Family Search for PF02153 (PDH_N)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF02153 hits 103 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

BSU22610 prephenate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
Aligns to 20:176 / 371 (42.3%), covers 99.4% of PF02153, 190.8 bits

• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...S. mutans Listeria innocua aroH tyrA Asn asnB BSU22690 BSU22610 No No 1.3.1.12 1COM 3DZB B. subtilis Streptococcus thermophilus BSU30540 No 6.3.5.4 1CT9 E. coli...”

TYRC_ZYMMO / Q04983 Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 from Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (see paper)
ZMO0420 Arogenate dehydrogenase from Zymomonas mobilis subsp. mobilis ZM4
Aligns to 19:173 / 293 (52.9%), covers 98.7% of PF02153, 189.7 bits

• function: Can function as either prephenate dehydrogenase or as arogenate dehydrogenase in the biosynthesis of L-tyrosine. Catalyzes two analogous reactions: converts prephenate to 4-hydroxyphenylpyruvate and transforms L-arogenate to L-tyrosine. Is not able to utilize NADP(+) instead of NAD(+) as cosubstrate.
  catalytic activity: L-arogenate + NAD(+) = CO2 + L-tyrosine + NADH (RHEA:12256)
  catalytic activity: NAD(+) + prephenate = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADH (RHEA:13869)
  subunit: Homodimer.
• Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
  Ong, PLoS computational biology 2020
  • “...Calculator [ 50 ] to have a similar translation rate as ZMO1503. The ZMO0421 and ZMO0420 genes in pRL814_ZMO0421_ZMO0420 were amplified from the genome with their natural spacing and sequences conserved. All plasmid inserts were confirmed via sequencing. Plasmids used in this work and primers used...”
  • “...additional data file. S6 Fig Overview of ZMO0421::Tn5 analysis. (A) Genomic region containing ZMO0421 and ZMO0420, which are in a single operon. (B) Partial pathways for tyrosine and histidine biosynthesis, showing the steps catalyzed by ZMO0421 and ZMO0420. (C) Summary of growth phenotypes of a aspC...”
• Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4
  Chang, Biotechnology for biofuels 2018
  • “...tyrosine, too. Besides, tyrosine can also be formed from l -arogenate by the catalyzation of ZMO0420. Thus, the down-regulation of ZMO0937 and ZMO0420 can lead to a decrease of phenylalanine and tyrosine, which was verified by our results of groups FA, AA, F, and H (Table...”
• Metabolic engineering of Synechocystis sp. PCC 6803 for the improved production of phenylpropanoids
  Kukil, Microbial cell factories 2024 (no snippet)

3gggD / O67636 The crystal structure of a. Aeolicus prephenate dehydrogenase in complex with tyrosine and NAD+ (see paper)
Aligns to 28:182 / 293 (52.9%), covers 99.4% of PF02153, 189.2 bits

• Ligands: nicotinamide-adenine-dinucleotide; tyrosine (3gggD)

O67636 prephenate dehydrogenase (EC 1.3.1.12) from Aquifex aeolicus (see paper)
Aligns to 45:199 / 311 (49.8%), covers 99.4% of PF02153, 189.0 bits

HP1380 prephenate dehydrogenase (tyrA) from Helicobacter pylori 26695
O25931 Prephenate dehydrogenase (TyrA) from Helicobacter pylori (strain ATCC 700392 / 26695)
Aligns to 5:155 / 265 (57.0%), covers 99.4% of PF02153, 179.9 bits

• Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
  Thiele, Journal of bacteriology 2005
  • “...(CHORM), HP1380 (PPND) UPPRT...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...DNA of H. pylori. Since the tyrA gene (HP1380), encoding chorismate mutase-prephenate dehydrogenase, is also present in the genome, the bacterium can synthesize...”
• Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
  Wei, ACS omega 2022
  • “...O25524 YheS 314 O25257 Cag1 315 O25982 ppiA 316 O25470 HP_0781 317 O25992 HP_1453 318 O25931 TyrA 319 P66185 rpmE 320 P56162 pyrE 321 O25853 nuoD 322 P56067 cysM 323 O24884 HP_0043 324 O25510 OmpP1 325 O25421 HP_0719 326 P56075 ndk 327 P55976 nusG 328 O24991...”
  • “...O25274 Cag20 366 O25151 tpx 367 O25852 HP_1262 368 P56022 rpsO 369 P56156 clpP 370 O25931 TyrA 371 O25614 gpsA 372 P56097 ftsZ H. pylori OMVs Promoted the Secretion of Inflammatory Factors of GES1 Cells H. pylori colonizes the gastric mucosa and causes acute and chronic...”

tyrAa / P73906 arogenate dehydrogenase monomer (EC 1.3.1.78) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see paper)
P73906 arogenate dehydrogenase (NADP+) (EC 1.3.1.78) from Synechocystis sp. PCC 6803 (see paper)
2f1kA / P73906 Crystal structure of synechocystis arogenate dehydrogenase (see paper)
slr2081 prephenate dehydrogenase from Synechocystis sp. PCC 6803
Aligns to 15:164 / 279 (53.8%), covers 99.4% of PF02153, 179.7 bits

• Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2f1kA)
• Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803
  Wang, Biotechnology for biofuels 2016
  • “...which was necessary to Synechocystis normal growth and 3-HP production [ 50 ]. Arogenate dehydrogenase Slr2081 involved in tyrosine biosynthesis pathway was up-regulated. The enzyme catalyzes the conversion of arogenate to tyrosine. In addition, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase Sll0603 was also found up-regulated, the enzyme is a key...”

D3S601 Prephenate dehydrogenase from Methanocaldococcus sp. (strain FS406-22)
Aligns to 21:166 / 446 (32.7%), covers 100.0% of PF02153, 157.7 bits

• Genetic linkage between von Hippel-Lindau disease and three microsatellite polymorphisms refines the localisation of the VHL locus.
  Crossey, Human molecular genetics 1993 (PubMed)
• Mapping the Von Hippel-Lindau disease tumour suppressor gene: identification of germline deletions by pulsed field gel electrophoresis.
  Richards, Human molecular genetics 1993 (PubMed)
• Detailed genetic mapping of the von Hippel-Lindau disease tumour suppressor gene.
  Richards, Journal of medical genetics 1993

5uyyA / Q81P63 Crystal structure of prephenate dehydrogenase tyra from bacillus anthracis in complex with l-tyrosine (see paper)
Aligns to 24:179 / 373 (41.8%), covers 99.4% of PF02153, 147.6 bits

• Ligand: tyrosine (5uyyA)

Q81P63 prephenate dehydrogenase (EC 1.3.1.12) from Bacillus anthracis (see paper)
Aligns to 29:184 / 378 (41.3%), covers 99.4% of PF02153, 147.5 bits

SCO3221 prephenate dehydrogenase from Streptomyces coelicolor A3(2)
Aligns to 16:161 / 284 (51.4%), covers 99.4% of PF02153, 146.4 bits

• Cytosolic copper is a major modulator of germination, development and secondary metabolism in Streptomyces coelicolor
  González-Quiñónez, Scientific reports 2019
  • “...0.4 SCO2782 Desferrioxamine biosynthesis 0.6 1.4 0.7 2.7 SCO3218 CDA biosynthesis 1.8 1 3.6 0.5 SCO3221 CDA biosynthesis 1.4 1.2 2.7 2.3 SCO5223 Albaflavenone biosynthesis 0.5 0.6 0.7 1.5 SCO5799 Siderophore biosynthesis 0.9 1 0.6 0.5 SCO6766 Hopene biosynthesis 0.6 0.8 1.5 0.6 SCO6768 1.4 1.1...”
• Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
  Alam, BMC genomics 2010
  • “...--0.66 SCO3246 pentadecanoyl-[acyl-carrier protein] synthesis fatty acid biosynthesis --0.63 SCO3595 D-alanine-D-alanine ligase D-alanine metabolism --0.63 SCO3221 prephenate dehydrogenase tryptophan biosynthesis --0.63 SCO6655 GTP cyclohydrolase II riboflavin metabolism --0.61 SCO6787 butyryl-CoA dehydrogenase propanoate metabolism --0.59 SCO2687 GTP cyclohydrolase II riboflavin metabolism --0.52 The most strongly anticorrelated genes...”
  • “...of the calcium dependent antibiotics (CDA) biosynthesis gene cluster (SCO3210-SCO3249) [ 17 ]. SCO3210 and SCO3221 are annotated as 2-dehydro-3-deoxyheptonate aldolase and prephenate dehydrogenase respectively, part of the shikimate pathway (tryptophan biosynthesis). Tryptophan is a precursor for CDA, and there are four anticorrelated genes (SCO3211-3214) which...”

BC2939 Arogenate dehydrogenase from Bacillus cereus ATCC 14579
Aligns to 17:172 / 366 (42.6%), covers 99.4% of PF02153, 145.6 bits

• l-tyrosine modulates biofilm formation of Bacillus cereus ATCC 14579
  Huijboom, Research in microbiology 2023 (PubMed) (secret)

Pfl01_4074 bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase from Pseudomonas fluorescens Pf0-1
Aligns to 17:173 / 735 (21.4%), covers 98.7% of PF02153, 137.2 bits

• Novel aroA of Glyphosate-Tolerant Bacterium Pseudomonas sp. Strain HA-09 Isolated from Roundup-Contaminated Garden Soils in Iran
  Ghaderitabar, Iranian journal of biotechnology 2020
  • “...aroA gene sequences of these selected bacteria (CP003150.1 locus-tag PSF113_1640; CP000076 locus-tag Pfl_4309; CP000094 locus-tag Pfl01_4074; CP002585.1 locus-tag PSEBR_a1552) were aligned using ClustalW. Forward and reverse primers were then designed based on the full length of their aroA gene sequences. PCR was performed with new forward...”

4wjiA / Q92MG1 Crystal structure of cyclohexadienyl dehydrogenase from sinorhizobium meliloti in complex with NADP and tyrosine
Aligns to 19:174 / 293 (53.2%), covers 98.1% of PF02153, 133.9 bits

• Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; tyrosine (4wjiA)

PSF113_1640 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase from Pseudomonas ogarae
Aligns to 17:173 / 735 (21.4%), covers 98.7% of PF02153, 133.7 bits

• Novel aroA of Glyphosate-Tolerant Bacterium Pseudomonas sp. Strain HA-09 Isolated from Roundup-Contaminated Garden Soils in Iran
  Ghaderitabar, Iranian journal of biotechnology 2020
  • “...the nucleotide BLAST in NCBI, the aroA gene sequences of these selected bacteria (CP003150.1 locus-tag PSF113_1640; CP000076 locus-tag Pfl_4309; CP000094 locus-tag Pfl01_4074; CP002585.1 locus-tag PSEBR_a1552) were aligned using ClustalW. Forward and reverse primers were then designed based on the full length of their aroA gene sequences....”

ELZ14_08510, PSEBR_a1552 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase from Pseudomonas brassicacearum subsp. brassicacearum NFM421
Aligns to 17:173 / 735 (21.4%), covers 98.7% of PF02153, 133.3 bits

• Novel aroA of Glyphosate-Tolerant Bacterium Pseudomonas sp. Strain HA-09 Isolated from Roundup-Contaminated Garden Soils in Iran
  Ghaderitabar, Iranian journal of biotechnology 2020
  • “...of these selected bacteria (CP003150.1 locus-tag PSF113_1640; CP000076 locus-tag Pfl_4309; CP000094 locus-tag Pfl01_4074; CP002585.1 locus-tag PSEBR_a1552) were aligned using ClustalW. Forward and reverse primers were then designed based on the full length of their aroA gene sequences. PCR was performed with new forward (5-ATGATCGGTCGCCTGGTGG-3) and reverse...”
• Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics
  Nelkner, Genes 2019
  • “...4.2.3.4; 3-dehydroquinate synthase 5.04 ELZ14_03505 ( aroQ ) EC 4.2.1.10; type II 3-dehydroquinate dehydratase 5.88 ELZ14_08510 ( aroA ) EC 2.5.1.19; 3-phosphoshikimate 1-carboxyvinyltransferase 6.40 ELZ14_11900 (-) n.a.; polyketide cyclase 2.67 ELZ14_25290 ( algD ) n.a.; nucleotide sugar dehydrogenase 9.65 ELZ14_25300 ( alg44 ) n.a.; alginate biosynthesis...”

