PaperBLAST
PaperBLAST Hits for sp|Q9RPT1|RHLG_PSEAE Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rhlG PE=1 SV=1 (256 a.a., MHPYFSLAGR...)
Show query sequence
>sp|Q9RPT1|RHLG_PSEAE Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rhlG PE=1 SV=1
MHPYFSLAGRIALVTGGSRGIGQMIAQGLLEAGARVFICARDAEACADTATRLSAYGDCQ
AIPADLSSEAGARRLAQALGELSARLDILVNNAGTSWGAALESYPVSGWEKVMQLNVTSV
FSCIQQLLPLLRRSASAENPARVINIGSVAGISAMGEQAYAYGPSKAALHQLSRMLAKEL
VGEHINVNVIAPGRFPSRMTRHIANDPQALEADSASIPMGRWGRPEEMAALAISLAGTAG
AYMTGNVIPIDGGFHL
Running BLASTp...
Found 250 similar proteins in the literature:
rhlG / Q9RPT1 NADPH-dependent β-ketoacyl reductase subunit (EC 1.1.1.100) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
2b4qA / Q9RPT1 Pseudomonas aeruginosa rhlg/NADP active-site complex (see paper)
PA3387 beta-ketoacyl reductase from Pseudomonas aeruginosa PAO1
NP_252077 3-oxoacyl-ACP reductase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2b4qA)
- Characterization of 3-Oxacyl-Acyl Carrier Protein Reductase Homolog Genes in Pseudomonas aeruginosa PAO1
Guo, Frontiers in microbiology 2019 - “...aeruginosa ( Kutchma et al., 1999 ; Hoang et al., 2002 ). RhlG, encoded by PA3387, the other OAR homolog, was first identified as a 3-ketoacyl reductase specifically involved in rhamnolipid synthesis ( Campos-Garcia et al., 1998 ). However, structural and genetic studies have shown that...”
- “...Tyr154-AAA-Lys158 adh_short; KR; Epimerase; adh_short_C2 PA3128 248 32.7 Gly9-ASR-Gly13-I-Gly15 Ser143, Tyr157-AAA-Lys161 adh_short; KR; Epimerase; adh_short_C2 PA3387 256 32.9 Gly16-GSR-Gly20-I-Gly22 Ser148, Tyr162-GPS-Lys166 adh_short; KR; Epimerase; adh_short_C2 PA4089 253 37.9 Gly13-AGQ-Gly17-I-Gly19 Ser142, Tyr156-AAS-Lys160 adh_short; KR; Epimerase; adh_short_C2 PA4389 252 34.7 Gly12-GCQ-Gly16-L-Gly18 Ser149, Tyr162-SAA-Lys166 adh_short; KR; adh_short_C2 PA4786 451...”
- Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Zhu, GigaScience 2018 - “...i PAO1, these reactions were associated with another 8 highly conserved isozymes (PA0182, PA1470, PA1827, PA3387, PA4089, PA4389, PA4786, and PA5524). Furthermore, condition-specific essential genes were predicted in i PAO1 by imposing transcriptomics constraints. Modification of lipid A with 4-amino-4-deoxy-L-arabinose (L-Ara4N) leads to polymyxin resistance in...”
- Induction by cationic antimicrobial peptides and involvement in intrinsic polymyxin and antimicrobial peptide resistance, biofilm formation, and swarming motility of PsrA in Pseudomonas aeruginosa
Gooderham, Journal of bacteriology 2008 - “...PA2893 PA2939 PA3077 PA3145 PA3148 PA3150 PA3152 PA3277 PA3327 PA3387 PA3409 PA3418 PA3427 PA3454 PA3630 nirJ nirH nirG nirC yeaG toxR coaA cbpD napB lcaD metE...”
- Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa
Skindersoe, Antimicrobial agents and chemotherapy 2008 - “...(rhlA, rhlB, rhlC, and rhlG; PA3479, PA3478, PA1130, and PA3387, respectively) (9, 46, 83). Rhamnolipid synthesis is turned on in early stationary phase of P....”
- Characterization of colony morphology variants isolated from Pseudomonas aeruginosa biofilms
Kirisits, Applied and environmental microbiology 2005 - “...Cell wall, LPS, capsule PA0763 PA0764 PA0765 PA0766d PA3387 Flagellar motility PA1100 PA1101 PA1102 PA1103 PA1104 PA1105 PA1443 PA1444 PA1445 PA1446 PA1447...”
- The Pseudomonas aeruginosa rhlG and rhlAB genes are inversely regulated and RhlG is not required for rhamnolipid synthesis.
Bazire, BMC microbiology 2014 - GeneRIF: rhlG was inversely regulated compared to rhlAB and rhlC.
PA14_20270 beta-ketoacyl reductase from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage
- BosR: A novel biofilm-specific regulator in Pseudomonas aeruginosa
Dostert, Frontiers in microbiology 2022 - “...Type VI effector chaperone for Tox-Rease 110.9 PA14_19990 (hasI) RNA polymerase ECF-subfamily sigma-70 factor 47.7 PA14_20270 rhlG Beta-ketoacyl reductase 4.6 PA14_20870 (plpD) Patatin-like protein 4.2 PA14_24040 xcpU Type II secretion outer membrane protein H precursor Essential PA14_34020 hsiF3 Type VI secretion protein Essential PA14_40330 (xphA) Type...”
D2S423 Short-chain dehydrogenase/reductase SDR from Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)
48% identity, 99% coverage
MSMEG_0121 rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium smegmatis str. MC2 155
MSMEG_0121 SDR family oxidoreductase from Mycolicibacterium smegmatis MC2 155
46% identity, 98% coverage
PADG_06006 uncharacterized protein from Paracoccidioides brasiliensis Pb18
41% identity, 87% coverage
- Paracoccidioides brasiliensis presents metabolic reprogramming and secretes a serine proteinase during murine infection
Lacerda, Virulence 2017 - “...the most enriched pathway, which includes acyl-CoA dehydrogenases (PADG_07604, PADG_05046, PADG_06335), short chain dehydrogenases/reductases (PADG_06247, PADG_06006), carnitine transport/metabolism (PADG_05773, PADG_06378), peroxisomal hydratase-dehydrogenase-epimerase (PADG_08651) and a 3-hydroxybutyryl-CoA dehydratase (PADG_05039). These genes demonstrated increase transcript abundance that ranged from 2.29 to 17.00 (TableS1). In addition, ethanol producing genes...”
PHYSODRAFT_252686 hypothetical protein from Phytophthora sojae
42% identity, 79% coverage
- Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
Pang, Scientific reports 2016 - “...family Transport 348690807 Hypothetical protein PHYSODRAFT_349569 Unclassified 348690475 Hypothetical protein PHYSODRAFT_323696 Unclassified 348689826 Hypothetical protein PHYSODRAFT_252686 Unclassified 348688971 Hypothetical protein PHYSODRAFT_537442 Unclassified 348688710 Hypothetical protein PHYSODRAFT_477401 Unclassified 348688366 Hypothetical protein PHYSODRAFT_353487 Unclassified 348687330 Hypothetical protein PHYSODRAFT_284057 Unclassified 348683932 Hypothetical protein PHYSODRAFT_485543 Unclassified 348683032 Hypothetical protein PHYSODRAFT_253833...”
PAAG_06953 short chain dehydrogenase/reductase family from Paracoccidioides lutzii Pb01
40% identity, 88% coverage
- Transcriptional and proteomic responses to carbon starvation in Paracoccidioides
Lima, PLoS neglected tropical diseases 2014 - “...sulfur metabolism PAAG_07811 sulfite oxidase # nitrogen, sulfur and selenium metabolism C-compound and carbohydrate metabolism PAAG_06953 short chain dehydrogenase/reductase family 2.96 carbohydrate metabolism_sugar epimerase family PAAG_04181 sorbitol utilization protein SOU2 # C-compound and carbohydrate metabolism PAAG_02653 acetyl-coenzyme A synthetase # C-compound and carbohydrate metabolism PAAG_00685 alpha-mannosidase...”
CH_124351 rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase from Magnaporthe grisea 70-15 (see paper)
44% identity, 96% coverage
AFUA_1G14540 oxidoreductase, short-chain dehydrogenase/reductase family from Aspergillus fumigatus Af293
41% identity, 86% coverage
- Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
Fan, Pathogens (Basel, Switzerland) 2021 - “...protein, putativeC2H2 finger domain protein, putative Intergenic Region * 1 3,885,980 G to A 2.74 AFUA_1G14540 Oxidoreductase, short-chain dehydrogenase/reductase family Non-coding Transcript Variant * 6 734,136 G to T 2.72 AFUA_6G03400-AFUA_6G03430 Uncharacterized proteinC6 finger transcription factor (FsqA) Intergenic Region Unique SNP sites are denoted by asterisks...”
- “...A 2.77 AFUA_4G09770 Velvet domain-containing protein Synonymous Variant (Leu193Leu) 1 3,885,980 G to A 2.74 AFUA_1G14540 Oxidoreductase, short-chain dehydrogenase/reductase family Non-coding Transcript Variant * 3 1,256,445 T to A 2.74 AFUA_3G04310-AFUA_3G05320 SnoRNA binding protein, putative C2H2 finger domain protein, putative Intergenic Region * 6 2,141,290 T...”
- The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro
Morton, PloS one 2011 - “...AFUA_3G11430 Arginase AFUA_5G14330 12-oxophytodienoate reductase Oxidation of fatty acids (p: 0.054) AFUA_6G03060 MFS monosaccharide transporter AFUA_1G14540 oxidoreductase, short-chain dehydrogenase/reductase family AFUA_2G04060 NADHflavin oxidoreductase AFUA_5G09400 carbonyl reductase AFUA_2G01440 mitochondrial carrier protein AFUA_3G03410 enoyl-CoA hydratase/isomerase family protein AFUA_1G04720 C-8 sterol isomerase (Erg-1) Disease, virulence and defense (p: 0.072)...”
SPBR_07600 rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase from Sporothrix brasiliensis 5110
38% identity, 87% coverage
BCV53_08150 SDR family oxidoreductase from Parageobacillus thermoglucosidasius
36% identity, 99% coverage
- A thermostable type I-B CRISPR-Cas system for orthogonal and multiplexed genetic engineering
Yang, Nature communications 2023 - “...detected a set of high abundance tgRNAs targeting several genes, including BCV53_12375, BCV53_09555, BCV53_01915, BCV53_09535, BCV53_08150 , and BCV53_10935 (Fig. 5d and Supplementary Table 3 ). To confirm that these targets negatively affected transformation efficiency, these positive tgRNAs were re-transformed into strain GtCom6, which substantially increased...”
- “...of the strain, such as growth rate (Supplementary Table 3 ). For instance, knockout of BCV53_08150 , encoding gluconate 5-dehydrogenase, resulted in decreased growth rate (Supplementary Fig. 10e, f ). To address this issue, we used the orthogonal tool to temporarily and simultaneously inhibit the expression...”
uxaD / Q9WYS2 fructuronate reductase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TM0441 oxidoreductase, short chain dehydrogenase/reductase family from Thermotoga maritima MSB8
38% identity, 99% coverage
- Structural basis of stereospecific reduction by quinuclidinone reductase
Takeshita, AMB Express 2014 - “...was solved by molecular replacement using Phaser (McCoy et al. 2007 ) with Thermotoga maritima TM0441 (PDB ID 1vl8) as a search model. The model was refined using REFMAC5 (Murshudov et al. 1997 ) and CNS (Brnger et al. 1998 ). The model was manually rebuilt...”
- The COMBREX project: design, methodology, and initial results
Anton, PLoS biology 2013 - “...were able to successfully investigate biochemical activities and enzyme kinetics for three previously uncharacterized proteins: TM0441 (results of different substrates further support the findings of Rodionova and colleagues [27] [and see Text S1 ]) and TM0542 from Thermotoga maritima , and Ta0880 from Thermoplasma acidophilum DSM1728...”
- Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima
Rodionova, Environmental microbiology 2012 - “...TM0439 (named UxaR) is a putative GntR family transcriptional regulator of hexuronic acid catabolic genes. TM0441 (named UxaD) encodes an uncharacterized enzyme, which is 40% identical to the NADP-dependent 5-keto-D-gluconate reductase IdnO from E. coli . TM0443 encodes a hypothetical FGGY-like sugar kinase that is 37%...”
- “...the recombinant proteins tm _UxaC (TM0064), tm _UxaE (TM0440), tm _UxuB (TM0068) and tm _UxaD (TM0441) were produced and characterized in vitro by direct and coupled enzymatic assays using spectrophotometry and GC-MS. Hexuronate isomerase In E. coli , the first step of D-GalA catabolism is catalysed...”
- Diversity and versatility of the Thermotoga maritima sugar kinome
Rodionova, Journal of bacteriology 2012 - “...kinase GntK is functionally coupled with 5-keto-D-gluconate reductase TM0441 (I. A. Rodionova, unpublished data). The L-rhamnulose kinase RhaB is linked to the...”
- Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and NADPH
Kubota, Acta crystallographica. Section F, Structural biology and crystallization communications 2010 - “...2010), with the coordinates of gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima (PDB code 1vl8; 39% sequence identity; Joint Center for Structural...”
- Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D
Carius, The Journal of biological chemistry 2010 - “...structure of gluconate 5-dehydrogenase from Thermotoga maritima (TM0441) (PDB entry 1VL8). The rotational and translational searches were performed with the...”
- Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra
Takeshita, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - “...by molecular replacement using the structure of Thermotoga maritima TM0441 (PDB code 1vl8) as a search model is currently under way using the programs Phaser...”
- Laboratory evolution of Pyrococcus furiosus alcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures
Machielsen, Extremophiles : life under extreme conditions 2008 - “...CT0609; PDB-ID 2BD0) (Supangat et al. 2006 ), the gluconate-5-dehydrogenase of Thermotoga maritima (22% identity; TM0441; PDB-ID 1VL8), and the human 17--hydroxysteroid dehydrogenase (23% identity, PDB-ID 1A27) (Breton et al. 1996 ; Mazza et al. 1998 ). Results Construction of a random mutant AdhA library and...”
1vl8B / Q9WYS2 Crystal structure of gluconate 5-dehydrogenase (tm0441) from thermotoga maritima at 2.07 a resolution
38% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (1vl8B)
alr4456 tropinone reductase homolog from Nostoc sp. PCC 7120
39% identity, 94% coverage
H16_A1531 short chain dehydrogenase from Ralstonia eutropha H16
H16_A1531 SDR family oxidoreductase from Cupriavidus necator H16
40% identity, 97% coverage
Q9RYV6 Oxidoreductase, short-chain dehydrogenase/reductase family from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
DRA0200, DR_A0200 oxidoreductase, short-chain dehydrogenase/reductase family from Deinococcus radiodurans R1
37% identity, 98% coverage
- iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C6+ heavy ion irradiation
Gao, BMC microbiology 2022 - “...Q9RYN6 Flavin monoamine oxidase-related protein oxidoreductase activity 20/0,80/0,160/0 Q9RV83 General stress protein 26 NA 20/0 Q9RYV6 Oxidoreductase, short-chain dehydrogenase/reductase family oxidoreductase activity 80/0,160/0 Q9RT75 Oxidoreductase D-threo-aldose 1- dehydrogenase activity 20/0 Q9RWD9 Oxidoreductase, short-chain dehydrogenase/reductase family oxidoreductase activity 20/0,80/0,160/0 Q9RYW1 Oxidoreductase, short-chain dehydrogenase/reductase family oxidoreductase activity 20/0,80/0...”
- Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants
Repar, Scientific reports 2021 - “...transport and catabolism 206,499..206960 DR_A0199 Nodulation protein N-like protein I Lipid transport and metabolism 206,957..207733 DR_A0200 Gluconate 5-dehydrogenase IQR Lipid transport and metabolism; secondary metabolites biosynthesis, transport and catabolism; general function prediction only 207,944..208807 DR_A0201 NAD synthetase H Coenzyme transport and metabolism 208,882..210270 DR_A0202 Cu/Zn family...”
- Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans
Schmid, Journal of bacteriology 2005 - “...clpB dnaJ dnaK lon DR1082 DR1019 DR0220 DR2307 DR2386 DRA0200 lrpA DR1473 DRC0007 DRB0012 DR1314 DR0392 DRB0083 pspA DR0194 a paaA 5.91 5.80 5.41 5.30 4.99 4.83...”
A8RST3 SDR family oxidoreductase from Enterocloster bolteae (strain ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351)
37% identity, 93% coverage
- Specific residues and conformational plasticity define the substrate specificity of short-chain dehydrogenases/reductases
Qian, The Journal of biological chemistry 2024 - “...cofactor NADH to the apo structures obtained from AlphafoldDB ( i.e. , KduD: P37769; DesE: A8RST3) based on GatDH (PDB 2wdz ), whose sequence identity is 36.25% and 35.91% to KduD and DesE, respectively. The substrate binding pockets in KduD and DesE were then located by...”
- “...cofactor NADH to the apo structures obtained from AlphaFoldDB ( i.e. , KduD: P37769; DesE: A8RST3) based on GatDH (PDB 2wdz ). The four selected regions residing along the substrate binding pocket are in the same color with the highlighted regions in Figure1 C . The...”
A2QAQ8 Contig An01c0370, genomic contig from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)
36% identity, 94% coverage
- Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Zhou, Microbial cell factories 2021 - “...Short-chain dehydrogenases/reductases (SDR) A2QVB0 Short-chain dehydrogenases/reductases (SDR) A2QLP8 Short-chain dehydrogenases/reductases (SDR) A2QL00 Short-chain dehydrogenases/reductases (SDR) A2QAQ8 Short-chain dehydrogenases/reductases (SDR) A2QGE1 Short-chain dehydrogenases/reductases (SDR) A2QZ10 Fatty acid metabolic process A2R9F2 Acyl-CoA dehydrogenase A2R9F4 Acyl-CoA dehydrogenase A2QI52 Acyl-CoA dehydrogenase A2R800 Acyl-CoA dehydrogenase A2QMT9 Acyl-CoA dehydrogenase A2QRU8 Aldehyde dehydrogenase...”
G3XRE5 gluconate 5-dehydrogenase (EC 1.1.1.69) from Aspergillus niger (see paper)
36% identity, 94% coverage
THTE_0865 SDR family NAD(P)-dependent oxidoreductase from Thermogutta terrifontis
37% identity, 97% coverage
- Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches
Elcheninov, Frontiers in microbiology 2017 - “...( Klimacek et al., 2003 ) were found. However, the genome contains several genes ( THTE_0865 , THTE_1784 , THTE_2229 , THTE_2632 , THTE_3060 , THTE_3480 , and THTE_3564 ), probably encoding proteins of the short-chain dehydrogenase/reductase family ( Jrnvall et al., 1995 ). One of...”
Clo1313_0815 SDR family NAD(P)-dependent oxidoreductase from Acetivibrio thermocellus DSM 1313
33% identity, 97% coverage
A2R1G3 Contig An13c0040, genomic contig from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)
32% identity, 86% coverage
- Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Zhou, Microbial cell factories 2021 - “...A2QGE2 TRANSMEMBRANE transporter A2R9U9 Short-chain dehydrogenases/reductases (SDR) A2R467 Short-chain dehydrogenases/reductases (SDR) A2R2M6 Short-chain dehydrogenases/reductases (SDR) A2R1G3 Short-chain dehydrogenases/reductases (SDR) A2QZJ2 Short-chain dehydrogenases/reductases (SDR) A2QYS5 Short-chain dehydrogenases/reductases (SDR) A2QVB0 Short-chain dehydrogenases/reductases (SDR) A2QLP8 Short-chain dehydrogenases/reductases (SDR) A2QL00 Short-chain dehydrogenases/reductases (SDR) A2QAQ8 Short-chain dehydrogenases/reductases (SDR) A2QGE1 Short-chain dehydrogenases/reductases...”
Cthe_1433 short-chain dehydrogenase/reductase SDR from Clostridium thermocellum ATCC 27405
33% identity, 97% coverage
TEGL_05600 3-oxoacyl-[acyl-carrier-protein] reductase from Terrisporobacter glycolicus ATCC 14880 = DSM 1288
34% identity, 98% coverage
- Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species
Böer, PloS one 2023 - “...TEPE_31750 TEGL_30950; TEGL_31000 Polar flagella ( Aeromonas ) fliP TEMA_40940 TEPE_11950 TEGL_11730 flmH - TEPE_06230 TEGL_05600 Type IV pili ( Neisseria ) pilT TEMA_31630 TEPE_02190 TEGL_02200 Regulation CheA/CheY ( Listeria ) cheY TEMA_41120 TEPE_12130 TEGL_11910 LisR/LisK ( Listeria ) lisR TEMA_11910 - - VirR/VirS ( Listeria...”
RB316 3-oxoacyl-[acyl-carrier-protein] reductase from Rhodopirellula baltica SH 1
RB316 3-oxoacyl-(acyl-carrier protein) reductase from Pirellula sp. 1
35% identity, 98% coverage
BBA_04090 short-chain dehydrogenase from Beauveria bassiana ARSEF 2860
40% identity, 86% coverage
- Transcriptomic landscape of the interaction between the entomopathogenic fungus Beauveria bassiana and its tolerant host Tribolium castaneum revealed by dual RNA-seq
Mannino, Scientific reports 2023 - “...domain-containing protein 299.338715 BBA_05848 Covalently linked cell wall protein 268.711487 BBA_03936 DUF1264 domain-containing protein 264.897766 BBA_04090 Short-chain dehydrogenase 238.594803 12 h BBA_00807 Glucose repressible protein Grg1 4151.953125 BBA_05166 Hypothetical protein 2071.314697 BBA_05679 HHE domain-containing protein 2057.088379 BBA_04088 Hypothetical protein 1753.269531 BBA_05252 Hydroxyproline-rich glycoprotein DZ-HRGP 1538.462036 BBA_06856...”
- “...h BBA_00807 Glucose repressible protein Grg1 6430.260254 BBA_04088 Hypothetical protein 3220.183838 BBA_06447 Hypothetical protein 3041.161133 BBA_04090 Short-chain dehydrogenase 2865.978516 BBA_06187 Hypothetical protein 2824.542236 BBA_05166 Hypothetical protein 2649.817627 BBA_05679 HHE domain-containing protein 2576.352539 BBA_01593 Quinone oxidoreductase 2274.452148 BBA_06629 Mannitol dehydrogenase 2208.681152 BBA_09598 Oxidoreductase 2C short-chain dehydrogenase/reductase family...”
NCU01904 2-deoxy-D-gluconate 3-dehydrogenase from Neurospora crassa OR74A
35% identity, 89% coverage
- Light-regulated promoters for tunable, temporal, and affordable control of fungal gene expression
Fuller, Applied microbiology and biotechnology 2018 - “...- Ta_46589 predicted protein 7.0 - - - X - - Ta_301399 tetrahydroxynaphthalene reductase 6.8 NCU01904 - - X - - Ta_143500 hypothetical protein similar to phenol 2-monooxygenase 6.4 - - - X - - Ta_40957 hypothetical protein similar to DEAD box RNA helicase Hca4 6.0...”
- Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
Sun, Eukaryotic cell 2012 - “...(NCU01328), 2-deoxy-D-gluconate 3-dehydrogenase (NCU01904), transaldolase (NCU02136), fructose-bisphosphate aldolase (NCU04401), xylulose-5-phosphate...”
- “...(PPP) genes (NCU01328, transketolase; NCU01904, 2-deoxy-D-gluconate 3-dehydrogenase; NCU02136, transaldolase; NCU04401, fructose-bisphosphate aldolase;...”
CD630_11820, CDIF630erm_01331 3-oxoacyl-[acyl-carrier-protein] reductase from Clostridioides difficile
Q18B45 3-oxoacyl-[acyl-carrier-protein] reductase from Clostridioides difficile (strain 630)
32% identity, 98% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...-0.16 3.61 0.50 CD630_11810 CDIF630erm_01330 fabD Malonyl CoA-acyl carrier protein transacylase 3.03 -0.18 3.87 0.41 CD630_11820 CDIF630erm_01331 fabG 3-oxoacyl-ACP reductase 3.65 -0.06 3.94 0.23 CD630_11830 CDIF630erm_01332 acpP Acyl carrier protein 2.95 4.28 CD630_11840 CDIF630erm_01333 fabF 3-oxoacyl-ACP synthase 2.98 0.07 4.71 0.69 01334 CRISPR/Cas and prophages CD630_29750...”
- “...3.61 0.50 CD630_11810 CDIF630erm_01330 fabD Malonyl CoA-acyl carrier protein transacylase 3.03 -0.18 3.87 0.41 CD630_11820 CDIF630erm_01331 fabG 3-oxoacyl-ACP reductase 3.65 -0.06 3.94 0.23 CD630_11830 CDIF630erm_01332 acpP Acyl carrier protein 2.95 4.28 CD630_11840 CDIF630erm_01333 fabF 3-oxoacyl-ACP synthase 2.98 0.07 4.71 0.69 01334 CRISPR/Cas and prophages CD630_29750 CDIF630erm_03259...”
- Structure features of <i>Streptococcus pneumoniae</i> FabG and virtual screening of allosteric inhibitors
Xu, Frontiers in molecular biosciences 2024 - “...in the multiple sequence alignment included Streptococcus pneumoniae FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), S. aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), E. coli FabG (P0AEK2), S. cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The amino acid sequences of...”
- “...This data can be found here: Streptococcus pneumoniae FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), Staphylococcus aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), Escherichia coli FabG (P0AEK2), Saccharomyces cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The X-ray crystallographic coordinates and...”
B6T8T5 3-oxoacyl-[acyl-carrier-protein] reductase from Zea mays
35% identity, 80% coverage
NP_196225 tropinone reductase, putative / tropine dehydrogenase, putative from Arabidopsis thaliana
AT5G06060 NAD(P)-binding Rossmann-fold superfamily protein from Arabidopsis thaliana
35% identity, 95% coverage
- Differentially expressed genes during contrasting growth stages of Artemisia annua for artemisinin content
Nair, PloS one 2013 - “...aldehyde delta-11(13) reductase (ACH61780.1) 1.006099 0.497891 T 35. Aa335 Tropine dehydrogenase [ Arabidopsis thaliana ] (NP_196225) 1.516377 0.349563 L 36. Aa340 Putative AX110P protein [ Arabidopsis thaliana ] (AAK76525) 1.328382 0.398215 L 37. Aa347 Clavaminate synthase-like protein [ Arabidopsis thaliana ] NAD(P)-linked oxidoreductase-like protein [ Arabidopsis...”
- A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry
Nembaware, BMC evolutionary biology 2004 - “...homologs: X. axonopodis A. thaliana NP_640439 NP_564216 short-chain dehydrogenase yes NP_641062 NP_196873 N-acetylglucosaminidase yes NP_642289 NP_196225 3-oxoacyl-[ACP] reductase yes NP_642965 NP_194767 hypothetical protein no NP_643053 NP_568712 amine oxidase related yes NP_643621 NP_173748 expressed protein no NP_644089 NP_182049 methionine aminopeptidase yes Recently, another example of a pathogen...”
- Dissecting the genetic basis of drought responses in common bean using natural variation
Labastida, Frontiers in plant science 2023 - “...Phvul.007G146100 24184160.24187772 AT4G02425 LYR motif-containing protein 7 8 b 13960516 8,32E-08 0,101 10,3 Phvul.008G116400 13963642.13964304 AT5G06060 Tropinone reductase homolog a Sites associated to SG; b sites associated to recovery. NA, not available. Putative candidate genes Most of the SNPs identified through GWAS were intergenic, except for...”
- Deciphering the Genetic Mechanisms of Salt Tolerance in Sorghum bicolor L.: Key Genes and SNP Associations from Comparative Transcriptomic Analyses
Jeon, Plants (Basel, Switzerland) 2023 - “...protein SKIP25 2 1 LOC8070845 two-component response regulator-like PRR37 2 2 LOC8073643 tropinone reductase homolog At5g06060 2 2 LOC8072215 ervatamin-B 2 2 LOC8073557 agmatine deiminase 2 2 LOC8076019 RING-H2 finger protein ATL8 2 3 LOC8056546 peroxidase 25 2 5 LOC8061413 tyrosine N-monooxygenase 1 1 LOC8069641 transcription...”
- Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs
Singh, Frontiers in genetics 2022 - “...transcription factor JAMYB-like Q.PHM.4 PHM LOC106759452 -178.201 tropinone reductase homolog LOC106758588 -69.349 tropinone reductase homolog At5g06060 Q.PHM.6.2 PHM LOC106764341 -82.244 steroid 5-alpha-reductase DET2 Q.PHM.11.1 PHM LOC106777611 -171.802 squamosa promoter-binding-like protein 14 LOC106777237 -112.535 cytochrome P450 71D11 LOC106777539 -82.108 pentatricopeptide repeat-containing protein At3g48810 Q.IL.1.1 IL LOC106766854 -33.322...”
- Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics
Chen, Frontiers in plant science 2021 - “...piperidine and pyridine alkaloid biosynthesis ath00960 ASP5, ASP2, MHK10.21, PAT, At4g12290, HISN6B, ASP3, At5g53970, At2g29300, At5g06060, ASP1, F23N14_50 12 7 Steroid biosynthesis ath00100 CYP710A2, 3BETAHSD/D2, SMT1, CAS1, DWF5, 3BETAHSD/D1, SMT2, CYP51G1, FK, DIM, SDP1 11 8 Carotenoid biosynthesis ath00906 CRTISO, ZDS1, CCD4, ABA2, PDS, NCED3, AAO3,...”
- Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach
Shaar-Moshe, BMC plant biology 2015 - “...loc_os12g29760 (AT4G33670, L-GalDH) loc_os02g44500 (AT4G11600, GPX6) Heme loc_os02g33020 (AT3G10130, SOUL heme-binding family protein Miscellaneous loc_os03g16210 (AT5G06060, tropinone reductase), loc_os03g04660 (AT4G39490, CYP96A10), loc_os07g48020 (AT5G05340, peroxidase), loc_os07g48050 (AT5G05340, peroxidase) Unspecified processes loc_os03g17470 (AT3G55040, GSTL2), loc_os01g08440 (AT4G15550, IAGLU), loc_os01g05840 (AT2G37540, SDR family protein), loc_os02g51930 (AT1G22400, UGT85A1), loc_os10g40570 (AT1G63370, FMO...”
- Phylloxera (Daktulosphaira vitifoliae Fitch) alters the carbohydrate metabolism in root galls to allowing the compatible interaction with grapevine (Vitis ssp.) roots
Griesser, Plant science : an international journal of experimental plant biology 2015 - “...Late embryogenesis abundant protein at1g52690 EE065926 i 3.39 1.42E07 17 0.00000 GSVIVT01016487001 VIT_13s0019g02180 Tropinone reductase at5g06060 EC941770 3.33 6.66E07 170 0.00011 GSVIVT01019892001 VIT_02s0025g04720 Leucoanthocyanidin dioxgenase at4g22880 TC106256 3.24 1.68E07 22 0.00000 GSVIVT01018903001 VIT_04s0023g02290 S-adenosyl- l -methionine:salicylic acid carboxyl methyltransferase At1g19640 TC111440 3.23 7.28E07 182 0.00013 GSVIVT01007987001...”
- The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns
Moummou, BMC plant biology 2012 - “...AT3G06060 SDR35C - ViridP 47,9 AT4G09750 SDR40C - ViridP* 70,8 AT1G54870 SDR57C - ViridP 58,0 AT5G06060 SDR65C Tropinone Reductase ViridP 53,3 AT3G03980 SDR68C TracheoP 57,0 AT5G54190 SDR73C Protochlorophyllide Oxidoreductase ViridP 74,5 AT3G50560 SDR84C - ViridP 60,4 AT1G52340 SDR110C ABA2 (xanthoxin oxidase), Tasselseed2, Secoisolariciresinol dehydrogenase, Momilactone A...”
- Expressed sequence tag analysis of khat (Catha edulis) provides a putative molecular biochemical basis for the biosynthesis of phenylpropylamino alkaloids
Hagel, Genetics and molecular biology 2011 - “...GABA-T Q6ZCF0 Oryza sativa transamination 032_C06-044 1.00E-101 PORA Q41249 Cucumis sativus reduction CL62Contig1 0 TR-like AT5G06060 Arabidopsis thaliana reduction CL440Contig1 1.00E-111 TR-like AT5G06060 Arabidopsis thaliana reduction 012_H02-002 2.00E-47 SDR AT3G50560 Arabidopsis thaliana reduction 041_B01-013 3.00E-99 TR-like ABG22472 Oryza sativa reduction 030_B02-014 7.00E-96 KAR Q0VH86 Gossypium hirsutum...”
LOC108197291 3-oxoacyl-[acyl-carrier-protein] reductase 4 from Daucus carota subsp. sativus
36% identity, 77% coverage
- De novo transcriptome assembly of Conium maculatum L. to identify candidate genes for coniine biosynthesis
Peddinti, Scientific reports 2022 - “...protein) reductase; PF08659.8 KR domain 1194 398 42.29 Daucus carota subsp. sativus 3-oxoacyl-[acyl-carrier-protein] reductase 4-like (LOC108197291), mRNA PKR2: TRINITY_DN99958_c0_g2_i3 1.1.1.100; 2.3.1.85 PF00106.23 short chain dehydrogenase; PF13561.4 Enoyl-(Acyl carrier protein) reductase; PF08659.8 KR domain 963 321 33.39 D. carota subsp. sativus 3-oxoacyl-[acyl-carrier-protein] reductase 4-like (LOC108197291), mRNA AAT...”
D7TAP7 3-oxoacyl-[acyl-carrier-protein] reductase from Vitis vinifera
37% identity, 75% coverage
- Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress
Prinsi, International journal of molecular sciences 2020 - “...3.22 211 D7T4I1 Biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (11) 4.35 105 D7TAP7 3-oxoacyl-[acyl-carrier-protein] reductase 2, chloroplastic (11, 26) 12.24 173 A5C5V3 Dihydroceramide fatty acyl 2-hydroxylase FAH1 (11) 32.25 188 D7TVI4 3-oxoacyl-[acyl-carrier-protein] synthase I, chloroplastic (11) d. N and amino acid metabolism (12,...”
- “...1.94 203 D7T4I1 Biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (11) 2.98 88 D7TAP7 3-oxoacyl-[acyl-carrier-protein] reductase 2, chloroplastic (11, 26) 3.19 125 A5C5V3 Dihydroceramide fatty acyl 2-hydroxylase FAH1 (11) 7.02 141 D7TVI4 3-oxoacyl-[acyl-carrier-protein] synthase I, chloroplastic (11) d. N and amino acid metabolism (12,...”
PD1772 tropinone reductase from Xylella fastidiosa Temecula1
36% identity, 96% coverage
BG05_RS14070 3-oxoacyl-ACP reductase FabG from Bacillus mycoides
35% identity, 98% coverage
B4FTC8 3-oxoacyl-[acyl-carrier-protein] reductase from Zea mays
35% identity, 77% coverage
A210_09220 SDR family NAD(P)-dependent oxidoreductase from Pseudomonas putida SJTE-1
36% identity, 96% coverage
PMN2A_1785 3-oxoacyl-[acyl-carrier protein] reductase from Prochlorococcus marinus str. NATL2A
36% identity, 98% coverage
- Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness
Biller, mSystems 2018 - “...tpiA 1.2E02 Fatty acid and lipid biosynthesis accA , accC , fabI , lpxC , PMN2A_1785 1.5E02 Fermentation acnB , icd , pdhB , pykF , PMN2A_1709 1.0E03 Photosynthesis glpX , tpiA , prkB , rpi , psaD , psbB , petD 2.0E03 Respiration acnB ,...”
- “...4.0E02 RubisCO shunt prkB , pykF , rpi 5.5E02 Unsaturated fatty acid biosynthesis fabI , PMN2A_1785 3.6E02 Enriched only in coculture Adenine and adenosine salvage apt 6.8E02 Lipoate salvage lplA 6.8E02 Proteinogenic amino acid degradation lpd , gltB , PMN2A_1709 1.0E01 Purine nucleotide degradation truB 6.8E02...”
Q93X62 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic from Brassica napus
LOC106367337 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic from Brassica napus
36% identity, 77% coverage
- STIC2 selectively binds ribosome-nascent chain complexes in the cotranslational sorting of Arabidopsis thylakoid proteins.
Stolle, The EMBO journal 2024 - “...s, m, l F6H7K5 Thiamine thiazole synthase 2 (THI42) Thiamine Psat6g209120.1 AT5G54770.1 s, m, l Q93X62 3-oxoacyl-reductase 1 (FABG1) Fatty acid Psat5g094480.1 AT1G24360.1 s, m, l P52418 Amidophosphoribosyltransferase (PUR1) Purine Psat7g181880.1 AT2G16570.1 s, m, l Proteins with functions in metabolic pathways for which an increased or...”
- Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis
Wickramasinghe, The Biochemical journal 2006 - “...with B. napus OAR (Bn ; Swiss-Prot accession number Q93X62) and E. coli OAR (Ec ; Swiss-Prot accession number P25716) using ClustalW. The potential signal...”
- “...study; data for B. napus are from [25,56] and Q93X62 (TrEMBL accession code); data for partially purified E. coli enzyme are from [43,57], E. coli enzyme...”
- Effects of Low Nighttime Temperature on Fatty Acid Content in Developing Seeds from Brassica napus L. Based on RNA-Seq and Metabolome
Mi, Plants (Basel, Switzerland) 2023 - “...RNA-seq analysis showed that the expression levels of SAD (LOC106366808), ECR (LOC106396280), KCS (LOC106419344), KAR (LOC106367337), HB1 (LOC106430193), and DOF5 (LOC111211868) in STSL seeds increased under LNT conditions. In STSL seeds, a base mutation in the cis -acting element involved in low-temperature responsiveness (LTR), the HB1...”
- “...analysis showed that the expression levels of SAD (LOC106366808), ECR (LOC106396280), KCS (LOC106419344), and KAR (LOC106367337) in the STSL seeds increased with increasing temperatures. Expression levels for these genes in the WTSL were slightly increased. While the expression level of SAD in the STSL seeds increased,...”
OA858_14210 3-oxoacyl-[acyl-carrier-protein] reductase from Pseudanabaena galeata CCNP1313
37% identity, 97% coverage
1edoA / Q93X62 The x-ray structure of beta-keto acyl carrier protein reductase from brassica napus complexed with NADP+ (see paper)
36% identity, 96% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (1edoA)
XP_002514996 3-oxoacyl-[acyl-carrier-protein] reductase 4 from Ricinus communis
36% identity, 75% coverage
alr1894 3-oxoacyl-[acyl-carrier protein] reductase from Nostoc sp. PCC 7120
37% identity, 98% coverage
SO_2776 3-oxoacyl-(acyl-carrier-protein) reductase from Shewanella oneidensis MR-1
34% identity, 100% coverage
- Shewanella oneidensis FabB: A β-ketoacyl-ACP Synthase That Works with C16:1-ACP
Luo, Frontiers in microbiology 2016 - “...(SO_4383) 420 6e-73 FabB 406 FabB (SO_3072) 411 0.0 3-oxoacyl-(acyl-carrier-protein) synthase I FabG 244 FabG1 (SO_2776) 248 2e-134 3-oxoacyl-(acyl-carrier-protein) reductase FabG2 (SO_4382) 241 3e-56 FabA 172 FabA (SO_1856) 171 9e-89 3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase FabZ 151 FabZ (SO_1640) 154 5e-67 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase FabV a 401 FabV (SO_1800) 400...”
- “...reductase FabI 262 SO_2397 275 9e-14 oxidoreductase, short chain dehydrogenase/reductase family SO_2813 249 1e-12 FabG (SO_2776) 248 1e-10 3-oxoacyl-(acyl-carrier-protein) reductase a V. cholerae FabV. Expression of S. oneidensis fabB rather than fabFs is affected by fatty acid species As shown above, in S. oneidensis there are...”
SPD_0384 3-oxoacyl-(acyl-carrier-protein) reductase from Streptococcus pneumoniae D39
Q8DR15 3-oxoacyl-[acyl-carrier-protein] reductase from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
spr0381 3-ketoacyl-acyl carrier protein reductase from Streptococcus pneumoniae R6
SPCG_RS02180 3-oxoacyl-[acyl-carrier-protein] reductase from Streptococcus pneumoniae
37% identity, 95% coverage
- The role of pneumococcal extracellular vesicles on the pathophysiology of the kidney disease hemolytic uremic syndrome
Battista, mSphere 2023 - “...Purine nucleoside phosphorylase DeoD-type (PNP) (EC 2.4.2.1) deoD SPD_0730 A0A0H2ZMC0 3-Oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) fabG SPD_0384 A0A0H2ZNV9 Glucose-1-phosphate adenylyltransferase, GlgD subunit (EC 2.7.7.27) glgD SPD_1007 Q04HZ0 Glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (glycerokinase) (GK) glpK SPD_2013 A0A0H2ZLA5 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) gnd SPD_0343 Q04JB4 2,3-Bisphosphoglycerate-dependent...”
- Inactivation of Transcriptional Regulator FabT Influences Colony Phase Variation of Streptococcus pneumoniae
Zhang, mBio 2021 - “...0.73 0.000 SPD_0382 fabK Enoyl-[acyl-carrier-protein] reductase FabK 2.05 0.000 SPD_0383 fabD ACP S-malonyltransferase 1.77 0.000 SPD_0384 fabG 3-oxoacyl-[acyl-carrier-protein] reductase 1.70 0.000 SPD_0385 fabF Beta-ketoacyl-ACP synthase II 1.76 0.000 SPD_0386 accB Acetyl-CoA carboxylase biotin carboxyl carrier protein 1.79 0.000 SPD_0387 fabZ 3-Hydroxyacyl-ACP dehydratase FabZ 1.63 0.000 SPD_0388...”
- Cadmium stress dictates central carbon flux and alters membrane composition in Streptococcus pneumoniae
Neville, Communications biology 2020 - “...fabK Trans-2-enoyl-ACP reductase II (EC:1.3.1.9) 2.27 SPD_0383 fabD Malonyl CoA-acyl carrier protein transacylase (EC:2.3.1.39) 2.18 SPD_0384 fabG 3-oxoacyl-[acyl-carrier-protein] reductase (EC:1.1.1.100) 2.19 SPD_0385 fabF 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC:2.3.1.179) 2.04 SPD_0386 accB Acetyl-CoA carboxylase, biotin carboxyl carrier protein 1.99 SPD_0387 fabZ 3-hydroxyacyl-[acyl-carrier-protein] dehydratase (EC:4.2.1.59) 1.92 SPD_0388 accC Acetyl-CoA...”
- High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae
Liu, Molecular systems biology 2017 - “...fabK ( SPD_0382 ) tarI ( SPD_1127 ) fabD ( SPD_0383 ) SPD_1200 fabG ( SPD_0384 ) licD3 ( SPD_1201 ) fabF ( SPD_0385 ) SPD_1620 accB ( SPD_0386 ) fabZ ( SPD_0387 ) accD ( SPD_0389 ) acpS ( SPD_1509 ) a The genes highlighted...”
- Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase
Al-Bayati, Scientific reports 2017 - “...synthase 2.4 SPD_0381 Acyl carrier protein 2.5 SPD_0382 enoyl-(acyl-carrier-protein) reductase 3.3 SPD_0383 Acyl-carrier-protein S-malonyltransferase 3.6 SPD_0384 3-ketoacyl-(acyl-carrier-protein) reductase 4.3 SPD_0385 3-oxoacyl-(acyl carrier protein) synthase 5.2 SPD_0386 Acetyl-CoA carboxylase 4.3 SPD_0387 (3R)-hydroxymyristoyl ACP dehydratase 4.6 SPD_0388 Acetyl-CoA carboxylase 6.3 SPD_0389 Acetyl-CoA carboxylase beta subunit 5.4 SPD_0390 Acetyl-CoA...”
- The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
Yadav, PloS one 2015 - “...activity -1.8 (0.01) SPD_0383 (fabD) malonyl CoA-acyl carrier protein transacylase [acyl-carrier-protein] S-malonyltransferase activity -2.2 (0.008) SPD_0384 (fabG) 3-oxoacyl-(acyl-carrier-protein) reductase -1.4 (0.05) SPD_0387 (fabZ) beta-hydroxyacyl-(acyl-carrier-protein) 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity fatty acid biosynthetic process -1.6 (0.03) SPD_0385 (fabF) 3-oxoacyl-[acyl-carrier-protein] synthase II beta-ketoacyl-acyl-carrier-protein synthase II activity fatty acid biosynthetic process...”
- Structure features of <i>Streptococcus pneumoniae</i> FabG and virtual screening of allosteric inhibitors
Xu, Frontiers in molecular biosciences 2024 - “...FabG and homologs used in the multiple sequence alignment included Streptococcus pneumoniae FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), S. aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), E. coli FabG (P0AEK2), S. cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The...”
- “...analyzed in this study. This data can be found here: Streptococcus pneumoniae FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), Staphylococcus aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), Escherichia coli FabG (P0AEK2), Saccharomyces cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The...”
- Integrated proteomic and metabolomic analysis reveals that rhodomyrtone reduces the capsule in Streptococcus pneumoniae
Mitsuwan, Scientific reports 2017 - “...uridylyltransferase 103 31 0.38 0.010 1C Q8DRG7 Glycosyltransferase, family 2 98 25 0.30 0.013 16C Q8DR15 3-ketoacyl-(acyl-carrier-protein) reductase 95 20 0.37 0.023 7C Q8DPM2 DNA gyrase A subunit 96 21 0.40 0.039 5C P64031 Elongation factor Tu 517 26 0.29 0.009 6B Q97SV1 50S ribosomal protein...”
- Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae
El, Scientific reports 2017 - “...spr0216 rplQ 50S ribosomal protein L17 1.34 spr0327 aliA oligopeptide ABC transporter substrate-binding protein 1.30 spr0381 fabG 3-ketoacyl-ACP reductase 1.19 spr0382 fabF 3-oxoacyl-ACP synthase 1.01 spr0383 accB acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 1.16 spr0384 fabZ (3R)-hydroxymyristoyl-ACP dehydratase 1.05 1.26 spr0386 accD acetyl-CoA carboxylase subunit...”
- The transcriptomic response of Streptococcus pneumoniae following exposure to cigarette smoke extract
Manna, Scientific reports 2018 - “...AccB 3.32 0.004 SPCG_RS02195 3-hydroxyacyl-ACP dehydratase FabZ 3.18 0.005 SPCG_RS02185 3-oxoacyl-ACP synthase FabF 3.11 0.004 SPCG_RS02180 3-ketoacyl-ACP reductase FabG 2.92 0.006 SPCG_RS02150 Enoyl-CoA hydratase FabM 2.82 0.026 SPCG_RS02175 ACP S-malonyltransferase FabD 2.76 0.011 SPCG_RS03620 Fatty acid-binding DegV family protein 2.59 0.006 SPCG_RS02170 Enoyl-[acyl-carrier-protein] reductase FabK 2.10...”
4jroC / Q8Y690 Crystal structure of 3-oxoacyl-[acyl-carrier protein]reductase (fabg) from listeria monocytogenes in complex with NADP+
LM6179_2577 3-oxoacyl-[acyl-carrier-protein] reductase from Listeria monocytogenes 6179
lmo1807 similar to 3-ketoacyl-acyl carrier protein reductase from Listeria monocytogenes EGD-e
34% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (4jroC)
- Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
Casey, Frontiers in microbiology 2014 - “...protein 18.25 LM6179_2579 plsX Phosphate:acyl-ACP acyltransferase 4.37 LM6179_2578 fabD Malonyl CoA:acyl carrier protein transacylase 3.56 LM6179_2577 fabG Beta-ketoacyl-acyl carrier protein reductase 7.04 LM6179_2981 fabHA Beta-ketoacyl-acyl carrier protein synthase III 3.51 LM6179_2980 fabF Beta-ketoacyl-acyl carrier protein synthase II 3.78 LM6179_1286 fabI Enoyl-acyl carrier protein reductase 4.41 LM6179_1679...”
- Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
Pleitner, Applied and environmental microbiology 2014 - “...included genes encoding acyl-carrier proteins (lmo0970, lmo1806, lmo1807, lmo2202, and lmo2450) responsible for membrane lipid production (36), which suggests...”
- “...Fatty acid and phospholipid metabolism lmo0970 lmo1806 lmo1807 lmo2202 lmo2450 Protein synthesis lmo0177 lmo0244 lmo0695 lmo1294 lmo1658 lmo1755 lmo2047 lmo2597...”
- The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
Stasiewicz, Applied and environmental microbiology 2011 - “...lmo0225 folPB) , fatty acid metabolism genes (lmo1806, lmo1807 acpP, fabG), iron ABC transport genes (lmo1957, lmo1959), oxidative stress genes (lmo0983 gpxA,...”
T260_09050 SDR family NAD(P)-dependent oxidoreductase from Geobacillus thermopakistaniensis
33% identity, 98% coverage
- Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1
Siddiqui, Genome announcements 2014 - “...(T260_04900), and glycosidase (T260_13695). It also contains five types of alcohol dehydrogenases (T260_01930, T260_06755, T260_07340, T260_09050, T260_12960) and lipases (T260_04645, T260_04700, T260_15915, T260_16665, T260_19075). According to the protein homology search analysis using the Basic Local Alignment Search Tool (BLAST) for five open reading frames annotated as...”
SP_0421 3-ketoacyl-(acyl-carrier-protein) reductase from Streptococcus pneumoniae TIGR4
37% identity, 95% coverage
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...2/9 Downregulated 38546 SP_0412, SP_0413 2/2 Downregulated 38547 SP_0416, SP_0417 2/2 Downregulated 38548 SP_0419, SP_0420, SP_0421, SP_0422, SP_0423, SP_0424, SP_0425, SP_0426, SP_0427, SP_0428, SP_0429, SP_0430, SP_0431 13/13 Downregulated 38571 SP_0526, SP_0527 2/3 Downregulated 38610 SP_0701, SP_0702 2/2 Downregulated 38617 SP_0737, SP_0738 2/2 Downregulated 38620 SP_0750, SP_0751,...”
- “...Location c TE5 Increased 6.1 0.03 SP_1220 L-lactate dehydrogenase 607 Cytoplasmic TE6 Increased 6.9 0.01 SP_0421 3-oxoacyl-[acyl-carrier protein] reductase 528 Cytoplasmic TE7 Decreased 4.6 0.04 SP_2055 Alcohol dehydrogenase, zinc-containing 535 Cytoplasmic TE8 Decreased 4.3 0.03 SP_2012 Glyceraldehyde-3-phosphate dehydrogenase 255 Cytoplasmic TS24 Increased 4.4 0.02 nanA Sialidase...”
- Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells
Kimaro, BMC genomics 2013 - “...CoA-acyl carrier protein transacylase 1.9 0.6 yes (99.5%) no Co-opted as part of an operon SP_0421 3-oxoacyl-[acyl-carrier protein] reductase 2.7 0.7 yes (99.4%) yes (SP) Up-regulated in the more adherent strain & Ratio index1.5 SP_0422 3-oxoacyl-(acyl-carrier-protein) synthase II 2.4 0.7 yes (99.8%) yes (SP) Up-regulated in...”
PF3D7_0922900, XP_001352100 3-oxoacyl-[acyl-carrier-protein] reductase from Plasmodium falciparum 3D7
33% identity, 83% coverage
- Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver
Franke-Fayard, NPJ vaccines 2022 - “...transacylase (FabD) no - 23 PBANKA_0308200 PF3D7_0211400 beta-ketoacyl-ACP synthase III (FabH) yes yes 23 PBANKA_0823800 PF3D7_0922900 3-oxoacyl-[acyl-carrier-protein] reductase (FabG) no - 23 PY17X_0715100 PF3D7_0815900 dihydrolipoyl dehydrogenase, apicoplast (PDH E3) no - PBANKA_0923800 PF3D7_1124500 pyruvate dehydrogenase E1 component subunit no - 73 alpha (PDH E1) PY17X_0934900 PF3D7_1114800...”
- Transcriptome analysis based detection of Plasmodium falciparum development in Anopheles stephensi mosquitoes
Oakley, Scientific reports 2018 - “...protein phosphatase PP1 PF3D7_1414400 Day 8 Metabolism 1-cys peroxiredoxin PF3D7_0802200 Day 6 3-oxoacyl-(acyl-carrier protein) reductase PF3D7_0922900 Day 8 protein DJ-1 PF3D7_0627500 Day 8 Adenosine deaminase PF3D7_1029600 Day 8 Adenosylhomocysteinase PF3D7_0520900 Day 8 ATP synthase F1, alpha subunit PF3D7_0217100 Day 6 Cytochrome c oxidase subunit 2 PF3D7_1430900...”
- South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains
Singh, F1000Research 2016 - “...protein-sorting protein VPS2 6.0 0.9 6.4 PF3D7_0410400 exosome complex component RRP4 (RRP4) 7.0 1.2 5.9 PF3D7_0922900 beta-ketoacyl-acyl carrier protein reductase (FabG) 11.0 2.0 5.5 PF3D7_0314100.1 vesicle transport v-SNARE protein 6.0 1.1 5.5 PF3D7_1124800 nuclear preribosomal assembly protein 8.0 1.5 5.4 PF3D7_0936000 ring-exported protein 2+(REX2) 13.0 2.6...”
- Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum
Bunnik, Genome biology 2013 - “...delay in translation for genes involved in metabolism, such as beta-ketoacyl-acyl carrier protein reductase (FabG; PF3D7_0922900) and acyl-CoA synthetase (ACS6; PF3D7_0401900). For FabG, the ratio of transcripts in steady-state versus polysome fractions was 1:47 at the ring stage, 2.6:1 at the trophozoite stage, and 3.5:1 at...”
- Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans
Ramakrishnan, Progress in lipid research 2013 - “...pathway ACP Acyl carrier protein Tb927.1.2100 LmjF.27.0290 PF3D7_0208500 TGME49_064080 KAR Ketoacyl ACP reductase Tb927.2.5210 LmjF27.2440 PF3D7_0922900 TGME49_017740 HAD Hydroxyacyl ACP dehydratase Tb927.8.1440 LmjF07.0430 LmjF07.0440 PF3D7_1323000 TGME49_121570 EAR Enoyl ACP reductase Tb927.10.11930 LmjF.04.0290 PF3D7_0420200 TGME49_051930 PPTase Phosphopantetheinyl transferase Tb927.3.1840 LmjF.25.1770 PF3D7_0420200 TGME49_003420 FASI pathway FASI Fatty acid...”
- Deciphering the key residues in Plasmodium falciparum beta-ketoacyl acyl carrier protein reductase responsible for interactions with Plasmodium falciparum acyl carrier protein.
Karmodiya, The FEBS journal 2008 (PubMed)- GeneRIF: Kinetic analysis and studies of direct binding between PfFabG and PfACP confirmed the identification of Arg187 and Arg230 as critical residues for the PfFabG-PfACP interactions.
- Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis.
Wickramasinghe, The Biochemical journal 2006 - GeneRIF: The biochemical properties and 1.5 A (crystal structure of OAR (3-oxoacyl acyl-carrier-protein reductase, or FabG), the second reductive step in fatty acid biosynthesis and its inhibition by hexachlorophene are reported.
- Production and purification of refolded recombinant Plasmodium falciparum beta-ketoacyl-ACP reductase from inclusion bodies.
Karmodiya, Protein expression and purification 2005 (PubMed)- GeneRIF: Recombinant beta-ketoacyl-ACP reductase was purified and characterized from Escherichia coli inclusion bodies.
PBANKA_0823800 3-oxoacyl-[acyl-carrier-protein] reductase, putative from Plasmodium berghei ANKA
33% identity, 84% coverage
- Plasmodium berghei oocysts possess fatty acid synthesis and scavenging routes
Saeed, Scientific reports 2023 - “...involves: (i) condensation of acyl-acyl carrier protein (acyl-ACP) with acetoacetyl-ACP, catalysed by acyl-ACP elongase (FabB/F, PBANKA_0823800); (ii) reduction of ketoacyl-ACP, catalysed by ketoacyl-ACP reductase (FabG, PBANKA_0823800); (iii) dehydration of hydroxyacyl-ACP, catalysed by hydroxyacyl-ACP dehydratase (FabZ, PBANKA_1338200); (iv) reduction of enoyl-ACP, catalysed by enoyl-ACP reductase (FabI, PBANKA_1229800)...”
- “...(FabG/GFP), an approximately 2.2kb fragment corresponding to the coding sequence (plus introns) and 5UTR of PBANKA_0823800 was PCR-amplified with primers FabG-F (TTGGGCTGCAGTCGAGGAATTTCCATAGCATCCATATATAC) and FabG-R (AATGAGGGCCCCTAAGCTGGTACCACTTGATAATCCACCATCAATTATAAATAC) and cloned into Sal I/ Hin dIII digested pBS-EGFP-hDHFR 10 by In-Fusion to give plasmid pBS-FabG/GFP. This plasmid was linearised with...”
- Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver
Franke-Fayard, NPJ vaccines 2022 - “...protein transacylase (FabD) no - 23 PBANKA_0308200 PF3D7_0211400 beta-ketoacyl-ACP synthase III (FabH) yes yes 23 PBANKA_0823800 PF3D7_0922900 3-oxoacyl-[acyl-carrier-protein] reductase (FabG) no - 23 PY17X_0715100 PF3D7_0815900 dihydrolipoyl dehydrogenase, apicoplast (PDH E3) no - PBANKA_0923800 PF3D7_1124500 pyruvate dehydrogenase E1 component subunit no - 73 alpha (PDH E1) PY17X_0934900...”
- Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Stanway, Cell 2019 - “...a drug-selectable marker in their genome. For genes PDH-E2 (PBANKA_0505000), HCS1 (PBANKA_0511000), FabD (PBANKA_1410500), FabG (PBANKA_0823800), FabH (PBANKA_0308200), LipA (PBANKA_1357500), ELO-A (PBANKA_0820900), KCR (PBANKA_0522400), CBR (PBANKA_1143400), USP (PBANKA_1232300), PMM (PBANKA_0501700), PGM3 (PBANKA_0918200), GFPT (PBANKA_0509300), LPD1 (PBANKA_1446900), IS-SDHA (PBANKA_1428800) and GCH1 (PBANKA_1438900), single knockout parasites were generated...”
Q86RB1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Plasmodium falciparum (see paper)
33% identity, 83% coverage
NCLIV_062520 3-ketoacyl-(Acyl-carrier-protein) reductase, related from Neospora caninum Liverpool
37% identity, 65% coverage
DR1943 3-oxoacyl-acyl carrier protein reductase from Deinococcus radiodurans R1
38% identity, 96% coverage
FABG_AQUAE / O67610 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 from Aquifex aeolicus (strain VF5)
aq_1716 3-oxoacyl-[acyl-carrier-protein] reductase from Aquifex aeolicus VF5
33% identity, 97% coverage
- function: Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis.
catalytic activity: a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + NADPH + H(+) (RHEA:17397)
subunit: Homotetramer. - The future of crystallography in drug discovery
Zheng, Expert opinion on drug discovery 2014 - “...should be critically evaluated. The unmodeled blobs (A) in the structure of crystal structure of aq_1716 from Aquifex aeolicus vt5 (PDB code: 2P68) should be more appropriately interpreted as PEG, rebuilt and refined as shown in (B). In both images, 2F o -F c electron density...”
