Cupriavidus gilardii strain FDAARGOS_639 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Cupriavidus.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (28-MAY-2020) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP054625.1.\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 Method :: canu v. 1.4\nGenome Coverage :: 656.77x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 03:26:08\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) :: 5,210\nCDSs (total) :: 5,134\nGenes (coding) :: 5,050\nCDSs (with protein) :: 5,050\nGenes (RNA) :: 76\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 3\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 27 of 84\nPseudo Genes (incomplete) :: 62 of 84\nPseudo Genes (internal stop) :: 9 of 84\nPseudo Genes (multiple problems) :: 11 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_018313763.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_019448404.1
COORDINATES: similar to AA sequence:RefSeq:WP_013956477.1
GO:0005215 - transporter activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006578559.1
GO:0004311 - farnesyltranstransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006578558.1
GO:0016767 - geranylgeranyl-diphosphate geranylgeranyltransferase activity [Evidence IEA]
GO:0016117 - carotenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019920999.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013956475.1
COORDINATES: similar to AA sequence:RefSeq:WP_012352658.1
COORDINATES: similar to AA sequence:RefSeq:WP_019427970.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
two-component system response regulator OmpR
COORDINATES: similar to AA sequence:RefSeq:WP_013956473.1
COORDINATES: similar to AA sequence:RefSeq:WP_004192241.1
COORDINATES: similar to AA sequence:RefSeq:WP_006155913.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020201243.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018004464.1
GO:0008685 - 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity [Evidence IEA]
GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway [Evidence IEA]
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
COORDINATES: similar to AA sequence:RefSeq:WP_006576347.1
GO:0050518 - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity [Evidence IEA]
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_013956466.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003690 - double-stranded DNA binding [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006155917.1
GO:0008777 - acetylornithine deacetylase activity [Evidence IEA]
GO:0006592 - ornithine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011615094.1
GO:0004180 - carboxypeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018311411.1
GO:0036424 - L-phosphoserine phosphatase activity [Evidence IEA]
GO:0006564 - L-serine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012352646.1
COORDINATES: similar to AA sequence:RefSeq:WP_020201237.1
COORDINATES: similar to AA sequence:RefSeq:WP_020201236.1
PepSY-associated TM helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR01783.1
COORDINATES: protein motif:HMM:NF016629.2
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015875628.1
GO:0004121 - cystathionine beta-lyase activity [Evidence IEA]
GO:0019346 - transsulfuration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006578564.1
GO:0008649 - rRNA methyltransferase activity [Evidence IEA]
GO:0070475 - rRNA base methylation [Evidence IEA]
23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