| Sep 15, 2020 |
PA0259
|
Pseudomonas aeruginosa
PAO1 |
New comment: In a previous release, we updated the start site to 291154 based on a recombinant tla3 gene with this start site being used in E. coli. There is no evidence for 291154 being the translation initiation site in P. aeruginosa so it have been reverted back to 291004.
|
Sophie Bleves, Institute of Microbiology of the Mediterranean, France
|
| Sep 15, 2020 |
PP_2674
|
Pseudomonas putida
KT2440 |
New comment: New function/Role: Initiates an alternative route for glycerol metabolism that provides a growth advantage by reducing the lag phase of the cells. New PMID: 32345644.
|
Janosch Klebensberger, University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2679
|
Pseudomonas putida
KT2440 |
New comment: New function/Role: Initiates an alternative route for glycerol metabolism that provides a growth advantage by reducing the lag phase of the cells. New PMID: 32345644.
|
Janosch Klebensberger, University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_3178
|
Pseudomonas putida
KT2440 |
New product name confidence: Class 1. New comment: New function/Role: Part of an alternative route for glycerol metabolism that provides a growth advantage by reducing the lag phase of the cells. New PMID: 32345644.
|
Janosch Klebensberger, University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PA2402
|
Pseudomonas aeruginosa
PAO1 |
New gene name: pvdI. New product name: pyoverdine peptide synthetase. New product name synonym: PvdI. New product name confidence: Class 1. New PMIDs: 12207696, 12686626, 10981704.
|
Iain Lamont, University of Otago, New Zealand
|
| Sep 15, 2020 |
PA2403
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2404
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2405
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2406
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2407
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2408
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2409
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2410
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part ABC transporter complex FpvWXYZCDEF coded by operons fpvWXYZCDEF and fpvF. New PMID: 28975384.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PKB_RS08575
|
Pseudomonas knackmussii
B13 |
New gene name synonym: PKB_1739.
|
Nicolas Wirth, DTU, Denmark
|
| Sep 15, 2020 |
PA2492
|
Pseudomonas aeruginosa
PAO1 |
New gene name: mexT. New comment: Contains an 8_bp insertion at 2807703-2807710 which is the result of a duplication of the preceding 8_bp GGCCAGCC sequence at 2807695-2807702. When translated from this start codon, premature termination occurs at 2807857-2807859 and a MexT polypeptide of 89 amino acids is encoded (PMID:31859619).; PAO1 strains containing the 8_bp insertion are unable to express MexEF-OprN due to a non-functional MexT(PMID: 11040437). New PMIDs: 31859619, 11040437.
|
Herbert P. Schweizer, University of Florida, USA
|
| Sep 15, 2020 |
PA0667
|
Pseudomonas aeruginosa
PAO1 |
New gene name: mepM. New product name: MepM. New product name confidence: Class 2. Name transferred from: UniProt:P0AFS9. New comment: Peptidoglycan cross-link hydrolase (based on homology to E.coli MepM). New PMID: 30018106.
|
Andrew Darwin, NYU School of Medicine, USA
|
| Sep 15, 2020 |
Y880_RS30035
|
Pseudomonas aeruginosa
PAK |
New gene name: mepM. New product name: MepM. New product name confidence: Class 2. Name transferred from: UniProt:P0AFS9. New comment: Peptidoglycan cross-link hydrolase (based on homology to E.coli MepM). New PMID: 30018106.
|
Andrew Darwin, NYU School of Medicine, USA
|
| Sep 15, 2020 |
PA4667
|
Pseudomonas aeruginosa
PAO1 |
New gene name: lbcA. New product name: LbcA. New product name synonym: lipoprotein binding partner of CtpA. New product name confidence: Class 1. New comment: Binding partner of CtpA (PA5134), required for CtpA proteolytic activity. New PMID: 30018106.