AM1_2942 prephenate dehydrogenase tyrA from Acaryochloris marina MBIC11017
Aligns to 15:164 / 278 (54.0%), covers 94.8% of PF02153, 132.1 bits

• Comparative Genomic Analysis of the Marine Cyanobacterium Acaryochloris marina MBIC10699 Reveals the Impact of Phycobiliprotein Reacquisition and the Diversity of Acaryochloris Plasmids
  Yamamoto, Microorganisms 2022
  • “...the two strains, and other genes such as petF (AM1_5442) and FNR ( petH ) (AM1_2942) had 99% identity with their counterparts in MB10699. Three isiA genes, AM1_3362, 3364, and 3366 of MB11017 are consecutively located on Chr and form an operon, and the corresponding, AM10699_02480,...”

EF1565 prephenate dehydrogenase from Enterococcus faecalis V583
H7C6X1 Prephenate dehydrogenase from Enterococcus faecalis (strain ATCC 700802 / V583)
Aligns to 17:170 / 364 (42.3%), covers 99.4% of PF02153, 131.6 bits

• Transcriptome, proteome, and metabolite analyses of a lactate dehydrogenase-negative mutant of Enterococcus faecalis V583
  Mehmeti, Applied and environmental microbiology 2011
  • “...were found to be downregulated significantly (EF1562, EF1564, EF1565, and EF1566). Among the three plasmids of the V583 strain, only pTEF2 carries genes that...”
• Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: the Fsr system of Enterococcus faecalis is more than the activator of gelatinase and serine protease
  Bourgogne, Journal of bacteriology 2006
  • “...tryptophan biosynthesis EF1561 EF1562 EF1563 EF1564 EF1565 EF1566 EF1567 EF1568 EF1569 aroE P-2-dehydro-3-deoxyheptonate aldolas aroB aroC Prephenate...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...Cell envelope Cell envelope Cell envelope Cell envelope Cell envelope EF0290 EF1565 EF2586 0.71 0.71 0 0 0 0.87 0 0 0.86 0 0 0 1.05 0 0 EF0849 EF0860 EF0887...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...Q831B4 6-aminohexanoate-cyclic-dimer hydrolase, putative Absent N/A 10 19.1 Q836S5 Prephenate dehydrogenase Absent N/A 7 23.4 H7C6X1 Mga domain-containing protein Absent N/A 6 15.6 Q82ZN7 Protease synthase and sporulation negative regulatory protein pai 1 Absent N/A 2 11.7 Q82ZP9 Transcriptional antiterminator, bglG family Absent N/A 3 7...”

MMP1514 Prephenate dehydrogenase from Methanococcus maripaludis S2
Aligns to 16:161 / 440 (33.2%), covers 100.0% of PF02153, 130.6 bits

• Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
  Hendrickson, Journal of bacteriology 2004
  • “...dehydratase (PheA; Mmp1528) and prephenate dehydrogenase (TyrA; Mmp1514) enzymes (70). In contrast, in many other organisms aroQ (encoding chorismate mutase) is...”

PA14_23310 EPSP synthase/prephenate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 29:185 / 746 (21.0%), covers 98.7% of PF02153, 130.5 bits

• The Peptide Chain Release Factor Methyltransferase PrmC Influences the Pseudomonas aeruginosa PA14 Endo- and Exometabolome
  Depke, Metabolites 2020
  • “...pathway with a significant difference between tn prmC and tn prmC :: prmC was 3-phosphoshikimate-1-carboxyvinyl-transferase (PA14_23310) [ 9 ]. This enzyme acts downstream of shikimate-3-phosphate and thus its downregulation cannot directly explain shikimate and shikimate-3-phosphate depletion. On the mRNA level, the transcripts for phzC1 and phzC2...”

IUJ47_RS10455 prephenate dehydrogenase from Enterococcus faecalis
Aligns to 17:170 / 364 (42.3%), covers 99.4% of PF02153, 130.5 bits

• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...3-dehydroquinate dehydratase ( IUJ47_RS11275 ), a 3-dehydroquinate synthase ( IUJ47_RS10445 ), a prephenate dehydrogenase ( IUJ47_RS10455 ), a 3-phosphoshikimate 1-carboxyvinyltransferase ( IUJ47_RS10460 ), a shikimate kinase ( IUJ47_RS10465 ), a chorismate synthase ( IUJ47_RS10450 ), and a prephenate dehydratase ( IUJ47_RS10470 ). Notably, nine DEGs in...”
  • “...IUJ47_RS10440 0.066 3-deoxy-7-phosphoheptulonate synthase biosynthesis IUJ47_RS11275 0.151 Type I 3-dehydroquinate dehydratase IUJ47_RS10445 0.154 3-dehydroquinate synthase IUJ47_RS10455 0.227 Prephenate dehydrogenase IUJ47_RS10460 0.262 3-phosphoshikimate 1-carboxyvinyltransferase IUJ47_RS10465 0.278 Shikimate kinase IUJ47_RS10450 0.3 Chorismate synthase IUJ47_RS10470 0.304 Prephenate dehydratase Carbon fixation IUJ47_RS00315 0.096 Flavocytochrome c pathways in prokaryotes IUJ47_RS01530 0.109...”

PA3164 still frameshift 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE prephenate dehydrogenase from Pseudomonas aeruginosa PAO1
Aligns to 29:185 / 746 (21.0%), covers 98.7% of PF02153, 129.5 bits

• Reconciling high-throughput gene essentiality data with metabolic network reconstructions
  Blazier, PLoS computational biology 2019
  • “...PA2964 pabC 4-Amino-4-deoxychorismate lyase Cofactors and Vitamins PA2969 plsX Fatty acid biosynthesis protein PlsX Lipid PA3164 Frameshift 3-phosphoshikimate-carboxyvinyltransferase prephenate dehydrogenase Amino Acid PA3296 phoA Alkaline phosphatase Cofactors and Vitamins PA3333 fabH2 3-Oxoacyl-[acyl-carrier-protein] synthase III Lipid PA3633 ygbP 4-Diphosphocytidyl-2-C-methylerythritol synthase Lipid PA3659 dapC Succinyldiaminopimelate transaminase Amino Acid...”
• Pseudomonas aeruginosa serA Gene Is Required for Bacterial Translocation through Caco-2 Cell Monolayers
  Yasuda, PloS one 2017
  • “...1 PA3818 extragenic suppressor protein SuhB suhB NP_252507.1 1 PA0316 D-3-phosphoglycerate dehydrogenase serA NP_249007.1 1 PA3164 still frameshift 3-phosphoshikimate 1-carboxyvinyltransferase aroA AE_004091.2 2 PA3763 phosphoribosylformylglycinamidine synthase purL NP_252452.1 1 PA5015 pyruvate dehydrogenase aceE NP_253702.1 3 PA0413 component of chemotactic signal transduction system chpA NP_249104.1 2 PA3115...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...nadBE, dapB, trpE, aotJ, phhA, phaF, PA0006, PA0400, PA0440, PA0530, PA1339-PA1342, PA1638, PA2084, PA2108, PA2740, PA3164, PA3271, PA3538, PA3589, PA3871, PA4180, PA4672, PA4774, PA4977, PA5093, PA5522 Amino acid and Fatty acid metabolism gcdH Carbohydrate transport and metabolism rpe, eno, ppsA, tpiA, pykF, pgm, chiC, PA3430 Nucleotide...”
• Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment
  Lucchetti-Miganeh, Pathogens (Basel, Switzerland) 2014
  • “...contains a right handed beta helix region that shares some similarity with pectate lyases. The PA3164 gene which in PAO1 strain seems to be a pseudogene due to frameshift is probably encoding a functional 3-phosphoshikimate 1-carboxyvinyltransferase prephenate dehydrogenase in both ST395 strains. Other discrete variations were...”
• A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
  Xu, PloS one 2013
  • “...21 1 1 PA1681( aroC ) 22 1 1 PA0548( tktA ) 23 1 1 PA3164( pseudogene ) 24 1 1 PA0330( rpiA ) 25 1 1 PA5038( aroB ) 26 2 1 PA4031( ppa ) 27 3 1 PA0904( lysC ) 28 4 1 PA2023(...”
• Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions
  Tielen, PloS one 2013
  • “...can be converted to chorismate in two sequential steps via the phenate dehydrogenase encoded by PA3164 and the chorismate dehydrogenase encoded by PA5184. Again, both genes were found to be induced. Subsequently, chorismate is converted by the anthranilate synthase PhnA to anthranilate, the direct precursor of...”
• A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
  Sigurdsson, PloS one 2012
  • “...metabolism UreB (PA4867) ArgB (PA5323) Aromatic amino acids AroC (PA1681), AroK (PA5039) AroB (PA5038), AroA (PA3164), AroE (PA0025) TrpA (PA0035), TrpB (PA0036), PheA (PA3166) Biosynthesis of cofactors, prosthetic groups and carriers, cell wall/ Lipopolysaccharide/ capsule UppS (PA3652) Biotin biosynthesis AccC (PA4848) Branched chain amino acid biosynthesis...”
• Identification of Pseudomonas aeruginosa genes involved in virulence and anaerobic growth
  Filiatrault, Infection and immunity 2006
  • “...norD PA1850 PA2637 PA2638 PA2639 PA2641 PA2642 PA2644 PA2645 PA2646 PA2648 PA2649 PA3164 1 1 2 2 1 4 2 1 1 5 1 1 PA3912 PA3913 PA3918 PA4049 PA5497 1 1 1 1 2...”
  • “...PA2639 PA2641 PA2642 PA2644 PA2645 PA2646 PA2648 PA2649 PA3164 PA3912 PA3913 PA3918 PA4049 PA5497 Gene Descriptionb nirQ norC norB norD Regulatory protein NirQ...”
• More

SXYL_01513 prephenate dehydrogenase from Staphylococcus xylosus
Aligns to 16:172 / 363 (43.3%), covers 99.4% of PF02153, 127.3 bits

• Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress
  Vermassen, Frontiers in microbiology 2014
  • “...0.5 0.4 SXYL_01503 trpE Anthranilate synthase component I 0.5 0.4 SXYL_01128 DAHP synthetase-chorismate mutase 0.5 SXYL_01513 tyrA Prephenate dehydrogenase 3.1 SXYL_00922 pheA Prephenate dehydratase 0.6 SXYL_02022 aroD 3-dehydroquinate dehydratase 1.7 SXYL_01261 aroE Shikimate dehydrogenase 0.6 SXYL_01316 aroK Shikimate kinase 0.5 Urea, arginine, aspartate SXYL_00296 ureA Urease...”

B488_11240 prephenate/arogenate dehydrogenase family protein from Liberibacter crescens BT-1
Aligns to 21:176 / 308 (50.6%), covers 98.1% of PF02153, 126.5 bits

• Identification of the Genes Required for the Culture of Liberibacter crescens, the Closest Cultured Relative of the Liberibacter Plant Pathogens
  Lai, Frontiers in microbiology 2016
  • “...indole-3-glycerol phosphate synthase ( B488_03020 ), 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase II ( B488_07360 ), cyclohexadienyl dehydrogenase ( B488_11240 ), and 3-dehydroquinate synthase ( B488_11320 ), which are involved in phenylalanine, tyrosine, and tryptophan biosynthesis/shikimate pathway. All of these are essential proteins for the growth of L. crescens on...”

T303_04385 prephenate dehydrogenase from Streptococcus thermophilus ASCC 1275
Aligns to 18:175 / 368 (42.9%), covers 99.4% of PF02153, 126.3 bits

• Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275
  Padmanabhan, Frontiers in microbiology 2018
  • “...8 . At 5 h, genes involved in phenyl alanine biosynthesis (T303_04365, T303_04370, T303_04375, T303_04380, T303_04385, T303_04400, T303_04405, T303_04410) were found to be significantly upregulated in M17-G, but these genes were downregulated in M17-S and M17-L. Sucrose and lactose supplemented media had higher number of upregulated...”

PP1770 prephenate dehydrogenase, putative/3-phosphoshikimate 1-carboxyvinyltransferase from Pseudomonas putida KT2440
Aligns to 28:184 / 746 (21.0%), covers 98.7% of PF02153, 125.3 bits

• Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440
  Molina-Henares, Microbial biotechnology 2009
  • “...(indole3glycerolphosphate synthase), TrpA (tryptophan synthase alphasubunit), TrpB (tryptophan synthase subunit beta), PheA (chorismate mutase/prephenate dehydratase), PP1770 or TyrA (prephenate dehydrogenase, putative/3phosphoshikimate 1carboxyvinyltransferase), TyrB1 (aromaticaminoacid aminotransferase) and PhhA (phenylalanine4hydrolase). Figure 2 Detailed biosynthetic pathway for tryptophan biosynthesis. Details are as in the legend for Fig.1 . This...”
  • “...restored by phenylalanine or tyrosine, the miniTn5 was inserted at the 84th codon of ORF PP1770 ( tyrA ). We then tested whether phenylpyruvate or 4hydroxyphenylpyruvate could replace the requirement for phenylalanine or tyrosine in all of the above pheA and tyrA mutants. As expected, all...”
• Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production
  Wierckx, Journal of bacteriology 2008
  • “...PP0074 (aroE-1), PP3002 (aroE-2), PP1769 (pheA), PP2170, PP1770, PP4490 (phhA), PP1972 (tyrB-1), PP3590 (tyrB-2), and PP4621 (hmgA). Expression profiles of...”
• Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
  Barbe, Nucleic acids research 2004
  • “...fusion is also present in P.aeruginosa (PA3164) and P.putida (PP1770) but not in P.syringae in which the ortholog to ACIAD2222 (PSPTO1748) aligns only on the...”

