: similar to AA sequence:RefSeq:WP_005260841.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005260840.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_005562465.1
COORDINATES: similar to AA sequence:RefSeq:WP_005249393.1
COORDINATES: similar to AA sequence:RefSeq:WP_005562469.1
COORDINATES: similar to AA sequence:RefSeq:WP_005562273.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF014814.2