Apr 30, 2018 |
XF14_RS22130
|
Burkholderia gladioli
SN82F6 |
New product name: T3SS-secreted prophage tail-like protein. New product name confidence: Class 2. New subcellular localization: Host Associated (Class 2). New subcellular localization evidence code (ECO): ECO:0000250. New subcellular localization PMID: 28864820. New PubMed ID: 28864820. New comment: .Annotation transferred from: GenBank:AOO34660.1.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
WQ49_RS20325
|
Burkholderia cenocepacia
K56-2 |
New product name: trimeric autotransporter adhesin. New product name confidence: Class 2. New PMIDs: 22919579, 20019083.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
WQ49_RS20305
|
Burkholderia cenocepacia
K56-2 |
New product name: vitronectin-binding trimeric autotransporter adhesin. New product name confidence: Class 1. New comment: A BCAM0223::Tp mutant was deficient in hemagglutination, affected in adherence to vitronectin and in biofilm formation and showed attenuated virulence in the Galleria mellonella model of infection. . New PMIDs: 22919579, 22848588, 20019083.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
WQ49_RS15905
|
Burkholderia cenocepacia
K56-2 |
New product name: trimeric autotransporter adhesin. New product name confidence: Class 2. New PMID: 22919579.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
WQ49_RS13910
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaA. New product name: PaaA. New product name confidence: Class 1. New PubMed ID: 18776009. New PubMed ID: 21247899. New comment: Putative monooxygenase subunit of ring 1,2-phenylacetyl-CoA epoxidase
.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS13905
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaB. New product name: PaaB. New product name synonym: putative subunit PaaB of ring 1,2-phenylacetyl-CoA epoxidase. New product name confidence: Class 2. New PubMed ID: 16997993. New comment:
. Annotation transferred from: UniProtKB:P76078.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS13900
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaC. New product name: PaaC. New product name synonym: putative subunit PaaC, structural subunit, of ring 1,2-phenylacetyl-CoA epoxidase. New product name confidence: Class 2. New PubMed ID: 21247899. New comment:
. Annotation transferred from: UniProtKB:P76079.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS13890
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaE. New product name: PaaE. New product name synonym: putative reductase subunit of ring 1,2-phenylacetyl-CoA epoxidase. New product name confidence: Class 2. New PubMed ID: 18776009. New PubMed ID: 21247899. New comment:
. Annotation transferred from: UniProtKB:P76081.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11520
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaK1. New product name: PaaK1. New product name synonym: phenylacetate-CoA ligase. New product name confidence: Class 1. New PubMed ID: 21388965. New comment:
.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11515
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaI. New product name: PaaI. New product name synonym: putative phenylacetatyl-CoA thioesterase. New product name confidence: Class 2. New PubMed ID: 16464851. New comment:
. Annotation transferred from: UniProtKB:P76084.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11510
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaG. New product name: PaaG. New product name synonym: putative 1,2-epoxyphenylacetyl-CoA isomerase/ 3,4-dehydroadipyl-CoA isomerase. New product name confidence: Class 2. New PubMed ID: 12846838. New comment:
. Annotation transferred from: UniProtKB:P77467.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11505
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaJ. New product name: PaaJ. New product name synonym: putative beta-ketothiolase (3-oxo-5,6-dehydrosuberyl-CoA thiolase). New product name confidence: Class 2. New PubMed ID: 12846838. New comment:
. Annotation transferred from: UniProtKB:P0C7L2.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11500
|
Burkholderia cenocepacia
K56-2 |
New gene name: pacL. New product name: PacL. New product name synonym: putative 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase. New product name confidence: Class 2. New PubMed ID: 21296885. New PubMed ID: 18776009. New comment: in E coli, paaZ encodes a bifunctional protein consisting of an N-terminal NADP-dependent aldehyde dehydrogenase domain and a C-terminal MaoC-like (R)-specific enoyl-CoA hydratase domain. In Burkholderia genomes, a gene incorrectly annotated as paaZ (e.g WQ49_RS11500) encodes only one of the two domains found in E.coli paaZ (the domain with semialdehyde dehydrogenase activity) and so is renamed PacL (PMID:21296885) but was also referred to as PaaZ-ALDH in the manuscript. In the same study , a separate A. aromaticum, protein (UniProtKB:Q5P232) with the (R)-hydratase activity was annotated as Ech-Aa and the Burkholderia ortholog was annotated as PaaZ-ECH.