- Crystallization and X-ray diffraction analysis of the beta-ketoacyl-acyl carrier protein reductase FabG from Aquifex aeolicus VF5
Mao, Acta crystallographica. Section F, Structural biology and crystallization communications 2007 - “...proteomics project, the gene product of fabG (locus aq_1716; SWISSPROT/TrEMBL accession No. 067610) from the thermophile Aquifex aeolicus VF5 was chosen for...”
- Characterization of the 3,4-Dichloroaniline Degradation Gene Cluster in Acinetobacter soli GFJ2
Gibu, Microorganisms 2024 - “...Dihydroanticapsin 7-dehydrogenase (BacC) from Bacillus subtilis 30 P39640 3-Oxoacyl-[acyl-carrier-protein] reductase (FabG) from Aquifex aeolicus 30 O67610 BEN76_01185 ( dcdA ) 46,014 (412) Indole dioxygenase (IifC) from Acinetobacter sp. 87 ARO76328 Styrene monooxygenase (StyA) from Pseudomonas sp. 29 O50214 BEN76_01190 ( dcdB ) 19,036 (172) Flavin reductase...”
JHW33_RS01075 gluconate 5-dehydrogenase from Rahnella aceris
32% identity, 99% coverage
NR_NARAP / A0A1C9II22 Noroxomaritidine/norcraugsodine reductase; NorRed; EC 1.1.1.- from Narcissus aff. pseudonarcissus MK-2014 (Daffodil) (see paper)
NR_NARPS / A0A1A9TAK5 Noroxomaritidine/norcraugsodine reductase; NorRed; EC 1.1.1.- from Narcissus pseudonarcissus (Daffodil) (see 2 papers)
5ff9B / A0A1A9TAK5 Noroxomaritidine/norcraugsodine reductase in complex with NADP+ and tyramine (see paper)
33% identity, 98% coverage
- function: In the Amaryllidaceae alkaloids biosynthesic pathway, catalyzes the conversion of noroxomaritidine to oxomaritidine, a precursor of haemanthamine- and crinamine-type alkaloids, promising anticancer agents (PubMed:27252378). Can also, to some extent, catalyze the condensation of 3,4-dihydroxybenzaldehyde (3,4-DHBA) and tyramine to produce norbelladine, and of isovanillin and tyramine to produce 4'- O-methylnorbelladine (PubMed:27252378).
catalytic activity: (10bR,4aS)-noroxomaritidine + NADPH + H(+) = (10bR,4aS)- oxomaritidine + NADP(+) (RHEA:63196)
catalytic activity: (10bS,4aR)-noroxomaritidine + NADPH + H(+) = (10bS,4aR)- oxomaritidine + NADP(+) (RHEA:63200) - function: In the Amaryllidaceae alkaloids biosynthesic pathway, catalyzes the conversion of noroxomaritidine to oxomaritidine, a precursor of haemanthamine- and crinamine-type alkaloids, promising anticancer agents (PubMed:27252378). Can also, to some extent, catalyze the condensation of 3,4-dihydroxybenzaldehyde (3,4-DHBA) and tyramine to produce norbelladine, and of isovanillin and tyramine to produce 4'- O-methylnorbelladine (PubMed:27252378).
catalytic activity: (10bR,4aS)-noroxomaritidine + NADPH + H(+) = (10bR,4aS)- oxomaritidine + NADP(+) (RHEA:63196)
catalytic activity: (10bS,4aR)-noroxomaritidine + NADPH + H(+) = (10bS,4aR)- oxomaritidine + NADP(+) (RHEA:63200) - Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; 4-(2-aminoethyl)phenol (5ff9B)
TR2 / Q6KF77 tropinone reductase (EC 1.1.1.236) from Solanum tuberosum (see paper)
34% identity, 96% coverage
L5014_12160 acetoacetyl-CoA reductase from Paraburkholderia tagetis
34% identity, 98% coverage
- Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato)
Chhetri, Frontiers in microbiology 2023 - “...) JAKLJA010000006 89,991 90,602 L5014_10525 203 Polyhydroxyalkanoate synthesis repressor ( phaR ) JAKLJA010000007 195,750 196,493 L5014_12160 247 Acetoacetyl-CoA reductase ( phbB ) JAKLJA010000026 54,246 54,989 L5014_25520 247 Acetoacetyl-CoA reductase ( phbB ) JAKLJA010000048 14,554 15,297 L5014_32695 247 Acetoacetyl-CoA reductase ( phbB ) JAKLJA010000093 5,639 6,382 L5014_38125...”
TGME49_017740, TGME49_217740 3-ketoacyl-(acyl-carrier-protein) reductase from Toxoplasma gondii ME49
37% identity, 65% coverage
TRNH3_ARATH / Q9ZW03 Tropinone reductase homolog At2g29150; EC 1.1.1.- from Arabidopsis thaliana (Mouse-ear cress) (see paper)
35% identity, 93% coverage
- function: Enantiospecific reductase active on cyclic monoterpenes and small flexible lipophilic carbonyls. No activity with tropinone, nitrogen-containing tropinone analogs, tropine or pseudotropine as substrate.
B5X54_RS06375 3-oxoacyl-[acyl-carrier-protein] reductase from Caldicellulosiruptor bescii
34% identity, 96% coverage
- Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii
Sander, Biotechnology for biofuels 2020 - “...Ketoacyl-ACP synthase III 3.8 2.3 2.2 B5X54_RS06370 Malonyl CoA-acyl carrier protein transacylase 3.8 2.5 2.2 B5X54_RS06375 Beta-ketoacyl-ACP reductase 3.7 2.2 2.1 B5X54_RS06380 Acyl carrier protein 2.1 1.5 1.3 B5X54_RS06385 Beta-ketoacyl-[acyl-carrier-protein] synthase II 2.8 1.8 1.7 B5X54_RS06390 Ribonuclease III 2.2 1.3 1.3 B5X54_RS06395 Radical SAM protein 2.3...”
VZ55_RS13980 SDR family oxidoreductase from Gluconobacter oxydans
34% identity, 97% coverage
F2VTN2 3-oxoacyl-[acyl-carrier-protein] reductase from Helianthus annuus
34% identity, 76% coverage
4nbuB Crystal structure of fabg from bacillus sp (see paper)
32% identity, 98% coverage
- Ligands: 1,4-dihydronicotinamide adenine dinucleotide; acetoacetyl-coenzyme a (4nbuB)
JI728_13095 SDR family oxidoreductase from Salmonella enterica subsp. enterica serovar Gallinarum/Pullorum
SEN1435 putative hexonate dehydrogenase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
33% identity, 99% coverage
- Integrated OMICs approach reveals energy metabolism pathway is vital for Salmonella Pullorum survival within the egg white
Kang, mSphere 2024 - “...response, amino acid metabolism, and carbohydrate metabolism were specifically affected. Additional upregulated functionally relevant genes (JI728_13095, JI728_13100, JI728_17960, JI728_10085, JI728_15605, and nhaA ) as mutants confirmed the susceptible phenotype. Furthermore, fim deletion resulted in an increased survival capacity in the egg white, consistent with the downregulated...”
- “...single gene deletion mutants were constructed using a previous method ( 18 ). Among them, JI728_13095 and JI728_13100 were considered as a whole for deletion due to their close genomic proximity and involvement in the metabolic process, while the other four were individually deleted (JI728_17960, encoding...”
- Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses
Baron, Frontiers in microbiology 2017 - “...1.94 SEN1433 L-idonate 5-dehydrogenase IdnD 3.05 3.21 5.17 SEN1434 Hexonate sugar transporter n.s. 2.70 5.68 SEN1435 Gluconate 5-dehydrogenase n.s. 3.07 .40 SEN1436 D-galactonate dehydratase family member SEN1436 n.s. 10.30 33.38 Highlighted fold changes correspond to up-regulated (dark gray) and down-regulated (light gray) genes. (n.s.), fold changes...”
fabG / P51831 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Bacillus subtilis (strain 168) (see 3 papers)
BSU15910 beta-ketoacyl-acyl carrier protein reductase from Bacillus subtilis subsp. subtilis str. 168
P51831 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Bacillus subtilis (strain 168)
33% identity, 97% coverage
R4QQK2 tropinone reductase I (EC 1.1.1.206) from Anisodus luridus (see paper)
37% identity, 92% coverage
P50164 Tropinone reductase 2 from Hyoscyamus niger
33% identity, 96% coverage
B2L2W9 tropinone reductase II (EC 1.1.1.236) from Anisodus acutangulus (see paper)
34% identity, 96% coverage
B2L2W8 tropinone reductase I (EC 1.1.1.206) from Anisodus acutangulus (see 3 papers)
36% identity, 92% coverage
FH974_05790 3-oxoacyl-ACP reductase FabG from Photobacterium ganghwense
34% identity, 98% coverage
BAB1_0483 Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase from Brucella melitensis biovar Abortus 2308
36% identity, 98% coverage
- Brucella abortus choloylglycine hydrolase affects cell envelope composition and host cell internalization
Marchesini, PloS one 2011 - “...5.42 29.3 27.1 5.7 BAB2_0883 C 39 3-ketoacyl-(acyl-carrier-protein) reductase gi|17987760 6.44 6.44 26.7 26.0 3.1 BAB1_0483 C 51 Chaperone protein DNAJ gi|17988284 6.34 6.51 42.6 41.1 2.3 BAB1_2130 C 59 Transcription antitermination protein NusG1 gi|17987027 5.99 6.64 20.9 19.7 2.6 BAB1_1269 U Exp.: experimental; Theor.: theoretical;...”
- “...6.13 47.2 36.3 2.8 BAB1_1741 C 31 3-ketoacyl-(acyl-carrier-protein) reductase gi|17987760 6.25 6.44 25.0 26.0 6.7 BAB1_0483 C 32 22 kDa Omp gi|17987000 6.19 8.59 23.3 19.4 2.7 BAB1_1302 OM 45 Argininosuccinate synthase gi|17988153 6.15 6.06 57.9 45.3 4.5 BAB1_0071 C 48 ATP synthase alpha chain 4...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...the inner membrane proteins 3-hydroxydecanoyl-ACP dehydratase FabA (BAB1_2174), Acetyl-CoA carboxylase (BAB1_0925) and 3-ketoacyl-acyl-carrier reductase FabG (BAB1_0483), as well as the glutaryl-CoA dehydrogenase GcdH (BAB1_1109), involved in the synthesis of fatty acids for membrane lipids, were all reduced early after infection, suggesting that Acetyl-CoA may be in...”
- “...71 BAB2_0233 Iron metabolism Ton B, Fiu-like 72 BAB2_0505 LPS synthesis BA14 lectin like 73 BAB1_0483 Lipid metabolism FabG 74 BAB1_0486 Lipid metabolism FabF 75 BAB1_2185 Lipid metabolism Ech 76 BAB1_2174 Lipid metabolism FabA 77 BAB2_0975 Lipid metabolism FabC 78 BAB2_1008 Cell division MepA 79 BAB1_1530...”
CPS_RS10230 3-oxoacyl-ACP reductase FabG from Colwellia psychrerythraea 34H
32% identity, 98% coverage
SM12261_RS07550 3-oxoacyl-[acyl-carrier-protein] reductase from Streptococcus mitis NCTC 12261
35% identity, 98% coverage
RPA3285 putative dehydrogenase from Rhodopseudomonas palustris CGA009
37% identity, 97% coverage
RC1_3949 acetoacetyl-CoA reductase from Rhodospirillum centenum SW
34% identity, 97% coverage
ltxD / Q5V8A5 lyngbyatoxin A monooxygenase from Lyngbya majuscula (see 3 papers)
34% identity, 97% coverage
Cbei_1071 3-ketoacyl-(acyl-carrier-protein) reductase from Clostridium beijerincki NCIMB 8052
31% identity, 97% coverage
LIMLP_00095 SDR family NAD(P)-dependent oxidoreductase from Leptospira interrogans serovar Manilae
31% identity, 99% coverage
VC2021 3-oxoacyl-(acyl-carrier-protein) reductase from Vibrio cholerae O1 biovar eltor str. N16961
32% identity, 100% coverage
- Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization
Sadauskas, Applied and environmental microbiology 2017 - “...AAC34814.1 AAC34813.1 F911_02001 F911_02004 F911_02003 4RL8 VC2021 GenBank accession no. or identifier AAB71539.1 Oxygenase component of anthranilate...”
- Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae
Hou, Journal of bacteriology 2016 - “...biovar El Tor strain N16961 (gene locus tag VC2021) and cloned into the pMCSG7 vector using a ligationindependent cloning (LIC) protocol (29). The recombinant...”
- Mechanism of Vibrio cholerae autoinducer-1 biosynthesis
Wei, ACS chemical biology 2011 - “...VC1059 has the highest activity, and two of the other four purified proteins, VCA0301 and VC2021, possess detectable activity in converting DK-CAI-1 to CAI-1 (Figure 6 a). We engineered deletions of vc1059 and vca0301 . VC2021 is the V. cholerae homologue of the E. coli FabG...”
- “...protein in fatty acid biosynthesis,( 26 ) so we could not construct a V. cholerae vc2021 deletion mutant. Lysate from the cqsA , vc1059 double mutant converted significantly less (50%) of the Ea-CAI-1 or DK-CAI-1 to CAI-1 than did lysate from the cqsA single mutant (Figure...”
- A systems biology approach to modeling vibrio cholerae gene expression under virulence-inducing conditions
Kanjilal, Journal of bacteriology 2010 - “...VC0460 VC0468 VC0585 VC0745 VC1231 VC1483 VC1827 VC1995 VC2021 VC2484 VCA0678 VC0196 VC0290 VC0612 VC1663 VC2055 VC2067 VC2368 Cholera enterotoxin, A subunit...”
Q01GL3 3-oxoacyl-[acyl-carrier-protein] reductase from Ostreococcus tauri
34% identity, 88% coverage
- Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses
Misra, Evolutionary bioinformatics online 2012 - “...1.1.1.100 KOG1200 K00059 GO:0004316 P33207, Q9SQR4, Q9SQR2 A8JBX4, Q84X75 D8TK78 * , D8TV99 * A4RQY6 Q01GL3 CMS393C 3-hydroxyacyl-ACP dehydrase (HAD) 4.2.1.- K02372 GO:0008659 Q9LX13, Q9SIE3 Q8LBU6 * , A8IX17 D8TV61 * A4RUS8 CMI240C Enoyl-ACP reductase (EAR) 1.3.1.9 KOG0725 K00208 GO:0004318 Q9SLA8, Q9M672, O04942, Q9FEF2 A8JFI7 D8UC03...”
SGO_1693 3-oxoacyl-(acyl-carrier-protein) reductase from Streptococcus gordonii str. Challis substr. CH1
35% identity, 98% coverage
A0A6B7HD48 tropinone reductase II (EC 1.1.1.236) from Przewalskia tangutica (see paper)
33% identity, 96% coverage
NBT05_09115 SDR family NAD(P)-dependent oxidoreductase from Aquimarina sp. ERC-38
33% identity, 99% coverage
- Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative β-agarase
Kang, Marine biotechnology (New York, N.Y.) 2023 - “...Aq1855 NBT05_09105 3,6-Anhydro-alpha-L-galactosidase 3P2N_A GH117 69.5% Aq1856 NBT05_09110 2-Dehydro-3-deoxy-L-galactonate 5-dehydrogenase 1E3J_A EC 1.1.1.389 31.2% Aq1857 NBT05_09115 2-Dehydro-3-deoxy-D-gluconate 5-dehydrogenase 4Z9Y_A EC 1.1.1.127 47.5% Aq1858 NBT05_09120 3,6-Anhydro-alpha-L-galactose dehydrogenase 6J75_A EC 1.2.1.92 69.3% Aq1859 NBT05_09125 3,6-Anhydro-L-galactonate cycloisomerase 5XD7_A EC 5.5.1.25 69.1% Each -agarase, Aq1828, Aq1829, Aq1830, Aq1832, Aq1839, and...”
AT1G24360 / P33207 3-oxoacyl-[acyl-carrier-protein] reductase, chloroplastic (EC 1.1.1.100) from Arabidopsis thaliana (see paper)
AT1G24360 NAD(P)-binding Rossmann-fold superfamily protein from Arabidopsis thaliana
P33207 3-oxoacyl-[acyl-carrier-protein] reductase, chloroplastic from Arabidopsis thaliana
NP_564216 3-oxoacyl-(acyl-carrier protein) reductase, chloroplast / 3-ketoacyl-acyl carrier protein reductase from Arabidopsis thaliana
34% identity, 77% coverage
- Specialized metabolism by trichome-enriched Rubisco and fatty acid synthase components
Ji, Plant physiology 2023 - “...to chloroplast, where it is elongated by the plastid FAS complex. Recently, a dual-localized KAR (AT1G24360) was reported in Arabidopsis ( Guan et al., 2020 ), and AT1G24360 is phylogenetically closely related to SpKAR1 ( Figure4C ; Supplemental Figure S5 ). This suggests the possibility that...”
- The Sunflower WRINKLED1 Transcription Factor Regulates Fatty Acid Biosynthesis Genes through an AW Box Binding Sequence with a Particular Base Bias
Sánchez, Plants (Basel, Switzerland) 2022 - “...target in sunflower seeds [ 45 ]. The corresponding gene in Arabidopsis ( 30AR , At1g24360 ) is also a putative WRI1 target due to its upregulation in WRI1-overexpressed plants [ 14 ]. We amplified and sequenced the upstream regions of both sunflower genes, confirming the...”
- “...Y-50 [ 46 ] HanXRQrChr05g0148701# KASIII-5g 1 Plastid Y-55 HanXRQr2Chr17g0801431 KASIII-17g 3 Plastid Y-5 KAR At1g24360 HanXRQr2Chr10g0464751 ( KAR2 ) 0 Plastid Y [ 45 ] HanXRQr2Chr17g0781961 ( KAR1 ) KAR-17g 1 Plastid Y-100 [ 45 ] HAD At2g22230 HanXRQr2Chr03g0102091 ( HAD2 ) 0 Plastid Y-25...”
- Heat stress leads to rapid lipid remodeling and transcriptional adaptations in Nicotiana tabacum pollen tubes
Krawczyk, Plant physiology 2022 - “...fatty acid synthesis LOC107779989 A0A1S3YUM8 AT1G23800 ALDH2B7 Aldehyde dehydrogenase 1.59 1.8 E 23 LOC107811394 A0A1S4BSN2 AT1G24360 KAR Ketoacyl-ACP reductase 1.24 8.1 E 08 LOC107789406 A0A1S3ZQ73 AT2G38040 -CT/CAC3 Carboxyltransferase alpha subunit of heteromeric ACCase 1.02 9.0 E 22 LOC107829909 A0A1S4DHM5 AT5G10160 HAD Hydroxyacyl-ACP dehydrase 1.06 5.2 E...”
- Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds
Moreno-Pérez, Plants (Basel, Switzerland) 2021 - “...Synthase III) At1g62640 HanXRQChr02g0049441 Yes Yes HanXRQChr05g0148701 Yes Yes HanXRQChr17g0550351 Yes Yes KAR (Ketoacyl-ACP Reductase) At1g24360 At1g62610 At3g46170 HanXRQChr17g0536131 Yes Yes At3g55290 HanXRQChr10g0318431 Yes Yes At3g55310 HAD (Hydroxyacyl-ACP Dehydrase) At2g22230 HanXRQChr03g0066951 Yes Yes At5g10160 ER (Enoyl-ACP Reductase) At2g05990 HanXRQChr02g0056711 No Yes HanXRQChr17g0564011 Yes Yes HACPS (Holo-ACP...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...Glutamyl-tRNA (Gln) amidotransferase subunit A 46, 47 Q9LI77, At3g25660 LIPID METABOLISM 3-oxoacyl-[acyl-carrier-protein] reductase 97 P33207, At1g24360 3-oxoacyl-[acyl-carrier-protein] synthase I 59, 85 P52410, At5g46290 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta 47, 59 P56765, AtCg00500 Biotin carboxyl carrier protein of acetyl-CoA carboxylase 1 86 Q42533, At5g16390 Biotin...”
- “...the condensing reaction, the 3-ketoacyl-ACP is reduced by 3-ketoacyl-ACP reductase (also known as 3-oxoacyl-ACP reductase, At1g24360, detected in spot 97), dehydrated, and finally the enoyl-ACP reductase (At2g05990, detected in spots 82 and 83) completes the formation of saturated fatty acids [ 54 ]. The presence of...”
- Homology modeling and molecular dynamics based insights into Chalcone synthase and Chalcone isomerase in Phyllanthus emblica L
Kumar, 3 Biotech 2020 - “...(x) Four 3-oxoacyl-[acyl-carrierprotein] synthase (KAS1, KAS2, AT1G24360, KAS), (xi) Embryo-specific protein 3 (AT5G62210), and (xii) Probable 3-ketoacyl-CoA...”
- Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism
Wang, Genomics, proteomics & bioinformatics 2019 - “...synthase Cre07.g324200 0.0E+00 NA NA #132 Cz01g34370 - P 3 3 3-oxoacyl-ACP reductase Cre03.g172000 2.0E120 AT1G24360 8.0E90 #137 Cz03g07200 P P 2 3 Trans-2-enoyl-CoA reductase Cre11.g476550 1.0E66 AT3G45770 1.0E24 #157 Cz02g12160 P P 3 2 Fatty acyl-CoA reductase Cre03.g171700 3.0E60 AT5G22500 3.0E23 #159 Cz14g12050 P P...”
- “...Cre08.g359350 0.0E+00 AT5G35360 0.0E+00 #179 Cz16g00050 P - 1 2 Beta-ketoacyl ACP reductase Cre03.g172000 2.0E23 AT1G24360 3.0E24 #187 Cz04g17090 - P 1 1 Glycerol-3-phosphate dehydrogenase (NAD) Cre09.g387763 7.0E142 AT2G40690 5.0E69 #200 UNPLg00026 - P 2 1 Patatin-like phospholipase NA NA AT2G26560 5.0E07 #212 Cz09g17170 P -...”
- A single-cell platform for reconstituting and characterizing fatty acid elongase component enzymes
Campbell, PloS one 2019 - “...by AT5G46290; KASII, encoded by AT1G74960; KASIII, encoded by AT1G62640), 3-ketoacyl-ACP reductase (KAR, encoded by AT1G24360), 3-hydroxyacyl-ACP dehydratase (HD, encoded by AT2G22230 and AT5G10160), and enoyl-ACP reductase (ER, encoded by AT2G05990). Construction of yeast expression cassettes All yeast expression cassettes used the galactose-inducible GAL1 promoter to...”
- More
- Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation
Félix, International journal of molecular sciences 2023 - “...immature stage ( Figure 7 A). The analysis of palmitate biosynthesis showed that 3-oxoacyl-[ACP] reductase (P33207) and 2,3,4-saturated fatty acyl-[ACP]: NAD+ oxidoreductase (Q9SLA8) were down-accumulated in the YGD, while the 3-hydroxyacyl-[ACP] dehydratase (Q9LX13) was up-accumulated, starting from log2FC 1.33 in the immature stage and increasing to...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...Synthesis Glutamyl-tRNA (Gln) amidotransferase subunit A 46, 47 Q9LI77, At3g25660 LIPID METABOLISM 3-oxoacyl-[acyl-carrier-protein] reductase 97 P33207, At1g24360 3-oxoacyl-[acyl-carrier-protein] synthase I 59, 85 P52410, At5g46290 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta 47, 59 P56765, AtCg00500 Biotin carboxyl carrier protein of acetyl-CoA carboxylase 1 86 Q42533, At5g16390...”
- Improving protein function prediction using protein sequence and GO-term similarities
Makrodimitris, Bioinformatics (Oxford, England) 2019 - “...dataset. As an example, consider query protein Q9SL78, whose best BLAST hit in Arabidopsis is P33207. These two proteins have 48% sequence identity and a BLAST E -value in the order of 10 - 74 . However, their Jaccard semantic similarity in the BPO is 0.0....”
- “...the RING-type zinc finger family. However, they have lower sequence similarity than the query and P33207 (39%). Their profile similarity was more similar, though. Importantly, they are both roughly equally similar (40%) to all the remaining members of the ATL subfamily, 30 of which were present...”
- Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
Liu, International journal of molecular sciences 2018 - “...Araip.10010555.1 1.74 Q9ZRA2 HGO lipid oxidation Araip.10008089.1 1.71 Q9C9P4 KAS2 lipid biosynthetic process Araip.10039818.1 1.71 P33207 At1g24360 fatty acid biosynthetic process Araip.10037915.1 1.67 Q9SQI8 LTA2 lipid biosynthetic process Araip.10019122.1 1.64 F4JML5 At4g16800 fatty acid metabolic process Araip.10020945.1 1.62 Q9SW21 ACP4 fatty acid biosynthetic process Araip.10014644.1 1.62...”
- “...cellular lipid metabolic process Araip.10028882.1 1.15 Q96242 CYP74A fatty acid derivative metabolic process Araip.10039818.1 1.09 P33207 At1g24360 fatty acid biosynthetic process Araip.10007632.1 1.01 Q06327 LOX1 fatty acid biosynthetic process Araip.10036036.1 1.05 Q9C5U1 AHK3 response to lipid Araip.10020945.1 1.11 Q9SW21 ACP4 fatty acid biosynthetic process Araip.10018212.1 1.24...”
- dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock
Misra, PloS one 2016 - “...KAS II/FabF 2.3.1.179 Q9C9P4 beta-ketoacyl-ACP Synthase III KAS III/FabH 2.3.1.180 P49243 3-ketoacyl-ACP Reductase KAR/FabG 1.1.1.100 P33207 3-hydroxyacyl-ACP Dehydratase HAD/FabZ/FabA 4.2.1.59 Q9LX13, Q9SIE3 Enoyl-ACP Reductase ENR/FabI 1.3.1.9 Q9SLA8 Triacylglycerol (TAG) assembly NAD-dependent Glycerol-3-phosphate dehydrogenase GPDH 1.1.1.8 Q9SCX9, Q949Q0 Glycerol-3-phosphate acyltransferase GPAT 2.3.1.15 Q8GWG0, Q43307 Lysophosphatidyl acyltransferase LPAT/LPAAT...”
- Microsome-associated proteome modifications of Arabidopsis seedlings grown on board the International Space Station reveal the possible effect on plants of space stresses other than microgravity
Mazars, Plant signaling & behavior 2014 - “...homolog 3 Q96242 AT5G42650 2.145 allene oxide synthase Q9C8P0 AT1G34430 1.976 pyruvate dehydrogenase E2 component P33207 AT1G24360 1.964 3-oxoacyl-[acyl-carrier-protein] reductase Q56WD9 AT2G33150 1.961 3-ketoacyl-CoA thiolase 2 Q9LM02 AT5G13710 1.939 cycloartenol-c-24-methyltransferase Q9LTV6 AT3G12800 1.914 peroxisomal 2,4-dienoyl-CoA reductase Q9LSQ0 AT3G16910 1.874 acyl-activating enzyme 7 C0Z3A0 1.793 AT3G06850 Q9ZPI5...”
- Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses
Misra, Evolutionary bioinformatics online 2012 - “...P49243, B9DHF9 A8JHL7 D8TXF1 * A4S7P4 Q00V15 CMD118C -ketoacyl-ACP reductase (KAR) 1.1.1.100 KOG1200 K00059 GO:0004316 P33207, Q9SQR4, Q9SQR2 A8JBX4, Q84X75 D8TK78 * , D8TV99 * A4RQY6 Q01GL3 CMS393C 3-hydroxyacyl-ACP dehydrase (HAD) 4.2.1.- K02372 GO:0008659 Q9LX13, Q9SIE3 Q8LBU6 * , A8IX17 D8TV61 * A4RUS8 CMI240C Enoyl-ACP reductase...”
- A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry
Nembaware, BMC evolutionary biology 2004 - “...obtained from the whole genome analyses. Proteins: Function: Bacterial homologs: X. axonopodis A. thaliana NP_640439 NP_564216 short-chain dehydrogenase yes NP_641062 NP_196873 N-acetylglucosaminidase yes NP_642289 NP_196225 3-oxoacyl-[ACP] reductase yes NP_642965 NP_194767 hypothetical protein no NP_643053 NP_568712 amine oxidase related yes NP_643621 NP_173748 expressed protein no NP_644089 NP_182049...”
NP_001263355 dehydrogenase/reductase SDR family member 4 from Tribolium castaneum
35% identity, 97% coverage
B1VK30 Tropinone reductase II from Solanum dulcamara
33% identity, 96% coverage
TRII / CAB52307.1 tropinone reductase II from Solanum tuberosum (see paper)
33% identity, 96% coverage
Q2RXC4 3-oxoacyl-[acyl-carrier-protein] reductase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
Rru_A0416 3-oxoacyl-(acyl-carrier-protein) reductase from Rhodospirillum rubrum ATCC 11170
36% identity, 98% coverage
CBO3600 3-ketoacyl-(acyl-carrier-protein) reductase from Clostridium botulinum A str. ATCC 3502
32% identity, 97% coverage
- Gene expression profiling of Clostridium botulinum under heat shock stress
Liang, BioMed research international 2013 - “...addition, two genes belonging to the same operon, fabF (CBO3599, 3-oxoacyl-ACP synthase II) and fabG (CBO3600, 3-oxoacyl-ACP reductase), were upregulated by 4.2- and 2.3-fold, respectively. Flagella are the most widely characterized of the bacterial motility structures [ 28 ]. Interestingly, we found that four genes involved...”