PSPTO1748 prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase family protein from Pseudomonas syringae pv. tomato str. DC3000
Aligns to 26:182 / 535 (29.3%), covers 98.7% of PF02153, 124.7 bits

• Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
  Barbe, Nucleic acids research 2004
  • “...not in P.syringae in which the ortholog to ACIAD2222 (PSPTO1748) aligns only on the C-terminal part of the protein (TyrA). The chorismate mutase activity of...”

Q8DUW0 prephenate dehydrogenase (EC 1.3.1.12) from Streptococcus mutans (see paper)
Aligns to 18:175 / 368 (42.9%), covers 99.4% of PF02153, 120.9 bits

lp_2034 prephenate dehydrogenase from Lactobacillus plantarum WCFS1
lp_2034 prephenate dehydrogenase from Lactiplantibacillus plantarum WCFS1
Aligns to 16:171 / 365 (42.7%), covers 98.1% of PF02153, 120.2 bits

• Molecular Responses of Lactobacilli to Plant Phenolic Compounds: A Comparative Review of the Mechanisms Involved
  López, Antioxidants (Basel, Switzerland) 2021
  • “...asp2 : alkaline shock protein p -CA + Human small intestine passage [ 92 ] lp_2034 lp_2035 lp_2037 tyrA ; prephenate dehydrogenase aroE ; 3-phosphoshikimate 1-carboxyvinyltransferase aroF ; chorismate synthase p -CA p -CA p -CA + + + Human small intestine passage [ 92 ]...”
• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...down-regulated. In addition, other genes related to respiration metabolism such as six genes ( lp_2033, lp_2034, lp_2035, lp_2036, lp_2037, lp_1084 ) involved in the synthesis of chorismate, which is the menaquinone precursor molecule, and two genes involved in the terpenoid backbone biosynthesis which are also required...”
• Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays
  Saulnier, Applied and environmental microbiology 2007
  • “...biosynthesis lp_0256 lp_0529 lp_1084 lp_1085 lp_1169 lp_2033 lp_2034 lp_2035 lp_2037 lp_2551 lp_2553 lp_2556 lp_2557 lp_2559 lp_2830 lp_3493 lp_3494 Cysteine...”

ACIAD2222 bifunctional protein [Includes: putative prephenate or cyclohexadienyl dehydrogenase; 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EPSP synthase) (EPSPS) (AroA)] from Acinetobacter sp. ADP1
Aligns to 21:178 / 748 (21.1%), covers 99.4% of PF02153, 118.3 bits

• Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
  Barbe, Nucleic acids research 2004
  • “...is fused with AroA, the 3phosphoshikimate 1-carboxyvinyltransferase (ACIAD2222). Synteny results show that this interesting fusion is also present in...”
  • “...but not in P.syringae in which the ortholog to ACIAD2222 (PSPTO1748) aligns only on the C-terminal part of the protein (TyrA). The chorismate mutase activity of...”

ABUW_1366 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase from Acinetobacter baumannii
Aligns to 21:178 / 748 (21.1%), covers 98.7% of PF02153, 118.0 bits

• Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
  Scribano, International journal of molecular sciences 2019
  • “...[AQA-ND]. Rs: 0.999 0.826 0.783 SpI score = 15.767 Cell envelope 0.571 A0A090C137 3-phosphoshikimate 1-carboxyvinyltransferase ABUW_1366 aroA Sec SP MLCS: 127 [IVA-EK]. Rs: 0.978 0.077 0.304 SpI score = 1.23597 Amino acid biosynthesis 0.194 V5VBJ4 Aconitate hydratase B ABUW_1593 acnB No SP. Rs: 0.989 0.386 0.091...”

ABBFA_001168 3-phosphoshikimate 1-carboxyvinyltransferase from Acinetobacter baumannii AB307-0294
A0A090C137 3-phosphoshikimate 1-carboxyvinyltransferase from Acinetobacter baumannii
AB57_2630 hypothetical protein from Acinetobacter baumannii AB0057
Aligns to 29:186 / 756 (20.9%), covers 98.7% of PF02153, 117.9 bits

• Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii
  Sutton, Acta crystallographica. Section F, Structural biology communications 2016
  • “...the A. baumannii strain 307-0294 aroA gene (ABBFA_001168) encoding EPSP synthase activity (corresponding to aminoacid residues Ala301-Gln756 of the transcribed...”
• In vivo-validated essential genes identified in Acinetobacter baumannii by using human ascites overlap poorly with essential genes detected on laboratory media
  Umland, mBio 2012
  • “...B7GXH9 ACIB300709 RT-PCR amplicon ABBFA_000787 carA 12 Carbamoyl-phosphate synthase small chain B7GY14 ACIB300758 RT-PCR amplicon ABBFA_001168 aroA 68 3-Phosphoshikimate 1-carboxyvinyltransferase B7GZU8 ACIB301129 RT-PCR amplicon ABBFA_001801 aroC 170 Chorismate synthase B7H3A6 ACIB301758 Genome organization ABBFA_001929 ostA 177 Organic solvent tolerance protein OstA B7H3N4 ACIB301886 RT-PCR amplicon ABBFA_002478...”
• Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
  Scribano, International journal of molecular sciences 2019
  • “...SP MLCS: 128 [AQA-ND]. Rs: 0.999 0.826 0.783 SpI score = 15.767 Cell envelope 0.571 A0A090C137 3-phosphoshikimate 1-carboxyvinyltransferase ABUW_1366 aroA Sec SP MLCS: 127 [IVA-EK]. Rs: 0.978 0.077 0.304 SpI score = 1.23597 Amino acid biosynthesis 0.194 V5VBJ4 Aconitate hydratase B ABUW_1593 acnB No SP. Rs:...”
• Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England
  Halachev, Genome medicine 2014
  • “...G A1S_2384 14 1600195 Bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase Gly Ser G GT A GT AB57_2630 15 3658279 Non-coding Intergenic 88 bp from start of serB 16 2448345 Plasmid replicase protein His Tyr C AC T AC ACINIS123_A0022 17 706757 Putative transport protein Ala Thr G...”

Tsac_1619 prephenate dehydrogenase/arogenate dehydrogenase family protein from Thermoanaerobacterium saccharolyticum JW/SL-YS485
Aligns to 17:171 / 281 (55.2%), covers 98.1% of PF02153, 117.5 bits

• The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum
  Zheng, PloS one 2018
  • “...Regulatory protein MarR Misc CTGAAATAATCATTTCAA -86 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...”

CC2224 cyclohexadienyl dehydrogenase from Caulobacter crescentus CB15
Aligns to 23:181 / 312 (51.0%), covers 98.1% of PF02153, 115.2 bits

• Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria
  Chen, Journal of bacteriology 2003
  • “...CC0655 CC0716 CC1135 CC2838 CC2867 CC3011 CC3071 CC3071 CC0562 CC0710 CC1019 CC2224 CC2833 CC3117 CC3367 51 18 54 178 54 1 71 14 126 1 89 21 23 35 5 1 Conserved...”

A1S_2276 hypothetical protein from Acinetobacter baumannii ATCC 17978
Aligns to 2:144 / 714 (20.0%), covers 87.7% of PF02153, 114.8 bits

• Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain
  Kentache, Molecular & cellular proteomics : MCP 2017
  • “...was predicted to interact with the accumulated AroA (A1S_2276, supplemental Table S2, supplemental Fig. S3). AroA (also designated as EPSP synthase) is involved...”

SA1197 prephenate dehydrogenase from Staphylococcus aureus subsp. aureus N315
Aligns to 16:172 / 363 (43.3%), covers 99.4% of PF02153, 112.4 bits

• Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New York City
  Pardos, Journal of clinical microbiology 2015
  • “...SAUSA300_2167 SAR0129 SAR0994 SAR2012 SAR2622 SA0131 SA0904 SA1197 SA1491 SA1706 deoD tyrA hemL Purine metabolism Antibiotic resistance? Shikimate pathway...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...membrane biogenesis sa_c4317s3671_at 2.1 2.5 2.5 ddl SA2074 D-alanylalanine synthetase sa_c1100s881_a_at 4.7 2.5 5 divlB SA1197 cell division protein sa_c8601s7554_a_at 5.4 2.5 2.5 dltA SA0935 D-alanine--D-alanyl protein ligase sa_c6835s5969_a_at * 3.5 2.5 2.5 gidB SA2736 glucose-inhibited division protein B sa_c1848s1571_a_at 3.4 2.5 2.5 femA SA1410 femA...”
• Isolation and characterization of biofilm formation-defective mutants of Staphylococcus aureus
  Tu, Infection and immunity 2007
  • “...SA2462 SA1909 SA2288 SA2354 SA2364 SA1885 SA1885 SA1142 SA1197 SA1323 SA1059 SA1064 SA1093 SA1098 SA1118 SA0909 SA0909 SA0909 SA0940 SA0641 SA0701 SA0874 SA0461...”
• Large-scale identification of genes required for full virulence of Staphylococcus aureus
  Benton, Journal of bacteriology 2004
  • “...trpF 366 230 383 211 263 132 367 53 SA1197 SA1228 SA1230 SA1203 IVT626 IVT627 IVT636 IVT638 aspB (B. circulans) pycA (B. halodurans) pyrC (B. halodurans) asd...”

MCR_0888 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase from Moraxella catarrhalis BBH18
Aligns to 36:190 / 767 (20.2%), covers 91.6% of PF02153, 111.7 bits

• Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells
  de, PloS one 2013
  • “...BBH18. Tn-seq log 2 adherent / non-adherent Locus tag Gene Product Functional class A549 Detroit MCR_0888 aroA 3-phosphoshikimate 1-carboxyvinyltransferase Amino acid biosynthesis -2.7 -1.8 MCR_1095 lgt1 glucosyltransferase Lgt1 Cell envelope -3.3 -2.6 MCR_1483 - putative lipoprotein Cell envelope -2.3 -1.7 MCR_1742 - outer membrane protein Cell...”

SAR1378 prephenate dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
Aligns to 16:172 / 363 (43.3%), covers 99.4% of PF02153, 110.8 bits

• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...3.52E-02 SAR2201 glyA serine hydroxymethyltransferase 3.55 8.43E-03 SAR2201 glyA serine hydroxymethyltransferase 2.15 3.74E-03 Carotenoid Biosynthesis SAR1378 prephenate dehydrogenase 2.37 8.08E-03 Miscellaneous SAR0218 putative pyruvate formate-lyase activating enzyme 2.60 3.46E-02 SAR0403 putative DNA binding protein 2.72 3.48E-02 SAR2007 putative oxygenase/mitric oxide synthase 2.04 7.13E-03 SAR2007 putative nitric...”

SAUSA300_1260 prephenate dehydrogenase from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1277 prephenate dehydrogenase from Staphylococcus aureus subsp. aureus str. Newman
SACOL1401 prephenate dehydrogenase from Staphylococcus aureus subsp. aureus COL
Aligns to 16:172 / 363 (43.3%), covers 99.4% of PF02153, 110.3 bits

• Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New York City
  Pardos, Journal of clinical microbiology 2015
  • “...Nonsynonymous Nonsynonymous SAUSA300_0138 SAUSA300_0954 SAUSA300_1260 SAUSA300_1614 SAUSA300_1871 SAUSA300_2158 SAUSA300_2167 SAR0129 SAR0994 SAR2012 SAR2622...”
• CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
  Pohl, Journal of bacteriology 2009
  • “...NWMN_0883 NWMN_1239 NWMN_1240 NWMN_1241 NWMN_1245 NWMN_1277 NWMN_1279 NWMN_1280 NWMN_1281 NWMN_1282 NWMN_1283 NWMN_1284 NWMN_1304 NWMN_1305 NWMN_1306 NWMN_1307...”
• Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
  Menzel, Antimicrobial agents and chemotherapy 2011
  • “...SACOL1304 SACOL1374 SACOL1375 SACOL1381 SACOL1382 SACOL1400 SACOL1401 SACOL1986 SACOL1987 SACOL2162 Transport- and cell wall-related genes Upregulated ORF...”
  • “...SACOL0823 SACOL0824 SACOL1304 SACOL1374 SACOL1382 SACOL1381 SACOL1400 SACOL1401 SACOL2089 SACOL2727 Gene VOL. 55, 2011 MT02 MODE OF ACTION AGAINST S. AUREUS...”

