Rhodococcus koreensis strain R85 plasmid unnamed4, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; Rhodococcus.
Complete Genome Sequences of Two Rhodococcus sp. Strains with Large and Linear Chromosomes, Isolated from Apple Rhizosphere
Microbiol Resour Announc 10 (24), e0015921 (2021)
Submitted (11-FEB-2021) Comparative Microbiome Analysis, Helmholtz Center Munich, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP070613.1.\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 Date :: MAY-2020\nAssembly Method :: Microbial Assembly v. May-2020\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 202x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 04:34:11\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) :: 10,075\nCDSs (total) :: 10,008\nGenes (coding) :: 9,623\nCDSs (with protein) :: 9,623\nGenes (RNA) :: 67\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 385\nCDSs (without protein) :: 385\nPseudo Genes (ambiguous residues) :: 0 of 385\nPseudo Genes (frameshifted) :: 224 of 385\nPseudo Genes (incomplete) :: 267 of 385\nPseudo Genes (internal stop) :: 41 of 385\nPseudo Genes (multiple problems) :: 137 of 385\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
rhizosphere of apple plantlets grown in replant diseased soil
COORDINATES: similar to AA sequence:RefSeq:WP_010080128.1
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_005254528.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019511300.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
cytochrome C oxidase subunit IV family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019509878.1
COORDINATES: similar to AA sequence:RefSeq:WP_005565159.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020497516.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014926098.1
COORDINATES: protein motif:HMM:NF012596.2
enoyl-CoA hydratase/isomerase family protein
COORDINATES: protein motif:HMM:NF015048.2
COORDINATES: similar to AA sequence:RefSeq:WP_014926109.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
PEP/pyruvate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017982141.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014926073.1
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: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_014926075.1
COORDINATES: similar to AA sequence:RefSeq:WP_019875100.1
COORDINATES: similar to AA sequence:RefSeq:WP_014926077.1
mycofactocin-coupled SDR family oxidoreductase
COORDINATES: protein motif:HMM:NF018595.2
COORDINATES: similar to AA sequence:RefSeq:WP_005463988.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011593695.1
COORDINATES: similar to AA sequence:RefSeq:WP_011600066.1
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF016777.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012689629.1
COORDINATES: similar to AA sequence:RefSeq:WP_012689630.1
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009760408.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012689632.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_009760410.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611377.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009472480.1
COORDINATES: protein motif:HMM:NF039405.1
COORDINATES: similar to AA sequence:RefSeq:WP_016884893.1
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_005242534.1
COORDINATES: similar to AA sequence:RefSeq:WP_015292640.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016692968.1
COORDINATES: similar to AA sequence:RefSeq:WP_005242513.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611796.1
COORDINATES: similar to AA sequence:RefSeq:WP_005264406.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007298864.1
COORDINATES: similar to AA sequence:RefSeq:WP_016883940.1
COORDINATES: similar to AA sequence:RefSeq:WP_005256026.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005254847.1
COORDINATES: similar to AA sequence:RefSeq:WP_016695746.1
COORDINATES: similar to AA sequence:RefSeq:WP_005566739.1
COORDINATES: similar to AA sequence:RefSeq:WP_005256028.1