WP_010563428 acetoacetyl-CoA reductase from Pseudomonas extremaustralis
34% identity, 96% coverage
DET1277 3-oxoacyl-acyl carrier protein reductase from Dehalococcoides ethenogenes 195
35% identity, 98% coverage
Q58LW6 D-arabinitol dehydrogenase (NADP+) (EC 1.1.1.287) from Gluconobacter oxydans (see paper)
34% identity, 97% coverage
MAC_05938 uncharacterized protein from Metarhizium acridum
35% identity, 77% coverage
A0A088MI02 tropinone reductase I (EC 1.1.1.206) from Brugmansia arborea (see paper)
34% identity, 92% coverage
FABG_SYNY3 / P73574 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see paper)
slr0886 3-oxoacyl-[acyl-carrier protein] reductase from Synechocystis sp. PCC 6803
34% identity, 98% coverage
- function: Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis (Probable). Is capable of reducing acetoacetyl-CoA, but less well than its paralog PhaB (PubMed:26358291).
catalytic activity: a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + NADPH + H(+) (RHEA:17397) - Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “.... For example, genes sll1655 and sll0053 for acetyl-CoA carboxylase, sll1069 for beta-ketoacyl synthase and slr0886 for beta-ketocayl-ACP reductase were all downregulated in slr1821 upon NH 4 + stress, while no notable change was observed in WT. Intriguingly, biosynthesis of another carbon storage polymer, glycogen, might...”
HMPREF1120_08985 gluconate 5-dehydrogenase from Exophiala dermatitidis NIH/UT8656
33% identity, 71% coverage
3op4A Crystal structure of putative 3-ketoacyl-(acyl-carrier-protein) reductase from vibrio cholerae o1 biovar eltor str. N16961 in complex with NADP+ (see paper)
32% identity, 99% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (3op4A)
9k8rA Structure of promiscuous short chain dehydrogenase spm14 in complex with NADPH
30% identity, 86% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (9k8rA)
H16_B0062 short chain dehydrogenase from Ralstonia eutropha H16
33% identity, 95% coverage
MS142 putative gluconate dehydrogenase from Microscilla sp. PRE1
33% identity, 98% coverage
F6476_22220 acetoacetyl-CoA reductase from Pseudomonas umsongensis
33% identity, 96% coverage
A0A6B7HCZ2 tropinone reductase I (EC 1.1.1.206) from Przewalskia tangutica (see paper)
35% identity, 92% coverage
3uf0A / C5BY10 Crystal structure of a putative NAD(p) dependent gluconate 5- dehydrogenase from beutenbergia cavernae(efi target efi-502044) with bound NADP (low occupancy)
34% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (3uf0A)
TR2 / P50163 tropinone reductase (EC 1.1.1.236) from Datura stramonium (see paper)
TRN2_DATST / P50163 Tropinone reductase 2; Tropinone reductase II; TR-II; EC 1.1.1.236 from Datura stramonium (Jimsonweed) (Common thornapple) (see paper)
P50163 tropinone reductase II (EC 1.1.1.236) from Datura stramonium (see 3 papers)
33% identity, 96% coverage
- function: Catalyzes the stereospecific reduction of tropinone to pseudotropine
catalytic activity: pseudotropine + NADP(+) = tropinone + NADPH + H(+) (RHEA:24244)
subunit: Homodimer.
2ae2A / P50163 Tropinone reductase-ii complexed with NADP+ and pseudotropine (see paper)
33% identity, 97% coverage
- Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; pseudotropine (2ae2A)
NCU01861 short chain dehydrogenase/reductase family protein from Neurospora crassa OR74A
32% identity, 70% coverage
- Genome-wide characterization of light-regulated genes in Neurospora crassa
Wu, G3 (Bethesda, Md.) 2014 - “...al. 1995 ). Also included in this cluster are several oxidoreductases ( mig-3 , NCU04452; NCU01861; and NCU08291) important in redox reactions. Genes in Cluster 5 are repressed by light, with repression being the strongest 60 to 120 min after light treatment. Although some light-repressed genes...”
- “...1.3 NCU03506 hypothetical protein 3.1 4.3 3.0 1.5 NCU05844 hypothetical protein 2.7 4.5 2.6 0.5 NCU01861 short chain dehydrogenase/reductase family 2.2 5.6 4.5 1.1 NCU06597 hypothetical protein 2.0 5.4 3.3 0.6 NCU04823 NADP-dependent alcohol dehydrogenase C 1.6 4.5 3.5 1.0 NCU05652 hypothetical protein 1.4 4.6 3.5...”
Tsac_1753 3-oxoacyl-[acyl-carrier-protein] reductase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
31% identity, 96% coverage
- The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum
Zheng, PloS one 2018 - “...Tsac_1550 hfsABCD Iron hydrogenases; sporulation protein Energy TTGTTAATAAATTAACTA -78 Tsac_1619 Prephenate dehydrogenase Carb GTGATTTTAAATGATCAA -10 Tsac_1753 3-oxoacyl-(acyl-carrier-protein) reductase Syn TTGATAAACTTTTATCCA -35 Tsac_1856 PHP domain protein Syn TTGTTTTTAGTTTAACAT -33 Tsac_1947 Fimbrial assembly family protein Mem ATGATTCAAAAAAATCAA -186 Tsac_1985 ABC transporter related Mem TTGAATTGAAATTTTCTA -82 Tsac_2078 ABC-2 type...”
kduD / Q05528 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (EC 1.1.1.127) from Dickeya dadantii (strain 3937) (see 3 papers)
KDUD_DICD3 / Q05528 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; 2-keto-3-deoxygluconate 5-dehydrogenase; 2-keto-3-deoxygluconate oxidoreductase; KDG oxidoreductase; EC 1.1.1.127 from Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937)) (see paper)
34% identity, 98% coverage
- function: Catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH.
catalytic activity: 2-dehydro-3-deoxy-D-gluconate + NAD(+) = 3-deoxy-D-glycero- 2,5-hexodiulosonate + NADH + H(+) (RHEA:24232)
NP_385248 PROBABLE 3-OXOACYL-ACYL-CARRIER PROTEIN REDUCTASE from Sinorhizobium meliloti 1021
36% identity, 98% coverage
A4RQY6 3-oxoacyl-[acyl-carrier-protein] reductase from Ostreococcus lucimarinus (strain CCE9901)
34% identity, 91% coverage
- Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses
Misra, Evolutionary bioinformatics online 2012 - “...(KAR) 1.1.1.100 KOG1200 K00059 GO:0004316 P33207, Q9SQR4, Q9SQR2 A8JBX4, Q84X75 D8TK78 * , D8TV99 * A4RQY6 Q01GL3 CMS393C 3-hydroxyacyl-ACP dehydrase (HAD) 4.2.1.- K02372 GO:0008659 Q9LX13, Q9SIE3 Q8LBU6 * , A8IX17 D8TV61 * A4RUS8 CMI240C Enoyl-ACP reductase (EAR) 1.3.1.9 KOG0725 K00208 GO:0004318 Q9SLA8, Q9M672, O04942, Q9FEF2 A8JFI7...”
2ekpA / Q53W82 Structure of tt0495 protein from thermus thermophilus (see paper)
35% identity, 96% coverage
- Ligand: nicotinamide-adenine-dinucleotide (2ekpA)
NPW32_RS02975 SDR family NAD(P)-dependent oxidoreductase from Staphylococcus epidermidis
32% identity, 98% coverage
SSU05_1803 3-ketoacyl-(acyl-carrier-protein) reductase from Streptococcus suis 05ZYH33
SSU1603 3-oxoacyl-[acyl-carrier protein] reductase from Streptococcus suis P1/7
36% identity, 98% coverage
- Peptidomics Analysis of Virulent Peptides Involved in Streptococcus suis Pathogenesis
Chaiden, Animals : an open access journal from MDPI 2021 - “...and 4--glucanotransferase (SSU05_0392) in SS14. Moreover, a peptide of fatty acid biosynthesis protein, 3-oxoacyl-[acyl-carrier-protein] reductase (SSU05_1803) was also identified in SS2, SS14, SS7, and SS27. Peptides involved in the membrane of the bacteria were also detected, consisting of a derived peptide of the PTS system ascorbate-specific...”
- “...(755) carbohydrate metabolism SSU05_1489 K01223 6-phospho-beta-glucosidase [EC-3.2.1.86] (474) carbohydrate metabolism SSU05_0392 4--glucanotransferase (364) carbohydrate metabolism SSU05_1803 3-oxoacyl-[acyl-carrier-protein] reductase (244) fatty acid biosynthesis SSU05_2063 PTS system ascorbate-specific transporter subunit IIC (482) cell membrane/membrane SSU05_1254 ABC transporter permease (197) transmembrane transporter SSU05_1106 ABC-type phosphate transport system (83) periplasmic...”
- Proteomic and Metabolomic Analyses Provide Insights into the Mechanism on Arginine Metabolism Regulated by tRNA Modification Enzymes GidA and MnmE of Streptococcus suis
Gao, Frontiers in cellular and infection microbiology 2020 - “...of acetyl-CoA carboxylase 0.4501 1 8.16 FabF SSU05_1802 3-oxoacyl-[acyl-carrier-protein] synthase 2 0.2011 8 26.52 FabG1 SSU05_1803 3-ketoacyl-ACP reductase 0.2392 13 80.33 FabD SSU05_1804 Malonyl CoA-acyl carrier protein transacylase 0.4979 6 23.86 FabI SSU05_1805 2-nitropropane dioxygenase 0.2211 2 39.56 AcpP SSU05_1806 Acyl carrier protein 0.5513 1 14.86...”
- MnmE, a Central tRNA-Modifying GTPase, Is Essential for the Growth, Pathogenicity, and Arginine Metabolism of Streptococcus suis Serotype 2
Gao, Frontiers in cellular and infection microbiology 2019 - “...SSU05_1800 3-hydroxyacyl-[acyl-carrier-protein] dehydratase 0.3717 2 17.14 FabF SSU05_1802 3-oxoacyl-[acyl-carrier-protein] synthase 2 0.18734 8 26.52 FabG1 SSU05_1803 3-ketoacyl-ACP reductase 0.2132 13 80.33 FabD SSU05_1804 Malonyl CoA-acyl carrier protein transacylase 0.4977 6 23.86 FabI SSU05_1805 2-nitropropane dioxygenase 0.2033 2 39.56 FadB SSU05_1809 Enoyl-CoA hydratase 0.4785 9 34.22 Virulence-Associated...”
- Precision Genome Engineering in Streptococcus suis Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
Gussak, ACS synthetic biology 2023 - “...SSU1598 accD 5.45 SSU1599 accC 5.81 SSU1600 fabZ 5.99 SSU1601 fabE 6.15 SSU1602 fabF 6.29 SSU1603 fabG 6.65 SSU1604 fabD 6.56 SSU1605 fabK 6.50 SSU1606 acpP 4.67 SSU1607 fabH 4.05 SSU1608 marR 3.78 SSU1609 phaB 5.05 tircarboxylic acid cycle SSU1040 Icd 2.98 SSU1041 citZ 2.92 SSU1042...”
RHE_RS07365 3-oxoacyl-[acyl-carrier-protein] reductase from Rhizobium etli CFN 42
36% identity, 98% coverage
ZMO1222 3-oxoacyl-(acyl-carrier-protein) reductase from Zymomonas mobilis subsp. mobilis ZM4
34% identity, 98% coverage
- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
Ong, PLoS computational biology 2020 - “...OGMEACPS_f, OPMEACPD_f, OPMEACPR_f, OPMEACPS_f, PMEACPE_f , S2FE2SR_f 13 ZMO0094, ZMO0423, ZMO0425, ZMO0426, ZMO0427, ZMO1067, ZMO1146, ZMO1222, ZMO1278, ZMO1692, ZMO1915, ZMO1917, ZMO1918, Biotin biosynthesis Modules with average cofitness scores below the significance threshold M45 0.497 5 E4PD_f , OHPBAT_f, PDX5PS_f, PERD_f , SINK_pydx5p_f 3 ZMO1313, ZMO1684, ZMO1708...”
- Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
Yan, Applied and environmental microbiology 2019 - “...ATCGCCTGCGTTGTGGTG GCATTCATGCGGATCATACCA reductase ZMO1222 3-oxoacyl-(acyl-carrier-protein) reductase TTAGCCGTGCCGTCATCAGA CGATCATGCCTGCCTTTGC ZMO1303...”
- “...ZMO0778 ZMO0157 ZMO1949 ZMO1335 ZMO1254 ZMO1984 ZMO1303 ZMO1222 ZMO0833 ZMO1993 ZMO1885 ZMO1772 ZMO1116 0 Hypotheticals 652 Fig. 5 Transcription level analysis...”
- Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
Yi, Biotechnology for biofuels 2015 - “...adenylyltransferase subunit 2 3.09 2.13 Energy metabolism ZMO1116 b Oxidoreductase 2.53 3.60 2.47 Lipid metabolism ZMO1222 3-oxoacyl-ACP reductase 2.73 2.11 Metabolism of cofactors and vitamins ZMO0006 Uroporphyrin-III C-methyltransferase 3.09 2.05 Metabolism of cofactors and vitamins ZMO0474 3,4-dihydroxy-2-butanone 4-phosphate synthase 2.71 2.34 Metabolism of cofactors and vitamins...”
- “...2-hydroxyacid dehydrogenase NAD binding, ZMO0788 encoded a gluconate 2-dehydrogenase, ZMO0833 encoded UDP- N -acetylenolpyruvoylglucosamine reductase, ZMO1222 encoded 3-oxoacyl-(acyl-carrier-protein) reductase, ZMO1254 encoded redoxin domain protein, ZMO1303 encoded a pyrroline-5-carboxylate reductase, ZMO1399 encoded fatty acid hydroxylase, ZMO1576 encoded short-chain dehydrogenase/reductase SDR, ZMO1696 encoding zinc-binding alcohol dehydrogenase, ZMO1984 encoded...”
SPO0595, YP_165855 gluconate 5-dehydrogenase from Silicibacter pomeroyi DSS-3
SPO0595 SDR family NAD(P)-dependent oxidoreductase from Ruegeria pomeroyi DSS-3
34% identity, 98% coverage
- Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria
Liu, The ISME journal 2024 - “...-, S -DHPS towards DHPS dehydrogenases on Biacore T200 (Cytiva). The purified proteins Rp HpsO (SPO0595), Rp HpsP (SPO0596), and Rp HpsN were first subjected to a gel-filtration column (Superdex 200 Increase 10/300 GL, Cytiva) with phosphate buffer (10mM, pH8.0) and then concentrated to ~1mg/ml using...”
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...Function YP_165853 SPO0593 Dihydroxypropanesulfonate (DHPS) TRAP transporter hpsM Function YP_165854 SPO0594 Dihydroxypropanesulfonate-3-dehydrogenase hpsN Function YP_165855 SPO0595 R or S-dihydroxypropanesulfonate-2-dehydrogenase hpsO Function YP_165856 SPO0596 S or R-dihydroxypropanesulfonate-2-dehydrogenase hpsP Function YP_165857 SPO0597 UspA stress protein hpsQ Function YP_165858 SPO0598 Membrane-bound sulfolactate dehydrogenase slcD Function YP_165912 SPO0657 Metallochaperone, putative...”
- “...hpsL Function YP_165853 SPO0593 Dihydroxypropanesulfonate (DHPS) TRAP transporter hpsM Function YP_165854 SPO0594 Dihydroxypropanesulfonate-3-dehydrogenase hpsN Function YP_165855 SPO0595 R or S-dihydroxypropanesulfonate-2-dehydrogenase hpsO Function YP_165856 SPO0596 S or R-dihydroxypropanesulfonate-2-dehydrogenase hpsP Function YP_165857 SPO0597 UspA stress protein hpsQ Function YP_165858 SPO0598 Membrane-bound sulfolactate dehydrogenase slcD Function YP_165912 SPO0657 Metallochaperone,...”
- Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux
Landa, The ISME journal 2019 - “...SPO3560 Regulation hpsP slcD SPO0596 SPO0598 cuyR hpsO SPO0595 SPOA0159 hpsN hpsM SPO0593 SPO0594 hpsL SPO0592 DHPS metabolism hpsK SPO0590 SPO0591 Regulation...”
Q1J2J0 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Deinococcus geothermalis (see paper)
35% identity, 98% coverage
TR1 / P50162 tropinone reductase (EC 1.1.1.206) from Datura stramonium (see paper)
TRN1_DATST / P50162 Tropinone reductase 1; Tropine dehydrogenase; Tropinone reductase I; TR-I; EC 1.1.1.206 from Datura stramonium (Jimsonweed) (Common thornapple) (see 2 papers)
P50162 tropinone reductase I (EC 1.1.1.206) from Datura stramonium (see 2 papers)
34% identity, 92% coverage
- function: Catalyzes the stereospecific reduction of tropinone to tropine.
catalytic activity: tropine + NADP(+) = tropinone + NADPH + H(+) (RHEA:18357)
subunit: Homodimer. - Comparative proteomics analyses of intraspecific differences in the response of Stipa purpurea to drought.
Li, Plant diversity 2016 - “...plasma membrane-associated protein-like Brachypodium distachyon M Q949H0 0.53 646 Ribosomal protein S7 Triticum aestivum S P50162 0.59 72 Tropinone reductase 1-like Brachypodium distachyon O P27521 0.33 575 Chlorophyll a-b binding protein 4, chloroplastic-like Brachypodium distachyon P Q06030 0.61 341 50S ribosomal protein L12, chloroplastic-like Setaria italica...”
1ae1B / P50162 Tropinone reductase-i complex with NADP (see paper)
34% identity, 97% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (1ae1B)
PGTG_15283 uncharacterized protein from Puccinia graminis f. sp. tritici CRL 75-36-700-3
34% identity, 83% coverage
gra-orf6 / BAD51477.1 ketoreductase from Streptomyces violaceoruber (see 3 papers)
Q65YY6 Ketoreductase from Streptomyces violaceoruber
37% identity, 96% coverage
Strop_2799 3-oxoacyl-(acyl-carrier-protein) reductase from Salinispora tropica CNB-440
37% identity, 96% coverage
- Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics
Lohman, Molecular bioSystems 2013 - “...kedU14 397 Strop_2801 (ABP55242) 71/81 Acyltransferase kedU15 407 Strop_2800 (ABP55241) 68/78 CoA transferase kedU16 247 Strop_2799 (ABP55240) 71/81 Ketoreductase kedU17 152 Strop_2798 (ABP55239) 43/53 Dehydratase kedU18 164 Strop_2797 (ABP55238) 59/72 Dehydratase kedU19 78 Strop_2796 (ABP55237) 76/93 ACP Unknown type II PKS locus d kedU20 402 Strop_2795...”
- Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine
Eustáquio, Proceedings of the National Academy of Sciences of the United States of America 2009 - “...6 -- -- Strop_1405, 35% Strop_0986, 69% -- Strop_2799, 35% Strop_1231, 36% Strop_1050 -- Strop_3612, 53% salG, 53% Sal., salinosporamide; n.d., not detected...”
- “...biochemical cross-talk with homologous dehydrogenases such as Strop_2799 (35% sequence identity). We hypothesized that the absence of SalM might furthermore...”
WP_011093956 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD from Pectobacterium atrosepticum
34% identity, 98% coverage
- [Genetic regulation of pathogenicity and virulence factors in bacteria Erwinia carotovora subsp. atroseptica: identification of kduD gene].
Miamin, Genetika 2004 (PubMed)- GeneRIF: located at 126.8 min of the Erwinia carotovora subsp. atroseptica genetic map; a mutant gene is responsible for failure to accomplish the catabolism of unsaturated digalacturonic acid
BRADO6616 putative oxidoreductase; putative Glucose/ribitol oxidoreductase from Bradyrhizobium sp. ORS278
34% identity, 97% coverage
- Identification and Validation of Reference Genes for Expression Analysis in Nitrogen-Fixing Bacteria under Environmental Stress
Parks, Life (Basel, Switzerland) 2022 - “...For ORS278, three genes BRADO6535, encoding a hypothetical protein, BRADO0162, encoding a phospholipid N-methyltransferase, and BRADO6616, encoding a putative oxidoreductase, were constitutively expressed during the day and night cycle ( Table 2 ). The target window of gene expression is a range of 0.8 < x...”
- “...( blr3561 ) hypothetical protein 0.8 0.3 BRADO0162 ( bll8166 ) phospholipid N-methyltransferase 1.0 0.1 BRADO6616 ( blr6358 ) putative oxioreducatase; putative glucose/ribitol oxioreductase 1.1 0.0 BRADO3450 (blr6296) hypothetical protein 1.6 0.1 a Gene names in parenthesis represent B. diazoefficiens USDA110 gene locus. Bold letters indicate...”
FABG_SALTY / P0A2C9 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM1195 3-oxoacyl-[acyl-carrier-protein] reductase from Salmonella typhimurium LT2
t1725 3-oxoacyl-[acyl-carrier protein] reductase from Salmonella enterica subsp. enterica serovar Typhi Ty2
T_RS08780 3-oxoacyl-ACP reductase FabG from Salmonella enterica subsp. enterica serovar Typhi str. Ty2
33% identity, 98% coverage
- function: Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis.
catalytic activity: a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + NADPH + H(+) (RHEA:17397)
subunit: Homotetramer. - Escherichia coli FabG 3-ketoacyl-ACP reductase proteins lacking the assigned catalytic triad residues are active enzymes
Hu, The Journal of biological chemistry 2021 - “...wildtype E.coli K-12 and S.enterica LT2 FabG sequences were taken from UniProtKB/Swiss-Prot entries P0AEK2 and P0A2C9, respectively. Circular dichroism measurements The CD spectra of FabG and mutant FabG proteins were obtained with a Chirascan (Applied Photophysics Limited) at 25 C using a 1.0-nm bandwidth, 1-mmcell, 1.0-nm...”
- Identifying essential genes in bacterial metabolic networks with machine learning methods
Plaimas, BMC systems biology 2010 - “...dehydrogenase STM0988 kdsB 2.7.7.38 CTP:CMP-KDO cytidylyltransferase * STM1194 fabD 2.3.1.39 Acyl carrier protein S-malonyltransferase * STM1195 fabG 1.1.1.100 3-ketoacyl-(acyl-carrier-protein) reductase ** STM1200 tmk 2.7.4.9 Thymidylate kinase STM1700 fabI 1.3.1.10 Enoyl-(acyl carrier protein) reductase STM2483 dapE 3.5.1.18 Succinyl-diaminopimelate desuccinylase STM2652 pssA 2.7.8.8 Phosphatidylserine synthase * STM3090 metK...”
- Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
Nickerson, EBioMedicine 2018 - “...0.0004 T_RS08555 t1680 2.46 0.0016 Sodiumpotassium/proton antiporter ChaA T_RS03960 t0786 2.44 0.0004 Glycosyl transferase T_RS08780 t1725 2.44 0.0004 Beta-ketoacyl-ACP reductase T_RS02535 t0501 2.43 0.0004 Colicin V production protein T_RS20635 t4059 2.42 0.0004 Elongation factor G T_RS03925 t0779 2.39 0.0004 CDP-6-deoxy-delta-3,4-glucoseen reductase T_RS14115 t2782 2.39 0.0004 Hypothetical...”
- Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
Nickerson, EBioMedicine 2018 - “...2.48 0.0004 T_RS08555 t1680 2.46 0.0016 Sodiumpotassium/proton antiporter ChaA T_RS03960 t0786 2.44 0.0004 Glycosyl transferase T_RS08780 t1725 2.44 0.0004 Beta-ketoacyl-ACP reductase T_RS02535 t0501 2.43 0.0004 Colicin V production protein T_RS20635 t4059 2.42 0.0004 Elongation factor G T_RS03925 t0779 2.39 0.0004 CDP-6-deoxy-delta-3,4-glucoseen reductase T_RS14115 t2782 2.39 0.0004...”
DDGLD_PSEA6 / Q15SS0 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; 2,5-diketo-3-deoxy-L-galactonate 5-reductase; EC 1.1.1.127 from Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087)
33% identity, 99% coverage
- function: Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the fourth step of the pathway, the reduction of 3-deoxy-D-glycero-2,5- hexodiulosonate (L-DDGal) to 2-dehydro-3-deoxy-D-gluconate (KDG).
catalytic activity: 2-dehydro-3-deoxy-D-gluconate + NAD(+) = 3-deoxy-D-glycero- 2,5-hexodiulosonate + NADH + H(+) (RHEA:24232)
A0A1E3M3N6 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) from Acinetobacter baumannii (see paper)
6zzsD / A0A1E3M3N6 Crystal structure of (r)-3-hydroxybutyrate dehydrogenase from acinetobacter baumannii complexed with NAD+ and 3-oxovalerate (see paper)
30% identity, 95% coverage
- Ligands: nicotinamide-adenine-dinucleotide; 3-oxidanylidenepentanoic acid (6zzsD)
A0A1D3K298 3-oxoacyl-[acyl-carrier-protein] reductase from Pseudomonas veronii 1YdBTEX2
36% identity, 98% coverage
- Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source
Zavala-Meneses, Microorganisms 2024 - “...peg.937 1.13.11.24 Quercetin 2,3-dioxygenase A0A1D3K115 peg.1907 1.13.11.24 Pirin A0A1D3JZS8 peg.1440 1.13.11.16 2,3-dihydroxyphenyl propionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase A0A1D3K298 peg.5553 1.1.1.100 3-oxoacyl-[acyl-c arrier-protein] reductase A0A1D3JWU0 peg.304 Oxidoreductase A0A1D3K7I1 peg.3568 1.14.11.- Fe2OG dioxygenase domain-containing protein Lyases A0A1D3K2B2 peg.5665 4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate aldolase A0A1D3K4Q4 peg.3296 4.1.3.27 Anthranilate synthase component 1 A0A1D3K4Q5 peg.3295...”
6t77A / W9B6I8 Crystal structure of klebsiella pneumoniae fabg(NADPH-dependent) NADP- complex at 1.75 a resolution (see paper)
33% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (6t77A)
FXV78_RS03230 3-oxoacyl-[acyl-carrier-protein] reductase from Mediterraneibacter gnavus ATCC 29149
35% identity, 98% coverage
A0A0M4UR95 L-xylulose reductase (EC 1.1.1.10) from Rhizomucor pusillus (see paper)
32% identity, 96% coverage
Q2RLD2 Short-chain dehydrogenase/reductase SDR from Moorella thermoacetica (strain ATCC 39073 / JCM 9320)
30% identity, 98% coverage
KDUD_BACSU / P50842 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; 2-keto-3-deoxygluconate 5-dehydrogenase; 2-keto-3-deoxygluconate oxidoreductase; KDG oxidoreductase; EC 1.1.1.127 from Bacillus subtilis (strain 168) (see paper)
33% identity, 99% coverage
- function: Catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH.
catalytic activity: 2-dehydro-3-deoxy-D-gluconate + NAD(+) = 3-deoxy-D-glycero- 2,5-hexodiulosonate + NADH + H(+) (RHEA:24232) - Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate
Zhong, Applied and environmental microbiology 2001 - “...ARSB_MOUSE_2 BAA86649 Q57517 BAA18061 F75583 P77989 Q57517 P50842 P25553 443131 P05149 P27125 P39217 48-351 1-237 51-127 31-286 28-428 31-185 1-153 1-418...”
STM4483 5-keto-D-gluconate-5-reductase from Salmonella typhimurium LT2
31% identity, 99% coverage
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3859, STM4066, STM4206, STM4215, STM4218, STM4447, STM4483, STM4498, STM4528, PSLT040, PSLT060, PSLT107, STY1049, STY2077, STY2364, STY3088, STY3688,...”
Q9X248 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
31% identity, 97% coverage
LOC101206201 tropinone reductase homolog from Cucumis sativus
33% identity, 92% coverage
- Uncovering waterlogging-responsive genes in cucumber through machine learning and differential gene correlation analysis
Zinati, Botanical studies 2024 - “...shown in Table 2 , these genes were LOC101213801, LOC101210665, LOC101205805, LOC101217277, LOC101213872, LOC101222503, LOC101206239, LOC101206201, LOC101212424, LOC101212625, LOC101203084, LOC101204590, LOC101210747, LOC101214385, LOC101213580, LOC116403322, LOC101205431, LOC101210491, LOC105435194, LOC101204309, and LOC101205898. Weight by SVM The SVM algorithm indicated that ten genes had values surpassing 0.90. As mentioned...”
- “...Correlation LOC101213801 1 LOC101210665 0.981792 LOC101205805 0.976468 LOC101217277 0.965222 LOC101213872 0.961903 LOC101222503 0.95507 LOC101206239 0.950225 LOC101206201 0.947782 LOC101212424 0.946504 LOC101212625 0.946377 LOC101203084 0.936201 LOC101204590 0.929242 LOC101210747 0.921718 LOC101214385 0.919868 LOC101213580 0.9143 LOC116403322 0.91381 LOC101205431 0.913398 LOC101210491 0.903276 LOC105435194 0.902187 LOC101204309 0.901909 LOC101205898 0.900742 SVM WRKY34 1...”
TRNHC_ARATH / Q9ZW19 Tropinone reductase homolog At2g29360; EC 1.1.1.- from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G29360 tropinone reductase, putative / tropine dehydrogenase, putative from Arabidopsis thaliana
34% identity, 93% coverage
- function: Oxidoreductase active on cyclic ketones, but not on tropinone or nortropinone.
- Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula
Subrahmaniam, The New phytologist 2025 - “...Stress Carbohydrates 1 N.V554 1 22319649 AT1G60600 ABC4 Nutrient Amino acid 2 N.V672 2 12605976 AT2G29360 SDR Metabolism Amino acids 1 N.V313 2 18065356 AT2G43500 NLP8 Nutrient Amino acids 1 N.V665* 3 8721212 AT3G24140 FAMA Signaling Amino acids 1 N.V665* 3 8764452 AT3G24220 NCED6 Metabolism Amino...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...AT4G34230, AT2G22990, AT1G51680, AT5G47000 Tropane, piperidine and pyridine alkaloid biosynthesis 5 0.26 0.03 AT2G29320, AT2G37040, AT2G29360, AT2G29340, AT3G53260 Stilbenoid, diarylheptanoid and gingerol biosynthesis 10 0.51 0.03 AT1G74550, AT4G37310, AT4G34050, AT3G26220, AT3G26200, AT2G30490, AT5G04660, AT3G53280, AT3G26280, AT3G26290 Table 6 Potential functions of the 43 transcripts presenting extensively...”