Cj0130 putative prephenate dehydrogenase from Campylobacter jejuni subsp. jejuni NCTC 11168
Aligns to 15:165 / 275 (54.9%), covers 98.7% of PF02153, 109.5 bits

• Active Packaging of Immobilized Zinc Oxide Nanoparticles Controls Campylobacter jejuni in Raw Chicken Meat
  Hakeem, Applied and environmental microbiology 2020 (secret)
• Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni
  Hoppe, PloS one 2013
  • “...5 cj0920c, 6 cj1380, 7 cj1381, 8 cj0669, 9 cj1624, 10 cj1320, 11 cj1486, 12 cj0130, 13 cj1366, 14 cj0016, 15 cj1575, 16 1576, 17 cj1729, 18 cj0571, 19 cj0926, 20 cj0927, 21 cj0623 and 22 cj1138. The pictures of the two gels as well as...”
  • “...length [aa] Size [kDa] Mean Q s.d. [n=25] Cj0016 [P0C634] 7-cyano-7-deazaguanine synthase 224 25.1 0.640.18 Cj0130 [Q0PC07] prephenate dehydrogenase 275 30.9 0.700.19 Cj0476 [Q9PI33] 50S ribosomal Protein L10 159 17.7 0.400.13 Cj0571 [Q0PAU6] Putative transcriptional regulator 290 34.3 0.520.21 Cj0623 [Q0PAP4] Hydrogenase isoenzymes formation protein 247...”

SAOUHSC_01364 prephenate dehydrogenase, putative from Staphylococcus aureus subsp. aureus NCTC 8325
Aligns to 16:172 / 363 (43.3%), covers 99.4% of PF02153, 108.1 bits

• Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin
  Rong, Frontiers in microbiology 2019
  • “...Tryptophanyl-tRNA synthetase 965494 SAOUHSC_00994 atl C/T K < - > K 43.90% Bifunctional autolysin 1307807 SAOUHSC_01364 tyrA G/T L < - > M 34.15% Prephenate dehydrogenase 1394043 SAOUHSC_01447 ebh G/A N < - > N 80.49% Extracellular matrix-binding protein 1612045 SAOUHSC_01705 C/T A < - >...”

NGO1515 putative oxidoreductase from Neisseria gonorrhoeae FA 1090
Aligns to 19:176 / 290 (54.5%), covers 97.4% of PF02153, 107.5 bits

• RpoH mediates the expression of some, but not all, genes induced in Neisseria gonorrhoeae adherent to epithelial cells
  Du, Infection and immunity 2006
  • “...NGO0633 NGO1988 NGO0234 NGO0721 NGO1366 NGO1291 NGO0199 NGO1515 NGO1493 NGO1439 NGO0989 NGO1831 NGO1841 NGO1668 NGO0637 NGO1773 NGO2180 NGO0962 NGO5041 NGO1587...”

DMB42_RS42860 prephenate dehydrogenase from Nonomuraea sp. WAC 01424
Aligns to 16:162 / 364 (40.4%), covers 98.7% of PF02153, 106.8 bits

• Genomic-Led Discovery of a Novel Glycopeptide Antibiotic by Nonomuraea coxensis DSM 45129
  Yushchuk, ACS chemical biology 2021
  • “...DMB42_RS42865 (6) (78%) VanY-carboxypeptidase noc28 dbv6 (95.9%) DMB42_RS42855 (8) (92%) response regulator noc29 dbv5 (92.8%) DMB42_RS42860 (7) (85%) prephenate dehydrogenase (Pdh) noc30 a a putative transposase nocRII dbv4 (94.4%) DMB42_RS42700 (38) (85%) StrR-like transcriptional regulator nocRI dbv3 (86.3%) DMB42_RS42695 (39) (70%) LuxR-like transcriptional regulator a Homologue...”

BCAL2953 putative prephenate dehydrogenase from Burkholderia cenocepacia J2315
Aligns to 25:188 / 312 (52.6%), covers 98.7% of PF02153, 104.9 bits

• Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS
  Wong, Frontiers in microbiology 2016
  • “...are genes involved in the conversion of chorismate to phenylalanine and tyrosine ( pheA , BCAL2953, and BCAL3004) as well as tryptophan ( trpA, trpC, trpD , and trpF ). We suspect that trp mutants may be tryptophan auxotrophs and are unable to grow in a...”
  • “...hisE, BCAL1874 Lysine biosynthesis dapF, BCAS0211 Phenylalanine, tyrosine, and tryptophan biosynthesis phhA, aroK, trpC, trpD, BCAL2953, pheA, BCAL3004, aroE, trpF, trpA, BCAS0366 Valine, leucine, and isoleucine biosynthesis ilvA, ilvI, leuD1, leuB, BCAS0025 FIGURE 6 Schematic diagram of KEGG-derived phenylalanine, tyrosine and tryptophan biosynthesis pathways. Boxes indicate...”

AORI_1476 prephenate dehydrogenase from Amycolatopsis keratiniphila
Aligns to 18:164 / 281 (52.3%), covers 99.4% of PF02153, 104.7 bits

• Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis
  Xu, BMC genomics 2014
  • “...D-alanyl-D-alanine dipeptidase - - AORI_1474 Hypothetical protein - - AORI_1475 vtr Regulator protein lcl|Y16952.3_cdsid_CAG25754.1 83.33 AORI_1476 pdh Prephenate dehydrogenase lcl|Y16952.3_cdsid_CAG25755.1 84.12 AORI_1477 ATP-binding cassette, subfamily B lcl|AJ223999.1_cdsid_CAA11793.1 88.89 AORI_1478 vcmA Non-ribosomal peptide synthetase lcl|AL078635.1_cdsid_CAB45052.1 81.31 AORI_1479 vcmB Non-ribosomal peptide synthetase lcl|AJ223999.1_cdsid_CAA11795.1 82.34 AORI_1480 vcmC Non-ribosomal peptide...”
  • “...of three non-protein amino acids were identified in the genome, i.e. , AORI_1492-AORI_1494 for L-Ht, AORI_1476, AORI_1491, AORI_1495-AORI_1496 for L-Hpg, and AORI_1502-AORI_1505 for L-Dpg. Figure 5 Metabolic pathway of vancomycin biosynthesis. Three steps are involved in the biosynthesis of vancomycin, and the related functional genes in...”

3b1fA / Q8DUW0 Crystal structure of prephenate dehydrogenase from streptococcus mutans (see paper)
Aligns to 21:174 / 286 (53.8%), covers 99.4% of PF02153, 104.6 bits

• Ligand: nicotinamide-adenine-dinucleotide (3b1fA)

Echvi_0125 prephenate dehydrogenase from Echinicola vietnamensis DSM 17526
Aligns to 16:167 / 282 (53.9%), covers 96.1% of PF02153, 104.1 bits

• GapMind: Automated Annotation of Amino Acid Biosynthesis
  Price, mSystems 2020
  • “...some defined media ( Fig.4B ). This bacterium also has a prephenate or arogenate dehydrogenase (Echvi_0125), which is important for growth in some defined media but not others ( Fig.4B ). It is difficult to understand why PAH is important for fitness in defined media unless...”

SCO1761 prephenate dehydrogenase from Streptomyces coelicolor A3(2)
Aligns to 16:163 / 361 (41.0%), covers 97.4% of PF02153, 102.4 bits

• Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
  Vaňková, Frontiers in microbiology 2022
  • “...are schematically shown for each sRNA. For as1791 and as1761 RNAs, fragments of sco1791 and sco1761 transcripts detected by Northern blotting are also shown in (A,B) . For scr1506, 5 ends was detected by 5 RACE (G,H) . Linguistic Search for Ms1 RNAs in Actinobacteria The...”
  • “...the opposite strand, a fragment of the sco1791 (1260 nt) mRNA. Str3 localizes to the sco1761 gene and similarly to Str1, Str3, is also an antisense RNA (130 nt, AS1711, Figure 1B ). Furthermore, we also detected two short transcripts (110 and 80 nt, respectively) from...”

J9XQS6 prephenate dehydrogenase (EC 1.3.1.12) from uncultured bacterium (see paper)
Aligns to 30:156 / 287 (44.3%), covers 74.0% of PF02153, 100.7 bits

CAC0893 Prephenate dehydrogenase from Clostridium acetobutylicum ATCC 824
Aligns to 22:178 / 286 (54.9%), covers 98.1% of PF02153, 99.4 bits

• Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
  Senger, Biotechnology and bioengineering 2008
  • “...CAC0939, CAC0938, CAC1369, CAC2727, CAC0937. List 10: CAC3162/CAC3163, CAC3161, CAC3159, CAC3160, CAC3157/CAC3158. List 11: CAC1234, CAC0893, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832. List 12: CAC1234, CAC0217, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832. List 13 (also shown in Fig. 5 ): CAC2391/CAC3020, CAC2388, CAC2389, CAC2390. Figure 5 Proposed pathway of l -glutamate biosynthesis in C. acetobutylicum given:...”

XNR_5061 prephenate dehydrogenase from Streptomyces albidoflavus
Aligns to 16:163 / 361 (41.0%), covers 98.1% of PF02153, 93.7 bits

• Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis
  Kittikunapong, Metabolites 2021
  • “...in regard to their associated pathways such as the previously mentioned overexpression of prephenate dehydrogenase (XNR_5061) to convert chorismate to L-tyrosine, a precursor leading to naringenin. With regards to another instance, in order to augment the availability of the L-paulomycose moiety on the basic paulomycin structure,...”

novF / Q9L9G2 prephenate dehydrogenase (EC 1.3.1.12) from Streptomyces niveus (see paper)
Aligns to 16:163 / 362 (40.9%), covers 97.4% of PF02153, 89.2 bits

A0A101IGG2 prephenate dehydrogenase (NADP+) (EC 1.3.1.13) from Methanothrix harundinacea (see paper)
Aligns to 26:168 / 310 (46.1%), covers 99.4% of PF02153, 87.7 bits

ACPL_8142 prephenate dehydrogenase/arogenate dehydrogenase family protein from Actinoplanes sp. SE50/110
Aligns to 15:162 / 313 (47.3%), covers 98.7% of PF02153, 84.4 bits

• Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production
  Wang, Frontiers in microbiology 2015
  • “...unique genes participated in amino acid synthesis directly or by supplying precursors. For example, gene ACPL_8142 participated in L-tyrosine synthesis, and genes ACPL_8304 and ACPL_887 participated in L-phenylalanine synthesis. In addition, genes ACPL_1328 and ACPL_1861 belong to the pentose phosphate pathway, but there was no flux...”

BBMN68_274 prephenate dehydrogenase/arogenate dehydrogenase family protein from Bifidobacterium longum subsp. longum BBMN68
Aligns to 17:171 / 355 (43.7%), covers 99.4% of PF02153, 81.8 bits

• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...imidazoleglycerol-phosphate dehydratase [EC:4.2.1.19] BBMN68_184 53.57 128 2.39 * E COG0118 hisH K02501, glutamine amidotransferase [EC:2.4.2.-] BBMN68_274 21.46 45.68 2.13 * E COG0287 pdhA K04517, prephenate dehydrogenase [EC:1.3.1.12] BBMN68_273 28.27 61.79 2.19 * E COG0077 pheA K14170, chorismate mutase/prephenate dehydratase [EC:5.4.99.5 4.2.1.51] BBMN68_312 52.76 202.97 3.85 *...”

MM1275 Prephenate dehydrogenase from Methanosarcina mazei Goe1
Aligns to 25:167 / 472 (30.3%), covers 98.7% of PF02153, 81.7 bits

• Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
  Krätzer, Journal of bacteriology 2009
  • “...MM1073 MM1074 MM1075 MM1112 MM1271 MM1272 MM1273 MM1274 MM1275 MM1647 MM1648 MM1761 MM1762 MM1977 MM2882 MM2933 MM3197 MM0011 MM0093 MM0496 MM0583 MM0671 MM0772...”

BMA0430 prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase from Burkholderia mallei ATCC 23344
Aligns to 1:108 / 673 (16.0%), covers 66.9% of PF02153, 75.1 bits

• Comparative genomics and an insect model rapidly identify novel virulence genes of Burkholderia mallei
  Schell, Journal of bacteriology 2008
  • “...mallei more likely resides in the BMA0430 protein, annotated as a bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyl transferase enzyme...”