. Annotation transferred from: UniProtKB:Q5P3J4.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS11495
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaF. New product name: PaaF. New product name synonym: putative 2,3-dehydroadipyl-CoA hydratase. New product name confidence: Class 2. New PubMed ID: 18776009. New PubMed ID: 20660314. New comment:
. Annotation transferred from: UniProtKB:P76082.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 20, 2020 |
WQ49_RS10080
|
Burkholderia cenocepacia
K56-2 |
New product name: trimeric autotransporter adhesin. New product name confidence: Class 2. New PMID: 22919579.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
WQ49_RS09590
|
Burkholderia cenocepacia
K56-2 |
New product name: trimeric autotransporter adhesin. New product name confidence: Class 2. New PMID: 22919579.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
WQ49_RS09445
|
Burkholderia cenocepacia
K56-2 |
New product name: putative (R)-specific oxepin-CoA hydratase. New product name synonym: PaaZ-ECH. New product name confidence: Class 2. New PubMed ID: 21296885. New comment: in E coli, paaZ encodes a bifunctional protein consisting of an N-terminal NADP-dependent aldehyde dehydrogenase domain and a C-terminal MaoC-like (R)-specific enoyl-CoA hydratase domain. In Burkholderia genomes, a gene incorrectly annotated as paaZ (e.g WQ49_RS11500) encodes only one of the two domains found in E.coli paaZ (the domain with semialdehyde dehydrogenase activity) and so is renamed PacL (PMID:21296885) but was also referred to as PaaZ-ALDH in the manuscript. In the same study , a separate A. aromaticum, protein (UniProtKB:Q5P232) with the (R)-hydratase activity was annotated as Ech-Aa and the Burkholderia ortholog was annotated as PaaZ-ECH.
. Annotation transferred from: UniProtKB:Q5P232.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 20, 2020 |
WQ49_RS07805
|
Burkholderia cenocepacia
K56-2 |
New product name: trimeric autotransporter adhesin. New product name confidence: Class 1. New PMIDs: 22919579, 32097539.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
WQ49_RS04260
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaH. New product name: PaaH. New product name synonym: putative 3-hydroxyadipyl-CoA dehydrogenase. New product name confidence: Class 2. New PubMed ID: 20660314. New PubMed ID: 12846838. New comment:
. Annotation transferred from: UniProtKB:P76083.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WQ49_RS04255
|
Burkholderia cenocepacia
K56-2 |
New gene name: paaK2. New product name: Paak2. New product name synonym: phenylacetate-CoA ligase. New product name confidence: Class 1. New PubMed ID: 21388965. New comment:
.