F6HL77 Tropinone reductase-like from Vitis vinifera
34% identity, 96% coverage
SEN4236 gluconate 5-dehydrogenase (ec 1.1.1.69) (5-keto-d-gluconate 5-reductase) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
31% identity, 99% coverage
Q31QF3 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Synechococcus elongatus PCC 7942 = FACHB-805 (see paper)
Synpcc7942_0684 3-oxoacyl-(acyl-carrier-protein) reductase from Synechococcus elongatus PCC 7942
39% identity, 98% coverage
- Synechococcus elongatus PCC 7942 as a Platform for Bioproduction of Omega-3 Fatty Acids
Santos-Merino, Life (Basel, Switzerland) 2022 - “...sites of the pMSM253 vector [ 33 ]. To overexpress the fabG gene of Se7942 (Synpcc7942_0684; GenBank Accession Number: NC_007604) in two neutral chromosomal regions, NS1 and NS2, plasmids pMSM310 and pMSM317 were constructed. Gene fabG was amplified with primer pair 380381, digested with EcoRI and...”
- “...performed the construction of pMSM319 to co-overexpress fabF and fabG genes of Se7942 (Synpcc7942_0537 and Synpcc7942_0684; GenBank Accession Number: NC_007604) in the neutral chromosomal region, NS2. To generate pMSM319, the P trc::fabG fragment was amplified from pMSM310 plasmid DNA using primers 364 and 384. The amplicon...”
azo1625 3-oxoacyl-[acyl-carrier-protein] reductase from Azoarcus sp. BH72
36% identity, 98% coverage
- Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72
Sarkar, PloS one 2014 - “...10.0 21.45.7 n/a n/a azo1566 clpB1 probable ATP-dependent Clp protease. 4.2 16.36.4 n/a n a azo1625 fabG1 3-oxoacyl-[acyl-carrier-protein] reductase 3.6 3.81.4 3.6 52.416.6 azo0720 rpsR SSU ribosomal protein S18P 2.9 2.51.5 3.1 41.2 azo0585 tlyA conserved hypothetical protein n/a n/a 6.1 12.73.2 azo1077 cysM cysteine synthase...”
- “..., middle panel). In accordance to expression data from microarray analysis, qRT-PCR further validated the azo1625 modulation, with down-regulation under N 2 response by -3.81.4 fold and activation by NifA by 52.416.6 fold. Although the expression of the gene cluster encoding for a T6SS was enhanced...”
Q9AR59 tropinone reductase I (EC 1.1.1.206) from Solanum tuberosum (see paper)
33% identity, 96% coverage
L0185 3-oxoacyl-acyl carrier protein reductase (EC 1.1.1.100) from Lactococcus lactis subsp. lactis Il1403
34% identity, 95% coverage
PHOF1_DIALO / A0A8J9S3B0 Short-chain dehydrogenase/reductase PhomF; Phomopsin biosynthesis cluster protein F; EC 1.-.-.- from Diaporthe leptostromiformis (Lupinosis disease fungus) (Phomopsis leptostromiformis) (see paper)
30% identity, 85% coverage
- function: Short-chain dehydrogenase/reductase; part of the gene cluster that mediates the biosynthesis of the phomopsins, a group of hexapeptide mycotoxins which infects lupins and causes lupinosis disease in livestock (PubMed:34608734). The role of phomF within the phomopsins biosynthesis pathway has still to be determined (Probable). The pathway starts with the processing of the precursor phomA by several endopeptidases including kexin proteases as well as the cluster-specific S41 family peptidase phomP1 and the oligopeptidase phomG to produce 10 identical copies of the hexapeptide Tyr-Val-Ile- Pro-Ile-Asp. After being excised from the precursor peptide, the core peptides are cyclized and modified post-translationally by enzymes encoded within the gene cluster. The timing and order of proteolysis of the phomA precursor and PTMs are still unknown. Two tyrosinase-like enzymes, phomQ1 and phomQ2, catalyze the chlorination and hydroxylation of Tyr, respectively. PhomYb, is proposed to be involved in the construction of the macrocyclic structure. The other 4 ustYa family proteins may be involved in PTMs that generate the unique structure of phomopsin A. PhomYa is required for the hydroxylation of C-beta of Tyr. PhomYc, phomYd, and phomYe are responsible for the biosynthesis of 2,3- dehydroisoleucine (dIle), 2,3-dehydroaspartic acid (dAsp), and 3,4- dehydroproline (dPro), respectively. While dIle formation by phomYc is indispensable for the installation of dAsp by phomYd, the order of the other PTMs have not been elucidated yet. Most of the biosynthetic enzymes likely have broad substrate specificity, and thus, there might be a metabolic grid from a precursor to phomopsin A. The enzyme(s) responsible for the biosynthesis of 3,4-dehydrovaline (dVal) have also not been identified yet. Finally, phomM acts as an S- adenosylmethionine-dependent alpha-N-methyltransferase that catalyzes two successive N-methylation reactions, converting N-desmethyl- phomopsin A to phomopsin A and phomopsin A further to an N,N- dimethylated congener called phomopsin E (Probable).
SAK_0422 3-oxoacyl-(acyl-carrier-protein) reductase from Streptococcus agalactiae A909
36% identity, 98% coverage
BTH_II0349 oxidoreductase, short chain dehydrogenase/reductase family superfamily from Burkholderia thailandensis E264
34% identity, 97% coverage
- Burkholderia thailandensis: Genetic Manipulation
Garcia, Current protocols in microbiology 2017 - “...(red arrows) that anneal to the Tn7L region of mini-Tn7 and either Bth_I0286 (Bth_RS13660) or Bth_II0349 (Bth_RS01810) are used to confirm a tt Tn7 insertion (for primer sequences, see Basic Protocol 2). In this example based on insertion from pUC18T-miniTn7T-Km ( Choi et al., 2005 ),...”
TRN1_COCOF / A7DY56 Tropinone reductase; EC 1.1.1.206; EC 1.1.1.236 from Cochlearia officinalis (Common scurvygrass) (see paper)
A7DY56 tropinone reductase I (EC 1.1.1.206); tropinone reductase II (EC 1.1.1.236) from Cochlearia officinalis (see paper)
32% identity, 92% coverage
- function: Oxidoreductase having both tropinone reductase I and II activities. Involved in the tropane alkaloids calystegines and cochlearine biosynthesis. Can use tropinone and nortropinone as substrates and produces both tropine and pseudotropine. Able to oxidize pseudotropine in the reverse reaction.
catalytic activity: tropine + NADP(+) = tropinone + NADPH + H(+) (RHEA:18357)
catalytic activity: pseudotropine + NADP(+) = tropinone + NADPH + H(+) (RHEA:24244)
ACICU_01774 dehydrogenase from Acinetobacter baumannii ACICU
29% identity, 95% coverage
- Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment
Wright, mBio 2017 - “...all clade C isolates and upstream by an additional isolate-specific IS Aba 1 insertion at ACICU_01774, in a region encoding a transcriptional regulator, transporters, and dehydrogenases of unannotated specificity. Point mutations in ACICU_03495 and ACICU_03498 (a TCRS hybrid sensor histidine kinase/response regulator) in ABUH66276 are associated...”
Csac_2718 2-deoxy-D-gluconate 3-dehydrogenase from Caldicellulosiruptor saccharolyticus DSM 8903
32% identity, 98% coverage
- Novel monosaccharide fermentation products in Caldicellulosiruptor saccharolyticus identified using NMR spectroscopy
Isern, Biotechnology for biofuels 2013 - “...candidate C. saccharolyticus gene for acetoin formation (presumably, acetolactate decarboxylase), though several candidate acetoin dehydrogenases (Csac_2718, 0357, 0868, or 1605) that could reduce acetoin to 2,3-butanediol have been identified in the genome [ 4 ]. C. saccharolyticus cells grew poorly in BA medium supplemented with 1%...”
- Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
van, Applied and environmental microbiology 2008 - “...genes (Csac_ 0356 and Csac_0357, as well as Csac_2718 and Csac_2719) that encode enzymes involved in the conversion of 5-keto-4deoxyuronate, an unsaturated...”
NT01EI_2369 3-oxoacyl-[acyl-carrier-protein] reductase, putative from Edwardsiella ictaluri 93-146
35% identity, 98% coverage
FabG / b1093 3-oxoacyl-[acyl-carrier-protein] reductase FabG (EC 1.1.1.100) from Escherichia coli K-12 substr. MG1655 (see 6 papers)
fabG / P0AEK2 3-oxoacyl-[acyl-carrier-protein] reductase FabG (EC 1.1.1.100) from Escherichia coli (strain K12) (see 22 papers)
FABG_ECOLI / P0AEK2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 from Escherichia coli (strain K12) (see 9 papers)
P0AEK2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Escherichia coli (see 2 papers)
NP_415611 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Escherichia coli str. K-12 substr. MG1655
AP_001719 3-oxoacyl-[acyl-carrier-protein] reductase from Escherichia coli W3110
b1093 3-oxoacyl-[acyl-carrier-protein] reductase from Escherichia coli str. K-12 substr. MG1655
S1177 3-oxoacyl-[acyl-carrier-protein] reductase from Shigella flexneri 2a str. 2457T
33% identity, 98% coverage
- function: Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis.
catalytic activity: a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + NADPH + H(+) (RHEA:17397)
catalytic activity: 3-oxobutanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxybutanoyl- [ACP] + NADP(+) (RHEA:41804)
catalytic activity: 3-oxopentanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxypentanoyl- [ACP] + NADP(+) (RHEA:55100)
catalytic activity: 3-oxohexanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxyhexanoyl- [ACP] + NADP(+) (RHEA:41824)
catalytic activity: 3-oxoheptanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxyheptanoyl- [ACP] + NADP(+) (RHEA:55104)
catalytic activity: 3-oxooctanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxyoctanoyl- [ACP] + NADP(+) (RHEA:41840)
catalytic activity: 3-oxononanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxynonanoyl- [ACP] + NADP(+) (RHEA:55108)
catalytic activity: 3-oxodecanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxydecanoyl- [ACP] + NADP(+) (RHEA:41856)
catalytic activity: 3-oxohexadecanoyl-[ACP] + NADPH + H(+) = (3R)- hydroxyhexadecanoyl-[ACP] + NADP(+) (RHEA:41904)
catalytic activity: 3-oxo-(9Z)-hexadecenoyl-[ACP] + NADPH + H(+) = (3R)-hydroxy- (9Z)-hexadecenoyl-[ACP] + NADP(+) (RHEA:54928)
catalytic activity: 4-methyl-3-oxopentanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxy-4- methylpentanoyl-[ACP] + NADP(+) (RHEA:55112)
catalytic activity: 5-methyl-3-oxohexanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxy-5- methylhexanoyl-[ACP] + NADP(+) (RHEA:55116)
catalytic activity: 4-methyl-3-oxohexanoyl-[ACP] + NADPH + H(+) = (3R)-hydroxy-4- methylhexanoyl-[ACP] + NADP(+) (RHEA:55120)
subunit: Homotetramer. - Functional complementation of the essential gene fabG1 of Mycobacterium tuberculosis by Mycobacterium smegmatis fabG but not Escherichia coli fabG.
Parish, Journal of bacteriology 2007 - GeneRIF: FabG1 activity can be replaced by the corresponding enzyme from the closely related species Mycobacterium smegmatis but not by the enzyme from Escherichia coli
- Escherichia coli FabG 3-ketoacyl-ACP reductase proteins lacking the assigned catalytic triad residues are active enzymes.
Hu, The Journal of biological chemistry - GeneRIF: Escherichia coli FabG 3-ketoacyl-ACP reductase proteins lacking the assigned catalytic triad residues are active enzymes.
- Structure features of <i>Streptococcus pneumoniae</i> FabG and virtual screening of allosteric inhibitors
Xu, Frontiers in molecular biosciences 2024 - “...S. aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), E. coli FabG (P0AEK2), S. cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The amino acid sequences of these eight FabG homologs were obtained from UniProt ( UniProt Consortium, 2023 ) and aligned to...”
- “...Staphylococcus aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), Escherichia coli FabG (P0AEK2), Saccharomyces cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The X-ray crystallographic coordinates and structure factor files for SpFabG structures are available in the Protein Data Bank ( http://www.rcsb.org )...”
- Structural assembly of the bacterial essential interactome
Gómez, eLife 2024 - “...binding pockets of both FabG and FabI. Uniprot codes used for AF2: AcpP: P0A6A8, fabG: P0AEK2, fabI: P0AEK4. Currently, the structure of the BirA-AccB binary complex remains unsolved. Hence, our model provides valuable functional insights into this complex. We show that the BPL catalytic domain of...”
- The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
Muñoz-Villagrán, International journal of molecular sciences 2024 - “...paaK 5.49 0.049 P0A8Y1 pyrimidine 5-nucleotidase YjjG yjjG 3.95 0.017 I. Lipid transport and metabolism P0AEK2 3-oxoacyl-[acyl-carrier-protein] reductase FabG fabG 7.02 0.015 P0AAI5 3-oxoacyl-[acyl carrier protein] synthase 2 fabF 5.43 0.011 P0AEK4 enoyl-[acyl-carrier-protein] reductase fabI 7.56 0.048 P0A9Q5 acetyl-CoA carboxyltransferase subunit beta accD 4.80 0.038 P37440...”
- Protein quaternary structures in solution are a mixture of multiple forms.
Marciano, Chemical science 2022 - “...units from the literature for PDB entries, predicts FabG to be a tetramer. In UniProt (P0AEK2) its subunit structure is registered as homo-tetramer. Initially, we purified FabG from the DE3 strain (FabG DE3 ), which has one free Cys residue at position 167. To our surprise,...”
- Escherichia coli FabG 3-ketoacyl-ACP reductase proteins lacking the assigned catalytic triad residues are active enzymes
Hu, The Journal of biological chemistry 2021 - “...10.6019/PXD023486. The wildtype E.coli K-12 and S.enterica LT2 FabG sequences were taken from UniProtKB/Swiss-Prot entries P0AEK2 and P0A2C9, respectively. Circular dichroism measurements The CD spectra of FabG and mutant FabG proteins were obtained with a Chirascan (Applied Photophysics Limited) at 25 C using a 1.0-nm bandwidth,...”
- Fatty acid activation and utilization by Alistipes finegoldii, a representative Bacteroidetes resident of the human gut microbiome
Radka, Molecular microbiology 2020 - “...P0AAI9 FabH ALFI_RS02965 Alfi_0603 2.00E-69 P0A6R0 FabF ALFI_RS01295 Alfi_0254 1.00E-104 P0AAI5 FabG ALFI_RS14995 Alfi_3068 5.00E-63 P0AEK2 FabZ ALFI_RS00450 Alfi_0083 2.00E-32 P0A6Q6 FabI ALFI_RS10055 Alfi_2059 8.00E-27 A0A1D3INF0 FabK ALFI_RS01405 Alfi_0277 1.00E-51 Q9FBC5 Phospholipid synthesis PlsX ALFI_RS02970 Alfi_0604 2.00E-53 P65739 PlsY ALFI_RS12850 Alfi_2636 7.00E-27 P67164 PlsC ALFI_RS14035 Alfi_2876...”
- Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves
Wang, G3 (Bethesda, Md.) 2019 - “...& Class II poly(R)-hydroxyalkanoic acid synthase 559 Q51513 PF07167 Escherichia coli fabG 3-Oxoacyl-[acyl-carrier-protein] reductase 244 P0AEK2 PF13561 Pseudomonas aeruginosa phaJ (R)-Enoyl-CoA hydratase/enoyl-CoA hydratase I 156 Q9LBK2 PF01575 Escherichia coli fabD Malonyl CoA-acyl carrier protein transacylase 209 P0AAI9 PF00698 Clostridium kluyveri sucD Succinic semialdehyde dehydrogenase 453 P38947...”
- Evolution by leaps: gene duplication in bacteria
Serres, Biology direct 2009 - “...the analysis included; Ribose Regulator and Transport proteins (P0ACQ0, P02925), Short Chain Dehydrogenase-Reductase family (P15047, P0AEK2, P0AEK4, P0AET8, P77646, P05707, P37769, P0A9P9, P37760, P32055, P09147, P67910, P37759, P0AC88, P27830), Class III Aminotransferase family (P36839, P94427, P53555, P71084, P30949, P33189, O34662, P38021, P22256, P50457, P12995, P23893, P48247,...”
- More
- Caenorhabditis elegans F09E10.3 encodes a putative 3-oxoacyl-thioester reductase of mitochondrial type 2 fatty acid synthase FASII that is functional in yeast
Gurvitz, Journal of biomedicine & biotechnology 2009 - “...lysine 155 (K) are shown in bold below the sequences. Accession numbers used were FabG; AP_001719; D1054.8, CAA98438; F09E10.3, AAB52488; YKL055c, P35731. Figure 2 Phenotype rescue of a yeast oar1 strain expressing F09E10.3. Mutant S. cerevisiae BY4741 oar1 cells producing native mitochondrial Oar1p (positive control), peroxisomal...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0417 b3771 b0091 b0914 b2838 b0420, b0421, b0423 b3774 b0954 b0915 b3359 b0475, b0750, b0907 b1093 b0918 b3433 b1096, b1208, b1210 b1094 b1094 b3809 b1277, b1662, b1740 b1288 b1215 s0001 b1812, b2103, b2153 b2323 b3198 b2315, b2320, b2400 b3176 b3633 b2515, b2530, b2564 b3189 b2574, b2615,...”
- Addendum
, Open forum infectious diseases 2019 - Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response
Lutay, PloS one 2014 - “...(T174), AMPK alpha2 (T172), beta-Catenin, Chk-2 (T68), c-Jun (S63), CREB (S133), EGF R (Y1086), eNOS (S1177), ERK1/2 (T202/Y204, T185/Y187), FAK (Y397), Fgr (Y412), Fyn (Y420), GSK-3 alpha/beta (S21/S9), Hck (Y411), HSP27 (S78/S82), HSP60, JNK pan (T183/Y185 T221/Y223), Lck (Y394), Lyn (Y397), MSK1/2 (S376/S360), p27 (T198), p38...”
- Serine phosphorylation of cortactin is required for maximal host cell invasion by Campylobacter jejuni
Samuelson, Cell communication and signaling : CCS 2013 - “...and maintained throughout the assay. The Erk 1/2 inhibitor PD98059 (Selleck, Houston, TX, Cat # S1177) was used at 50 M. The c-Src inhibitor PP2 (Sigma, Cat # P0042) was used at 5, 10, 20, and 40 g/mL. The transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) (Sigma, Cat #...”
Smed_0745 3-ketoacyl-(acyl-carrier-protein) reductase NodG from Sinorhizobium medicae WSM419
36% identity, 98% coverage
AT2G29260 tropinone reductase, putative / tropine dehydrogenase, putative from Arabidopsis thaliana
32% identity, 78% coverage
YPO2539 gluconate 5-dehydrogenase from Yersinia pestis CO92
31% identity, 99% coverage
YP_3535 2-deoxy-D-gluconate 3-dehydrogenase from Yersinia pestis biovar Medievalis str. 91001
34% identity, 98% coverage
Q9Z8P2 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Chlamydia pneumoniae
35% identity, 98% coverage
H16_A2002 acetoacetyl-CoA reductase from Cupriavidus necator H16
H16_A2002 Acetoacetyl-CoA reductase from Ralstonia eutropha H16
36% identity, 96% coverage
FHQ17_00510 SDR family NAD(P)-dependent oxidoreductase from Staphylococcus epidermidis
32% identity, 98% coverage
- The Genome of Staphylococcus epidermidis O47
Raue, Frontiers in microbiology 2020 - “...dehydrogenase FHQ17_00820 tributyrin esterase FHQ17_00780 K05846 osmoprotectant transport system permease protein FHQ17_00765 mqo2 malate:quinone oxidoreductase FHQ17_00510 Mobile Genetic Elements Like other staphylococci, S. epidermidis contains several mobile genetic elements ( Table 4 ). Besides the housekeeping recombinases ( recA, recD, recF, recG, recJ, recN, recO, recQ,...”
WP_026707247 SDR family NAD(P)-dependent oxidoreductase from Flavobacterium frigidarium DSM 17623
35% identity, 97% coverage
- Identification of a 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase, FlRed, in an alginolytic bacterium Flavobacterium sp. strain UMI-01
Inoue, Marine drugs 2015 - “...Cellulophaga algicola [ 26 ], Cytophaga fermentans [ 27 ] Flavobacterium frigidarium (GenBank accession number, WP_026707247) and Lewinella cohaerens (GenBank accession number, WP_020539555) have not been identified as alginolytic bacteria. Specific sequence motifs of SDR-family enzymes, i.e. , the catalytic tetrad Asn-Tyr-Lys-Ser [ 28 ], the...”
- “...KMM 3901 (GenBank accession number, CDF80389); Flavobacterium, short-chain dehydrogenase from Flavobacterium frigidarium (GenBank accession number, WP_026707247); Cytophaga, short-chain dehydrogenase from Cytophaga fermentans (GenBank accession number, WP_027472031); Lewinella, short-chain dehydrogenase from Lewinella cohaerens (GenBank accession number, WP_020539555); Cellulophaga, short-chain dehydrogenase from Cellulophaga algicola (GenBank accession number WP_013552902);...”
O54438 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Pseudomonas aeruginosa (see paper)
PA14_25660 3-oxoacyl-[acyl-carrier-protein] reductase from Pseudomonas aeruginosa UCBPP-PA14
PA2967 3-oxoacyl-[acyl-carrier-protein] reductase from Pseudomonas aeruginosa PAO1
37% identity, 98% coverage
- Structure features of <i>Streptococcus pneumoniae</i> FabG and virtual screening of allosteric inhibitors
Xu, Frontiers in molecular biosciences 2024 - “...FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), S. aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), E. coli FabG (P0AEK2), S. cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The amino acid sequences of these eight FabG homologs were obtained from UniProt...”
- “...FabG (UniProt accession Q8DR15), Clostridioides difficile FabG (Q18B45), Staphylococcus aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), Escherichia coli FabG (P0AEK2), Saccharomyces cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The X-ray crystallographic coordinates and structure factor files for SpFabG structures are available...”
- Vanillic acid from Actinidia deliciosa impedes virulence in Serratia marcescens by affecting S-layer, flagellin and fatty acid biosynthesis proteins
Sethupathy, Scientific reports 2017 - “...P. syringae pv. tabaci (A0A0W0PM71) and 63.2 and 75.3% identity and similarity, respectively to fabG (O54438) of P. aeruginosa . Hence it is hypothesized that down-regulation of fabG by vanillic acid could have a negative effect on QS-regulated virulence factors production in S. marcescens . In...”
- Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity
Blanka, Journal of bacteriology 2014 - “...PA14_09400 PA14_17220 PA14_17270 PA14_20750 PA14_25650 PA14_25660 PA14_25670 PA14_25900 PA14_40560 PA14_41575 PA14_41590 PA14_42310 PA14_42350 PA14_42380...”
- A novel role for an ECF sigma factor in fatty acid biosynthesis and membrane fluidity in Pseudomonas aeruginosa
Boechat, PloS one 2013 - “...2.12 ND PA14_25650 (FabD) malonyl-CoA-[acyl-carrier-protein] transacylase 6.42 2.40 PA14_68360 (FabY) -oxoacyl synthase I/II 4.19 0.28 PA14_25660 (FabG) -oxoacyl-(acyl-carrier-protein) reductase 3.30 0.63 PA14_57050 (FabG2) -oxoacyl-(acyl-carrier-protein) reductase 6.80 0.78 PA14_25900 (FabV) trans-2-enoyl-CoA reductase 5.24 0.76 PA14_21540 (FabH3) -oxoacyl-(acyl carrier protein) synthase III 4.12 1.19 PA14_43690 (FabB) -oxoacyl -(acyl...”
- “...73 , 78 , 79 ] and a report where attempts to create a fabG (PA14_25660) disruption failed [ 76 ] suggest that this gene product would act as the constitutive reductase. Another FabG isoform, coded by PA14_57050 (PA4389 in PAO1) and here denominated FabG2, was...”
- Anaerobic biosynthesis of rhamnolipids by Pseudomonas aeruginosa: performance, mechanism and its application potential for enhanced oil recovery
Zhao, Microbial cell factories 2021 - “...1.85 2.57E12 3-oxoacyl-acyl carrier protein synthase II PA2968 fabD 702.6 439.7 0.68 6.68E03 malonyl-CoA-[acyl-carrier-protein] transacylase PA2967 fabG 2143.7 926.5 1.21 5.82E07 3-oxoacyl-[acyl-carrier-protein] reductase PA3333 fabH2 677.1 10.0 6.08 2.65E70 3-oxoacyl-[acyl-carrier-protein] synthase III PA3476 rhlI 5429.4 92.4 5.88 1.56E87 autoinducer synthesis protein RhlI PA3477 rhlR 13664.1 732.3...”
- Characterization of 3-Oxacyl-Acyl Carrier Protein Reductase Homolog Genes in Pseudomonas aeruginosa PAO1
Guo, Frontiers in microbiology 2019 - “...characterized the functions of these genes with biochemical and genetic techniques. With the exception of PA2967, which encodes FabG, an essential protein in fatty acid synthesis, only the PA4389 and PA4786 gene products had OAR activity, and the single deletion of these two genes reduced the...”
- “...OAR homologs, are poorly understood. To date, only two OAR homologs have been studied. fabG (PA2967), located in the fabD - fabG - acpP - fabF gene cluster, is an essential gene in the fatty acid synthetic pathway of P. aeruginosa ( Kutchma et al., 1999...”
- Acyl Carrier Protein 3 Is Involved in Oxidative Stress Response in Pseudomonas aeruginosa
Chen, Frontiers in microbiology 2018 - “...purification. Locus Protein Function SC a SC Abundance b p -Value c AcpP PAO1 CW20 PA2967 FabG 3-Oxo-acyl-ACP reductase 0 174 340.24 2.14E-54 PA3645 FabZ 3-Hydroxyacyl-ACP dehydratase 0 53 158.08 1.02E-17 PA2907 CobL Precorrin-6YC(5,15)-methyltransferase 0 121 137.18 2.31E-38 PA5552 GlmU Bifunctional enzyme of LPS/peptidoglycan synthesis 0...”
- “...Cytosol aminopeptidase 0 49 46 1.70E-16 PA3583 GlpR Glycerol-3-phosphate regulon repressor 0 23 41 1.64E-08 PA2967 FabG 3-Oxo-acyl-ACP reductase 0 8 15.6 8.68E-04 PA4277 Tuf1 Elongation factor Tu 0 13 15 2.19E-05 Acp3 PAO1 CW21 PA3814 IscS Cysteine desulfurase 0 69 77.29 1.37E-22 PA3333 FabH2 3-Oxo-acyl-ACP...”
- Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Zhu, GigaScience 2018 - “...accuracy of essential genes; e.g., 3-ketoacyl-ACP reductase (EC 1.1.1.100) reactions in iPae1146 were associated with PA2967 only [ 31 ], whereas in i PAO1, these reactions were associated with another 8 highly conserved isozymes (PA0182, PA1470, PA1827, PA3387, PA4089, PA4389, PA4786, and PA5524). Furthermore, condition-specific essential...”
- To Hit or Not to Hit, That Is the Question - Genome-wide Structure-Based Druggability Predictions for Pseudomonas aeruginosa Proteins
Sarkar, PloS one 2015 - “...9 39.4966.50 9 / 0 / 0 Beta-ketoacyl carrier protein synthase II fabF1 119 (30) PA2967 1doh / NID 8 34.2337.70 7 / 0 / 1 3-oxoacyl-[acyl carrier protein] reductase fabG 80 (21) PA3883 1a27 / EST 9 34.8135.19 9 / 0 / 0 Probable short-chain...”
- Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa
Cukier, ACS chemical biology 2013 - “...its native promoter and attempted the deletion of the native copy of fabG at the PA2967 locus. The suicide mini-CTX2 plasmid based method 28 was utilized for site-specific integration of the second copy of fabG . We successfully obtained a PAO1 strain with a dual copy...”
- “...methods as described above. We were able to replace the fabG gene at the chromosomal PA2967 locus by the gentamicin resistance casette in the presence of the second copy at the attB site. These clones were gentamicin-resistant, carbenicillin-sensitive, and sucrose-resistant. The replacement of the fabG sequence...”
- A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
Xu, PloS one 2013 - “...fabI ),PA1959( bacA ),PA2165( glgA ), PA2584( pgsA ),PA2629( purB ),PA2962( tmk ),PA2964( pabC ), PA2967( fabG ),PA2977( murB ),PA2979( kdsB ),PA2981( lpxK ), PA3088( yfjB ),PA3108( purF ),PA3111( folC ),PA3112( accD ), PA3163( cmk ),PA3337( rfaD ),PA3636( kdsA ),PA3637( pyrG ), PA3643( lpxB ),PA3644( lpxA...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...74 PA2965 fabF1 Betaketoacylacyl carrier synthase IQ C 43.5 45 5.62 5.64 0.654 0.034 75 PA2967 fabG Oxoacylacyl carrier reductase IQR C 25.6 24 6.16 6.09 0.604 0.176 76 PA2968 fabD Malonyl CoA acyl carrier transacylase I U 32.4 32 5.05 5.00 0.595 0.253 77 PA3148...”