TyrAAT1 / Q944B6 arogenate dehydrogenase (EC 1.3.1.78) from Arabidopsis thaliana (see paper)
TYRA1_ARATH / Q944B6 Arogenate dehydrogenase 1, chloroplastic; TYRATC; TyrAAT1; EC 1.3.1.78 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
Q944B6 arogenate dehydrogenase (NADP+) (EC 1.3.1.78) from Arabidopsis thaliana (see 2 papers)
AT5G34930 arogenate dehydrogenase from Arabidopsis thaliana
2 alignments in 67:528 / 640 (41.7%), covering up to 72.1% of PF02153, 74.3 bits

• function: Involved in the biosynthesis of tyrosine. Has no prephenate dehydrogenase activity.
  catalytic activity: L-arogenate + NADP(+) = CO2 + L-tyrosine + NADPH (RHEA:15417)
• An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana
  Sanjaya, Plants (Basel, Switzerland) 2021
  • “...AtMBD2 (At5g35330) and AtMBD12 (At5g35338). Five genes encoded known chloroplast-targeted proteins, namely TYRAAt1 / TyrA1 (At5g34930), encoding arogenate dehydrogenase [ 53 ]; AtCYP28 (At5g35100), encoding thylakoid lumen-localized cyclophilin [ 54 ]; AMK5 (At5g35170), encoding an envelope- and thylakoid-associated adenylate kinase protein [ 55 ]; PTM (At5g35210),...”
  • “...(1.0) ECA1 gametogenesis family protein AT5G34908 Signal peptide (1.0) a ECA1 gametogenesis related family protein AT5G34930 Chloroplast stroma TYRAAt1/TyrA1; arogenate dehydrogenase [ 53 , 60 ] AT5G34940 Signal peptide (1.0) ATGUS3/GUS3; glucuronidase 3 [ 61 ] AT5G35067 Other (1.0) hypothetical protein AT5G35069 Other (0.6), Mitochondrion (0.3)...”
• Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana
  de, The Plant journal : for cell and molecular biology 2019 (PubMed) (secret)
• Genetic dissection of vitamin E biosynthesis in tomato
  Almeida, Journal of experimental botany 2011
  • “...(TyrA, EC 1.3.1.78) At1g15710 ( 358) Chloroplast U567861 (1) Chloroplast SL2.31sc03731 C2_At5g34850 7 (0.4 cM) At5g34930 (640) Chloroplast ( Rippert et al., 2009 ) U570951 (2) Chloroplast SL2.31sc03771 T1212 9 (48 cM) Tyrosine aminotransferase (TAT, EC 2.6.1.5) At5g53970 (414) nd U577103(1) nd SL2.31sc05925 C2_At1g53000 10 (7.5...”
• The Biosynthetic Pathways for Shikimate and Aromatic Amino Acids in Arabidopsis thaliana
  Tzin, The arabidopsis book 2010
  • “...two genes encoding TyrA enzymes were identified: TyrA1 (At5g34930) and TyrA2 (At1g15710) (Rippert and Matringe, 2002b, a; Rippert et al., 2009). A second...”
  • “...3 3 PAT TyrA1, ADS1 TyrA2, ADS2 At5g34930 At1g15710 2.6.1.79 1.3.1.43 1.3.1.43 Prephenate Aminotransferase Arogenate Dehydrogenase Arogenate Dehydrogenase PDH...”
• Coordinations between gene modules control the operation of plant amino acid metabolic networks
  Less, BMC systems biology 2009
  • “...mutase 32 CM1 AT3G29200 257746_at CM2 AT5G10870 250407_at CM3 AT1G69370 260360_at arogenate dehydrogenase 33 AAT1 AT5G34930 255859_at AAT2 AT1G15710 259486_at tyrosine aminotransferase 34 TAT3 d AT2G24850 263539_at TAT AT5G53970 248207_at prephenate dehydratase 35 PD1 AT2G27820 266257_at PD AT1G08250 261758_at PD AT1G11790 262825_at PD AT3G07630 259254_at PD...”
• Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling
  Stracke, The Plant journal : for cell and molecular biology 2007
  • “...flavanone 3-hydroxylase (TT6) 253195_at At4g35420 94.7 P 32.9 P 2.9 Dihydroflavonol 4-reductase family protein 252215_at At5g34930 21.3 P 7.7 P 2.8 Arogenate dehydrogenase 266851_at At2g26820 24.3 P 8.8 A 2.8 Avirulence-responsive family protein 261773_at At1g76250 28.5 P 10.4 A 2.7 Expressed protein 258241_at At3g27650 52.9 P...”
  • “...noteworthy putative PFG target genes are At1g53270 , encoding an ABC transporter family protein, and At5g34930 , encoding an arogenate dehydrogenase. The ABC transporter might be able to facilitate the transport of flavonols across the tonoplast. In the study of Tohge et al. (2005) two transporters...”
• Dynamic evolution at pericentromeres
  Hall, Genome research 2006
  • “...F-CTTCTTGATTTCCTCCGTCTCC, R-CCTCT TTGGTACGCTGTTAGGC; and At5g34930, F-TCTTCTCCTT CAATACTTACCT, R-TTCCAAACCCGACGACGATACCAAT. BACs identified with the peri-CEN5...”

NP_001331736 arogenate dehydrogenase from Arabidopsis thaliana
2 alignments in 89:550 / 662 (40.3%), covering up to 72.1% of PF02153, 74.1 bits

• Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana.
  de, The Plant journal : for cell and molecular biology 2019 (PubMed)
  • GeneRIF: These results revealed that TyrA1 and TyrA2 have distinct and overlapping functions in flower and leaf development, respectively, and that imbalance of tyrosine, caused by altered TyrA activity and regulation, impacts growth and development of Arabidopsis. [TyrA1]

all0418 chorismate mutase/prephenate dehydrogenase from Nostoc sp. PCC 7120
Aligns to 40:161 / 281 (43.4%), covers 78.6% of PF02153, 70.0 bits

• Molecular genetics and genomic analysis of scytonemin biosynthesis in Nostoc punctiforme ATCC 29133
  Soule, Journal of bacteriology 2007
  • “...(79) all0414, trpE (81) all0417, aroB (71) None None all0418, tyrA (72) all0422 (55) all0423 (47) all0424 (71) all0426, leuDH (79) all0425 (61) all0427 (74)...”

Ddes_0334 Prephenate dehydrogenase from Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774
Aligns to 53:180 / 292 (43.8%), covers 72.7% of PF02153, 69.3 bits

• Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide
  Cadby, Scientific reports 2017
  • “...Glycosyl transferase family 9 1.75 0.00129 Ddes_0333 Major facilitator family membrane transport protein 1.79 0.00336 Ddes_0334 Prephenate dehydrogenase 1.85 0.00164 Ddes_0335 3-phosphoshikimate 1-carboxyvinyltransferase 2.29 4.16e-5 Ddes_0336 Chorismate mutase 2.47 3.53e-6 Ddes_0337 3-dehydroquinate synthase 1.87 0.00292 Ddes_0525 4Fe-4S ferredoxin family 1.94 0.00030 Ddes_0526 Pyridoxamine 5-phosphate oxidase-related FMN-binding...”
  • “...0.00303 H Ddes_0289 SAM-binding methylase 2.41 1.59E-06 R Ddes_0290 alaS Alanyl-tRNA synthetase 1.49 0.0132 J Ddes_0334 Prephenate dehydrogenase 1.52 0.0206 E Ddes_0335 3-phosphoshikimate 1-carboxyvinyltransferase 1.35 0.0377 E Ddes_0336 Chorismate mutase 1.56 0.00875 E Ddes_0337 3-dehydroquinate synthase 1.45 0.0119 E Ddes_0338 Fructose-bisphosphate aldolase 1.34 0.0334 G Ddes_0339...”

DIP0245 Putative prephenate dehydrogenase from Corynebacterium diphtheriae NCTC 13129
Aligns to 22:179 / 336 (47.0%), covers 94.8% of PF02153, 69.2 bits

• Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology
  Guimarães, BMC genomics 2015
  • “...DIP0247 tadA tRNA-specific adenosine deaminase cur_1934 CU7111_1857 Cp1002_0131 DIP0246 - Hypothtical protein cur_1935 CU7111_1858 Cp1002_0130 DIP0245 tyrA Prephenate dehydrogenase cur_1939 CU7111_1861 Cp1002_0120 DIP0179 - Putative dicarboxylate uptake system The genomes of C. urealyticum strains DSM 7109 and DSM 7111, C. pseudotuberculosis 1002, and C. diphtheriae NCTC...”

Cp1002_0130 prephenate dehydrogenase from Corynebacterium pseudotuberculosis 1002
Aligns to 22:180 / 337 (47.2%), covers 92.2% of PF02153, 69.0 bits

• Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology
  Guimarães, BMC genomics 2015
  • “...Cp1002_0132 DIP0247 tadA tRNA-specific adenosine deaminase cur_1934 CU7111_1857 Cp1002_0131 DIP0246 - Hypothtical protein cur_1935 CU7111_1858 Cp1002_0130 DIP0245 tyrA Prephenate dehydrogenase cur_1939 CU7111_1861 Cp1002_0120 DIP0179 - Putative dicarboxylate uptake system The genomes of C. urealyticum strains DSM 7109 and DSM 7111, C. pseudotuberculosis 1002, and C. diphtheriae...”

Ga0059261_2298 prephenate and/or arogenate dehydrogenase (EC 1.3.1.13) from Sphingomonas koreensis DSMZ 15582
Aligns to 16:149 / 249 (53.8%), covers 83.8% of PF02153, 68.8 bits

• mutant phenotype: Important for fitness in defined media. 31% identical to arogenate dehydrogenase from Arabidopsis (Q9LMR3). The substrate could be prephenate (dehydrogenation first) or arogenate (transamination followed by dehydrogenation).

Rv3754 prephenate dehydrogenase from Mycobacterium tuberculosis H37Rv
Aligns to 2:153 / 301 (50.5%), covers 92.2% of PF02153, 68.4 bits

• Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
  Fang, BMC systems biology 2010
  • “...Let the conversion to CTP and glutamate from UTP and glutamine be reversible 23 28 Rv3754 tyrA FP Amino acid metabolism Functions as prephenate dehydrogenase (1) Allowed the uptake of tyrosine 24 29 Rv3042c serB2 FN Amino acid metabolism Remove a phosphate group from phosphoserine to...”
• The two chorismate mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: biochemical analysis and limited regulation of promoter activity by aromatic amino acids
  Schneider, Journal of bacteriology 2008
  • “...were promptly identified: they correspond to ORFs Rv3838c and Rv3754, respectively, and do not possess any associated CM domain (13). Thus, at least one CM...”
  • “...our results, the predicted PheA (Rv3838c) and TyrA (Rv3754) proteins from M. tuberculosis have been recently purified (42, 55), and no associated CM activity...”

TYRA_MYCTU / O69721 Prephenate dehydrogenase; PDH; EC 1.3.1.12 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
Aligns to 22:175 / 323 (47.7%), covers 92.2% of PF02153, 68.3 bits

• function: Catalyzes the NAD(+)-dependent conversion of prephenate to p- hydroxyphenylpyruvate, with the elimination of carbon dioxide. Is a key regulatory enzyme in tyrosine biosynthesis. Displays no chorismate mutase (CM) activity, in contrast to TyrA from E.coli and some other bacteria, that are bifunctional and possess a CM domain.
  catalytic activity: NAD(+) + prephenate = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADH (RHEA:13869)

Npun_R1269 prephenate dehydrogenase from Nostoc punctiforme
Aligns to 108:221 / 359 (31.8%), covers 73.4% of PF02153, 63.5 bits

• Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy
  Gao, Marine drugs 2021
  • “...substrates [ 60 , 66 , 67 ]. Except Npun_R1268 (encoding a DSBA oxidoreductase) and Npun_R1269 (encoding a prephenate dehydrogenase), other genes in Module II have at least two homologous genes. The redundancy of the aromatic amino acid biosynthetic genes should be beneficial for providing more...”
• Mutational Studies of Putative Biosynthetic Genes for the Cyanobacterial Sunscreen Scytonemin in Nostoc punctiforme ATCC 29133
  Ferreira, Frontiers in microbiology 2016
  • “...oxidative deamination of L -tryptophan to provide indole-3 pyruvic acid ( Figure 1A ). TyrA (Npun_R1269), a putative prephenate dehydrogenase, is thought to be responsible for the oxidation of prephenate to p -hydroxyphenylpyruvic acid ( Gao and Garcia-Pichel, 2011 ). Subsequently ScyA (Npun_R1276), a thiamin-dependent enzyme,...”