|
Dustin Lavallee and Silvia Cardona, University of Manitoba
|
Apr 30, 2018 |
WJ59_RS21240
|
Burkholderia gladioli
MSMB1756 |
New product name: T3SS-secreted prophage tail-like protein. New product name confidence: Class 2. New subcellular localization: Host Associated (Class 2). New subcellular localization evidence code (ECO): ECO:0000250. New subcellular localization PMID: 28864820. New PubMed ID: 28864820. New comment: .Annotation transferred from: GenBank:AOO34660.1.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS65806
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2568766..2568918 (+ strand). New start coordinate: 2568766. New end coordinate: 2568918. New gene name: ncS37. New product name: small regulatory ncRNA ncS37. New product name confidence: Class 1. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
QU43_RS64696
|
Burkholderia cenocepacia
J2315 |
New PMID: 29359187.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS64696
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2304213..2304378 (- strand). New start coordinate: 2304213. New end coordinate: 2304378. New gene name: ncS35. New product name: small regulatory ncRNA ncS35. New product name confidence: Class 1. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS63756
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2089713..2089769 (+ strand). New start coordinate: 2089713. New end coordinate: 2089769. New gene name: ncS62. New product name: double-hairpin RNA ncS62. New product name confidence: Class 1. New PubMed ID: 29142288. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
QU43_RS53446
|
Burkholderia cenocepacia
J2315 |
New gene name: bdhR1. New gene name synonym: ncS27. New product name: Burkholderia double-hairpin sRNA regulator bdhR1. New product name confidence: Class 1. New PMID: 31464662.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS53446
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 3666557..3666648 (- strand). New start coordinate: 3666557. New end coordinate: 3666648. New gene name: ncS27. New product name: double-hairpin RNA ncS27. New product name confidence: Class 1. New PubMed ID: 29142288. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS51716
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 3297991..3298074 (- strand). New start coordinate: 3297991. New end coordinate: 3298074. New gene name: ncS25. New product name: small regulatory ncRNA ncS25. New product name confidence: Class 1. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS49841
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2912201..2912283 (+ strand). New start coordinate: 2912201. New end coordinate: 2912283. New gene name: ncS16. New product name: small regulatory ncRNA ncS16. New product name confidence: Class 1. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS48121
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2548559..2548685 (+ strand). New start coordinate: 2548559. New end coordinate: 2548685. New gene name: ncS63. New product name: small regulatory ncRNA ncS63. New product name synonym: BTH_s39. New product name confidence: Class 1. New PubMed ID: 29142288. New PubMed ID: 24884623. New comment: Confirmed by Northern Blot. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS48101
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 2545296..2545503 (- strand). New start coordinate: 2545296. New end coordinate: 2545503. New gene name: ncS11. New product name: small regulatory ncRNA ncS11. New gene name synonym: ncRNA13. New product name confidence: Class 1. New PubMed ID: 29142288. New PubMed ID: 19234113. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS41981
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 1179680..1179807 (+ strand). New start coordinate: 1179680. New end coordinate: 1179807. New gene name: ncS54. New product name: small regulatory ncRNA ncS54. New product name confidence: Class 1. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS39311
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 603652..603910 (+ strand). New start coordinate: 603652. New end coordinate: 603910. New gene name: ncS06. New product name: small regulatory ncRNA ncS06. New gene name synonym: ncRNA7. New product name synonym: BTH_s1. New product name confidence: Class 1. New PubMed ID: 29142288. New PubMed ID: 24884623. New PubMed ID: 19234113. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS38736
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 479440..479506 (- strand). New start coordinate: 479440. New end coordinate: 479506. New gene name: ncS05. New product name: double-hairpin RNA ncS05. New product name confidence: Class 1. New PubMed ID: 29142288. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS37856
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 292949..293053 (+ strand). New start coordinate: 292949. New end coordinate: 293053. New gene name: ncS04. New product name: small regulatory ncRNA ncS04. New product name synonym: anti-hemB. New product name confidence: Class 1. New PubMed ID: 29142288. New PubMed ID: 23282220. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS37471