- More
SMU_1740, SMU_RS07910 3-oxoacyl-[acyl-carrier-protein] reductase from Streptococcus mutans UA159
33% identity, 98% coverage
- Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans
Qin, Microbiology spectrum 2024 - “...Acetyl-CoA carboxylase carboxyl transferase subunit alpha, AccA SMU_RS07890 2.6 Acetyl-CoA carboxylase biotin carboxylase subunit, AccC SMU_RS07910 2.5 3-oxoacyl-[acyl-carrier-protein] reductase, FabG SMU_RS07905 2.2 Beta-ketoacyl-ACP synthase II, FabF SMU_RS07915 2 2 ACP S-malonyltransferase, FabD Lipid metabolism SMU_RS01590 2.8 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase, GpsA SMU_RS06690 2.8 SDR family oxidoreductase DNA...”
- Characterization of FtsH Essentiality in Streptococcus mutans via Genetic Suppression
Wang, Frontiers in genetics 2021 - “...1490737 T SMU_RS07100 SMU_1565 4-alpha-glucanotransferase G376F C 1568890 T intergenic intergenic A 1646995 G SMU_RS07910 SMU_1740 3-oxoacyl-ACP reductase V108A G 1701085 A SMU_RS08255 SMU_1799 nicotinate-nucleotide adenylyltransferase R101C Construction of S. mutans S877 The strain S877 was constructed by a previously described markerless mutagenesis approach ( McKenna...”
- “...G 1490737 T SMU_RS07100 SMU_1565 4-alpha-glucanotransferase G376F C 1568890 T intergenic intergenic A 1646995 G SMU_RS07910 SMU_1740 3-oxoacyl-ACP reductase V108A G 1701085 A SMU_RS08255 SMU_1799 nicotinate-nucleotide adenylyltransferase R101C Construction of S. mutans S877 The strain S877 was constructed by a previously described markerless mutagenesis approach (...”
PP_1914 3-oxoacyl-(acyl-carrier-protein) reductase from Pseudomonas putida KT2440
35% identity, 98% coverage
- β-oxidation-polyhydroxyalkanoates synthesis relationship in Pseudomonas putida KT2440 revisited
Liu, Applied microbiology and biotechnology 2023 - “...Their expression level in WT under non-limited nitrogen condition was firstly analysed (Fig. 3a ). PP_1914 showed the highest expression level during the log phase of growth compared with other four fabG homologous, while PP_2540 and PP_2783 had very low expression. In addition, PP_0581 showed 4.8-fold...”
- “...expression level at late-log phase compared with the early-log phase, respectively. The results indicated that PP_1914, PP_0581 and PP_1852 could potentially contribute to PHA synthesis. Therefore, the gene expression level of these three fabG homologous was further analysed in WT, P. putida phaJ1phaJ4 and P. putida...”
Q308C1 D-arabinitol 4-dehydrogenase (EC 1.1.1.11); D-arabinitol dehydrogenase (NADP+) (EC 1.1.1.287) from Gluconobacter oxydans (see paper)
34% identity, 97% coverage
blr3225 oxidoreductase from Bradyrhizobium japonicum USDA 110
33% identity, 97% coverage
- Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism
Quelas, International journal of molecular sciences 2024 - “...the membrane and their conversion to fructose-6-P, namely, blr3224, coding for putative mannitol transport system; blr3225, coding for mannitol dehydrogenase; blr3226, coding for ribitol kinase and blr3227; coding for D-fructokinase were downregulated at transcriptional level ( Tables S1 and S3 ). Of these four proteins, Blr3225...”
- Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO2 Fixation, O2 Consumption, and Lateral-Flagellum Production
Cogo, Frontiers in microbiology 2018 - “...Mtl blr3224 Q89QA6 ABC transporter ATP-binding protein. Putative sorbitol/mannitol transport system. In only Mtl NS blr3225 Q89QA5 Oxidoreductase. Similar to putative Glucose/ribitol oxidoreductase. 5.0927 In only Mtl blr3226 Q89QA4 Ribitol kinase 3.9234 - blr3227 Q89QA3 Putative fructokinase. In only Mtl - bll3754 Q89NT0 gph Phosphoglycolate phosphatase....”
- “...gene encoding that enzyme was not annotated in the B. diazoefficiens genome. We observed that Blr3225, which enzyme is similar to the glucose/ribitol oxidoreductase, is present in the MtlDP. The corresponding structural gene is a neighbor of three genes encoding proteins also found in MtlDPnamely the...”
Csac_0357 2-deoxy-D-gluconate 3-dehydrogenase from Caldicellulosiruptor saccharolyticus DSM 8903
32% identity, 98% coverage
Q2RXR7 3-oxoacyl-[acyl-carrier-protein] reductase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
Rru_A0273 Acetoacetyl-CoA reductase from Rhodospirillum rubrum ATCC 11170
33% identity, 97% coverage
- Study of the Production of Poly(Hydroxybutyrate-co-Hydroxyhexanoate) and Poly(Hydroxybutyrate-co-Hydroxyvalerate-co-Hydroxyhexanoate) in Rhodospirillum rubrum
Cabecas, Applied and environmental microbiology 2022 (secret) - The metabolic pathways of carbon assimilation and polyhydroxyalkanoate production by Rhodospirillum rubrum in response to different atmospheric fermentation
Tang, PloS one 2024 - “...), PHA polymerase homologous gene ( Rru_A1816 ), ketothiolase ( Rru_A0274 ), acetoacetyl-CoA reductase ( Rru_A0273 ), carbon-monoxide dehydrogenase ( Rru_A1427 ) and pyruvate carboxylase ( Rru_A2317 ). The expression levels were normalized to the expression of a 16S rRNA gene ( Rru_A0064 ). Primers are...”
- “...key enzymes of PHA synthesis pathway (phaA, phaB and phaC; separately coded by Rru_A0274 , Rru_A0273 , and Rru_A0275 ) under both fermentation conditions. Interestingly, one of the homologous PHA polymerase gene phaC3 ( Rru_A1816 ) and a phasin ( Rru_2817 ) associated with PHA granules...”
- Effects of Mixing Volatile Fatty Acids as Carbon Sources on Rhodospirillum rubrum Carbon Metabolism and Redox Balance Mechanisms
Cabecas, Microorganisms 2021 - “...pathway tr|Q2RXX3 Rru_A0217 1.97 1.38 10 2 0.72 4.46 10 1 6 Citrate lyase tr|Q2RXR7 Rru_A0273 0.556 1.00 10 1 0.74 7.70 10 3 5 3-oxoacyl-eductase tr|Q2RV43 Rru_A1201 1.48 8.73 10 4 1.34 3.48 10 1 6 MaoC-like dehydratase tr|Q2RTB0 Rru_A1835 1.97 1.43 10 2 1.49...”
- New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions
De, BMC microbiology 2020 - “...Acetoacetyl-CoA thiolase 3.7 d 2e-02 2 0.8 3e-02 0.8 1e-02 1.2 7e-03 0.9 2e-01 3 Rru_A0273 Acetoacetyl-CoA reductase 0.3 4e-07 5 0.8 7e-05 0.9 2e-02 1.2 8e-05 1.4 1e-05 6 Rru_A2964 (R)-specific enoyl-CoA hydratase 0.9 5e-01 6 0.8 4e-01 1.2 9e-01 0.7 7e-01 1.7 6e-03 5...”
- “...n.a. n.a. n.a. Rru_A3079 3-hydroxyacyl-CoA dehydrogenase 0.45 1.16 2e-02 Rru_A1946 Acetoacetyl-CoA thiolase 0.06 0.03 7e-01 Rru_A0273 b Acetoacetyl-CoA reductase n.a. n.a. n.a. Rru_A2964 (R)-specific enoyl-CoA hydratase 0.04 0.79 9e-05 Rru_A2413 Poly(R)-hydroxyalkanoic acid synthase 0.48 0.11 3e-02 Rru_A2817 b Phasin n.a. n.a. n.a. Rru_A3283 a Activator of...”
- Genetic Plasticity and Ethylmalonyl Coenzyme A Pathway during Acetate Assimilation in Rhodospirillum rubrum S1H under Photoheterotrophic Conditions
De, Applied and environmental microbiology 2018 - “...2.5) and could complement the acetoacetyl-CoA reductase (Rru_A0273) that was retained as an acetate-specific candidate to reduce 3-acetoacetyl-CoA into...”
- “...was assigned to the acetoacetyl-CoA reductase (Rru_A0273) (13). The situation is reversed through acetate acclimatization: Rru_A3079 was clearly...”
- Evaluating PHA productivity of bioengineered Rhodosprillum rubrum
Jin, PloS one 2014 - “...gene resides in the PHA biosynthetic operon that also includes the phaA (Rru_A0274) and phaB (Rru_A0273) genes. The products of this phaC1-phaA-phaB operon, are enzymes that sequentially catalyze condensation of two acetyl-CoA molecules to form acetoacetyl-CoA, the reduction of acetoacetyl-CoA to ( R )-3-hydroxybutyryl-CoA, and the...”
L5014_32695 acetoacetyl-CoA reductase from Paraburkholderia tagetis
33% identity, 98% coverage
5u9pB / B4EEX4 Crystal structure of a gluconate 5-dehydrogenase from burkholderia cenocepacia j2315 in complex with NADP and tartrate
33% identity, 96% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (5u9pB)
Q4J702 alcohol dehydrogenase (EC 1.1.1.1) from Sulfolobus acidocaldarius (see paper)
29% identity, 95% coverage
BG05_RS24540 acetoacetyl-CoA reductase from Bacillus mycoides
32% identity, 98% coverage
LNN31_12060 SDR family NAD(P)-dependent oxidoreductase from Acetobacterium wieringae
30% identity, 96% coverage
- Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y
Jin, mBio 2022 - “...only low abundances with an MS intensityof (4.80.4)10 8 ( Fig.7 ). The putative ER LNN31_12060 belonging to the SDR family oxidoreductase was slightly upregulated (FC,1.5; FDR,<0.002; MS intensity,[1.40.1]10 8 ) ( Fig.7 ). FIG7 Abundances of expressed putative ene-reductases in isoprene-fed (ISO-1) cultures and cultures...”
RPA3304 putative 3-oxoacyl-acyl carrier protein reductase from Rhodopseudomonas palustris CGA009
33% identity, 91% coverage
P55336 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Vibrio harveyi
32% identity, 98% coverage
AMED_5426 SDR family NAD(P)-dependent oxidoreductase from Amycolatopsis mediterranei U32
35% identity, 98% coverage
AMK58_26800 acetoacetyl-CoA reductase from Azospirillum brasilense
32% identity, 96% coverage
PHOF2_DIALO / A0A142I726 Short-chain dehydrogenase/reductase PhomF'; Phomopsin biosynthesis cluster protein F'; EC 1.-.-.- from Diaporthe leptostromiformis (Lupinosis disease fungus) (Phomopsis leptostromiformis) (see paper)
30% identity, 85% coverage
- function: Short-chain dehydrogenase/reductase; part of the gene cluster that mediates the biosynthesis of the phomopsins, a group of hexapeptide mycotoxins which infects lupins and causes lupinosis disease in livestock (PubMed:34608734). The role of phomF' within the phomopsins biosynthesis pathway has still to be determined (Probable). The pathway starts with the processing of the precursor phomA by several endopeptidases including kexin proteases as well as the cluster-specific S41 family peptidase phomP1 and the oligopeptidase phomG to produce 10 identical copies of the hexapeptide Tyr-Val-Ile- Pro-Ile-Asp. After being excised from the precursor peptide, the core peptides are cyclized and modified post-translationally by enzymes encoded within the gene cluster. The timing and order of proteolysis of the phomA precursor and PTMs are still unknown. Two tyrosinase-like enzymes, phomQ1 and phomQ2, catalyze the chlorination and hydroxylation of Tyr, respectively. PhomYb, is proposed to be involved in the construction of the macrocyclic structure. The other 4 ustYa family proteins may be involved in PTMs that generate the unique structure of phomopsin A. PhomYa is required for the hydroxylation of C-beta of Tyr. PhomYc, phomYd, and phomYe are responsible for the biosynthesis of 2,3- dehydroisoleucine (dIle), 2,3-dehydroaspartic acid (dAsp), and 3,4- dehydroproline (dPro), respectively. While dIle formation by phomYc is indispensable for the installation of dAsp by phomYd, the order of the other PTMs have not been elucidated yet. Most of the biosynthetic enzymes likely have broad substrate specificity, and thus, there might be a metabolic grid from a precursor to phomopsin A. The enzyme(s) responsible for the biosynthesis of 3,4-dehydrovaline (dVal) have also not been identified yet. Finally, phomM acts as an S- adenosylmethionine-dependent alpha-N-methyltransferase that catalyzes two successive N-methylation reactions, converting N-desmethyl- phomopsin A to phomopsin A and phomopsin A further to an N,N- dimethylated congener called phomopsin E (Probable).
phaB / BAC45231.1 3-keto-acyl-CoA reductase from Bacillus sp. INT005 (see paper)
31% identity, 98% coverage
A5HIF6 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Pseudomonas putida (see paper)
35% identity, 98% coverage
GSU1603 3-oxoacyl-(acyl-carrier-protein) reductase from Geobacter sulfurreducens PCA
33% identity, 98% coverage
U5PUZ1 tropinone reductase I (EC 1.1.1.206) from Withania somnifera (see paper)
34% identity, 92% coverage
WP_009406831 3-oxoacyl-ACP reductase FabG from Pseudomonas putida
35% identity, 98% coverage
GLRG_09591 short chain dehydrogenase from Colletotrichum graminicola M1.001
36% identity, 95% coverage
Q4AE87 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) from Pseudomonas sp. (see paper)
fabG / BAE19680.1 3-oxoacyl-(acyl-carrier-protein) reductase from Pseudomonas sp. 61-3 (see paper)
37% identity, 98% coverage
BC1317, NP_831099 Acetoacetyl-CoA reductase from Bacillus cereus ATCC 14579
31% identity, 98% coverage
- Methionine Residues in Exoproteins and Their Recycling by Methionine Sulfoxide Reductase AB Serve as an Antioxidant Strategy in Bacillus cereus
Madeira, Frontiers in microbiology 2017 - “...synthase 2.16 Folate biosynthesis NP_833540 BC3819 Dxr2 1-deoxy-D-xylulose 5-phosphate reductoisomerase 2.75 Terpenoid backbone biosynthesis NP_831099 BC1317 PhaB Acetoacetyl-CoA reductase 2.53 Uncategorized NP_829927 BC0025 Unknown 2.67 NP_832675 BC2927 Prolyl endopeptidase 4.18 NP_831667 BC1894 Phage protein 2.84 NP_831673 BC1901 phage protein 2.43 NP_834610 BC4938 NADH dehydrogenase 2.03 NP_834043...”
- “...NP_830056 BC0188 GlmM Phosphoglucosamine mutase 3.81 Nucleotide NP_835123 BC5468 AdSS Adenylosuccinate synthetase 2.53 Butanoate NP_831099 BC1317 PhaB Acetoacetyl-CoA reductase 2.56 Gamma Hexachlorocyclohexane degradation NP_834220 BC4511 LppC Acid phosphatase 2.34 Ubiquinone and other terpenoid-quinone NP_832068 BC2305 DhbB Isochorismatase 2.45 Toxins NP_832699 BC2952 EntB Enterotoxin/cell-wall binding protein 2.25...”
- “...tetrahydrobiopterin synthase 2.16 Folate biosynthesis NP_833540 BC3819 Dxr2 1-deoxy-D-xylulose 5-phosphate reductoisomerase 2.75 Terpenoid backbone biosynthesis NP_831099 BC1317 PhaB Acetoacetyl-CoA reductase 2.53 Uncategorized NP_829927 BC0025 Unknown 2.67 NP_832675 BC2927 Prolyl endopeptidase 4.18 NP_831667 BC1894 Phage protein 2.84 NP_831673 BC1901 phage protein 2.43 NP_834610 BC4938 NADH dehydrogenase 2.03...”
- “...sugar NP_830056 BC0188 GlmM Phosphoglucosamine mutase 3.81 Nucleotide NP_835123 BC5468 AdSS Adenylosuccinate synthetase 2.53 Butanoate NP_831099 BC1317 PhaB Acetoacetyl-CoA reductase 2.56 Gamma Hexachlorocyclohexane degradation NP_834220 BC4511 LppC Acid phosphatase 2.34 Ubiquinone and other terpenoid-quinone NP_832068 BC2305 DhbB Isochorismatase 2.45 Toxins NP_832699 BC2952 EntB Enterotoxin/cell-wall binding protein...”
CAC3574 3-ketoacyl-acyl carrier protein reductase from Clostridium acetobutylicum ATCC 824
31% identity, 97% coverage
7emgB Carbonyl reductase variant 4 (r123c/l209p/f183y/v61k) from serratia marcescens complexed with NADP+ (see paper)
33% identity, 98% coverage
- Ligand: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (7emgB)
YjgU / b4266 5-keto-D-gluconate 5-reductase (EC 1.1.1.69) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
idnO / P0A9P9 5-keto-D-gluconate 5-reductase (EC 1.1.1.69) from Escherichia coli (strain K12) (see 4 papers)
IDNO_ECOLI / P0A9P9 5-keto-D-gluconate 5-reductase; EC 1.1.1.69 from Escherichia coli (strain K12) (see paper)
b4266 gluconate 5-dehydrogenase from Escherichia coli str. K-12 substr. MG1655
32% identity, 99% coverage
- function: Catalyzes the reduction of 5-keto-D-gluconate to D-gluconate, using either NADH or NADPH. Is likely involved in an L-idonate degradation pathway that allows E.coli to utilize L-idonate as the sole carbon and energy source. Is also able to catalyze the reverse reaction in vitro, but the D-gluconate oxidation by the enzyme can only proceed with NAD.
catalytic activity: D-gluconate + NAD(+) = 5-dehydro-D-gluconate + NADH + H(+) (RHEA:23940)
catalytic activity: D-gluconate + NADP(+) = 5-dehydro-D-gluconate + NADPH + H(+) (RHEA:23936) - Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
White-Ziegler, Journal of bacteriology 2007 - “...entE b0594 2,3-Dihydroxybenzoate-AMP ligase idnO b4266 5-Keto-D-gluconate 5-reductase srlD b2705 Glucitol (sorbitol)-6-phosphate dehydrogenase yeiN b2165...”
- An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
Reed, Genome biology 2003 - “...NAD(P)-binding Acetoin dehydrogenase, diacetyl reductase 1.1.1.5 b2137 yohF Putative oxidoreductase Acetoin dehydrogenase, diacetyl reductase 1.1.1.5 b4266 idnO 5-Keto-D-gluconate-5-reductase Acetoin dehydrogenase, diacetyl reductase 1.2.1.19 b1385 feaB Phenylacetaldehyde dehydrogenase Aminobutyraldehyde dehydrogenase 1.2.1.19 b1444 ydcW Putative aldehyde dehydrogenase Aminobutyraldehyde dehydrogenase 1.2.1.19 b3588 aldB Aldehyde dehydrogenase B (lactaldehyde dehydrogenase) Aminobutyraldehyde...”
- Evolution by leaps: gene duplication in bacteria
Serres, Biology direct 2009 - “...Transport proteins (P0ACQ0, P02925), Short Chain Dehydrogenase-Reductase family (P15047, P0AEK2, P0AEK4, P0AET8, P77646, P05707, P37769, P0A9P9, P37760, P32055, P09147, P67910, P37759, P0AC88, P27830), Class III Aminotransferase family (P36839, P94427, P53555, P71084, P30949, P33189, O34662, P38021, P22256, P50457, P12995, P23893, P48247, P18335, P77581, O30508, Q9I606, Q9I6 M4,...”
AFUA_1G17380 3-oxoacyl-(acyl-carrier-protein) reductase, putative from Aspergillus fumigatus Af293
32% identity, 91% coverage
- Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment
Rhodes, Nature microbiology 2022 - “...secreted polygalacturonase GH-28 Intron AFUB_016620 AFUA_1G17230 >1 0.000359083 Orthologue(s) have carbon-oxygen lyase activity P466T AFUB_016750 AFUA_1G17380 >1 0.000200224 Has domain(s) with predicted oxidoreductase activity I68V AFUB_016800 AFUA_1G17430 >1 0.00000228 Orthologue(s) have monophenol monooxygenase activity E586D AFUB_016830 AFUA_1G17470 >1 0.00000305 nrtB Intron AFUB_016850 AFUA_1G17490 >1 0.001152366 Has...”
- Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
Fan, Pathogens (Basel, Switzerland) 2021 - “...For both MIC resistance thresholds, the results showed that the three previously noted SNPs, in AFUA_1G17380, AFUA_3G09040 and AFUA_3G09070, were again significantly associated with itraconazole resistance. After removal of the 21 strains and using both MIC thresholds, two of these SNPs, AFUA_3G09040 and AFUA_3G09070, were now...”
- “...associated with both itraconazole and pan-azole resistance. These three SNPs were a missense variant in AFUA_1G17380, AFUA_3G09040, and AFUA_3G09070. Using both MIC thresholds, the tests also identified the previous AFUA_7G06290 missense variant to be significantly associated with pan-azole resistance. Lastly, another set of Fishers Exact test...”
LA14_RS05540 SDR family oxidoreductase from Lactobacillus acidophilus La-14
33% identity, 97% coverage
- Functional Characterization of c-di-GMP Signaling-Related Genes in the Probiotic Lactobacillus acidophilus
He, Frontiers in microbiology 2018 - “...cenocepacia B4EIC5 Fazli et al., 2011 NA BdcA, E. coli PF00106 Ma et al., 2011 LA14_RS05540 BcsE, E. coli P37657.1 Fang et al., 2014 NA BrlR, P. aeruginosa Q9HUT5 Chambers et al., 2014 LA14_RS09635 LA14_RS05180 CLP, Xanthomonas campestris P22260 Chin et al., 2010 NA PgaC, E....”
gno / P50199 D-gluconate 5-dehydrogenase monomer from Gluconobacter oxydans (strain 621H) (see paper)
GNO_GLUOX / P50199 Gluconate 5-dehydrogenase; D-gluconate 5-dehydrogenase (NADP); Gluconate:NADP 5-oxidoreductase; GNO; EC 1.1.1.- from Gluconobacter oxydans (strain 621H) (Gluconobacter suboxydans) (see paper)
GOX2187 Gluconate 5-dehydrogenase from Gluconobacter oxydans 621H
31% identity, 100% coverage
- function: Catalyzes the reversible NADP-dependent oxidation of gluconate to 5-ketogluconate. Is involved in the non-phosphorylative, ketogenic oxidation of glucose. Is almost inactive with NAD as cosubstrate. Displays high substrate specificity since D-Glucose, D- sorbitol, and D-mannitol are not oxidized by the enzyme, and 2- ketogluconate and L-sorbose are not reduced. Can accept D-fructose as a substrate, with a rate that is only 10% of the rate of 5-ketogluconate reduction.
catalytic activity: D-gluconate + NADP(+) = 5-dehydro-D-gluconate + NADPH + H(+) (RHEA:23936)
subunit: Homodimer. - Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...synthase (GOX1999); gnd , 6-phosphogluconate dehydrogenase (GOX1705); gnk , gluconokinase (GOX1709); gno , gluconate 5-dehydrogenase (GOX2187); gpm phosphoglyceromutase (GOX0330); icd , isocitrate dehydrogenase (GOX1336); lpd , dihydrolipoamide dehydrogenase (GOX2292); mqo , malate:quinone oxidoreductase (GOX2070); odhA , 2-oxoglutarate dehydrogenase E1 component (GOX0882); odhB , dihydrolipoamide succinyltransferase E2...”
- (13)C Tracers for Glucose Degrading Pathway Discrimination in Gluconobacter oxydans 621H
Ostermann, Metabolites 2015 - “...this conversion. Intracellular gluconate can be converted to 5-ketogluconate by a gluconate-5-dehydrogenase ( gno , GOX2187), or phosphorylated by a gluconate kinase ( gnk , GOX1709) [ 2 , 16 ]. The metabolite 6-phosphogluconate (6-PG) exclusively serves as a precursor molecule for both intracellular glucose degradation...”
- Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and NADPH
Kubota, Acta crystallographica. Section F, Structural biology and crystallization communications 2010 - “...5KGR-coding gene from G. suboxydans IFO12528 (GenBank code GOX2187; Prust et al., 2005) was cloned into the NcoI/BamHI Acta Cryst. (2010). F66, 1680-1682...”
- Preparation of enzymes required for enzymatic quantification of 5-keto-D-gluconate and 2-keto-D-gluconate
Saichana, Bioscience, biotechnology, and biochemistry 2007 (PubMed)- “...the genome of Gluconobacter oxydans 621H and was identified as GOX2187. On the other hand, the gene for 2KGR was identified in this study as GOX0417 from the...”
- “...purified enzyme. Several plasmids were constructed to express GOX2187 and GOX0417, and the final constructed plasmids showed good expression of 5KGR and 2KGR in...”
- L-sorbose reductase and its transcriptional regulator involved in L-sorbose utilization of Gluconobacter frateurii
Soemphol, Journal of bacteriology 2007 - “...(30% identity each). 5-Keto D-gluconate reductase (GOX2187), D-glucose 1-dehydrogenase (GOX2015), and xylitol dehydrogenase (GOX0865) genes also showed identity...”
- Identification of the yqhE and yafB genes encoding two 2, 5-diketo-D-gluconate reductases in Escherichia coli
Yum, Applied and environmental microbiology 1999 - “...searches with the amino acid sequences of 5KDGR (SP: P50199) of G. oxydans (21) and 25DKGR (PIR:I40838) of Corynebacterium sp. (6) as query sequences. As a...”
- Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli
Bausch, Journal of bacteriology 1998 - “...e G. oxydans gluconate:NADP 5-oxidoreductase encoded by gno (P50199). f E. coli gluconate transporter encoded by gntT (P39835). g E. coli gluconate regulator...”
- Cloning, nucleotide sequence, and overexpression of smoS, a component of a novel operon encoding an ABC transporter and polyol dehydrogenases of Rhodobacter sphaeroides Si4
Stein, Journal of bacteriology 1997 - “...oxydans (Gno_Glo), SwissProt accession no. P50199 (23); N-acyl-D-mannosamine dehydrogenase from Flavobacterium sp. strain 141-8 (Dhma_Flas1), SwissProt...”
TTHB016 oxidoreductase, short-chain dehydrogenase/reductase family from Thermus thermophilus HB8
37% identity, 97% coverage
LOC103972276 tropinone reductase homolog At5g06060-like from Musa acuminata AAA Group
32% identity, 93% coverage
Q84X75 3-oxoacyl-[acyl-carrier-protein] reductase from Chlamydomonas reinhardtii
35% identity, 76% coverage
WP_013552902 SDR family NAD(P)-dependent oxidoreductase from Cellulophaga sp. L1A9
33% identity, 96% coverage
BH1511 oxidoreductase (short chain dehydrogenase/reductase family) from Bacillus halodurans C-125
32% identity, 86% coverage
- Phenotypic and genotypic characterization of some lactic Acid bacteria isolated from bee pollen: a preliminary study
Belhadj, Bioscience of microbiota, food and health 2014 - “...54 potent LAB isolates as determined by carbohydrate fermentation Cluster A 18 isolates Cluster B (BH1511) Cluster C 6 isolates Cluster D (BH0400 BH0500) Cluster E 12 isolates Cluster F 4 isolates Cluster G (BH0600) Cluster H (BH2722 BH2422) Cluster I 8 isolates D-Arabinose 5.5 0...”
- “...strains Sequences of the 16S rRNA gene (approximately 1,500 bp) of ten LAB isolates, BH0900, BH1511, AH3133, BH0500, AH5655, AH3030, BH1711, BH0600, BH2422, and AH3433A, were determined. The 16S rRNA nucleotide sequences of the isolates were aligned with homologous regions from various LAB, and a phylogenetic...”
- Global analysis of the general stress response of Bacillus subtilis
Petersohn, Journal of bacteriology 2001 - “...fluorescens (6e-10) Oxidoreductase (short chain DH/Red.) BH1511, B. halodurans (e-104) Probable oxidoreductase PA1127, P. aeruginosa (e-112) YxiE, B....”
pRL80037 putative short-chain dehydrogenase from Rhizobium leguminosarum bv. viciae 3841
35% identity, 98% coverage
THTE_2632 SDR family NAD(P)-dependent oxidoreductase from Thermogutta terrifontis
30% identity, 93% coverage
- Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches
Elcheninov, Frontiers in microbiology 2017 - “...were found. However, the genome contains several genes ( THTE_0865 , THTE_1784 , THTE_2229 , THTE_2632 , THTE_3060 , THTE_3480 , and THTE_3564 ), probably encoding proteins of the short-chain dehydrogenase/reductase family ( Jrnvall et al., 1995 ). One of its biochemically characterized representatives, an oxidoreductase...”
- “...was hypothesized for altronate oxidoreductases (see above), we suggest that some of short-chain reductases/dehydrogenases (THTE_2229, THTE_2632, THTE_3060, THTE_3480, THTE_3564 and THTE_3622) with unknown specificity, especially the up-regulated THTE_3564, may act as a mannonate oxidoreductase. In most cases, the majority of enzymes involved in both the trehalose...”
4bo4C / O54438 Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (fabg) from pseudomonas aeruginosa in complex with n-(2-methoxyphenyl)-3,4- dihydro-2h-quinoline-1-carboxamide at 2.7a resolution (see paper)
36% identity, 99% coverage
- Ligand: n-(2-methoxyphenyl)-3,4-dihydro-2h-quinoline-1-carboxamide (4bo4C)
PA1827 probable short-chain dehydrogenase from Pseudomonas aeruginosa PAO1
34% identity, 100% coverage
- Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations
Ruparel, Drug target insights 2023 - “...reductase subunit B 5.44 0 7 norC Nitric oxide reductase subunit B 5.04 0 8 PA1827 3-oxoacyl-[acyl-carrier protein] reductase 4.52 3.77E-06 9 PA1013.1 tRNA-Ser 4.50 0.002 10 atuE Isohexenylglutaconyl-CoA hydratase 4.50 0.009 11 PA1492 Hypothetical protein 4.20 0.001 12 PA2085 Ring-hydroxylating dioxygenase small subunit 4.16 0.01...”