|
Andrew Darwin, NYU School of Medicine, USA
|
| Sep 15, 2020 |
Y880_RS21705
|
Pseudomonas aeruginosa
PAK |
New gene name: lbcA. New product name: LbcA. New product name synonym: lipoprotein binding partner of CtpA. New product name confidence: Class 1. New comment: Binding partner of CtpA (PA5134), required for CtpA proteolytic activity. New PMID: 30018106.
|
Andrew Darwin, NYU School of Medicine, USA
|
| Sep 15, 2020 |
PP_5538
|
Pseudomonas putida
KT2440 |
New gene name: pedA1. New product name: PedA1. New comment: Essential for PedH-dependent growth under low (nM) concentrations of lanthanides. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2669
|
Pseudomonas putida
KT2440 |
New gene name: pedA2. New product name: PedA2. New comment: Essential for PedH-dependent growth under low (nM) concentrations of lanthanides. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2668
|
Pseudomonas putida
KT2440 |
New gene name: pedB. New product name: PedB. New comment: Essential for PedH-dependent growth under low (nM) concentrations of lanthanides. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2667
|
Pseudomonas putida
KT2440 |
New gene name: pedC. New product name: PedC. New comment: Essential for PedH-dependent growth under low concentrations (nM) of lanthanides. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2674
|
Pseudomonas putida
KT2440 |
New gene name: pedE. New product name: PedE. New comment: The lanthanum-dependent transcriptional repression through PedR2 is influenced by the environmental concentration of iron. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PP_2679
|
Pseudomonas putida
KT2440 |
New gene name: pedH. New product name: PedH. New comment: PedH-dependent growth with 2-phenylethanol under low (nM) concentrations of lanthanides relies on the ABC transporter PedA1A2BC. New PMID: 31736923.
|
Janosch Klebensberger, University of Stuttgart, Institute of Technical Biochemistry, Stuttgart, Germany
|
| Sep 15, 2020 |
PA1300
|
Pseudomonas aeruginosa
PAO1 |
New gene name: hxuI. New product name: HxuI. New product name synonym: ECF sigma factor HxuI. New product name confidence: Class 1. New PMID: 31390127.
|
Maria A. Llamas, Dept. Environmental Protection, Estacion Experimental del Zaidin-CSIC, Granada, Spain
|
| Sep 15, 2020 |
PA1301
|
Pseudomonas aeruginosa
PAO1 |
New gene name: hxuR. New product name: HxuR. New product name synonym: anti-sigma factor HxuR. New product name confidence: Class 1. New PMID: 31390127.
|
Maria A. Llamas, Dept. Environmental Protection, Estacion Experimental del Zaidin-CSIC, Granada, Spain
|
| Sep 15, 2020 |
PA1302
|
Pseudomonas aeruginosa
PAO1 |
New gene name: hxuA. New product name: HxuA. New product name synonym: Heme receptor HxuA. New product name confidence: Class 1. New PMID: 31390127.
|
Maria A. Llamas, Dept. Environmental Protection, Estacion Experimental del Zaidin-CSIC, Granada, Spain
|
| Sep 15, 2020 |
PA3409
|
Pseudomonas aeruginosa
PAO1 |
New product name confidence: Class 1. New PMID: 31390127.
|
Maria A. Llamas, Dept. Environmental Protection, Estacion Experimental del Zaidin-CSIC, Granada, Spain
|
| Sep 15, 2020 |
PA3410
|
Pseudomonas aeruginosa
PAO1 |
New product name confidence: Class 1. New PMID: 31390127.