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 221314..221372 (+ strand). New start coordinate: 221314. New end coordinate: 221372. New gene name: ncS03. New product name: double-hairpin RNA ncS03. New product name confidence: Class 1. New PubMed ID: 29142288. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
QU43_RS36586
|
Burkholderia cenocepacia
J2315 |
New ncRNA gene identified at 20581..20691 (+ strand). New start coordinate: 20581. New end coordinate: 20691. New gene name: ncS01. New product name: small regulatory ncRNA ncS01. New PubMed ID: 29142288. New comment: Confirmed by Northern Blot. 3'end confirmed by RACE. 3'end defined in dRNA-Seq data.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
LA03_RS18415
|
Burkholderia gladioli
UCD-UG_CHAPALOTE |
New product name: T3SS-secreted prophage tail-like protein. New product name confidence: Class 2. New subcellular localization: Host Associated (Class 2). New subcellular localization evidence code (ECO): ECO:0000250. New subcellular localization PMID: 28864820. New PubMed ID: 28864820. New comment: .Annotation transferred from: GenBank:AOO34660.1.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
KS03_RS21965
|
Burkholderia glumae
ATCC 33617 |
New gene name: tepR. New product name: toxoflavin and eps regulator, TepR. New product name confidence: Class 2. New PubMed ID: 28036242. New comment: .Annotation transferred from: BGLU_RS04835.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
KS03_RS20605
|
Burkholderia glumae
ATCC 33617 |
New gene name: ntpR. New product name: NtpR. New product name synonym: negative regulator of toxoflavin production LysR . New product name confidence: Class 2. New PubMed ID: 28036242. New comment: .Annotation transferred from: BGLU_RS03475.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS29310
|
Burkholderia cenocepacia
H111 |
New gene name: copA. New product name: Copper-exporting P-type ATPase, CopA. New product name confidence: Class 2. Name transferred from: UniProtKB:Q59385. New comment: Required for growth in the presence of 20__M CuSO4 (PMID:32090500). New PMIDs: 32090500, 12832075.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS25090
|
Burkholderia cenocepacia
H111 |
New gene name: tecA. New product name: type VI secretion system effector protein TecA. New product name confidence: Class 2. New subcellular localization: Extracellular (Class 2). New subcellular localization evidence code (ECO): ECO:0000250. New subcellular localization cross-ref: BGD:BCAM1857. New subcellular localization PMID: 27133449. New PubMed ID: 27133449. New comment: .Annotation transferred from: BGD:BCAM1857.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21130
|
Burkholderia cenocepacia
H111 |
New gene name: bceU. New product name: acyltransferase BceU. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Since bceU is found in the genome sequences of all Bcc strains as well as in B. thailandensis, B. oklahomensis, and B. pseudomallei strains, the authors of PMID:19948863 considered it to belong as part of bce-II gene cluster.. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4480.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21125
|
Burkholderia cenocepacia
H111 |
New gene name: bceT. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4479.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21120
|
Burkholderia cenocepacia
H111 |
New gene name: bceS. New product name: acyltransferase BceS. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Note that another gene (BCAM1494) for a two-component sensor kinase in B. cenocepacia J2315 was also assigned the name bceS at a later date (PMID:25519693).. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4477.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21115
|
Burkholderia cenocepacia
H111 |
New gene name: bceR. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Disruption of the bceQ and bceR genes, in B. cepacia IST408 (PMID:19948863) resulted in the abolishment of cepacian biosynthesis. . New comment: Note that another gene (BCAM1493) for a two-component response regulator in B. cenocepacia J2315 was also assigned the name bceR at a later date (PMID:25519693).. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4476.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21110
|
Burkholderia cenocepacia
H111 |
New gene name: bceQ. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Disruption of the bceQ and bceR genes, in B. cepacia IST408 (PMID:19948863) resulted in the abolishment of cepacian biosynthesis. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4475.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21105
|
Burkholderia cenocepacia
H111 |
New gene name: bceP. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4474.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21100
|
Burkholderia cenocepacia
H111 |
New gene name: bceO. New product name: acyltransferase BceO. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4473.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21095
|
Burkholderia cenocepacia
H111 |
New gene name: bceN. New product name: GDP-D-mannose 4,6-dehydratase BceN. New product name confidence: Class 2. New PubMed ID: 23460819. New PubMed ID: 19948863. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:BCAM1004.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS21090
|
Burkholderia cenocepacia
H111 |
New gene name: bceM. New product name: GDP-6-deoxy-D-lyxo-4-hexulose reductase BceM. New PubMed ID: 19948863. New comment: Member of the bce-II gene cluster.Annotation transferred from: BGD:Bcep1808_4471.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20395
|
Burkholderia cenocepacia
H111 |
New gene name: bceK. New product name: BceK. New product name confidence: Class 2. New PubMed ID: 19948863. New PubMed ID: 22919582. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4210.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20390
|
Burkholderia cenocepacia
H111 |
New gene name: bceJ. New product name: BceJ. New product name confidence: Class 2. New PubMed ID: 19948863. New PubMed ID: 22919582. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4209.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20385
|
Burkholderia cenocepacia
H111 |
New gene name: bceI. New product name: BceI. New product name confidence: Class 2. New PubMed ID: 14637140. New PubMed ID: 19948863. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4208.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20380
|
Burkholderia cenocepacia
H111 |
New gene name: bceH. New product name: BceH. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4207.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20375
|
Burkholderia cenocepacia
H111 |
New gene name: bceG. New product name: BceG. New product name confidence: Class 2. New PubMed ID: 14637140. New PubMed ID: 19948863. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4206.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20370
|
Burkholderia cenocepacia
H111 |
New gene name: bceF. New product name: tyrosine kinase BceF. New product name confidence: Class 2. New PubMed ID: 17114319. New PubMed ID: 23435894. New PubMed ID: 25486990. New PubMed ID: 26590274. New PubMed ID: 19948863. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4205.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20365
|
Burkholderia cenocepacia
H111 |
New gene name: bceE. New product name: BceE. New product name confidence: Class 2. New PubMed ID: 19948863. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4204.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20360
|
Burkholderia cenocepacia
H111 |
New gene name: bceD. New product name: phosphotyrosine phosphatase BceD. New product name confidence: Class 2. New PubMed ID: 17114319. New PubMed ID: 19948863. New PubMed ID: 26590274. New PubMed ID: 25486990. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4203.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20355
|
Burkholderia cenocepacia
H111 |
New gene name: bceC. New product name: UDP-Glucose Dehydrogenase BceC. New product name confidence: Class 2. New PubMed ID: 19948863. New PubMed ID: 21602353. New PubMed ID: 20208157. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:Bcep1808_4202.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20350
|
Burkholderia cenocepacia
H111 |
New gene name: bceB. New product name: undecaprenyl-phosphate glycosyl-1-phosphate transferase BceB. New PubMed ID: 19948863. New PubMed ID: 15995219. New PubMed ID: 18667584. New comment: Member of the bce-I gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS20345
|
Burkholderia cenocepacia
H111 |
New gene name: bceA. New product name: bifunctional exopolysaccharide biosynthesis protein (phosphomannose isomerase and GDP-D-mannose pyrophosphorylase) BceA. New product name confidence: Class 1. New PubMed ID: 19948863. New PubMed ID: 17184737. New PubMed ID: 18668237. New comment: Member of the bce-I gene cluster.Annotation transferred from: BGD:BCAM0854.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS18940
|
Burkholderia cenocepacia
H111 |
New gene name: dfsA. New product name: diffusible factor synthase A. New gene name synonym: rpfF. New product name confidence: Class 2. New PubMed ID: 18049456. New PubMed ID: 23231487. New PubMed ID: 25681189. New PubMed ID: 26725701. New PubMed ID: 22221091. New comment: .Annotation transferred from: BGD:BCAM0581.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS18935
|
Burkholderia cenocepacia
H111 |
New gene name: rpfR. New product name: cis-2-dodecenoic acid receptor RpfR. New product name confidence: Class 1. New PubMed ID: 22949660. New PubMed ID: 28956352. New PubMed ID: 28463102. New PubMed ID: 23815566. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS18335
|
Burkholderia cenocepacia
H111 |
New gene name: copD. New product name confidence: Class 2. New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS18330
|
Burkholderia cenocepacia
H111 |