- “...208964.PA1020 1 34 PA1211 208964.PA1211 1 35 PA1221 208964.PA1221 1 36 PA1470 208964.PA1470 1 37 PA1827 208964.PA1827 1 38 PA2136 208964.PA2136 1 39 PA2433 208964.PA2433 1 40 PA3016 208964.PA3016 1 41 PA3224 208964.PA3224 1 42 PA3450 208964.PA3450 1 43 PA3859 208964.PA3859 1 44 PA5071 208964.PA5071 1...”
- The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
Coleman, Applied and environmental microbiology 2021 (secret) - Characterization of 3-Oxacyl-Acyl Carrier Protein Reductase Homolog Genes in Pseudomonas aeruginosa PAO1
Guo, Frontiers in microbiology 2019 - “...Tyr159-AMS-Lys163 adh_short; KR; Epimerase; adh_short_C2 PA1470 245 33.7 Gly12-ASR-Gly16-I-Gly18 Thr140, Tyr153-IAS-Lys157 adh_short; KR; Epimerase; adh_short_C2 PA1827 253 39.9 Gly15-GSS-Gly19-I-Gly21 Ser142, Tyr157-AAA-Lys161 adh_short; KR; Epimerase; adh_short_C2 PA2142 286 33.7 Gly49-GDS-Gly53-I-Gly55 Ser178, Tyr191-SST-Lys195 adh_short; KR; Epimerase; adh_short_C2 PA2967 247 63.6 Gly12-ASR-Gly16-I-Gly18 Ser141, Tyr154-AAA-Lys158 adh_short; KR; Epimerase; adh_short_C2 PA3128...”
- “...the 42 SDR encoded in the P. aeruginosa genome, nine are putative OARs: PA0182, PA1470, PA1827, PA2967 (FabG), PA3387 (RhlG), PA4089, PA4389, PA4786, and PA5524. We also included PA2142, PA3128, and PA5150 in this study because their putative proteins share high identities with P. aeruginosa FabG...”
- Validation of the anti-infective potential of a polyherbal 'Panchvalkal' preparation, and elucidation of the molecular basis underlining its efficacy against Pseudomonas aeruginosa
Joshi, BMC complementary and alternative medicine 2019 - “...]. A brief description of the differently expressed QS-associated genes follows. Five of the genes (PA1827, PA0182, fabI , PA1470, PA5071) involved in the production of the autoinducer 3-oxo-C 12 -HSL/ C 4 -HSL were down-regulated in the range of 2.024.52 fold. These two acylhomoserine lactones...”
- Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Zhu, GigaScience 2018 - “...in i PAO1, these reactions were associated with another 8 highly conserved isozymes (PA0182, PA1470, PA1827, PA3387, PA4089, PA4389, PA4786, and PA5524). Furthermore, condition-specific essential genes were predicted in i PAO1 by imposing transcriptomics constraints. Modification of lipid A with 4-amino-4-deoxy-L-arabinose (L-Ara4N) leads to polymyxin resistance...”
- Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
Rahmani-Badi, Frontiers in microbiology 2015 - “...mdcA, atuC,PA0098, PA0182,PA0286, PA0493, PA0506-PA0508, PA0745-PA0746, PA0879, PA1020-PA1022, PA1187, PA1240, PA1470, PA1535, PA1576, PA1628-PA1629, PA1631, PA1827, PA1869, PA2550, PA2552, PA2815, PA2841, PA2887-PA2891, PA2893, PA3286, PA3426, PA3589, PA3591, PA3593, PA3924,PA4089, PA4330, PA4912, PA4979-PA4980, PA4995, PA5020, PA5524 Protein and Amino acid metabolism thrS, folC, glnA, gmk, tgt, dadA,...”
BB0649 probable short chain dehydrogenase from Bordetella bronchiseptica RB50
37% identity, 95% coverage
- BosR (BB0647) controls the RpoN-RpoS regulatory pathway and virulence expression in Borrelia burgdorferi by a novel DNA-binding mechanism
Ouyang, PLoS pathogens 2011 - “.... Of note, the sequences of this operon and its flanking genes ( bb0645 and bb0649 ) are identical between both strains 297 and B31 (data not shown). Thus, the same strategies used in the creation of the bosR mutant in B31 [34] were employed to...”
- “...were obtained. To cis -complement the bosR mutation, the suicide plasmid pOY83 [34] containing the bb0649 - bb0648 - bosR -P flgB - aadA cassette was introduced into the bosR mutants. As a result, two streptomycin-resistant clones (OY33/A6 and OY33/F7) were isolated. The inactivation and complementation...”
Achr_22890 acetoacetyl-CoA reductase from Azotobacter chroococcum NCIMB 8003
32% identity, 96% coverage
- Holistic view of biological nitrogen fixation and phosphorus mobilization in Azotobacter chroococcum NCIMB 8003
Biełło, Frontiers in microbiology 2023 - “...Poly-hydroxybutyrate (PHB) and alginate biosynthesis-related proteins decreased in BNF compared to C. Acetoacetyl-CoA reductase (A0A0C4WQB3, Achr_22890) and PHB synthase (A0A0C4WTR3, Achr_22910), involved in PHB biosynthesis, and Alg44, Algk, AlgJ, AlgX, AlgV, and AlgF proteins, which are required for alginate biosynthesis, decrease their levels in BNF under...”
Pput_1909 short chain dehydrogenase from Pseudomonas putida F1
31% identity, 98% coverage
4dmmB / Q31QF3 3-oxoacyl-[acyl-carrier-protein] reductase from synechococcus elongatus pcc 7942 in complex with NADP
39% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (4dmmB)
AFE_1857 glucose 1-dehydrogenase from Acidithiobacillus ferrooxidans ATCC 23270
35% identity, 96% coverage
- Proteomics Reveal Enhanced Oxidative Stress Responses and Metabolic Adaptation in Acidithiobacillus ferrooxidans Biofilm Cells on Pyrite
Bellenberg, Frontiers in microbiology 2019 - “...phosphorylases. Three different glucose dehydrogenases were found, a putative glucose 1-dehydrogenase (AFE_0748), a glucose dehydrogenase (AFE_1857), a glucose-6-phosphate dehydrogenase (AFE_2025). The first two enzymes are probably involved in generating D -gluconate, while the third one generates D-gluconate-6-phosphate. These can be precursors for pyruvate, ribulose-5 phosphate or...”
- Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog
Mamani, Frontiers in microbiology 2016 - “...the glycolysis [ pyk (AFE_1801), AFE_1802, gpmL (AFE_1815)], the pentose phosphate pathway [ tal (AFE_0419), AFE_1857, and AFE_2024] and the glycogen biosynthesis/degradation pathway [AFE_1799, AFE_2082, AFE_2083, and glgB (AFE_2836)]. In the case of glycolysis, this could mean that the pathway was directed toward - D -fructose-1,6-bisphosphate,...”
BCG_1967c putative short-chain type dehydrogenase/reductase from Mycobacterium bovis BCG str. Pasteur 1173P2
P95286 Probable short-chain type dehydrogenase/reductase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Rv1928c short chain dehydrogenase from Mycobacterium tuberculosis H37Rv
Mb1963c PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE from Mycobacterium bovis AF2122/97
33% identity, 98% coverage
- Facile metabolic reprogramming distinguishes mycobacterial adaptation to hypoxia and starvation: ketosis drives starvation-induced persistence in M. bovis BCG
Davis, Communications biology 2024 - “...upregulated succinyl-CoA:3-ketoacid-CoA transferase ( scoA, scoB ) and to BHB by upregulated 3-hydroxybutyrate dehydrogenase ( BCG_1967c ). Proteins levels for BCG_3587, ScoA, and ScoB were not quantified. Key: Relative transcript and proteins abundances are visualized after counts are normalized to their levels at Log (hence not...”
- “...AcAc-CoA (Fig. 4a, b ). Further action by succinyl-CoA:3-ketoacid-CoA transferase (ScoA, ScoB) and 3-hydroxybutyrate dehydrogenase (BCG_1967c) can convert AcAc-CoA to AcAc and BHB which was observed to increase during starvation (Figs. 3 e and 4b ). Ketogenesis: an Achilles heel for starvation-induced NRP mycobacteria Ketosis has...”
- Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Chekesa, PloS one 2024 - “...Isocitrate lyase 2 Q8VJU4 766 0 24 5.18E-09 9.31E-06 3.58E-07 LP Rv1928c Short-chain type dehydrogenase/reductase P95286 255 26 8 5.18E-09 9.31E-06 3.58E-07 HP PE_PGRS20 PE-PGRS family protein P9WIF9 463 26 11 2.51E-07 0.0005 1.46E-05 HP Rv3093c Oxidoreductase O05772 334 26 13 2.46E-06 0.004 0.0001 HP fadD34...”
- Universal Lineage-Independent Markers of Multidrug Resistance in Mycobacterium tuberculosis
Hlanze, Microorganisms 2024 - “...other antibiotics. Additionally, mutations in another protein potentially involvement in redox potential maintenance, short-chain dehydrogenase/reductase Rv1928c, showed associations with MDR. The involvement of this gene in INH resistance was reported [ 64 ]. It is likely that Rv3093c and Rv3346c are also involved in the oxidative...”
- “...TB drugs, ultimately leading to high-level resistance [ 73 ]. Amino acid substitutions in OpcA, Rv1928c, the oxidoreductase Rv3093c, and the transmembrane protein Rv3346c are likely to be part of the anti-oxidative mechanisms that Mtb employs to survive antibiotic exposure. Statistical analysis using attributable risk statistics...”
- Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Chekesa, PloS one 2024 - “...remaining six were non-annotated hypothetical protein-coding genes ( Table 1 ). Specifically, four genes ( Rv1928c , Rv3093c , Rv0025 , and PE_PGRS20 ) showed significant associations with the highly prevalent L4.6.3 sublineage, while the other seven genes ( Rv0071 , vapC28 , Rv3098A , icl2...”
- “...5.05E-13 7.22E-14 LP icl2/aceA Isocitrate lyase 2 Q8VJU4 766 0 24 5.18E-09 9.31E-06 3.58E-07 LP Rv1928c Short-chain type dehydrogenase/reductase P95286 255 26 8 5.18E-09 9.31E-06 3.58E-07 HP PE_PGRS20 PE-PGRS family protein P9WIF9 463 26 11 2.51E-07 0.0005 1.46E-05 HP Rv3093c Oxidoreductase O05772 334 26 13 2.46E-06...”
- Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i>
Poonawala, Antimicrobial agents and chemotherapy 2024 (secret) - Rv0687 a Putative Short-Chain Dehydrogenase Is Required for In Vitro and In Vivo Survival of Mycobacterium tuberculosis
Bhargavi, International journal of molecular sciences 2024 - “...Mtb possess 23 SDRs, namely Rv0148, Rv0484c, Rv0687, Rv0851c, Rv0927c, Rv0945, Rv1144, Rv1245c, Rv1865c, Rv1882c, Rv1928c, Rv1941, Rv2214c, Rv2509, Rv2766c, Rv2857c, Rv3085, Rv3174, Rv3224, Rv3485c, Rv3502c, Rv3548c and Rv3549c (as listed in Mycobrowser) and only a few of these are characterized [ 25 , 26 ]....”
- Comparative Analysis on Proteomics Profiles of Intracellular and Extracellular M.tb and BCG From Infected Human Macrophages
Liu, Frontiers in genetics 2022 - “...10 up-regulated proteins in intracellular M.tb compared with extracellular M.tb include Rv1498A, RpsF, Rv1405c, TB22.2, Rv1928c, LppE, Rv2466c, PPE41, FbpB, and Rv1674c. Rv1498A was the mostly up-regulated (four point one folds up), but the protein currently uncharacterized. RspF, 30S ribosomal protein S6, was modified by ATP-dependent...”
- “...protein S6 Up Rv1405c 2.26984127 http://www.uniprot.org/uniprot/P9WLY7 Putative methyltransferase Up TB22.2 2.091614333 http://www.uniprot.org/uniprot/I6YF08 hypothetical protein Up Rv1928c 2.063829787 http://www.uniprot.org/uniprot/P95286 Short-chain dehydrogenase Up lppE 2.016712009 http://www.uniprot.org/uniprot/O07750 lipoprotein LppE Up Rv2466c 1.998148148 http://www.uniprot.org/uniprot/O53193 Uncharacterized protein Up PPE41 1.907282133 http://www.uniprot.org/uniprot/Q79FE1 PPE family protein PPE41 Up fbpB 1.894904459 http://www.uniprot.org/uniprot/P9WQP1 diacylglycerol acyltransferase/mycolyltransferase...”
- The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Mycobacterium tuberculosis Strain in Aragon Using Whole-Genome Sequencing
Comín, Frontiers in cellular and infection microbiology 2022 - “...monophosphate to nucleotide monophosphate CLS-2.2 1301938 PE12 Synonymous Pe/ppe PE family protein PE12 CLS-1 2180630 Rv1928c I196M Non-synonymous (neutral) Intermediary metabolism and respiration Short-chain type dehydrogenase/reductase CLS-2.4 2544858 lppN A54V Non-synonymous (neutral) Cell wall and cell processes Lipoprotein LppN CLS-1.1 2770751 pepN V589A Non-synonymous (deleterious) Intermediary...”
- The Epistatic Landscape of Antibiotic Resistance of Different Clades of Mycobacterium tuberculosis
Muzondiwa, Antibiotics (Basel, Switzerland) 2021 - “...evolution of antibiotic resistance started from a mutation in codon 55 in a putative dehydrogenase/reductase Rv1928c whose involvement in INH resistance was hypothesized in a recent paper [ 56 ]. This mutation made it possible for several other DR mutations to occur independently from each other:...”
- An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis
Furió, Communications biology 2021 - “...IR aao d -Amino acid oxidase Rv1908c IR katG Catalase-peroxidase-peroxynitritase T, main isoniazid resistance gene Rv1928c IR Rv1928c Short-chain type dehydrogenase/reductase Rv2021c IR Rv2021c Transcriptional regulator IG_Rv2208_Rv2209 IR Rv2209 Conserved membrane protein Rv2214c IR ephD Short-chain type dehydrogenase, thought to be involved in detoxification reactions following...”
- More
- Functional analysis of a clonal deletion in an epidemic strain of Mycobacterium bovis reveals a role in lipid metabolism
Wheeler, Microbiology (Reading, England) 2008 (PubMed)- “...of deletion, termed RDbovis(d)_0173, of seven genes between Mb1963c and Mb1971. Three of these genes have functions annotated in lipid metabolism. To explore...”
- “...al., 2005). This deletion affects seven genes between Mb1963c and Mb1971 (M. tuberculosis H37Rv designation Rv1928c-Rv1936), three of which are annotated as...”
P43713 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0155 3-ketoacyl-acyl carrier protein reductase (fabG) from Haemophilus influenzae Rd KW20
33% identity, 98% coverage
- Structure features of <i>Streptococcus pneumoniae</i> FabG and virtual screening of allosteric inhibitors
Xu, Frontiers in molecular biosciences 2024 - “...Clostridioides difficile FabG (Q18B45), S. aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), E. coli FabG (P0AEK2), S. cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The amino acid sequences of these eight FabG homologs were obtained from UniProt ( UniProt Consortium, 2023...”
- “...Clostridioides difficile FabG (Q18B45), Staphylococcus aureus FabG (Q6G9Y2), Pseudomonas aeruginosa FabG (O54438), Haemophilus influenzae FabG (P43713), Escherichia coli FabG (P0AEK2), Saccharomyces cerevisiae FabG (P35731) and Homo sapiens FAS (P49327). The X-ray crystallographic coordinates and structure factor files for SpFabG structures are available in the Protein Data...”
- Identification of genes transcribed by Actinobacillus pleuropneumoniae in necrotic porcine lung tissue by using selective capture of transcribed sequences
Baltes, Infection and immunity 2004 - “...ZP_00135280 ZP_00135039 34 34 ZP_00134291 ZP_00133817 ZP_00134532 P43713 ZP_00134954 ZP_00134371 P95510 78/82 238 81/81 156 20 84/86 174 34 rpoB, RNA...”
- Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor
López-López, mSystems 2022 - “...ED no. Gene Enzyme Lipid metabolism FASII HI0154 ( acpP ) Acyl carrier protein 1.1.1.100 HI0155 ( fabG ) 3-Oxoacyl-[acyl-carrier-protein] reductase FabG 2.3.1.39 HI0156 ( fabD ) Malonyl CoA-acyl carrier protein transacylase 2.3.1.180 HI0157 ( fabH ) 3-Oxoacyl-[acyl-carrier-protein] synthase 3 2.1.3.15 HI0406 ( accA ) Acetyl-coenzyme...”
IF655_12535 3-oxoacyl-ACP reductase FabG from Streptomyces sp. DSM 110735
34% identity, 95% coverage
BP951000_0534 3-oxoacyl-[acyl-carrier-protein] reductase from Brachyspira pilosicoli 95/1000
31% identity, 98% coverage
4za2D Crystal structure of pectobacterium carotovorum 2-keto-3-deoxy-d- gluconate dehydrogenase complexed with NAD+ (see paper)
33% identity, 98% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4za2D)
CPF_0396 2-deoxy-D-gluconate 3-dehydrogenase from Clostridium perfringens ATCC 13124
30% identity, 97% coverage
- Molecular identification of hyaluronate lyase, not hyaluronidase, as an intrinsic hyaluronan-degrading enzyme in Clostridium perfringens strain ATCC 13124
Kumon, Scientific reports 2024 - “...genetic cluster. Name ATCC13124 Nutrient-poor+HA/nutrient-poor Nutrient-poor+mucin/nutrient-poor hysA CPF_0394 1.82 4.80 kduI CPF_0395 9.62 10.99 kduD CPF_0396 7.83 9.41 kdgA CPF_0397 9.63 11.97 kdgK CPF_0398 9.57 11.88 kduI CPF_0399 2.28 6.87 ugl CPF_0400 2.16 8.36 PTS-EIIB CPF_0401 2.76 8.67 PTS-EIIC CPF_0402 2.43 7.96 PTS-EIID CPF_0403 2.41 8.03...”
- “...structure of which with substrate analogs has recently reported in Lactocaseibacillus 44 , and KduD (CPF_0396). The resultant metabolites finally flow into glycolysis. This study is a significant finding that newly identified hyaluronate lyase as an HA-degrading enzyme distinct from conventional hyaluronidases in C. perfringens ....”
AT2G29370 tropinone reductase, putative / tropine dehydrogenase, putative from Arabidopsis thaliana
31% identity, 95% coverage
- Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants
Petegrosso, Plant phenomics (Washington, D.C.) 2020 - “...feature [ 37 ]. Note that this enrichment of alkaloid term only involves 2 genes, AT2G29370 and AT1G31690, with a weak association. Network-based HCCA does capture AT1G31690 and reports a p value of 0.08 for the enrichment which is only slightly off the 0.05 cutoff. It...”
- HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings
Veerappan, BMC plant biology 2014 - “...(AGL15, At5g13790 ), At2g41260 (Late-embryogenesis-abundant protein), At3g22640 (cupin family seed storage protein), At1g04660 (glycine-rich protein), At2g29370 (NAD(P)-binding Rossmann-fold superfamily protein), At5g45830 ( DOG1, DELAY OF GERMINATION1), At2g34700 (putative proline-rich glycoprotein). As previously reported, a number of seed maturation-related structural genes are derepressed in hsi2-4 mutant seedlings...”
- “...specific to At2g41260 (Late-embryogenesis-abundant (LEA) protein), At3g22640 (cupin family seed storage protein), At1g04660 (glycine-rich protein), At2g29370 (NAD(P)-binding Rossmann -fold superfamily protein), At5g45830 ( Delay of Germination1, DOG1 ) and At2g34700 (proline-rich glycoprotein). These seed maturation genes were previously reported to be targets of H3K27 hypermethylation [...”
- Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana
Pierce, PloS one 2013 - “...4.53 1.24E-08 AT3G15210 ATERF-4,Ethylene responsive binding factor 4 DNA binding/protein binding/transcription factor/transcriptional repressor 4.64 1.31E-08 AT2G29370 Tropinone reductase, putative/tropine dehydrogenase, putative 5.36 3.83E-09 AT2G20630 Protein phosphatase 2C, putative/PP2C, putative 5.37 3.23E-09 AT1G07400 17.8 kDa class I heat shock protein (HSP17.8-CI) 5.57 3.11E-09 AT3G27540 Glycosyl transferase family...”
- Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply
Armengaud, Molecular plant 2010 - “...0.7 0.7 0.6 0.6 At4g05020 NDB2 A. thaliana cDNA W43435 6.4 0.8 0.6 0.6 0.6 At2g29370 Putative tropinone reductase 11.8 0.5 0.1 0.7 0.6 At5g19550 ASP2 Aspartate aminotransferase 2 12.6 0.5 0.8 0.8 0.7 At4g34710 ADC2 Arginine decarboxylase SPE2 9.9 1.7 0.2 0.3 0.4 At1g69930 GSTU11...”
B7G1R8 3-oxoacyl-[acyl-carrier-protein] reductase from Phaeodactylum tricornutum (strain CCAP 1055/1)
34% identity, 96% coverage
- Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum
Wu, Biotechnology for biofuels 2021 - “...(B7FRX6), malonyl CoA: ACP transacylase (B7G3D4), 3-ketoacyl-ACP synthase II (A0A1P8BJW1), 3-oxoacyl-ACP synthase (B7GCM0), 3-oxoacyl-ACP reductase (B7G1R8), enoyl-ACP reductase (B7FS72) and long chain acetyl-CoA synthase (B7FXX6 and B7FYK0), were significantly upregulated 1.27- to 3.49-fold under HC conditions but downregulated 0.23- to 0.78-fold under LC conditions, respectively. The...”
- Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion
Longworth, Algal research 2016 - “...10 1.58 B7FT67 Triosephosphate isomerase 6 1.42 B7G3C1 Triosephosphate isomerase 4 1.46 Fatty acid biosynthesis B7G1R8 3-oxoacyl-[acyl-carrier protein 11 1.71 B7GCM0 3-oxoacyl-[acyl-carrier-protein] synthase 10 1.51 B7G7H8 3R-hydroxyacyl-[acyl carrier protein] dehydrase 4 1.41 A0T0F8 Acyl carrier protein 2 1.96 B7FRX6 Acyl carrier protein 3 2.00 B7G3D4 Malonyl-CoA:ACP...”
WP_013993961 SDR family NAD(P)-dependent oxidoreductase from Zobellia galactanivorans
32% identity, 95% coverage
tpdE / M1WXK8 aminoalcohol dehydrogenase from Rhodococcus sp. TMP1 (see paper)
tpdE / CCN27364.1 aminoalcohol dehydrogenase from Rhodococcus sp. TMP1 (see paper)
33% identity, 98% coverage
Q8X7R8 SDR family oxidoreductase from Escherichia coli O157:H7
30% identity, 96% coverage
D0Z05_11900 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD from Enterobacter hormaechei
33% identity, 98% coverage
aknA / Q9L553 aclacinomycin polyketide synthase reductase from Streptomyces galilaeus (see paper)
Q9L553 AknA from Streptomyces galilaeus
32% identity, 94% coverage
- Rethinking Biosynthesis of Aclacinomycin A
Xu, Molecules (Basel, Switzerland) 2023 - “...of the akn genes. Gene Product Number of Amino Acid Residues Uniprot Functions AknA 261 Q9L553 -ketoreductase AknB 423 Q9L551 KS AknC 407 Q9L550 KS AknD 91 Q9L549 Acyl carrier protein (ACP) AknE1 450 Q9L554 Aromatase (ARO) AknE2 368 Q9L548 Determines the starter unit AknF 347...”
Atu3141 2-deoxy-D-gluconate 3-dehydrogenase from Agrobacterium tumefaciens str. C58 (Cereon)
35% identity, 99% coverage
- Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58
Yoon, Journal of bacteriology 2009 - “...about 150 kb. In A. tumefaciens, the genes Atu3140, Atu3141, Atu3142, and Atu3145 adjacent to udh are kdgD, kduD, kduI, and kdgF, respectively, and are related...”
4nbtA / A9NFJ2 Crystal structure of fabg from acholeplasma laidlawii (see paper)
31% identity, 98% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4nbtA)
ETEC_2966 SDR family oxidoreductase from Escherichia coli ETEC H10407
30% identity, 96% coverage
SAG13_ARATH / Q9ZW18 Senescence-associated protein 13; Tropinone reductase homolog SAG13; EC 1.1.1.- from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT2G29350 SAG13; alcohol dehydrogenase/ oxidoreductase from Arabidopsis thaliana
33% identity, 93% coverage
- function: Unspecific reductase providing both diastereomeric alcohols from the prochiral ketones. Active on cyclic monoterpenes and small flexible lipophilic carbonyls. No activity with tropinone, nitrogen- containing tropinone analogs, tropine or pseudotropine as substrate.
- ZmNF-YB10, a maize NF-Y transcription factor, positively regulates drought and salt stress response in Arabidopsis thaliana
Wang, GM crops & food 2025 - “...marker gene DRE-binding protein 2A ( AtDREB2A , AT5G05410), senescence-associated gene 13 ( AtSAG13 , AT2G29350), cold-regulated gene 15 ( AtCOR15 , AT2G42540), and salt tolerance-associated gene SAL1 phosphorothionein ( AtCOR15 , AT2G42540) in drought and salt stress-treated transgenic plants. associated gene 13 ( AtSAG13 ,...”
- <i>ALLENE OXIDE SYNTHASE</i> (<i>AOS</i>) induces petal senescence through a novel JA-associated regulatory pathway in <i>Arabidopsis</i>
Wu, Physiology and molecular biology of plants : an international journal of functional plant biology 2024 - “...four senescence associated genes (SAG), namely SAG 13 (AT2G29350), SAG 21 (AT4G02380), SAG 24 (AT1G66580), and SAG 29 (AT5G13170). One senescence related gene...”
- “...bHLH17 (At2g46510), URH2 (At1g05620), SAG13 (At2g29350), SAG21 (At4g02380), SAG24 (At1g66580), SAG29 (At5g13170), SRG1 (At1g17020). Declarations Conflict...”
- Transcriptome analysis reveals role of transcription factor WRKY70 in early N-hydroxy-pipecolic acid signaling
Foret, Plant physiology 2024 - “...1 2.3 AT3G45860 CRK4 Cysteine-rich receptor-like protein kinase 2.1 AT5G51500 PME60 Pectin methylesterase inhibitor 1.7 AT2G29350 SAG13 SENESCENCE-ASSOCIATED GENE 13 1.3 Late strong AT3G22231 PCC1 PATHOGEN AND CIRCADIAN CONTROLLED 1 3.8 3.9 Selection of genes upregulated by NHP in Col-0 and sid2-2 seedlings. Clusters defined for...”
- m6A RNA methylation counteracts dark-induced leaf senescence in Arabidopsis
Sheikh, Plant physiology 2024 - “...quantitative analyses are presented as mean SD or mean SEM. Accession numbers SAG12 (AT5G45890), SAG13 (AT2G29350), SAG113 (AT5G59220), SEN4 (AT4G30270), SARD1 (AT1G73805), WRKY6 (AT1G62300), WRKY53 (AT4G23810), OXI1 (AT3G25250), Trxh5(AT1G45145), CAB1 (AT1G29930), RBCS (AT1G67090), NYE1 (AT4G22920), GLK1 (AT2G20570), CP33B (AT2G35410), PIF4 (AT2G43010), ORE1/NAC2/NAC092 (AT5G39610), NAP(AT1G69490), TUB (AT5G62690),...”
- Metabolic changes associated with dark-induced leaf senescence in Arabidopsis nadk2 mutants
Chaomurilege,, Plant signaling & behavior 2023 - “...(KAPA Biosystems) and an ABI Prism 7500 system (Applied Biosystems). The following primers were used: AT2G29350 ( SAG13 , forward, 5-CAGCTTGCCCACCCATTGTTA-3; reverse, 5-GTCGTACGCACCGCTTCTTTC-3), AT5G45890 ( SAG12 , forward, 5-TTGAGCATATAAAAGCGACTG-3; reverse, 5-GTGCACTCTCCAGTGAACACA-3), and AT4G35770 ( SEN1 , forward, 5-CCACTGCTTTTAACACAACATCA-3; reverse, 5-AGCAGTGAGAAGATCAGTTGAGG-3), while Actin8 (forward, 5-TGAGCCAGATCTTCATCGTC-3, reverse, 5-TCTCTTGCTCGTAGTCGACA-3)...”
- Nitrile-Specific Protein NSP2 and Its Interacting Protein MPK3 Synergistically Regulate Plant Disease Resistance in Arabidopsis
Zhai, Plants (Basel, Switzerland) 2023 - “...found that four proteins were upregulated in NSP2 -OE and downregulated in nsp2 (AT1G10940, AT1G24280, AT2G29350, AT5G62440), while another four proteins were upregulated in nsp2 and downregulated in NSP2 -OE (AT2G03870, AT3G01520, AT5G04420, AT5G08060). It is worth noting that two of these eight genes, AT1G10940 (SnrK2.4)...”
- Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis
Tsai, Metabolites 2023 - “...2.7 3.9 AT5G42600 MRN1 8.3 31.1 AT5G48010 THAS1 2.0 9.1 -alkaloids AT2G30750 CYP71A12 3.0 4.4 AT2G29350 SAG13 4.6 6.6 -glucosinolates AT1G21100 IGMT1 2.2 2.4 AT1G21110 IGMT3 2.8 2.8 AT1G21120 IGMT2 2.3 2.4 AT1G76790 IGMT5 2.0 2.2 AT5G57220 CYP81F2 2.9 2.3 - phytoalexin AT4G31970 CYP82C2 2.7 9.1...”