COO91_00780 bifunctional chorismate mutase/prephenate dehydrogenase from Nostoc flagelliforme CCNUN1
Aligns to 107:222 / 362 (32.0%), covers 73.4% of PF02153, 63.4 bits

• Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy
  Gao, Marine drugs 2021
  • “...dense exopolysaccharide matrix provides an ideal environment for accommodating scytonemin. In addition to COO91_00781 , COO91_00780 , and COO91_00775 (the homologous genes of Npun_R1268 , Npun_R 1269 , and Npun_R1274 , respectively), other scytonemin-biosynthetic genes all have paralogous genes in the N. flagelliforme genome. Its genetic...”

E1R5M5 arogenate dehydrogenase [NAD(P)+] (EC 1.3.1.79) from Sediminispirochaeta smaragdinae (see paper)
Aligns to 18:156 / 251 (55.4%), covers 98.7% of PF02153, 62.0 bits

DVU0464 prephenate and/or arogenate dehydrogenase from Desulfovibrio vulgaris Hildenborough JW710
DVU0464 prephenate dehydrogenase from Desulfovibrio vulgaris Hildenborough
Aligns to 20:141 / 255 (47.8%), covers 44.2% of PF02153, 62.0 bits

• mutant phenotype: # important for fitness in defined media, and rescued by added tyrosine. This is the second or third step in tyrosine synthesis from chorismate via prephenate; it is not clear if dehydrogenation or transamination occurs first.
• Response of Desulfovibrio vulgaris to alkaline stress
  Stolyar, Journal of bacteriology 2007
  • “...DVU0285 DVU0286 DVU0339 DVU0460 DVU0461 DVU0462 DVU0463 DVU0464 DVU0465 DVU0466 DVU0467 DVU0468 DVU0469 DVU0470 DVU0471 DVU0663 DVU0890 DVU1466 DVU1585 DVU1609...”

CU7111_1858 prephenate dehydrogenase from Corynebacterium urealyticum DSM 7111
Aligns to 39:182 / 336 (42.9%), covers 57.8% of PF02153, 58.2 bits

• Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology
  Guimarães, BMC genomics 2015
  • “...CU7111_1856 Cp1002_0132 DIP0247 tadA tRNA-specific adenosine deaminase cur_1934 CU7111_1857 Cp1002_0131 DIP0246 - Hypothtical protein cur_1935 CU7111_1858 Cp1002_0130 DIP0245 tyrA Prephenate dehydrogenase cur_1939 CU7111_1861 Cp1002_0120 DIP0179 - Putative dicarboxylate uptake system The genomes of C. urealyticum strains DSM 7109 and DSM 7111, C. pseudotuberculosis 1002, and C....”

cur_1935 hypothetical protein from Corynebacterium urealyticum DSM 7109
Aligns to 52:195 / 349 (41.3%), covers 57.8% of PF02153, 58.1 bits

• Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology
  Guimarães, BMC genomics 2015
  • “...cur_1933 CU7111_1856 Cp1002_0132 DIP0247 tadA tRNA-specific adenosine deaminase cur_1934 CU7111_1857 Cp1002_0131 DIP0246 - Hypothtical protein cur_1935 CU7111_1858 Cp1002_0130 DIP0245 tyrA Prephenate dehydrogenase cur_1939 CU7111_1861 Cp1002_0120 DIP0179 - Putative dicarboxylate uptake system The genomes of C. urealyticum strains DSM 7109 and DSM 7111, C. pseudotuberculosis 1002, and...”

TM0344 prephenate dehydrogenase from Thermotoga maritima MSB8
Aligns to 15:153 / 253 (54.9%), covers 97.4% of PF02153, 55.4 bits

• Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima
  Frock, Applied and environmental microbiology 2013
  • “...genes involved in the biosynthesis of tyrosine (TM0344), leucine (TM0548-TM0555), cysteine (TM0882), and lysine (TM1519-TM1520), among others. Genes involved in...”

A8AAX2 prephenate dehydrogenase (NADP+) (EC 1.3.1.13) from Ignicoccus hospitalis (see 2 papers)
Aligns to 111:252 / 348 (40.8%), covers 67.5% of PF02153, 55.4 bits

Fisuc_2559 Prephenate dehydrogenase from Fibrobacter succinogenes subsp. succinogenes S85
Aligns to 17:180 / 396 (41.4%), covers 85.7% of PF02153, 54.2 bits

• Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
  Wu, Scientific reports 2017
  • “...protein Fisuc_2123 2.3 0.002766 4Fe-4S ferredoxin iron-sulfur binding domain protein Fisuc_2558 1.9 2.99E-15 Chorismate mutase Fisuc_2559 2.0 1.03E-16 Prephenate dehydrogenase Fisuc_2908 2.1 0.000191 (Sulfur transfer protein involved in) thiamine biosynthesis protein ThiS Acid survival for E . coli knockout mutants To date, genetic manipulation tools are...”

FTN_0055 prephenate dehydrogenase from Francisella tularensis subsp. novicida U112
Aligns to 28:141 / 278 (41.0%), covers 64.9% of PF02153, 53.1 bits

• Francisella tularensis metabolism and its relation to virulence
  Meibom, Frontiers in microbiology 2010
  • “...absent in the Schu S4 strain but present in both LVS (FTL_048) and subsp. novicida (FTN_0055). Bruce Stocker's pioneer work on the genetics of Salmonella enterica serovar Typhimurium ( S. typhimurium ) has demonstrated the crucial importance of the aromatic biosynthetic pathway for bacterial virulence. Mutations...”
  • “...pulmonary and systemic infection in mice (Kraemer et al., 2009 ). The gene tyrA ( FTN_0055 ), which encodes the enzyme prephenate dehydrogenase converting chorismate to tyrosine, was also hit in this in vivo screen, as was aroC . Notably, the tyrA gene is absent in...”
• Genome-wide screen in Francisella novicida for genes required for pulmonary and systemic infection in mice
  Kraemer, Infection and immunity 2009
  • “...were lost in all three organs. These were tyrA (FTN_0055) and folD (FTN_0417), both involved in amino acid metabolism; the intracellular growth locus protein D...”
  • “...Berkeley FTN_0008 FTN_0012 FTN_0023 FTN_0028 FTN_0031 FTN_0045 FTN_0055 FTN_0111 FTN_0132 FTN_0133 FTN_0143 Gene name GENOME-WIDE SCREEN IN F. NOVICIDA VOL. 77,...”
• Working toward the future: insights into Francisella tularensis pathogenesis and vaccine development
  Pechous, Microbiology and molecular biology reviews : MMBR 2009
  • “...FTN_0023 FTN_0028 FTN_0031 FTN_0035 FTN_0036 FTN_0045 FTN_0055 FTN_0090, FTN_1556, FTN_1061, FTN_0954 FTN_0096 FTN_0097 carA tmpT FTN_0028 FTN_0031 pyrF...”

FTL_0048 prephenate dehydrogenase. from Francisella tularensis subsp. holarctica
Aligns to 30:142 / 220 (51.4%), covers 63.0% of PF02153, 51.7 bits

• Francisella tularensis metabolism and its relation to virulence
  Meibom, Frontiers in microbiology 2010
  • “...the tyrA gene is absent in the Schu S4 strain but present in LVS ( FTL_0048 ). aroC encodes the enzyme performing the last step of chorismic acid synthesis. The gene aroE1 , which encodes shikimate-5-dehydrogenase, the fourth step of the biosynthetic pathway, was identified in...”

2pv7B / P43902 Crystal structure of chorismate mutase / prephenate dehydrogenase (tyra) (1574749) from haemophilus influenzae rd at 2.00 a resolution (see paper)
Aligns to 25:149 / 280 (44.6%), covers 43.5% of PF02153, 50.7 bits

• Ligands: tyrosine; nicotinamide-adenine-dinucleotide (2pv7B)

VP0547 chorismate mutase/prephenate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
Aligns to 122:235 / 375 (30.4%), covers 63.6% of PF02153, 50.3 bits

• Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus
  Kalburge, Infection and immunity 2017
  • “...VPA0639) (Fig. S4A), phenylalanine/tyrosine biosynthesis (VP0546 to VP0547 and VP0555), and histidine biosynthesis (VP1137 to VP1138). qPCR analysis confirmed...”

P43902 prephenate dehydrogenase (EC 1.3.1.12) from Haemophilus influenzae (see paper)
HI1290 chorismate mutase / prephenate dehydrogenase (tyrA) from Haemophilus influenzae Rd KW20
Aligns to 117:239 / 377 (32.6%), covers 43.5% of PF02153, 49.9 bits

• Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis
  Wong, Frontiers in cellular and infection microbiology 2012
  • “...a HI1431 trpB Tryptophan synthase subunit beta a HI1432 trpA Tryptophan synthase subunit alpha a HI1290 tyrA Bifunctional chorismate mutase/prephenate dehydrogenase a HI0086 metB Cystathionine gamma-synthase a, d HI0122 metC Cystathionine beta-lyase a HI1702 metE 5-Methyltetrahydropteroyltriglutamate homocysteine methyltransferase a HI1263 metX Homoserine O -acetyltransferase a HI0465...”
• Analysis of the pmsCEAB gene cluster involved in biosynthesis of salicylic acid and the siderophore pseudomonine in the biocontrol strain Pseudomonas fluorescens WCS374
  Mercado-Blanco, Journal of bacteriology 2001
  • “...prephenate dehydrogenase; T protein) of Haemophilus influenzae (P43902), Erwinia herbicola (Q02287), and E. coli (P07023). The homology was located in the...”

Q02287 T-protein from Enterobacter agglomerans
Aligns to 124:239 / 373 (31.1%), covers 59.1% of PF02153, 48.5 bits

• Analysis of the pmsCEAB gene cluster involved in biosynthesis of salicylic acid and the siderophore pseudomonine in the biocontrol strain Pseudomonas fluorescens WCS374
  Mercado-Blanco, Journal of bacteriology 2001
  • “...T protein) of Haemophilus influenzae (P43902), Erwinia herbicola (Q02287), and E. coli (P07023). The homology was located in the N-terminal domain of TyrA. TyrA...”

ECs3463 chorismate mutase-T / prephenate dehydrogenase from Escherichia coli O157:H7 str. Sakai
Aligns to 124:240 / 373 (31.4%), covers 63.6% of PF02153, 48.5 bits

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...purL -2.45 1 ECs4366 yhiO 4.26 2 ECs3448 trxC 2.24 2 ECs4481 lldP 2.39 2 ECs3463 tyrA 3.67 3 ECs4490 gpmI -3.35 1 ECs3464 aroF 3.30 3 ECs4512 rpmB -2.38 1 ECs3471 yfjA -3.58 1 ECs4553 O157 -2.10 1 ECs3546 emrR -3.47 1 ECs4575 escC -2.00...”

A0A140N544 T-protein from Escherichia coli (strain B / BL21-DE3)
Aligns to 124:240 / 373 (31.4%), covers 63.6% of PF02153, 48.5 bits

• Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli
  Chang, Biotechnology for biofuels and bioproducts 2022
  • “...1.05 1.20 Amino acid transport and metabolismrelated proteins Inner-membrane translocator A0A140N716 livH 1.03 2.99 T-protein A0A140N544 tyrA 1.66 2.29 Carbohydrate transport and metabolismrelated proteins Fructose-bisphosphate aldolase A0A140N821 fba 1.56 1.27 d -Erythrose-4-phosphate dehydrogenase A0A140N827 epd 1.97 1.35 Ribulose-phosphate 3-epimerase A0A140SS41 alsE 1.23 4.07 PTS system, fructose...”

