Gordonia alkanivorans strain YC-RL2 plasmid pYYC01, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Gordoniaceae; Gordonia.
Complete genome sequence of a phthalic acid esters degrading strain Gordonia alkanivorans strain YC-RL2
Submitted (22-FEB-2018) Biology Department, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, Beijing 100081, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP027115.1.\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 :: NOV-2017\nAssembly Method :: PacBio RS II v. P6-C4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 04:58:20\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,538\nCDSs (total) :: 4,475\nGenes (coding) :: 4,364\nCDSs (with protein) :: 4,364\nGenes (RNA) :: 63\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 111\nCDSs (without protein) :: 111\nPseudo Genes (ambiguous residues) :: 0 of 111\nPseudo Genes (frameshifted) :: 53 of 111\nPseudo Genes (incomplete) :: 63 of 111\nPseudo Genes (internal stop) :: 17 of 111\nPseudo Genes (multiple problems) :: 19 of 111\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_005199800.1
GO:0046872 - metal ion binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005199799.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005199797.1
COORDINATES: similar to AA sequence:RefSeq:WP_012834396.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005199795.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005199794.1
COORDINATES: protein motif:HMM:NF028506.2
COORDINATES: similar to AA sequence:RefSeq:WP_006945647.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199789.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_014928799.1
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: similar to AA sequence:RefSeq:WP_005199783.1
COORDINATES: similar to AA sequence:RefSeq:WP_020171063.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199780.1
COORDINATES: protein motif:HMM:NF023505.2
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: protein motif:HMM:NF013265.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611217.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007240673.1
COORDINATES: similar to AA sequence:RefSeq:WP_012834428.1
COORDINATES: protein motif:HMM:NF013335.2
COORDINATES: similar to AA sequence:RefSeq:WP_014928860.1
COORDINATES: similar to AA sequence:RefSeq:WP_017681394.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199730.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928774.1
COORDINATES: similar to AA sequence:RefSeq:WP_019953214.1
COORDINATES: similar to AA sequence:RefSeq:WP_006438310.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199737.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199738.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: protein motif:HMM:NF025378.2
COORDINATES: similar to AA sequence:RefSeq:WP_012834424.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005199820.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005199819.1
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_017975738.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199817.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006438336.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199814.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199813.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199812.1
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_012834426.1
COORDINATES: similar to AA sequence:RefSeq:WP_005199810.1
vitamin K epoxide reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005199809.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_012834429.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012834401.1
GO:0016491 - oxidoreductase activity [Evidence IEA]