New gene name: copC. New product name: CopC. New product name confidence: Class 2. New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS18325
|
Burkholderia cenocepacia
H111 |
New gene name: cusF. New product name: CusF. New product name confidence: Class 2. New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS18300
|
Burkholderia cenocepacia
H111 |
New gene name: copR. New product name: CopR. New product name confidence: Class 2. Name transferred from: UniProtKB:Q47456. New PMID: 11004187.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS18295
|
Burkholderia cenocepacia
H111 |
New gene name: copS. New product name: CopS. New product name confidence: Class 2. Name transferred from: UniProtKB:Q47457. New PMID: 11004187.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS17890
|
Burkholderia cenocepacia
H111 |
New gene name: atsR. New product name: hybrid two-component system kinase-response regulator protein AtsR. New product name confidence: Class 1. New PubMed ID: 22830644. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS15965
|
Burkholderia cenocepacia
H111 |
New comment: Required for growth in the presence of 20__M CuSO4 (PMID:32090500). New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS15645
|
Burkholderia cenocepacia
H111 |
New gene name: rqpR. New product name: two-component regulatory system, response regulator RqpR. New product name confidence: Class 1. New PubMed ID: 29363827. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS15640
|
Burkholderia cenocepacia
H111 |
New gene name: rqpS. New product name: two-component regulatory system, sensor histidine kinase RqpS. New product name confidence: Class 1. New PubMed ID: 29363827. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS12975
|
Burkholderia cenocepacia
H111 |
New gene name: cueO. New product name: CueO. New product name confidence: Class 2. New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS11185
|
Burkholderia cenocepacia
H111 |
New gene name: cueR. New product name: CueR. New product name confidence: Class 2. Name transferred from: UniProtKB:P0A9G4. New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS10755
|
Burkholderia cenocepacia
H111 |
New gene name: ntrC. New product name: NtrC. New PubMed ID: 28662146. New comment:
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS02045
|
Burkholderia cenocepacia
H111 |
New gene name: pacL. New product name: PacL. New product name synonym: putative 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase. New product name confidence: Class 2. New PubMed ID: 21296885. New PubMed ID: 18776009. New comment: in E coli, paaZ encodes a bifunctional protein consisting of an N-terminal NADP-dependent aldehyde dehydrogenase domain and a C-terminal MaoC-like (R)-specific enoyl-CoA hydratase domain. In Burkholderia genomes, a gene incorrectly annotated as paaZ (e.g WQ49_RS11500) encodes only one of the two domains found in E.coli paaZ (the domain with semialdehyde dehydrogenase activity) and so is renamed PacL (PMID:21296885) but was also referred to as PaaZ-ALDH in the manuscript. In the same study , a separate A. aromaticum, protein (UniProtKB:Q5P232) with the (R)-hydratase activity was annotated as Ech-Aa and the Burkholderia ortholog was annotated as PaaZ-ECH.
. Annotation transferred from: UniProtKB:Q5P3J4.
|
Geoff Winsor, Simon Fraser University. Transferred annotation from the B. cenocepacia annotation provided by D. Lavellee and S. Cardona.
|
Apr 30, 2018 |
I35_RS01775
|
Burkholderia cenocepacia
H111 |
New gene name synonym: bcsA. New product name confidence: Class 2. New PubMed ID: 18316384. New PubMed ID: 21178498. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01770
|
Burkholderia cenocepacia
H111 |
New gene name: tssM. New product name: type VI secretion system protein TssM. New gene name synonym: icmF. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 22102820. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01765
|
Burkholderia cenocepacia
H111 |
New gene name: tagF. New product name: type VI secretion system-associated protein TagF. New gene name synonym: bcsC. New product name confidence: Class 2. New PubMed ID: 18316384. New PubMed ID: 22411981. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01760
|
Burkholderia cenocepacia
H111 |
New gene name: tagL. New product name: type VI secretion system-associated protein TagL. New gene name synonym: bcsD. New product name confidence: Class 2. New PubMed ID: 18316384. New PubMed ID: 21178498. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01755
|
Burkholderia cenocepacia
H111 |
New gene name: tssA. New product name: type VI secretion system protein TssA. New gene name synonym: bcsE. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01750
|
Burkholderia cenocepacia
H111 |
New gene name: tssH. New product name: type VI secretion system protein TssH. New gene name synonym: clpV. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 19131969. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01745
|
Burkholderia cenocepacia
H111 |
