Rhodococcus fascians D188 plasmid pFiD188, 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\nCP015236.1.\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+
incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014533.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011689737.1
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_008720822.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331724.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720814.1
COORDINATES: protein motif:HMM:NF020250.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005560297.1
COORDINATES: protein motif:HMM:NF024792.2
pilus assembly protein TadG-related protein
COORDINATES: protein motif:HMM:NF015649.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR04541.1
GO:0050332 - thiamine pyridinylase activity [Evidence IEA]
GO:0009230 - thiamine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011731432.1
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_006932157.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005257955.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005255841.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720766.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009472305.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019436.2
COORDINATES: similar to AA sequence:RefSeq:WP_018760813.1
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: protein motif:HMM:TIGR00711.1
COORDINATES: protein motif:HMM:TIGR01509.1
COORDINATES: protein motif:HMM:NF041195.1
ScbA/BarX family gamma-butyrolactone biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_013838846.1
COORDINATES: protein motif:HMM:NF037005.2
COORDINATES: protein motif:HMM:NF002964.0
LysR family transcriptional regulator ArgP
COORDINATES: protein motif:HMM:NF013933.2
COORDINATES: protein motif:HMM:TIGR00838.1
GO:0004056 - argininosuccinate lyase activity [Evidence IEA]
GO:0042450 - arginine biosynthetic process via ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011745179.1
GO:0004055 - argininosuccinate synthase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0006526 - arginine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012760.2
GO:0016742 - hydroxymethyl-, formyl- and related transferase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012596.2
enoyl-CoA hydratase/isomerase family protein
COORDINATES: protein motif:HMM:NF012936.2
asparagine synthase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014698.2
COORDINATES: protein motif:HMM:NF012711.2
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017603204.1
GO:0004358 - glutamate N-acetyltransferase activity [Evidence IEA]
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
COORDINATES: similar to AA sequence:RefSeq:WP_006378941.1
COORDINATES: similar to AA sequence:RefSeq:WP_006378713.1
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004003370.1
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:NF018595.2
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_017619957.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009943247.1
COORDINATES: similar to AA sequence:RefSeq:WP_006378774.1
COORDINATES: protein motif:HMM:NF020826.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00730.1
COORDINATES: similar to AA sequence:RefSeq:WP_015308965.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
NtaA/DmoA family FMN-dependent monooxygenase
COORDINATES: protein motif:HMM:NF028221.2
COORDINATES: protein motif:HMM:NF013265.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: similar to AA sequence:RefSeq:WP_008720664.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720660.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF013727.2
COORDINATES: similar to AA sequence:RefSeq:WP_007299954.1
COORDINATES: similar to AA sequence:RefSeq:WP_006367542.1
GO:0042586 - peptide deformylase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF013226.2
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006338025.1
COORDINATES: similar to AA sequence:RefSeq:WP_018223540.1
COORDINATES: similar to AA sequence:RefSeq:WP_011603695.1
FMN-binding negative transcriptional regulator
COORDINATES: protein motif:HMM:NF003417.0
putative nonribosomal peptide synthetase; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR00641.1
GO:0016866 - intramolecular transferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012759.2
COORDINATES: similar to AA sequence:RefSeq:WP_019634554.1
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: similar to AA sequence:RefSeq:WP_015802435.1
GO:0043880 - crotonyl-CoA reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013862147.1
cobalamin B12-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR00750.1
GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:1903826 - L-arginine transmembrane transport [Evidence IEA]; GO:0015819 - lysine transport [Evidence IEA]; GO:0015822 - ornithine transport [Evidence IEA]
methylmalonyl Co-A mutase-associated GTPase MeaB
COORDINATES: similar to AA sequence:RefSeq:WP_015036233.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720164.1
COORDINATES: protein motif:HMM:NF019350.2
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018658042.1
COORDINATES: protein motif:HMM:NF021134.2
GO:0016758 - hexosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016699383.1
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: protein motif:HMM:NF014068.2
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: protein motif:HMM:NF012503.2
GO:0016831 - carboxy-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0019752 - carboxylic acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017577315.1
COORDINATES: similar to AA sequence:RefSeq:WP_020171615.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_006368073.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720555.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020109358.1
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_008720549.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720547.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720544.1
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: similar to AA sequence:RefSeq:WP_012686791.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720538.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008720536.1
COORDINATES: similar to AA sequence:RefSeq:WP_012880222.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599953.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720531.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720522.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720520.1
COORDINATES: similar to AA sequence:RefSeq:WP_017554919.1
COORDINATES: protein motif:HMM:NF014045.2
COORDINATES: protein motif:HMM:NF025720.2
COORDINATES: protein motif:HMM:NF018884.2
GO:0016791 - phosphatase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF028007.2
COORDINATES: protein motif:HMM:NF013279.2
GO:0051301 - cell division [Evidence IEA]
FtsW/RodA/SpoVE family cell cycle protein