TyrA / b2600 fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
tyrA / P07023 fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) from Escherichia coli (strain K12) (see 12 papers)
P07023 T-protein from Escherichia coli (strain K12)
b2600 fused chorismate mutase T/prephenate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
Aligns to 124:240 / 373 (31.4%), covers 63.6% of PF02153, 47.2 bits

• Identification of enzymes and regulatory proteins in Escherichia coli that are oxidized under nitrogen, carbon, or phosphate starvation
  Noda, Proceedings of the National Academy of Sciences of the United States of America 2007
  • “...P0A9P1 P0A6M9 P0A6Q0 Q59346 P23847 P0A7A0 P23721 P0AD61 P07023 Protein name Protein MW Protein PI Dihydrolipoyl dehydrogenase, 3 Elongation factor G (EF-G), 2...”
• Analysis of the pmsCEAB gene cluster involved in biosynthesis of salicylic acid and the siderophore pseudomonine in the biocontrol strain Pseudomonas fluorescens WCS374
  Mercado-Blanco, Journal of bacteriology 2001
  • “...influenzae (P43902), Erwinia herbicola (Q02287), and E. coli (P07023). The homology was located in the N-terminal domain of TyrA. TyrA proteins are larger than...”
• Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli
  Frick-Cheng, mBio 2022
  • “...sufE Cysteine desulfuration protein 3.8 b1679 sufS Selenocysteine lyase 4.1 b1680 tyrA Chorismate mutase 3.7 b2600 ybdZ Enterobactin biosynthesis protein 6.1 b4511 ybgS Uncharacterized protein 4.3 b0753 ybiX PKHD-type hydroxylase 3.7 b0804 yciG Uncharacterized protein 4.5 b1259 yddM Putative DNA-binding transcriptional regulator 4.6 b1477 ydiE Uncharacterized...”
• Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
  Orth, BMC systems biology 2012
  • “...(b0073) 2.00E-15 R00732 (R) III aroA (b0908) 5.00E-32 murA (b3189) 7.00E-8 R00733 (R) III tyrA (b2600) 2.80E-2 R01393 (R) I global orphan R01618 (R) IV glgP (b3428) 2.10 R01713 (F) I global orphan R01731 (F) IV tyrB (b4054) * R01785 (R) III rhaD (b3902) * R01902...”
• More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
  Göhler, BMC systems biology 2011
  • “...0.977 2.124 b0628 lipA * -0.075 3.914 b1596 ynfM 0.927 0.007 b4052 dnaB -0.018 3.864 b2600 tyrA 0.915 2.065 b0085 murE $ 0.167 3.659 b2505 yfgH 0.820 0.425 b0822 ybiV 0.284 3.653 b0333 prpC 0.729 0.021 b2683 ygaH -0.077 3.628 b0331 prpB 0.713 0.024 b0436 tig...”
• Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
  Xu, BMC bioinformatics 2009
  • “...b1260 b0914 b1098 b1136 b1261, b1262 s0001 b2827 b1263, b1264 b3648 b1693, b2329 s0001 b2599, b2600 b3389 SS AAM FM ACM HM CM genes b0928 b1415 b1415 b2019, b2020 b2750, b2751 b3941 b3608 b2021, b2022 b2752, b2762 b2023, b2024 b2763, b2764 b2025, b2026 b3607 SS IITM...”
• Experimental and computational assessment of conditionally essential genes in Escherichia coli
  Joyce, Journal of bacteriology 2006
  • “...(b1261) trpC (b1262) trpD (b1263) trpE (b1264) tyrA (b2600) Group 8262 JOYCE ET AL. J. BACTERIOL. two experimentally defined essential genes. We then examined...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...hdeB b3524 b2601 b1261 b1264 b1493 b3517 b3320 b1263 b2600 b1260 b1973 b1262 b3340 b1779 b3321 b3308 b3304 b3616 b3339 b2155 b3829 b3317 b3296 b2913 b0631 b2416...”
  • “...b1264 b1493 b3517 b3774 b1289 b2553 b0698 b1004 b0179 b2600 b1260 b3509 b1261 b2342 b2800 b3460 b3458 b1263 b1783 b0907 b0461 b2464 b0812 b0903 b1262 b0126...”

YP_0399 T-protein [includes: chorismate mutase and prephenate dehydrogenase] from Yersinia pestis biovar Medievalis str. 91001
Aligns to 124:239 / 373 (31.1%), covers 72.1% of PF02153, 46.8 bits

• TyrR, the regulator of aromatic amino acid metabolism, is required for mice infection of Yersinia pestis
  Deng, Frontiers in microbiology 2015
  • “...tyrR /WT) Annotation RNA-seq qPCR YP_0398 aroF Chromosome 421761 422837 + 39.5 52.0 Phospho-2-dehydro-3-deoxyheptonate aldolase YP_0399 tyrA Chromosome 422850 423971 + 19.4 Bifunctional chorismate mutase/prephenate dehydrogenase YP_0720 aroL Chromosome 777603 778127 + 4.7 Shikimate kinase II YP_pMT067 pMT1 plasmid 56720 56986 3.3 Hypothetical protein YP_0263 aroP1...”

SO1362 chorismate mutase/prephenate dehydrogenase from Shewanella oneidensis MR-1
Aligns to 120:244 / 379 (33.0%), covers 61.7% of PF02153, 44.8 bits

• Design and analysis of mismatch probes for long oligonucleotide microarrays
  Deng, BMC genomics 2008
  • “...Mm Na+/H+ exchanger MMP0926 44921025 Mm Chemotaxis protein cheB MMP1559 45047480 Mm Formatedehydrogenase alpha subunit SO1362 24371479 So Chorismate mutase/prephenate dehydrogenase (tyrA) SO1779 24371479 So Decaheme cytochrome c (omcA) SO2452 24371479 So Alcohol dehydrogenase, zinc-containing *DvH: Desulfovibrio vulgaris str. Hildenborough ; Mm: Methanococcus maripaludis ; So:...”

Dde_3485 Prephenate dehydrogenase from Desulfovibrio desulfuricans G20
Dde_3485 prephenate dehydrogenase/arogenate dehydrogenase family protein from Oleidesulfovibrio alaskensis G20
Aligns to 4:121 / 260 (45.4%), covers 44.2% of PF02153, 44.7 bits

• Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
  Jawaharraj, Scientific reports 2023
  • “...P-II Dde_0508 4.05 0.99 Signal peptide peptidase SppA, 36K type Dde_2791 3.97 0.46 Arsenical-resistance protein Dde_3485 3.88 0.94 Prephenate dehydrogenase Up (EC-3) Dde_4057 8.35 0.11 DNA binding domain protein, excisionase family Dde_3199 7.67 0.09 Uncharacterized protein Dde_3198 7.49 0.15 Dinitrogenase iron-molybdenum cofactor biosynthesis protein Dde_4005 6.90...”

ETAE_2836 bifunctional chorismate mutase/prephenate dehydrogenase from Edwardsiella tarda EIB202
Aligns to 131:239 / 373 (29.2%), covers 69.5% of PF02153, 42.9 bits

• Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches
  Wang, PloS one 2009
  • “...dehydrogenase ETAE_2695 folD Methylenetetrahydrofolate dehydrogenase (NADP(+)) ETAE_2705 dltE Short chain dehydrogenase ETAE_2787 guaB Inositol-5-monophosphate dehydrogenase ETAE_2836 tyrA Bifunctional chorismate mutase/prephenate dehydrogenase ETAE_2856 sdhA Succinate dehydrogenase flavoprotein subunit ETAE_2857 sdhD Succinate dehydrogenase hydrophobic membrane anchor protein ETAE_2858 sdhC Succinate dehydrogenase cytochrome b-556 subunit ETAE_2934 aroE Shikimate 5-dehydrogenase...”

BT3933 prephenate dehydrogenase (EC 1.3.1.13) from Bacteroides thetaiotaomicron VPI-5482
Aligns to 24:151 / 257 (49.8%), covers 68.8% of PF02153, 41.9 bits

• mutant phenotype: Important for fitness in defined media. Distantly related (under 25% identity) to the prephenate dehydrogenase portion of E. coli tyrA. This is sometimes annotated as chorismate mutase as well, but it lacks that domain.

O30012 prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) from Archaeoglobus fulgidus (see paper)
AF0227 chorismate mutase/prephenate dehydratase (pheA) from Archaeoglobus fulgidus DSM 4304
Aligns to 29:138 / 620 (17.7%), covers 48.7% of PF02153, 39.5 bits

• Characterization of a key trifunctional enzyme for aromatic amino acid biosynthesis in Archaeoglobus fulgidus
  Lim, Extremophiles : life under extreme conditions 2009 (PubMed)
  • “...proteins or fusions combining two activities. Gene locus AF0227 of Archaeoglobus fulgidus is predicted to encode a fusion protein, AroQ, containing all three...”
  • “...to be particularly interesting since its gene at locus AF0227 is predicted to encode a protein containing three domains harboring putative CM, PDT, and PDHG...”
• Evolution of gene fusions: horizontal transfer versus independent events
  Yanai, Genome biology 2002
  • “...of the fused gene (Figure 4a,4b ). The single archaeal fusion, the Arachaeoglobus fulgidus protein AF0227, belongs to one of these clusters and shows a strongly supported affinity with the ortholog from the hyperthermophilic bacterium Thermotoga maritima . (Figure 4a,4b ). Given the broad distribution of...”
  • “...(COG1605); (b) prephenate dehydratase (COG0077). Protein designations are as in Figure 2 . The protein AF0227 contains a prephenate dehydrogenase domain in addition to the chorismate mutase and prephenate dehydratase domains. Figure 5 Phylogenetic trees for fusion-linked COGs: and subunits of acetyl-CoA carboxylase. (a) subunit (domain)...”
• Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus
  Tang, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...() AF1049 () AF1987 () AF1017 () AF0790 () AF2390 () AF0227 () AF0896 () AF0701 () AF1489 () AF1277 () AF1444 () AF0208 () AF0595 () AF0592 () AF0597 () AF2236...”
• Prephenate dehydratase from the aphid endosymbiont (Buchnera) displays changes in the regulatory domain that suggest its desensitization to inhibition by phenylalanine
  Jiménez, Journal of bacteriology 2000
  • “...pombe, O14361), PDTARCFU (Archaeoglobus fulgidus, O30012), PDTAQUAE (Aquifex aeolicus, O67085), PDTXANCA (Xanthomonas campestris, O87954), PDTPSEAER (P....”

TyrAAT2 / Q9LMR3 arogenate dehydrogenase (EC 1.3.1.78) from Arabidopsis thaliana (see paper)
TYRA2_ARATH / Q9LMR3 Arogenate dehydrogenase 2, chloroplastic; TyrAAT2; EC 1.3.1.78 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q9LMR3 arogenate dehydrogenase (NADP+) (EC 1.3.1.78) from Arabidopsis thaliana (see 2 papers)
NP_173023 prephenate dehydrogenase family protein from Arabidopsis thaliana
AT1G15710 prephenate dehydrogenase family protein from Arabidopsis thaliana
Aligns to 73:223 / 358 (42.2%), covers 95.5% of PF02153, 38.3 bits

• function: Involved in the biosynthesis of tyrosine. Has a weak prephenate dehydrogenase activity.
  catalytic activity: L-arogenate + NADP(+) = CO2 + L-tyrosine + NADPH (RHEA:15417)
• Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana.
  de, The Plant journal : for cell and molecular biology 2019 (PubMed)
  • GeneRIF: These results revealed that TyrA1 and TyrA2 have distinct and overlapping functions in flower and leaf development, respectively, and that imbalance of tyrosine, caused by altered TyrA activity and regulation, impacts growth and development of Arabidopsis. [TyrA2]
• The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism
  Wu, Science advances 2024
  • “...and growth conditions The Arabidopsis ( A. thaliana ) T-DNA insertion mutants adh2 (SALK_001765, in At1g15710) and vas1-1 (SALK_207250, in At1g80360) are in the Col-0 background. The adh2 mutant was provided by Y. Qi (Tsinghua University, China). The vas1 mutant was purchased from AraShare ( http://arashare.cn...”
• Two independently evolved natural mutations additively deregulate TyrA enzymes and boost tyrosine production in planta
  Lopez-Nieves, The Plant journal : for cell and molecular biology 2022 (PubMed) (secret)
• TRUEE; a bioinformatic pipeline to define the functional microRNA targetome of Arabidopsis
  Wong, The Plant journal : for cell and molecular biology 2022
  • “...miR5021 Yes AT3G23890 3.559 TOPII Topoisomerase II miR414 Yes AT5G40340 2.765 Tudor/PWWP/MBT superfamily protein miR8177 AT1G15710 2.618 Prephenate dehydrogenase family protein miR5652 AT1G62670 2.529 RPF2 rna processing factor 2 a miR414 Yes AT3G11810 2.118 (1 of 2) PTHR33133:SF7 F26K24.10 miR414 Yes AT5G55300 2.118 TOP1ALPHA DNA topoisomerase...”
• Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana
  de, The Plant journal : for cell and molecular biology 2019 (PubMed) (secret)
• Transcriptional analyses of natural leaf senescence in maize
  Zhang, PloS one 2014
  • “...protein chloroplast GRMZM2G454719 1.52 0.96 AT1G22410 \ class-II DAHP synthetase-like protein chloroplast GRMZM2G365961 2.51 2.33 AT1G15710 \ prephenate dehydrogenase family protein chloroplast GRMZM2G164562 1.44 1.99 AT1G48850 EMB1144 chorismate synthase chloroplast, stroma GRMZM2G115841 2.17 1.41 AT2G27820 PD1 arogenate dehydratase 3 chloroplast GRMZM2G003109 2.09 0.39 AT5G05730 ASA1 anthranilate...”
• Genetic dissection of vitamin E biosynthesis in tomato
  Almeida, Journal of experimental botany 2011
  • “...At2g22250 (475) Chloroplast U567172 Chloroplast SL2.31sc06101 C2_At4g39830 4 (61 cM) Arogenate dehydrogenase (TyrA, EC 1.3.1.78) At1g15710 ( 358) Chloroplast U567861 (1) Chloroplast SL2.31sc03731 C2_At5g34850 7 (0.4 cM) At5g34930 (640) Chloroplast ( Rippert et al., 2009 ) U570951 (2) Chloroplast SL2.31sc03771 T1212 9 (48 cM) Tyrosine aminotransferase...”
• Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development
  Schmidt, PLoS biology 2011
  • “...factors. Arabidopsis PUMILIO23 (AtPUM23 ) is an RNA-binding protein located in the nucleus [40] . AT1G15710 is a prehenate dehydrogenase potentially involved in tyrosin biosynthesis. Also YUCCA2 , a gene involved in auxin biosynthesis and AT1G29440 , encoding an auxin-responsive gene related to SMALL AUXIN UPREGULATED68...”
• The Biosynthetic Pathways for Shikimate and Aromatic Amino Acids in Arabidopsis thaliana
  Tzin, The arabidopsis book 2010
  • “...TyrA enzymes were identified: TyrA1 (At5g34930) and TyrA2 (At1g15710) (Rippert and Matringe, 2002b, a; Rippert et al., 2009). A second possible route of Tyr...”
  • “...PAT TyrA1, ADS1 TyrA2, ADS2 At5g34930 At1g15710 2.6.1.79 1.3.1.43 1.3.1.43 Prephenate Aminotransferase Arogenate Dehydrogenase Arogenate Dehydrogenase PDH AAAAT...”
• More