|
Maria A. Llamas, Dept. Environmental Protection, Estacion Experimental del Zaidin-CSIC, Granada, Spain
|
| Sep 15, 2020 |
PA0277
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative Zn-dependent peptidase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3C37: putative peptidase Zn-dependent from Geobacter sulfurreducens (root-mean-square deviation: 1.5 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA0371
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative Zn-dependent peptidase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3AMJ: metallopeptidase from Sphingomonas SP. A1 (root-mean-square deviation: 1.0 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1005
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative beta-barrel assembly-enhancing protease. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 6AIT: beta-Barrel Assembly-Enhancing Protease BepA from Escherichia coli (root-mean-square deviation: 0.8 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4632
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative Zn-dependent peptidase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3C37: putative peptidase Zn-dependent from Geobacter sulfurreducens (root-mean-square deviation: 1.0 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2448
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative hydrolase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3IGH: uncharacterized metal-dependent hydrolase from Pyrococcus horikoscii (root-mean-square deviation: 0.9 angstroms) Hydrolase. New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1304
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 2XE4: oligopeptidase B from Leishmania major (root-mean-square deviation: 0.6 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2854
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative L,D-transpeptidase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 4LZH: L,D-transpeptidase from Klebsiella pneumoniae (root-mean-square deviation: 0.7 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3054
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative carboxypeptidase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 1H8L: human carboxypeptidase M (root-mean-square deviation: 2.2 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5134
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 4C2E: carboxyprotease from Tetradesmus obliquus (root-mean-square deviation: 1.6 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1046
|
Pseudomonas aeruginosa
PAO1 |
New product name: beta-agarase. New product name confidence: Class 1. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 4BQ3: B-agarase (root-mean-square deviation: 0.8 angstroms) ; 99% identical to beta-1,3-glucanase (GenBank: KY865343.1) in P. aeruginosa CAU 342A . New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy. Further literature review by Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2352
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative glycerophosphoryl diester phosphodiesterase. New comment: Structural similarity to 2OOG: glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus (root-mean-square deviation: 1.5 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3238
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative lipase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 1HLG: human gastric lipase (root-mean-square deviation: 1.4 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4621
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 1RM6: 4-hydroxybenzoyl-CoA reductase from Thauera aromatica (root-mean-square deviation: 0.8 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3125
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative transferase. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3SKV: Salicylyl-Acyltransferase SsfX3 from Streptomyces (root-mean-square deviation: 1.0 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1579
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative lipid binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2R55: START-related lipid transfer protein 5 from Homo sapiens (root-mean-square deviation: 1.0 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3785
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative copper binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2K6W: copper protein from Thermus thermophilus (root-mean-square deviation: 1.5 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4453
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative phospholipid binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2QGU: phospholipid binding protein from Ralstonia Solanacearum (root-mean-square deviation: 1.1 angstroms). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2407
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1XVL (Mn transporter from Synechocystis 6803, root-mean-square deviation: 0.9 angstroms). Sequence similarity to 1PSZ (97%/23,84%) (ZN). Final predicted ligand: metal Ion (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5498
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 2XQV (zinc transporter ZnuA from Salmonella enterica, root-mean-square deviation: 1.7 angstroms). Sequence similarity to 4BBP (98%/39,72%) (ZN). Final predicted ligand: zinc Ion (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2913