- The Arabidopsis thaliana onset of leaf death 12 mutation in the lectin receptor kinase P2K2 results in an autoimmune phenotype
Zhao, BMC plant biology 2023 - “...CERK1 (AT3G21630), ICS1 (AT1G74710), PAD4 (AT3G52430), EDS1 (AT3G48090), PR1 (AT2G14610), PR2 (AT3G57260), PR5 (AT1G75040), SAG13 (AT2G29350), SAG101 (AT5G14930), SAG113 (AT5G59220), NPR1 (AT1G64280), NPR2 (AT4G26120), MES1 (AT2G23620), BSMT1 (AT3G11480) and SID2 (AT1G74710). Supplementary Information Additional file 1: Fig. S1. Early-senescence phenotype of old12 under short-day condition. Fig....”
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Z4085 putative oxidoreductase from Escherichia coli O157:H7 EDL933
30% identity, 88% coverage
- Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
Wang, Infection and immunity 1992 - “...I, IIa Z4103 I, IIa Z3928, Z3929, Z3930, Z3931, Z4085, Z4086, Z4087, Z4088, Z4089 I, IIa Z4312, Z4313, Z4314, Z4315, Z4316, Z4317 I, IIa Z4713, Z4715, Z4716,...”
LOC100273624 uncharacterized protein LOC100273624 from Zea mays
36% identity, 95% coverage
PP_2783 3-oxoacyl-(acyl-carrier-protein) reductase from Pseudomonas putida KT2440
32% identity, 96% coverage
LOC107811394 3-oxoacyl-[acyl-carrier-protein] reductase 4-like from Nicotiana tabacum
33% identity, 66% coverage
LINX_SPHIU / D4Z260 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- from Sphingobium indicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S) (Sphingobium japonicum) (see paper)
32% identity, 98% coverage
- function: Catalyzes the degradation of 2,5-dichloro-2,5-cyclohexadiene- 1,4-diol (2,5-DDOL) into 2,5-dichlorohydroquinone (2,5-DCHQ) in vitro. LinX appears not to be involved in gamma-hexachlorocyclohexane (gamma- HCH) degradation pathway, in contrast to LinC which has the same enzymatic activity.
catalytic activity: 2,5-dichlorocyclohexa-2,5-dien-1,4-diol + NAD(+) = 2,5- dichlorohydroquinone + NADH + H(+) (RHEA:15741)
Ssal_01803 3-oxoacyl-[acyl-carrier-protein] reductase from Streptococcus salivarius 57.I
33% identity, 98% coverage
WP_020539555 SDR family NAD(P)-dependent oxidoreductase from Lewinella cohaerens DSM 23179
31% identity, 97% coverage
- Identification of a 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase, FlRed, in an alginolytic bacterium Flavobacterium sp. strain UMI-01
Inoue, Marine drugs 2015 - “...[ 27 ] Flavobacterium frigidarium (GenBank accession number, WP_026707247) and Lewinella cohaerens (GenBank accession number, WP_020539555) have not been identified as alginolytic bacteria. Specific sequence motifs of SDR-family enzymes, i.e. , the catalytic tetrad Asn-Tyr-Lys-Ser [ 28 ], the cofactor-binding sequence motif Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold...”
- “...Cytophaga fermentans (GenBank accession number, WP_027472031); Lewinella, short-chain dehydrogenase from Lewinella cohaerens (GenBank accession number, WP_020539555); Cellulophaga, short-chain dehydrogenase from Cellulophaga algicola (GenBank accession number WP_013552902); Zobellia, short-chain dehydrogenase from Zobellia galactanivorans (GenBank accession number, WP_013993961); A1-R, NADPH-dependent DEH reductase A1-R from Sphingomonas sp. A1 [...”
BA3989 3-oxoacyl-(acyl-carrier-protein) reductase from Bacillus anthracis str. Ames
31% identity, 97% coverage
- Crystal structure of a putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 Å resolution
Dinh, Acta crystallographica. Section F, Structural biology communications 2023 - “...(Dutta et al., 2012); OAR from Bacillus anthracis (BA3989), 2uvd (Zaccai et al., 2008); FabG from Listeria monocytogenes (with NADP+), 4jro (Center for...”
- “...is highlighted in hot pink. OAR from Bacillus anthracis (BA3989; PDB entry 2uvd, black; Zaccai et al., 2008) and FabG from Synechocystis sp. PCC 6803 (PDB entry...”
- Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis
Porter, Acta crystallographica. Section F, Structural biology communications 2022 - “...et al. , 2008 ) with PDB entry 2uvd , a 3-oxoacyl-(acyl carrier protein) reductase (Ba3989) from Bacillus anthracis (Zaccai et al. , 2008 ), as the search model. Bs FolM was solved with MoRDa (Vagin & Lebedev, 2015 ) using Bc FolM (PDB entry 5bt9...”
- “...Both structures have structural differences from the molecular-replacement search model, the 3-oxoacyl-(acyl carrier protein) reductase (Ba3989) from Bacillus anthracis , and have an r.m.s.d. of 2.12 on superposing all main-chain atoms (Fig.3 ). While the cofactor-binding cavities of Bs FolM, Bc FolM and the Trypanosoma proteins...”
- Structural insight into the tetramerization of an iterative ketoreductase siam through aromatic residues in the interfaces
Wang, PloS one 2014 - “...structure was solved by molecular replacement with the program Phaser using the 3-oxoacyl-(acylcarrier protein) reductase (BA3989) from Bacillus anthracis (PDB ID: 2UVD) as the search model [20] . Auto-model building was performed using Phenix which was followed by the manual model building performed by Coot [21]...”
- “...Nettleship JE , et al ( 2008 ) Crystal structure of a 3-oxoacyl-(acylcarrier protein) reductase (BA3989) from Bacillus anthracis at 2.4-A resolution . Proteins 70 : 562 567 . 17894349 30 Rao ST , Rossmann MG ( 1973 ) Comparison of super-secondary structures in proteins ....”
- Crystal structure of a 3-oxoacyl-(acylcarrier protein) reductase (BA3989) from Bacillus anthracis at 2.4-A resolution
Zaccai, Proteins 2008 (PubMed)- “...a 3-oxoacyl-(acyl carrier protein) reductase (BA3989) from Bacillus anthracis at 2.4-A resolution Nathan R. Zaccai,1 Lester G. Carter,1 Nick S. Berrow,1 Sarah...”
- “...This study reports the structure of gene product BA3989, a 3-oxoacyl-(ACP) reductase of 246 residues, determined to a resolution of 2.4 A using protein...”
Reut_B3865 Acetoacetyl-CoA reductase from Ralstonia eutropha JMP134
33% identity, 90% coverage
ECH_0669 3-oxoacyl-(acyl-carrier-protein) reductase from Ehrlichia chaffeensis str. Arkansas
31% identity, 98% coverage
- Multiple Ehrlichia chaffeensis genes critical for persistent infection in a vertebrate host are identified as nonessential for its growth in the tick vector; Amblyomma americanum
Jaworski, Frontiers in cellular and infection microbiology 2023 - “...B5-1 ECH_0600 606371 + 70/144 Hypothetical protein D3-1a ECH_0614 619640 334/696 DUF3023 domain-containing protein** A4-1 ECH_0669 683268 740/744 3-oxoacyl=(acyl-carrier-protein) reductase S34A2 ECH_0843 861495 + 581/588 Recombination mediator RecR C3-2 ECH_1127 1150113 + 117/840 Major outer membrane protein OMP-IV (P44/Msp2 family outer membrane protein**) B6-1 ECH_1144 1165318...”
- “...S34C8 ECH_0445 tRNA guanosine(34) transglycosylase Tgt** 8/10 C1-1 ECH_0475 Signal recognition particle protein 1/10 A4-1 ECH_0669 3-oxoacyl=(acyl-carrier-protein) reductase 1/10 S34A2 ECH_0843 Recombination mediator RecR 1/10 C3-2 ECH_1127 Major outer membrane protein OMP-IV (P44/Msp2 family outer membrane protein**) 3/10 B6-1 ECH_1144 Major outer membrane protein P28-1 (P44/Msp2...”
- Multiple Ehrlichia chaffeensis Genes Critical for Its Persistent Infection in a Vertebrate Host Are Identified by Random Mutagenesis Coupled with In Vivo Infection Assessment
Wang, Infection and immunity 2020 - “...ECH_0665 Phage uncharacterized protein 676091 907/1,410 14 C2-1 ECH_0666 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase 678007 1182/1,281 15 A4-1 ECH_0669 3-Oxoacyl-(acyl-carrier-protein) reductase 683268 740/744 16 s34 A2 ECH_0843 Recombination protein RecR 861495 + 581/588 17 s33 E8 ECH_0878 Hypothetical protein 898815 456/1,230 18 C4-2 ECH_1038 Hypothetical protein 1065224 5217/5,892 19...”
- “...protein 11 D3-1 ECH_0614 Hypothetical protein 14 C2-1 ECH_0666 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (biotin biosynthesis) 15 A4-1 ECH_0669 3-Oxoacyl-(acyl-carrier-protein) reductase (fatty acid biosynthesis) 16 s34 A2 ECH_0843 Recombination protein RecR (DNA repair) 20 s34 D8 ECH_1110 Dethiobiotin synthetase (biotin biosynthesis) 21 C3-2 ECH_1127 Major outer membrane protein OMP-1V/OMP-6...”
VVA1616 dehydrogenase from Vibrio vulnificus YJ016
33% identity, 98% coverage
Gmet_2059 Short-chain dehydrogenase/reductase SDR from Geobacter metallireducens GS-15
Q39TY6 3-oxoacyl-[acyl-carrier-protein] reductase from Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
31% identity, 98% coverage
4hp8B / A9CEQ9 Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from agrobacterium tumefaciens (target efi-506435) with bound NADP
35% identity, 98% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (4hp8B)
A0A2K9VPX3 D-arabinitol 4-dehydrogenase (EC 1.1.1.11) from Gluconobacter sp. JX-05 (see paper)
32% identity, 97% coverage
CNA01160 LSDR from Cryptococcus neoformans var. neoformans JEC21
29% identity, 87% coverage
Q8RX32 Tropinone reductase homolog At1g07450 from Arabidopsis thaliana
AT1G07450 tropinone reductase, putative / tropine dehydrogenase, putative from Arabidopsis thaliana
35% identity, 96% coverage
AFO85456.1 reductase/oxidase from Marinactinospora thermotolerans (see paper)
35% identity, 97% coverage
SCO1681 gluconate dehydrogenase from Streptomyces coelicolor A3(2)
30% identity, 99% coverage
- Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145
Tsypik, BioMed research international 2017 - “...(gntP) encodes gluconate permease that transports the molecule into a cell. The next two genes, SCO1681 - SCO1682 (gntZ - gntZ2) , overlap by 4 nucleotides and encode gluconate dehydrogenase and zinc-binding alcohol dehydrogenase, respectively. RT-PCR confirmed transcriptional coupling of genes SCO1679-1680-1681 ( Figure 1(b) )....”
- “...RTSCO1679-r GCCCGTTCGGTGATCTCCTC RTSCO1680-f TGTTCTTCGAGGTCGGCATC RT-PCR analysis of SCO1680 RTSCO1680-r CTTGAGCAGCATCAGCACGA RTSCO1681-f TCGACATCCTGGTCAACAAC RT-PCR analysis of SCO1681 RTSCO1681-r GGTGCTGAACTCCTCGTCCT RTSCO4991-f ACCGGTCTGATCTTCGGCAT RT-PCR analysis of SCO4991 RTSCO4991-r ATCCAGGCGGAGAACACCCA RTgntR-K_f ACTCGACGAGGTGCATGGAC RT-PCR of gntR-K intergeneric region RTgntR-K_r GCCGTCATCTTGGCGATGTT RTgntK-P_f TGATCGAGGACCGGATGTCG RT-PCR of gntK-P intergeneric region RTgntK-P_r TGGTGATGACCTTGTCCAGC RTgntP-Z_f ACATGTCGACCACGCACGC...”
BSU38970 3-hydroxybutyrate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
P42317 Uncharacterized oxidoreductase YxjF from Bacillus subtilis (strain 168)
30% identity, 95% coverage
Q5HPW0 3-oxoacyl-[acyl-carrier-protein] reductase FabG from Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)
34% identity, 96% coverage
ETAE_1899 2-deoxy-D-gluconate 3-dehydrogenase from Edwardsiella tarda EIB202
33% identity, 98% coverage
H16_A2171 acetoacetyl-CoA reductase from Cupriavidus necator H16
34% identity, 96% coverage
- De Novo Assembly of the Polyhydroxybutyrate (PHB) Producer <i>Azohydromonas lata</i> Strain H1 Genome and Genomic Analysis of PHB Production Machinery
Traversa, Microorganisms 2025 - “...JAXOJX010000034 acetyl-CoA C-acyltransferase H16_A1438 phaA Acetyl-CoA acetyltransferase SM757_22340 738 JAXOJX010000042 * acetoacetyl-CoA reductase H16_A1439; H16_A2002; H16_A2171 phaB1; phaB2; phaB3 Acetoacetyl-CoA reductase SM757_08215 750 JAXOJX010000009 3-oxoacyl-ACP reductase FabG H16_A1439; H16_A2002; H16_A2171 phaB1; phaB2; phaB3 Acetoacetyl-CoA reductase SM757_31855 741 JAXOJX010000100 3-oxoacyl-ACP reductase FabG H16_A1439; H16_A2002; H16_A2171 phaB1; phaB2;...”
- Microaerobic insights into production of polyhydroxyalkanoates containing 3-hydroxyhexanoate via native reverse β-oxidation from glucose in Ralstonia eutropha H16
Huong, Microbial cell factories 2024 - “...out through homologous recombination using pk18mobsacB-based suicide vectors, where the targeted genes were phaB1 ( h16_A2171 ), phaB2-C2 ( h16_A2002-A2003 ), phaB3 ( h16_A2171 ), had ( h16_A0602 ), paaH1 ( h16_A0282 ), crt2 ( h16_A3307 ), bktB ( h16_A1445 ), phaJ4a ( h16_A1070 ), h16_A3330...”
- The Overexpression of Phasin and Regulator Genes Promoting the Synthesis of Polyhydroxybutyrate in Cupriavidus necator H16 under Nonstress Conditions
Tang, Applied and environmental microbiology 2022 (secret) - Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol
Gascoyne, Metabolic engineering 2021 - “...in the C. necator genome ( Lindenkamp et al., 2012 ) and acetoacetyl-CoA reductase PhaB3 (H16_A2171) possessing reduced rate compared to PhaB1 ( Budde et al., 2010 ). Fig. 4 Improvement of (R) -1,3-BDO production by overexpression of phaAB . Batch fermentation profile data for strains...”
- Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
Shimizu, BMC microbiology 2013 - “...when grown on fructose [ 37 ]. The expression behaviors of phaB2 (H16_A2002) and phaB3 (H16_A2171), as well as the negligible transcription of the second PHA synthase gene phaC2 (H16_A2003) were well agreed with the previous microarray analyses [ 17 , 22 , 38 ]. The...”
- Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays
Peplinski, Applied microbiology and biotechnology 2010 - “...catalyze the transfer of acyl groups to a substrate, and phaB3 encoding an acetoacetyl-CoA reductase (H16_A2171; two- to fivefold) were found to be induced during cultivation in presence of TDP (Table 1A ). phaB3 represents a homolog to phaB1 which is part of the phaCAB operon...”
- “...H16_A0217 Hypothetical membrane-associated protein 3.16 3.11 40.29 30.94 H16_A1954 Predicted acyltransferase 4.09 2.04 2.61 x H16_A2171 phaB3 Acetoacetyl-CoA reductase 4.68 2.20 3.97 x H16_B1292 phnT Acetyltransferase (GNAT) family 6.36 2.74 3.46 x H16_B2322 frnE Predicted dithiol-disulfide isomerase 2.99 6.25 5.80 5.26 Genes putatively involved in detoxification...”
Z1545 putative fatty acyl chain reductase from Escherichia coli O157:H7 EDL933
31% identity, 99% coverage
- Identification of four fimbria-encoding genomic islands that are highly specific for verocytotoxin-producing Escherichia coli serotype O157 strains
Shen, Journal of clinical microbiology 2005 - “...Z1543-F1 Z1543-R1 Z1544 Z1544-F2 Z1544-R2 Z1545 Z1545-F1 Z1545-R1 Z1546 Z1546-F1 Primer sequence (5-3) CGACCAACGCCATTAAAGTTCA GCCCTGGATGCAGTCAAATC...”
- “...Z1540 and -41; 12, Z1542; 13, Z1543; 14, Z1544; 15, Z1545; 16, Z1546; 17, Z1547; 18, Z1548; 19, Z1549; 20, Z1550; 21, Z1551; 22, Z1552; 23, Z1553; 24, Z1554;...”
RHTO_07844 D-arabinitol dehydrogenase from Rhodotorula toruloides NP11
31% identity, 69% coverage
- Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
Reķēna, PLoS computational biology 2023 - “...by the presence of two genes in the R . toruloides genome encoding D-arabinitol dehydrogenase, RHTO_07844 and RHTO_07702. Only protein RHTO_07844 was detected in our proteomics analysis (1913 g/g_protein) ( S10 Fig ), suggesting its role as D-arabinitol 4-dehydrogenase (DAD-4), converting D-xylulose to D-arabinitol. Arabinitol dehydrogenase...”
- “...found a match with 98.5% identity. Interestingly, in strain IFO 0880 orthologs of both genes RHTO_07844 and RHTO_07702 were identified as DAD-2 and DAD-4, respectively, and both were using NAD/NADH as the cofactor [ 9 ]. While it is not known, which cofactor of DAD-2/LXR enzyme...”
- Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery
Pinheiro, Frontiers in bioengineering and biotechnology 2020 - “...Proteins belonging to arabitol metabolism, such as L-xylulose reductase (LXR, RHTO_00373), and D-arabitol dehydrogenase (DAD, RHTO_07844), and L-iditol 2-dehydrogenase, identified by Bommareddy et al. (2015) as L-arabitol dehydrogenase (LAD, RHTO_01629) were all down-regulated under nitrogen- limiting conditions. Approximately four-fold increased transketolase (TKT, RHTO_03248) abundance compared to...”
D8TK78 3-oxoacyl-[acyl-carrier-protein] reductase from Volvox carteri f. nagariensis
36% identity, 75% coverage
BT_3771 3-oxoacyl-[acyl-carrier protein] reductase from Bacteroides thetaiotaomicron VPI-5482
31% identity, 98% coverage
- Identification and characterization of 3-ketosphinganine reductase activity encoded at the BT_0972 locus in Bacteroides thetaiotaomicron
Lee, Journal of lipid research 2022 - “...the short-chain dehydrogenase/reductase family. Specifically, interrogation of the multiple sequence alignment identified that BT_2380, BT_1433, BT_3771, and BT_0972 included conserved serine, tyrosine, and lysine residues (based on the S.cerevisiae numbering in the sequence alignment in supplemental Fig.S2 : Ser167, Tyr180, and Lys184) that correspond to the...”
- “...components contain sphingolipids. Interestingly, BT_0972 successfully converted 3-KDS to SA, where candidates BT_2380, BT_1433, and BT_3771 failed ( Fig 2 C, E). Indeed, supplementing the media with PA alk led to the successful conversion of 3-ketosphinganine alkyne (3-KDS alk ) to SA alk , further validating...”
LMON_0351 SDR family oxidoreductase from Listeria monocytogenes EGD
lmo0344 similar to dehydrogenase/reductase from Listeria monocytogenes EGD-e
LMOf2365_0364 short chain dehydrogenase from Listeria monocytogenes str. 4b F2365
29% identity, 98% coverage
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...9 1.86 2.79 2.18 1.23 2.70 LMON_0350 Transaldolase lmo0343 5 1.88 2.03 1.56 0.27 4.16 LMON_0351 3-oxoacyl-[acyl-carrier protein] reductase lmo0344 5 2.35 1.71 1.30 0.62 4.34 LMON_0352 Ribose 5-phosphate isomerase B lmo0345 5 2.75 2.30 1.25 0.26 4.61 LMON_0353 Triosephosphate isomerase lmo0346 5 2.38 1.95 1.75...”
- Anti-Biofilm Effects of Z102-E of Lactiplantibacillus plantarum against Listeria monocytogenes and the Mechanism Revealed by Transcriptomic Analysis
Wei, Foods (Basel, Switzerland) 2024 - “...1 Top significantly up-regulated genes. Gene Name Gene Description FC (T/C) Log 2 FC (T/C) lmo0344 short chain dehydrogenase 22.077 4.464464 lmo0345 sugar-phosphate isomerase 21.196 4.405722 lmo0343 transaldolase 21.032 4.394532 lmo0342 transketolase 18.269 4.191303 lmo0347 dihydroxyacetone kinase 16.727 4.064068 lmo0348 dihydroxyacetone kinase 14.344 3.842421 lmo1249 hypothetical...”
- The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells
Quendera, NPJ biofilms and microbiomes 2023 - “...pentose phosphate pathway ( lmo0342 , lmo0343 , and lmo0345 ), in glycerol metabolism ( lmo0344 , lmo0347 , and lmo0348 ) and in glycolysis ( lmo0346 ) 63 , 64 . Altogether, the higher expression of these genes suggests that the metabolism of carbohydrates is...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...1.23 2.70 LMON_0350 Transaldolase lmo0343 5 1.88 2.03 1.56 0.27 4.16 LMON_0351 3-oxoacyl-[acyl-carrier protein] reductase lmo0344 5 2.35 1.71 1.30 0.62 4.34 LMON_0352 Ribose 5-phosphate isomerase B lmo0345 5 2.75 2.30 1.25 0.26 4.61 LMON_0353 Triosephosphate isomerase lmo0346 5 2.38 1.95 1.75 0.45 4.38 LMON_0354 Phosphoenolpyruvate-dihydroxyacetone...”
- Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons
Mujahid, BMC microbiology 2013 - “...2.96 beta-glucosidase bglA Energy metabolism Sugars Lmo0343 3.94 transaldolase tal2 Energy metabolism Pentose phosphate pathway Lmo0344 4.69 short chain dehydrogenase lmo0344 Energy metabolism Biosynthesis and degradation of polysaccharides Lmo0345 6.04 ribose 5-phosphate isomerase B lmo0345 Energy metabolism Pentose phosphate pathway Lmo0346 2.74 triosephosphate isomerase tpiA2 Energy...”
- Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
Oliver, Applied and environmental microbiology 2010 - “...lmo0136 lmo0264 lmo0265 lmo0292 lmo0321 lmo0342 lmo0343 lmo0344 lmo0345 lmo0346 lmo0348 lmo0398 lmo0399 lmo0400 lmo0401 lmo0402 lmo0439 lmo0449 lmo0584 lmo0589...”
- Proteomic analyses of a Listeria monocytogenes mutant lacking sigmaB identify new components of the sigmaB regulon and highlight a role for sigmaB in the utilization of glycerol
Abram, Applied and environmental microbiology 2008 - “...Lmo1602 Lmo0956 Lmo0398 Lmo0292 Lmo2824 PyrF ProS TcsA Lmo0344 Lmo0443 DaaA Lmo0342 DeoD Lmo1699 Lmo1681 DltD Lmo0560 Lmo1057 Lmo0521 Lmo2363 Lmo1604 Lmo2258...”
- “...proteins were negatively influenced by B (Lmo2824, Lmo0344, Lmo0342, Lmo1057, Lmo2258, Lmo1867, Lmo0521, Lmo0536, PyrF, DeoD, Lmo0560, DaaA, and Lmo1681)....”
- Glycerol metabolism and PrfA activity in Listeria monocytogenes
Joseph, Journal of bacteriology 2008 - “...lmo0265 lmo0278 lmo0298 lmo0299a lmo0300 lmo0342 lmo0343 lmo0344 lmo0345 lmo0346 lmo0347 lmo0348 lmo0358 lmo0384a,b lmo0385 lmo0386b lmo0400 lmo0405 lmo0415...”
- Contributions of a LysR Transcriptional Regulator to Listeria monocytogenes Virulence and Identification of Its Regulons
Abdelhamed, Journal of bacteriology 2020 (secret)
SCO1815 3-oxacyl-(ACP) reductase from Streptomyces coelicolor A3(2)
32% identity, 96% coverage
- Role of Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase in Oleaginous Streptomyces sp. Strain G25
Röttig, Applied and environmental microbiology 2016 - “...shows the highest similarity (89%) to the characterized FabG (SCO1815) from S. coelicolor (25, 52). The redundancy of fabH and fabG genes in Streptomyces sp....”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...kinase [EC:2.7.2.8] SCO1579 argJ, SCL24.15c Putative glutamate N-acetyltransferase [EC:2.3.1.1 2.3.1.35] SCO1580 argC N-Acetyl-gamma-glutamyl-phosphate reductase [EC:1.2.1.38] SCO1815 fabG, SCI28.09c Probable 3-oxacyl-(acyl-carrier-protein) reductase [EC:1.1.1.100] SCO2126 glk, SC6E10.20c Glucokinase [EC:2.7.1.2] SCO2296 Integral membrane protein SCO2513 Hypothetical protein SCO2930 Putative permease membrane component SCO2986 Hypothetical protein SCO3138 galT, SCE66.17c Galactose-1-phosphate...”
- Characterization of FabG and FabI of the Streptomyces coelicolor dissociated fatty acid synthase
Singh, Chembiochem : a European journal of chemical biology 2015 (PubMed)- “...gene (SCO1814) and three likely fabG genes (SCO1815, SCO1345, and SCO1846). We report the expression, purification, and characterization of the corresponding...”
- “...data presented provide the first experimental evidence that SCO1815, SCO1346, and SCO1814 have the catalytic capability to process intermediates in both fatty...”
- Fatty acid biosynthesis in actinomycetes
Gago, FEMS microbiology reviews 2011 - “...3 ). SCO1814 is 47 % identical in a 263 aa overlap with InhA, and SCO1815 is 50.8% identical in a 455 aa overlap with MabA. Based on homology and synteny with the M. tuberculosis (3 R )-hydroxyacyl-ACP dehydratase components ( Sacco et al. , 2007...”
- Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues
Mo, Journal of the American Chemical Society 2011 - “...of the host, as is the case with type II PKS initiation modules. 15 Indeed, SCO1815, a FabG (the -ketoacyl-ACP reductase of fatty acid biosynthesis) homolog from the genome of Streptomyces coelicolor A3(2), was shown to function as the -ketoacy l-ACP reductase component of the R1228...”
- Structural and biochemical analyses of regio- and stereospecificities observed in a type II polyketide ketoreductase
Javidpour, Biochemistry 2011 - “...patch has been identified as the putative ACP-docking site for both actKR and the homologous SCO1815 KR from S. coelicolor ( 52 ) and its presence would restrict the attached polyketide to a single side of the pocket ( 17 , 18 ). The above analysis...”
- Biochemical and genetic insights into asukamycin biosynthesis
Rui, The Journal of biological chemistry 2010 - “...ZhuH (PDB 1MZJ) ZhuG (AAG30194.1) PaaI (P76084) Sco1815 (PDB 2NM0) HadC (NP_215151.1) HadB (YP_001281933.1) Putative open reading frame ZhuN (AAG30201.1) AcmACP...”
- Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase
Erb, Proceedings of the National Academy of Sciences of the United States of America 2009 - “...dehydrogenase and the keto-acyl carrier protein reductase Sco1815 (type II polyketide synthase, PKS) involved in R1128 biosynthesis from S. coelicolor (36)...”
- More
XCC1018 3-oxoacyl-[ACP] reductase from Xanthomonas campestris pv. campestris str. ATCC 33913
34% identity, 98% coverage
- A novel 3-oxoacyl-ACP reductase (FabG3) is involved in the xanthomonadin biosynthesis of Xanthomonas campestris pv. campestris
Yu, Molecular plant pathology 2019 - “...Yu et al. , 2016 ; Zhou et al. , 2015 ). Four genes, fabG1 (XCC1018), fabG2 (XCC0416), fabG3 (XCC4003) and fabG4 (XCC0384), encode putative OARs in the Xcc genome (Qian et al. , 2005 ). FabG1 plays the major role in catalysing the reduction of...”
- Novel Xanthomonas campestris Long-Chain-Specific 3-Oxoacyl-Acyl Carrier Protein Reductase Involved in Diffusible Signal Factor Synthesis
Hu, mBio 2018 - “...( 6 ). The X. campestris pv. campestris genome carries four putative OAR genes: fabG1 (XCC1018), fabG2 (XCC0416), fabG3 (XCC4003), and fabG4 (XCC0384) ( Fig.1C ). XCC1018 ( fabG1 ) is located within a cluster of fatty acid synthesis genes, and 69.1% of the residues of...”
- The Multiple DSF-family QS Signals are Synthesized from Carbohydrate and Branched-chain Amino Acids via the FAS Elongation Cycle
Zhou, Scientific reports 2015 - “...the genes required for the FAS elongation cycle, including Xcc0582 (FabA), Xcc0581 (FabB), Xcc1020 (FabF), Xcc1018 (FabG), Xcc0115 (FabV) and Xcc1362 (FabZ) ( Fig. 6a ). This led us to further investigate whether DSF-family signals are synthesized via the FAS elongation cycle in Xcc. Since the...”
- “...cycle ( Fig. 6a ) 22 , we first attempted to delete the FabG-encoding gene Xcc1018 . However, these experiments were not successful probably due to the fact that Xcc1018 is an essential gene. As an alternative approach, we overexpressed Xcc1018 in the rpfC strain, and...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory