Paraburkholderia phytofirmans PsJN plasmid pBPHYT01, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN
Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN
Complete sequence of plasmid1 of Burkholderia phytofirmans PsJN
Submitted (28-APR-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001054.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4002732\nSource DNA and bacteria available from James Tiedje\n(tiedjej@msu.edu)\nContacts: James Tiedje (tiedjej@msu.edu)\n David Bruce (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LLNL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 14:43:53\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) :: 7,433\nCDSs (total) :: 7,347\nGenes (coding) :: 7,226\nCDSs (with protein) :: 7,226\nGenes (RNA) :: 86\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 121\nCDSs (without protein) :: 121\nPseudo Genes (ambiguous residues) :: 0 of 121\nPseudo Genes (frameshifted) :: 43 of 121\nPseudo Genes (incomplete) :: 99 of 121\nPseudo Genes (internal stop) :: 16 of 121\nPseudo Genes (multiple problems) :: 32 of 121\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Paraburkholderia phytofirmans
COORDINATES: protein motif:HMM:NF022136.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012652.2
type II secretory pathway component PulF-like protein
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_011487796.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024212.2
COORDINATES: protein motif:HMM:NF013161.2
COORDINATES: protein motif:HMM:NF039910.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007175954.1
COORDINATES: similar to AA sequence:RefSeq:WP_012427050.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256992.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_007176046.1
COORDINATES: protein motif:HMM:NF024852.2
COORDINATES: similar to AA sequence:RefSeq:WP_014190185.1
COORDINATES: similar to AA sequence:RefSeq:WP_007589985.1
COORDINATES: similar to AA sequence:RefSeq:WP_010485401.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182959.1
COORDINATES: similar to AA sequence:RefSeq:WP_011487795.1
COORDINATES: similar to AA sequence:RefSeq:WP_012777666.1
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008649422.1
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_014194226.1
COORDINATES: similar to AA sequence:RefSeq:WP_010106347.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014750904.1
COORDINATES: similar to AA sequence:RefSeq:WP_007160855.1
COORDINATES: similar to AA sequence:RefSeq:WP_004636902.1
COORDINATES: similar to AA sequence:RefSeq:WP_008333815.1
COORDINATES: similar to AA sequence:RefSeq:WP_013207108.1
COORDINATES: similar to AA sequence:RefSeq:WP_008060734.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875746.1
COORDINATES: similar to AA sequence:RefSeq:WP_007250677.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094712.1
COORDINATES: similar to AA sequence:RefSeq:WP_008918740.1
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_012406682.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406685.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406686.1
COORDINATES: similar to AA sequence:RefSeq:WP_012428292.1
COORDINATES: protein motif:HMM:NF023926.2
COORDINATES: protein motif:HMM:NF021897.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF041492.1
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF015118.2
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR02788.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007182586.1
COORDINATES: similar to AA sequence:RefSeq:WP_000105175.1
COORDINATES: similar to AA sequence:RefSeq:WP_016245689.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase-like protein
COORDINATES: similar to AA sequence:RefSeq:WP_012435707.1
COORDINATES: similar to AA sequence:RefSeq:WP_003238204.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700153.1
COORDINATES: similar to AA sequence:RefSeq:WP_006409555.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645421.1
COORDINATES: similar to AA sequence:RefSeq:WP_011876237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011695148.1
COORDINATES: similar to AA sequence:RefSeq:WP_011876229.1
COORDINATES: protein motif:HMM:NF014814.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_013696300.1
COORDINATES: protein motif:HMM:NF027824.2
COORDINATES: similar to AA sequence:RefSeq:WP_012435631.1
lytic transglycosylase domain-containing protein