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 4MLZ (periplasmic binding protein from Jonesia denitrificans, root-mean-square deviation: 2.1 angstroms). Sequence similarity to 4MLZ (93%/28,67%)(no ligand). Final predicted ligand: No Ligand (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3836
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 3LKV (conserved domain protein from Vibrio cholerae, root-mean-square deviation: 0.6 angstroms). Sequence similarity to 3LKV (96%/50%) (PHE). Final predicted ligand: phenylalanine (PMID: 31631799). New PMID: 31631799.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1810
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 4ONY (ABC transporter from Brucella melitensis da Thermotoga maritima, root-mean-square deviation:0.3 angstroms). Sequence similarity to 4ONY (96%/42,44%) (no ligand). Final predicted ligand: No Ligand (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4496
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1DPE (dipeptide binding protein from Escherichia coli, root-mean-square deviation: 0.5 angstroms). Sequence similarity to 1DPP (99%/53,06%) (G-L). Final predicted ligand: dipeptide (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4500
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1DPE (dipeptide binding protein from Escherichia coli, root-mean-square deviation: 0.4 angstroms). Sequence similarity to 1DPP (98%/53,16%) (G-L). Final predicted ligand: dipeptide (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4502
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1DPE (dipeptide binding protein from Escherichia coli, root-mean-square deviation: 0.5 angstroms). Sequence similarity to 1DPP (99%/50,20%) (G-L). Final predicted ligand: dipeptide (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5317
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1DPE (dipeptide binding protein from Escherichia coli, root-mean-square deviation: 0.6 angstroms). Sequence similarity to 1DPE (99%/44,86%) (G-L). Final predicted ligand: dipeptide (PMID: 31631799). New PMID: 31631799.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA0295
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 1A99 (putrescine-binding protein from Escherichia coli, root-mean-square deviation: 0.6 angstroms). Sequence similarity to 1A99 (99%/37,54%) (PUT). Final predicted ligand: putrescine (PMID: 31631799). New PMID: 31631799.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA0602
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 4I1D (ABC transporter substrate-binding protein from Bradyrhizobium japonicum, root-mean-square deviation: 0.8 angstroms). Sequence similarity to 4EUO (91%/33,44%) (ABU). Final predicted ligand: gamma-aminobutyric acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA0604
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 4I1D (ABC transporter substrate-binding protein from Bradyrhizobium japonicum, root-mean-square deviation: 0.8 angstroms). Sequence similarity to 4EUO (99%/36,22%) (ABU). Final predicted ligand: gamma-aminobutyric acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3520
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic substrate binding protein. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 5T1P (periplasmic solute-binding protein from Campylobacter jejuni, root-mean-square deviation: 0.4 angstroms). Sequence similarity to 5T1P (97%/68,42%) (GPE). Final predicted ligand: L-alpha-glycerophosphoryl-ethanolamine (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5217
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative binding protein of iron ABC transporter. New comment: Structural similarity to 2PT2 (iron-binding protein, FutA1, from Synechocystis 6803, root-mean-square deviation: 0.6 angstroms). Sequence similarity to 6G7N (98%/44,09%) (FE). Final predicted ligand: iron ion (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3779
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic substrate binding protein. New comment: Structural similarity to 4P47 (TRAP periplasmic solute binding protein from Ochrobactrum anthropi, root-mean-square deviation: 1.2 angstroms). Sequence similarity to 4N8G (98%/63,99%) (DAL). Final predicted ligand: dipeptide (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5167
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 4MX6 (TRAP periplasmic solute binding protein from Shewanella oneidensis, root-mean-square deviation: 0.5 angstroms). Sequence similarity to 4O94 (98%/60,07%) (SIN). Final predicted ligand: succinic acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA1342
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative acidic amino acid ABC transporter substrate-binding protein. New comment: Structural similarity to 2VHA (periplasmic l-aspartate/l-glutamate binding protein from Shigella flexneri, root-mean-square deviation: 0.5 angstroms). Sequence similarity to 2VHA (96%/62,22%) (GLU). Final predicted ligand: acidic amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2204
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative binding protein component of ABC transporter. New comment: Structural similarity to 3VV5 (amino acid ABC transporter from Thermus thermophilus, root-mean-square deviation: 0.7 angstroms). Sequence similarity to 4ZV1 (89%/39,11%) (ARG). Final predicted ligand: L-amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2594
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic aliphatic sulfonate binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3E4R:alkansulphonate-binding protein SsuA from Xanthomonas axonopodis, root-mean-square deviation:0.6 angstroms). Sequence similarity to 2X26 (98%/42,91%) (no ligand). Final predicted ligand: aliphatic sulphonate (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA2599
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic aliphatic sulfonate-binding protein . New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 3E4R (alkansulphonate-binding protein from Xanthomonas axonopodis, root-mean-square deviation:0.6 angstroms). Sequence similarity to 2X26 (86%/33,33%) (no ligand). Final predicted ligand: aliphatic sulphonate (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3865
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic lysine-, arginine-, ornithine-binding protein. New comment: Structural similarity to 1LAF (Lys/Arg/His-binding protein from Salmonella typhimurium, root-mean-square deviation:0.4 angstroms). Sequence similarity to 6FT2 (98%/46,58%) (ARG). Final predicted ligand: basic amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3931
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative methionine-binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 1XS5 (Lipoprotein Tp32 from Treponema pallidum, root-mean-square deviation: 0.6 angstroms). Sequence similarity to 4K3F (100%/72,38%) (MSE). Final predicted ligand: methionine (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4049
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2Q2C (Arg/Lys/His-binding protein ArtJ from Geobacillus stearothermophilu, root-mean-square deviation: 1.5 angstroms). Sequence similarity to 3TQL (60%/24%) (ARG). Final predicted ligand: basic amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA4195
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative amino acid ABC transporter substrate-binding protein. New comment: Structural similarity to 2YJP (solute receptors for L-cysteine from Neisseria gonorrhoeae, root-mean-square deviation: 1.4 angstroms). Sequence similarity to 4ZV1 (88%/35,24%) (ARG). Final predicted ligand: L-amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5076
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative amino acid ABC transporter substrate-binding protein. New comment: Structural similarity to 5T0W (ancestral amino acid-binding protein AncCDT-1, root-mean-square deviation: 0.8 angstroms). Sequence similarity to 3K4U (96%/52,99%) (LYS). Final predicted ligand: L-amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5138
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2PYY (L-glutamate-binding protein from Nostoc Punctiforme, root-mean-square deviation: 1.6 angstroms). Sequence similarity to 1GPM (17%/37,50%) (no ligand). Final predicted ligand: glutamic acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5139
|
Pseudomonas aeruginosa
PAO1 |
New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2PYY (L-glutamate-binding protein from Nostoc Punctiforme, root-mean-square deviation: 1.6 angstroms). Sequence similarity to No result. Final predicted ligand: glutamic acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5153
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 4ZV1 (ancestral arginine-binding protein, root-mean-square deviation: 1.0 angstroms). Sequence similarity to 3TQL (97%/40,97%) (ARG). Final predicted ligand: arginine (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5378
|
Pseudomonas aeruginosa
PAO1 |
New comment: Structural similarity to 2REG (ABC-transporter choline binding protein from Rhizobium meliloti, root-mean-square deviation: 0.4 angstroms). Sequence similarity to 2REG (99%/60%) (CHT). Final predicted ligand: choline (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5472
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative basic amino acid ABC transporter substrate-binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 2Q2C (Arg/Lys/His-binding protein ArtJ from Geobacillus stearothermophilus, root-mean-square deviation: 1.4 angstroms). Sequence similarity to 3RYO (10%/44%) (no ligand). Final predicted ligand: basic amino acid (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA5545
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative glutamate/glutamine-binding protein. New product name confidence: Class 3. New subcellular localization: Periplasmic. New subcellular localization confidence: Class 1. New PMID for subcellular localization: PMID:19333994. New comment: Structural similarity to 1US5 ( putative glutamate/glutamine-binding protein from Thermus thermophilus, root-mean-square deviation: 0.5 angstroms). Sequence similarity to 1US5 (99%/41,83%) (GLU). Final predicted ligand: glutamic Acid, glutamine (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA3313
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative periplasmic organophosphorous compound-binding protein. New product name confidence: Class 3. New comment: Structural similarity to 5LQ1 (phosphonate Binding Protein PtxB from Trichodesmium erythraeum, root-mean-square deviation:0.8 angstroms). Sequence similarity to 5LQ5 (75%/39,25%) (PO3). Final predicted ligand: organophosphorus compounds (PMID: 31631799). New PMIDs: 31631799, 19333994.
|
Fabio Polticelli, Department of Sciences, Roma Tre University, Italy
|
| Sep 15, 2020 |
PA0243
|
Pseudomonas aeruginosa
PAO1 |
New gene name: pip. New product name: Pip. New product name confidence: Class 1. New comment: Deletion of pip causes decreased pyocyanin biosynthesis in P. aeruginosa (PMID:32707314). New PMID: 32707314.
