Paraburkholderia ginsengisoli strain FDAARGOS_1049 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (08-DEC-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\nCP066077.1.\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. 1.8\nGenome Coverage :: 689.62x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/31/2022 03:10:46\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) :: 5,904\nCDSs (total) :: 5,813\nGenes (coding) :: 5,713\nCDSs (with protein) :: 5,713\nGenes (RNA) :: 91\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 100\nCDSs (without protein) :: 100\nPseudo Genes (ambiguous residues) :: 0 of 100\nPseudo Genes (frameshifted) :: 37 of 100\nPseudo Genes (incomplete) :: 70 of 100\nPseudo Genes (internal stop) :: 17 of 100\nPseudo Genes (multiple problems) :: 18 of 100\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015602012.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004536487.1
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_006029518.1
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018420487.1
COORDINATES: similar to AA sequence:RefSeq:WP_007577647.1
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_007740894.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011711650.1
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_076611570.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013093476.1
COORDINATES: similar to AA sequence:RefSeq:WP_006491127.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007182694.1
COORDINATES: similar to AA sequence:RefSeq:WP_007749694.1
COORDINATES: similar to AA sequence:RefSeq:WP_006049832.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700267.1
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016355205.1
GO:0008795 - NAD+ synthase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
frameshifted; internal stop; 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_011084489.1
COORDINATES: similar to AA sequence:RefSeq:WP_008919003.1
COORDINATES: similar to AA sequence:RefSeq:WP_018418421.1
COORDINATES: similar to AA sequence:RefSeq:WP_008917337.1
COORDINATES: similar to AA sequence:RefSeq:WP_011850860.1
COORDINATES: protein motif:HMM:NF026057.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
transposase DNA-binding-containing protein
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_012427131.1
COORDINATES: similar to AA sequence:RefSeq:WP_012404801.1
COORDINATES: similar to AA sequence:RefSeq:WP_013689964.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152391.1
COORDINATES: similar to AA sequence:RefSeq:WP_020070899.1
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: similar to AA sequence:RefSeq:WP_011872570.1
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.
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009652972.1
GO:0030599 - pectinesterase activity [Evidence IEA]
GO:0042545 - cell wall modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012355561.1
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_013094002.1
GO:0004650 - polygalacturonase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013587663.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194869.1
COORDINATES: protein motif:HMM:NF019542.2
COORDINATES: similar to AA sequence:RefSeq:WP_013801313.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182647.1
COORDINATES: similar to AA sequence:RefSeq:WP_012723264.1
COORDINATES: similar to AA sequence:RefSeq:WP_008643887.1
COORDINATES: similar to AA sequence:RefSeq:WP_015001934.1
COORDINATES: similar to AA sequence:RefSeq:WP_013587331.1
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF039385.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_007741253.1
COORDINATES: similar to AA sequence:RefSeq:WP_007584160.1
COORDINATES: similar to AA sequence:RefSeq:WP_011408623.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_004711842.1
COORDINATES: similar to AA sequence:RefSeq:WP_004711839.1
twin-arginine translocation signal domain-containing protein
COORDINATES: protein motif:HMM:NF018352.2
COORDINATES: similar to AA sequence:RefSeq:WP_018421078.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094623.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071510.1
COORDINATES: similar to AA sequence:RefSeq:WP_012464922.1
COORDINATES: similar to AA sequence:RefSeq:WP_014723932.1
COORDINATES: similar to AA sequence:RefSeq:WP_011880698.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344524.1
COORDINATES: similar to AA sequence:RefSeq:WP_007578722.1
COORDINATES: similar to AA sequence:RefSeq:WP_012218138.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344520.1
COORDINATES: protein motif:HMM:NF040438.1
alpha/beta hydrolase domain-containing protein
COORDINATES: protein motif:HMM:NF014566.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family glutamic-type intramembrane protease
COORDINATES: similar to AA sequence:RefSeq:WP_008919199.1
COORDINATES: similar to AA sequence:RefSeq:WP_012427638.1