New gene name: tssG. New product name: type VI secretion system protein TssG. New gene name synonym: bcsG. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 23921384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01740
|
Burkholderia cenocepacia
H111 |
New gene name: tssF. New product name: type VI secretion system protein TssF. New gene name synonym: bcsH. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01735
|
Burkholderia cenocepacia
H111 |
New gene name: tssE. New product name: type VI secretion system protein TssE. New gene name synonym: bcsI. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01730
|
Burkholderia cenocepacia
H111 |
New gene name: tssD. New product name: type VI secretion system protein TssD. New gene name synonym: hcp. New product name synonym: hemolysin-coregulated protein Hcp. New product name confidence: Class 1. New subcellular localization: Extracellular (Class 1). New subcellular localization evidence code (ECO): ECO:0000333. New subcellular localization PMID: 18316384. New PubMed ID: 8557353. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01725
|
Burkholderia cenocepacia
H111 |
New gene name: tssC. New product name: type VI secretion system protein TssC. New gene name synonym: bcsK. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 20729192. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01720
|
Burkholderia cenocepacia
H111 |
New gene name: tssB. New product name: type VI secretion system protein TssB. New gene name synonym: bcsL. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 20729192. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01715
|
Burkholderia cenocepacia
H111 |
New gene name synonym: bcsM. New product name confidence: Class 2. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01710
|
Burkholderia cenocepacia
H111 |
New gene name: tssJ. New product name: type VI secretion system protein TssJ. New gene name synonym: bcsN. New product name confidence: Class 2. New PubMed ID: 18316384. New PubMed ID: 22102820. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster.Annotation transferred from: PDB:3RX9.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01705
|
Burkholderia cenocepacia
H111 |
New gene name: tssK. New product name: type VI secretion system protein TssK. New gene name synonym: bcsO. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 23921384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
I35_RS01700
|
Burkholderia cenocepacia
H111 |
New gene name: tssL. New product name: type VI secretion system protein TssL. New gene name synonym: bcsP. New product name confidence: Class 1. New PubMed ID: 18316384. New PubMed ID: 26364149. New comment: Part of the T6SS gene cluster
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
I35_RS01625
|
Burkholderia cenocepacia
H111 |
New product name confidence: Class 2. New comment: Required for growth in the presence of 20__M CuSO4 (PMID:32090500). New PMID: 32090500.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
DM80_RS04270
|
Burkholderia multivorans
DDS 15A-1 |
New gene name: ampC1. New gene name synonym: ampC. New product name synonym: AmpC1. New product name confidence: Class 2. New PMID: 30012762.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
D590_RS24420
|
Burkholderia gladioli
3848s-5 |
New product name: T3SS-secreted prophage tail-like protein. New product name confidence: Class 2. New subcellular localization: Host Associated (Class 2). New subcellular localization evidence code (ECO): ECO:0000250. New subcellular localization PMID: 28864820. New PubMed ID: 28864820. New comment: .Annotation transferred from: GenBank:AOO34660.1.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 30, 2018 |
CH72_RS04090
|
Burkholderia ambifaria
AMMD |
New gene name: kdoO. New product name: Kdo 3-hydroxylase KdoO. New product name confidence: Class 1. New PubMed ID: 21178073. New PubMed ID: 25204504. New comment: Responsible for Ko formation with Kdo2-lipid A as a substrate
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Apr 20, 2020 |
C6Q10_RS14220
|
Burkholderia multivorans
AU19564 |
New gene name: ampC2. New gene name synonym: ampC. New product name: class C beta-lactamase. New product name synonym: AmpC2. New product name confidence: Class 2. New PMID: 30012762.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
Jan 25, 2011 |
Bxe_C0458
|
Burkholderia xenovorans
LB400 |
New product name confidence: Class 2. New pathway: VirB4/D4 Type IV Secretion System. New GO Accession: GO:0030255(ISS). New PubMed reference: 15342570. New PubMed reference: 19744991. New PubMed reference: 18824538.
|
Literature review. Geoffrey L. Winsor (Brinkman Lab). Simon Fraser University, Canada
|
Jan 25, 2011 |
Bxe_C0458
|
Burkholderia xenovorans
LB400 |
New product name confidence: Class 2. New pathway: VirB4/D4 Type IV Secretion System. New GO accession: GO:0030255 [ISS]. New evidence reference (PMID): 15342570. New evidence reference (PMID): 19744991. New evidence reference (PMID): 18824538.
|
Literature review. Geoffrey L. Winsor (Brinkman Lab). Simon Fraser University, Canada
|