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Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA5253
|
Pseudomonas aeruginosa
PAO1 |
New product name synonym: Hp-1. New PMID: 32634088.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA5512
|
Pseudomonas aeruginosa
PAO1 |
New comment: MifS only responds with high specificity to the C5-dicarboxylate alpha-ketoglutarate (PMID:32553056). New PMID: 32553056.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA4132
|
Pseudomonas aeruginosa
PAO1 |
New gene name: mpaR. New product name: MpaR. New product name synonym: MvfR-mediated PQS and anthranilate regulator. New product name confidence: Class 1. New comment: Deletion of mpaR caused increased biofilm formation, but reduced pyocyanin production (PMID:32748556);Deletion of mpaR leads to increased expression of the ant operon and the catechol production (PMID:32748556). New PseudoCAP function class : Transcriptional regulators . New PMID: 32748556.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA5295
|
Pseudomonas aeruginosa
PAO1 |
New gene name: proE. New product name: ProE. New product name synonym: phosphodiesterase regulator of EPS. New product name confidence: Class 1. New comment: Mutation of proE results in wrinkly colony morphology in P. aeruginosa PAO1 (PMID:32582123);ProE negatively regulates the transcriptional expression of pel and psl (PMID:32582123). New PMID: 32582123.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0805.1
|
Pseudomonas aeruginosa
PAO1 |
New product name confidence: Class 1. New PMIDs: 32430407, 29587634.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0728.1
|
Pseudomonas aeruginosa
PAO1 |
New gene name: pfiA. New product name: PfiT antitoxin, PfiA. New product name confidence: Class 1. New PMID: 32246813.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0729
|
Pseudomonas aeruginosa
PAO1 |
New gene name: pfiT. New product name: Pf4 inhibition toxin, PfiT. New product name confidence: Class 1. New PMID: 32246813.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA3361
|
Pseudomonas aeruginosa
PAO1 |
New comment: Basolaterally applied LecB binds beta1-integrin and causes its internalization (PMID:32156827);LecB inhibits cell migration and epithelial wound healing (PMID:32156827). New PMID: 32156827.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2887
|
Pseudomonas aeruginosa
PAO1 |
New product name: AtuB. New product name confidence: Class 1. New comment: . New PMID: 31964529.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA1726
|
Pseudomonas aeruginosa
PAO1 |
New product name: BglX. New product name confidence: Class 1. New PMID: 31877028.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA5487
|
Pseudomonas aeruginosa
PAO1 |
New gene name: dgcH. New product name: DgcH. New product name synonym: diguanylate cyclase. New product name confidence: Class 1. New PMID: 31444209.
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Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0285
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative phosphodiesterase. New product name confidence: Class 3. New PMID: 31444209.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0290
|
Pseudomonas aeruginosa
PAO1 |
New product name: putative diguanylate cyclase. New product name confidence: Class 3. New PMID: 31444209.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0176
|
Pseudomonas aeruginosa
PAO1 |
New gene name synonym: mcpB. New product name synonym: methyl-accepting chemotaxis protein, McpB. New comment: Part of cluster II che genes involved in chemotaxis. New PMIDs: 31511598, 12142407, 16824098.
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Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA2652
|
Pseudomonas aeruginosa
PAO1 |
New PMID: 29391435.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA0180
|
Pseudomonas aeruginosa
PAO1 |
New comment: Part of cluster II che genes involved in chemotaxis. New PMID: 12142407.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA1244
|
Pseudomonas aeruginosa
PAO1 |
New product name synonym: LasR-specific antiactivator QslA. New PMIDs: 31405911, 24319092.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PA14_48150
|
Pseudomonas aeruginosa
UCBPP-PA14 |
New gene name: qslA. New product name: QslA. New product name synonym: LasR-specific antiactivator QslA. New product name confidence: Class 1. New PMIDs: 31405911, 24319092.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|
| Sep 15, 2020 |
PALES_40681
|
Pseudomonas aeruginosa
LESB58 |
New gene name: qslA. New product name: QslA. New product name synonym: LasR-specific antiactivator QslA. New product name confidence: Class 1. New PMIDs: 31405911, 24319092.
|
Literature review. Geoff Winsor, Brinkman Lab, Simon Fraser University, Canada
|