COORDINATES: similar to AA sequence:RefSeq:WP_008919197.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344459.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344461.1
COORDINATES: similar to AA sequence:RefSeq:WP_018417845.1
COORDINATES: similar to AA sequence:RefSeq:WP_018417846.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012427641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012372150.1
COORDINATES: similar to AA sequence:RefSeq:WP_018417849.1
COORDINATES: similar to AA sequence:RefSeq:WP_007730194.1
COORDINATES: similar to AA sequence:RefSeq:WP_007181774.1
COORDINATES: similar to AA sequence:RefSeq:WP_006047345.1
COORDINATES: similar to AA sequence:RefSeq:WP_017475148.1
COORDINATES: protein motif:HMM:NF018319.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612094.1
COORDINATES: similar to AA sequence:RefSeq:WP_017423776.1
COORDINATES: similar to AA sequence:RefSeq:WP_018443843.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012354590.1
COORDINATES: similar to AA sequence:RefSeq:WP_017333754.1
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: protein motif:HMM:NF015648.2
COORDINATES: similar to AA sequence:RefSeq:WP_007182904.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017161000.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_007182898.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007182897.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_007182894.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_007182892.1
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019303572.1
COORDINATES: similar to AA sequence:RefSeq:WP_006402578.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182886.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013094770.1
COORDINATES: protein motif:HMM:NF020251.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017775293.1
COORDINATES: protein motif:HMM:NF014567.2
hybrid sensor histidine kinase/response regulator
COORDINATES: protein motif:HMM:NF012401.2
COORDINATES: similar to AA sequence:RefSeq:WP_012367283.1
GO:0016740 - transferase activity [Evidence IEA]
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006484960.1
COORDINATES: similar to AA sequence:RefSeq:WP_011350132.1
GO:0004400 - histidinol-phosphate transaminase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006482547.1
COORDINATES: similar to AA sequence:RefSeq:WP_008554466.1
catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF018152.2
COORDINATES: similar to AA sequence:RefSeq:WP_006749856.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731363.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731368.1
COORDINATES: similar to AA sequence:RefSeq:WP_018441931.1
COORDINATES: similar to AA sequence:RefSeq:WP_006749863.1
COORDINATES: similar to AA sequence:RefSeq:WP_013592245.1
COORDINATES: similar to AA sequence:RefSeq:WP_011695131.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_011546968.1
COORDINATES: similar to AA sequence:RefSeq:WP_004532132.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010116282.1
COORDINATES: protein motif:HMM:NF025217.2
50S ribosomal protein L11 methyltransferase
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_014917755.1
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_008351121.1
GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: similar to AA sequence:RefSeq:WP_007182868.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014066.2
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_008346150.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406636.1
COORDINATES: similar to AA sequence:RefSeq:WP_016346799.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013691841.1
COORDINATES: similar to AA sequence:RefSeq:WP_013339698.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_007674967.1
COORDINATES: similar to AA sequence:RefSeq:WP_006413500.1
COORDINATES: protein motif:HMM:NF019315.2
COORDINATES: similar to AA sequence:RefSeq:WP_018420346.1
internal stop; 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_018420717.1
COORDINATES: similar to AA sequence:RefSeq:WP_006413910.1
COORDINATES: similar to AA sequence:RefSeq:WP_009901820.1
acyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010110849.1
COORDINATES: similar to AA sequence:RefSeq:WP_004529537.1
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: similar to AA sequence:RefSeq:WP_009894438.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004530641.1
COORDINATES: similar to AA sequence:RefSeq:WP_010110842.1
COORDINATES: similar to AA sequence:RefSeq:WP_018746934.1
outer membrane lipoprotein-sorting protein
COORDINATES: similar to AA sequence:RefSeq:WP_012213626.1
COORDINATES: similar to AA sequence:RefSeq:WP_010463267.1
COORDINATES: similar to AA sequence:RefSeq:WP_015603822.1
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: similar to AA sequence:RefSeq:WP_006754864.1
COORDINATES: protein motif:HMM:NF015252.2