LOC100284089 arogenate dehydrogenase from Zea mays
Aligns to 105:218 / 403 (28.3%), covers 70.8% of PF02153, 37.9 bits

• Identification and characterization of the maize arogenate dehydrogenase gene family
  Holding, Journal of experimental botany 2010
  • “...amino acid similarities in the maize AroDH family AroDH-1 AroDH-2 AroDH-3 AroDH-4 Accession no. BT085368.1 LOC100284089 LOC100281078 BT068692.1 Transcript (bp) 1477 1417 1336 1327 Protein (amino acids) 360 406 349 392 ID to AroDH-1 mRNA (coverage and max ID) 73% and 85% 83% and 93% 65%...”

AroDH-1 / B4FY98 arogenate dehydrogenase 1 (EC 1.3.1.43) from Zea mays (see paper)
Aligns to 96:230 / 360 (37.5%), covers 69.5% of PF02153, 37.9 bits

B6SS03 arogenate dehydrogenase [NAD(P)+] (EC 1.3.1.79) from Zea mays (see paper)
GRMZM2G365961, LOC100281078 arogenate dehydrogenase from Zea mays
Aligns to 83:197 / 349 (33.0%), covers 68.8% of PF02153, 37.3 bits

• Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection
  Yue, BMC plant biology 2018
  • “...acids pathway, one significantly induced protein (C0P3B4) and five significantly reduced proteins (K7VBU7, K7VC35, B8A068, B6SS03 and K7U2E4) were identified and in the purine metabolism pathway, one significantly induced protein (K7TPZ5) and one significantly reduced protein (K7UGQ5) were identified (Table 1 ). Table 1 Identification of...”
  • “...0.025750889 K7VC35 Zm.66568 S-adenosylmethionine synthethase 42.54 0.770235935 0.025440529 B8A068 Zm.20018 S-adenosylmethionine synthethase 43.072 0.757097792 0.012769647 B6SS03 Zm.155641 Arogenate dehydrogenase isoform 2 38.561 0.77589852 0.023596168 K7U2E4 Zm.24636 Amine oxidase 82.989 0.779698303 0.04484565 Purine metabolism K7TPZ5 Zm.138895 Aminoimidazolecarboximide ribonucleotide transformylase 65.704 1.222222222 0.0327844 K7UGQ5 LOC100275070 Putative adenine phosphoribosyltransferase...”
• Chloroplast-associated metabolic functions influence the susceptibility of maize to Ustilago maydis
  Kretschmer, Molecular plant pathology 2017 (secret)
• Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations
  Li, BMC genomics 2016
  • “...0.66 + PH GRMZM2G430680 Inside gene Glucan synthase-like 12 0.34 6 85797877 0.25 + PH GRMZM2G365961 52 Prephenate dehydrogenase family protein 0.15 6 88935877 0.40 + PH GRMZM2G150302 13001 Nucleotide-diphospho-sugar transferases superfamily protein/glycosyltransferase family 43 protein 0.41 6 119695193 0.50 - HKW GRMZM2G368678 Inside gene Binding/expressed...”
• Transcriptional analyses of natural leaf senescence in maize
  Zhang, PloS one 2014
  • “...class-II DAHP synthetase-like protein chloroplast GRMZM2G454719 1.52 0.96 AT1G22410 \ class-II DAHP synthetase-like protein chloroplast GRMZM2G365961 2.51 2.33 AT1G15710 \ prephenate dehydrogenase family protein chloroplast GRMZM2G164562 1.44 1.99 AT1G48850 EMB1144 chorismate synthase chloroplast, stroma GRMZM2G115841 2.17 1.41 AT2G27820 PD1 arogenate dehydratase 3 chloroplast GRMZM2G003109 2.09 0.39...”
• Identification and characterization of the maize arogenate dehydrogenase gene family
  Holding, Journal of experimental botany 2010
  • “...acid similarities in the maize AroDH family AroDH-1 AroDH-2 AroDH-3 AroDH-4 Accession no. BT085368.1 LOC100284089 LOC100281078 BT068692.1 Transcript (bp) 1477 1417 1336 1327 Protein (amino acids) 360 406 349 392 ID to AroDH-1 mRNA (coverage and max ID) 73% and 85% 83% and 93% 65% and...”

G7J2F0 Prephenate dehydrogenase from Medicago truncatula
Aligns to 22:146 / 239 (52.3%), covers 55.2% of PF02153, 35.5 bits

• Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets
  Babaei, ACS synthetic biology 2024
  • “...phosphoketolase (WP_101428637); EcAroL, E. coli shikimate kinase II (P0A6E1); MtPDH1 , Medicago truncatula prephenate dehydrogenase (G7J2F0); AtPAL2, Arabidopsis thaliana phenylalanine ammonia lyase (P45724); AtC4H, A. thaliana cinnamate 4-hydroxylase (P92994); AtCPR, A. thaliana cytochrome P450 reductase 2 (Q9SUM3); FjTAL, Flavobacterium johnsoniae tyrosine ammonia lyase (A5FKY3); BvCYP76AD1 W13L,F309L...”

5t9fB / I1MYY4 Prephenate dehydrogenase n222d mutant from soybean (see paper)
Aligns to 17:137 / 253 (47.8%), covers 68.8% of PF02153, 35.2 bits

• Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; tyrosine (5t9fB)

G7J2E9 prephenate dehydrogenase (NADP+) (EC 1.3.1.13) from Medicago truncatula (see paper)
Aligns to 22:146 / 268 (46.6%), covers 55.2% of PF02153, 35.2 bits

PAPC_STRPR / P72540 4-amino-4-deoxyprephenate dehydrogenase; EC 1.3.1.121 from Streptomyces pristinaespiralis (see paper)
Aligns to 23:165 / 296 (48.3%), covers 62.3% of PF02153, 34.0 bits

• function: Involved in pristinamycin I biosynthesis (PubMed:9044253). Probably catalyzes the formation of 3-(4-aminophenyl)pyruvate from 4- amino-4-deoxyprephenate (Probable).
  catalytic activity: 4-amino-4-deoxyprephenate + NAD(+) = 3-(4-aminophenyl)pyruvate + CO2 + H(+) + NADH (RHEA:59380)

CC1574 conserved hypothetical protein from Caulobacter crescentus CB15
Aligns to 15:135 / 286 (42.3%), covers 73.4% of PF02153, 32.2 bits

• CtrA, a global response regulator, uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus
  Spencer, Journal of bacteriology 2009
  • “...coli chemotaxis protein MotB (20). The MotB/CC1573 and CC1574 genes are positioned divergently, implying that the intervening DNA (114 bp) contains two...”

PPTG_08889 pyrroline-5-carboxylate reductase from Phytophthora parasitica INRA-310
Aligns to 102:212 / 356 (31.2%), covers 59.7% of PF02153, 32.1 bits

• Transcriptomic and Ultrastructural Signatures of K⁺-Induced Aggregation in Phytophthora parasitica Zoospores
  Bassani, Microorganisms 2020
  • “...genes identified 12 genes putatively involved in transport and metabolism of organic molecules. Among them, PPTG_08889 (2578 FPKM) encoded D1-pyrroline-5-carboxylate reductase (P5CR), the enzyme catalyzing the last step of proline biosynthesis [ 54 ]. P5CR is of particular importance for osmoregulation during zoospore release, as proline...”

HVO_1312 Prephenate dehydrogenase from Haloferax volcanii DS2
Aligns to 16:147 / 272 (48.5%), covers 64.3% of PF02153, 32.0 bits

• Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery
  Kiljunen, BMC biology 2014
  • “...synthase [NADPH] large chain H295/24-65 Proline 1,051,586; - HVO_1153 Hypothetical protein H295/12-1 Tyrosine 1,198,243; + HVO_1312 Prephenate dehydrogenase H295/16-1 Isoleucine 578,651; - HVO_0644, leuA1 2-isopropylmalate synthase/(R)-citramalate synthase H295/24-63 Phenylalanine 399,114; - HVO_0449, pheA1 Prephenate dehydratase H295/9-8 Valine, Leucine, Isoleucine 1,374,516; - HVO_1506, ilvC Ketol-acid reductoisomerase H295/4-26...”
  • “...subunit) and the other in HVO_1153 (hypothetical protein). In the tyrosine auxotroph the transposon interrupted HVO_1312 (prephenate dehydrogenase, a known enzyme on the tyrosine biosynthesis pathway). The isoleucine auxotroph harbored the transposon in leuA1 , proposed to encode either 2-isopropylmalate synthase or highly similar (R)-citramalate synthase....”

K4C5K7 Arogenate dehydrogenase from Solanum lycopersicum
Aligns to 26:148 / 272 (45.2%), covers 73.4% of PF02153, 31.3 bits

• Proteome-wide identification of non-histone lysine methylation in tomato during fruit ripening
  Xiao, Journal of advanced research 2022
  • “...A0A3Q7HE49 91, K Peptide-methionine (R)-S-oxide reductase Methyl chloroplast A0A3Q7HK83 206, K Glutathione peroxidase Trimethyl chloroplast K4C5K7 262, K Arogenate dehydrogenase Methyl chloroplast P00060 80, K Cytochrome c Dimethyl,Trimethyl mitochondria 94, K Trimethyl A0A3Q7F9X5 81, K; 82, K;95, K;96, K;100, R PREDICTED: cytochrome c Methyl mitochondria P27065...”
  • “...bystin-like protein Methyl cytoplasm K4B3H5 161, R NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 Methyl chloroplast K4C5K7 260, R Arogenate dehydrogenase Methyl chloroplast A9LRT7 188, K Isopentenyl diphosphate isomerase Methyl chloroplast Methylated proteins related to carbohydrate biosynthetic P27065 14, K Ribulose bisphosphate carboxylase large chain Dimethyl, Trimethyl...”

PF1703 prephenate dehydrogenase from Pyrococcus furiosus DSM 3638
Aligns to 18:148 / 148 (88.5%), covers 61.0% of PF02153, 28.5 bits

• Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins
  Weinberg, Journal of bacteriology 2005
  • “...Aromatic amino acid biosynthesis PF1701 PF1702 PF1703 Tungstoenzyme-4 PF1960 PF1961 PF1973 PF2032 [Chorismate mutase] [Aspartate aminotransferase] [Prephenate...”
  • “...aromatic amino acid biosynthesis (PF1701 to PF1703), carbohydrate metabolism (aldose reductase [PF1960]), proteolysis (serine protease [PF1670]), transport...”
• Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
  Schut, Journal of bacteriology 2003
  • “...amino acid biosynthesis] PF1699 PF1700 PF1701 PF1702 PF1703 PF1706 PF1708 PF1709 PF1710 PF1711 PF1713 PF1739 [Maltose transport] PF1740 PF1741 PF1742 PF1784...”

papC / BAD21141.1 4-amino-4-deoxyprephenate dehydrogenase from Streptomyces venezuelae (see paper)
Aligns to 20:136 / 322 (36.3%), covers 46.8% of PF02153, 27.1 bits

Or search for genetic data about PF02153 in the Fitness Browser