PaperBLAST
PaperBLAST Hits for BRENDA::P29976 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (Arabidopsis thaliana) (525 a.a., MALSNASSLS...)
Show query sequence
>BRENDA::P29976 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (Arabidopsis thaliana)
MALSNASSLSTRSIYGGDLSHRPSNRQSSFTFHPAVNTKPKSVNLVTAVHAAEPARNAVS
VKESVASSSSGALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLE
ERLADAAVGKAFLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMA
GQFAKPRSDAFEEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRA
FATGGYAAIQRVTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDHPLMTTTDF
YTSHECLLLPYEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIK
VSNKMDPFELVKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCD
PMHGNTIKAPCGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRT
VTYDDLSSRYHTHCDPRLNASQSLELAFIVAERLRKRRTGSQRVS
Running BLASTp...
Found 87 similar proteins in the literature:
P29976 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) from Arabidopsis thaliana (see paper)
AT4G39980 DHS1 (3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE 1); 3-deoxy-7-phosphoheptulonate synthase from Arabidopsis thaliana
100% identity, 100% coverage
- Photosynthetic Electron Flows and Networks of Metabolite Trafficking to Sustain Metabolism in Photosynthetic Systems
Fakhimi, Plants (Basel, Switzerland) 2024 - “...7-phosphate (DAHP) [ 112 ]. The Arabidopsis genome contains three DAHPS genes: At DAHPS 1 (AT4G39980), At DAHPS 2 (At4g33510), and At DAHPS 3 (At1g22410). Based on homology to Arabidopsis DAHPS, we identified a single putative DAHPS locus (Cre17.g726750_4532) on the Chlamydomonas genome. The Chlamydomonas protein...”
- Chromoplast plastoglobules recruit the carotenoid biosynthetic pathway and contribute to carotenoid accumulation during tomato fruit maturation
Zita, 2022 - Chromoplast plastoglobules recruit the carotenoid biosynthetic pathway and contribute to carotenoid accumulation during tomato fruit maturation
Zita, PloS one 2022 - “...superfamily protein 4 0 AT5G51010 - - - Solyc11g009080.2.1 DAHP synthetase 1 (DHS1) 5 2 AT4G39980 - - - Solyc05g053100.2.1 Dihydrolipoamide dehydrogenase 6 0 AT4G16155 - - - Solyc06g050590.3.1 Biotin/lipoyl attachment domain-containing protein 5 0 AT3G56130 - - - Solyc01g005910.2.1 DUF1212 0 3 AT3G12685 - -...”
- Point mutations that boost aromatic amino acid production and CO2 assimilation in plants
Yokoyama, Science advances 2022 - “...and/or sota -like F 2 progenies identified high-frequency missense mutations from all eight lines in At4g39980, At4g33510, or At1g22410, which are the three loci encoding 3-deoxy- d - arabino -heptulosonate 7-phosphate synthase (DAHP synthase or DHS) isoforms (fig. S3 and table S1). DHS catalyzes the first...”
- The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation
Yokoyama, The Plant cell 2021 - “...thaliana has three type II DHS enzymes, AthDHS1, 2, and 3, which are encoded by AT4G39980, AT4G33510, and AT1G22410, respectively ( Supplemental Figure S1 ; Entus et al., 2002 ; Richards et al., 2006 ; Tohge et al., 2013 ). AthDHS1 has been biochemically characterized as...”
- “...did not exhibited drastic phenotypes under standard growth condition. (A) Schematic structural models of AthDHS1 (AT4G39980), AthDHS2 (AT4G33510), and AthDHS3 (AT1G22410) genes, with exons and introns shown in gray boxes and solid lines, respectively. The positions of the T-DNA insertion are indicated by triangles for dhs1...”
- Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis
Xu, Biomolecules 2021 - “...hormones (auxins) [ 150 ], which was mapped with three CRGs, i.e., TAT3 (AT2G24850), DHS1 (AT4G39980), and tryptophan synthase (AT5G28237); in contrast, the pathway of -linolenic acid (ALA) metabolism is related to the biosynthesis of JAs, which modulate the production of secondary metabolites [ 151 ,...”
- “...SLAH3 (AT5G24030) Cell cycle CDKG1 (AT5G63370) Secondary metabolism AtGES (AT1G61120), CYP82G1 (AT3G25180), TAT3 (AT2G24850), DHS1 (AT4G39980), Tryptophan synthase (AT5G28237) Cell wall assembly and remodeling XTH16 (AT3G23730), XTH23 (AT4G25810), XTH33 (AT1G10550), CSLA3 (AT1G23480), LRX2 (AT1G62440), AtGH9C2 (AT1G64390), KOR2 (AT1G65610), EXPA12 (AT3G15370), EXPA15 (AT2G03090), GALS1 (AT2G33570), FLA13 (AT5G44130),...”
- Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues
Mangeot-Peter, International journal of molecular sciences 2016 - “...to produce 3-deoxy- d -arabino-heptulosonate 7-phosphate. Three isoforms are present in Arabidopsis ( DHS1 - At4g39980 , DHS2 - At4g33510 and DHS3 - At1g22410 ), however in hemp only two contigs were retrieved ( Table S1 ). Notably, two isoforms were also found in jute (...”
- Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis thaliana
Hussain, Frontiers in plant science 2016 - “...key enzymes by at least 10-folds e.g., 3-deoxy- d -arabino-heptulosonate 7-phosphate synthase 1 ( DHS1 -AT4G39980) and 5-enolpyruvylshikimate 3-phosphate synthase ( EPSP synthsae-AT2G45300), which is involved in the shikimate pathway (Supplementary Figure S4 ). Genes involved in the tocopherol biosynthesis pathway, the products of which often...”
- More
- The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades
Ojosnegros, International journal of molecular sciences 2022 - “...9434-771_1_ORF2 Q9SUT5 SGT1B Protein SGT1 homolog B 39 358 8.74 10 118 Biotic stress 30827-456_4_ORF1 P29976 DHS1 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic 57 525 0 Biotic stress tr|D7MBC8|D7MBC8_ARALL Q9M084 IBI1 Aspartate-tRNA ligase 2, cytoplasmic 62 558 0 Biotic stress 3234-1184_1_ORF1 Q9M8L4 ACP4 Glycerol kinase 56 522 0...”
- A chloroplast processing enzyme functions as the general stromal processing peptidase
Richter, Proceedings of the National Academy of Sciences of the United States of America 1998 - “...Arabidopsis thaliana 18 19 20 21 P23321* P07030* P07854* P29976 Pisum sativum Pisum sativum Silene pratensis 22 7 23 P09886* U25111 P04669* volume of 20 mM...”
O24046 Phospho-2-dehydro-3-deoxyheptonate aldolase from Morinda citrifolia
78% identity, 98% coverage
- Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor.
Zamboni, BMC genomics 2009 - “...Phe biosynthesis CLU083 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase precursor O24051 TC74975 x 1611211_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase precursor O24046 TC57386 x 1614440_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase Q6YH16 TC54321 x 1619357_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase O24046 TC57642 x 1621405_at Plastidic 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2 O22407 TC51974 x 1609646_at 3-Dehydroquinate synthase-like protein Q9FKX0...”
I1JGU8 Phospho-2-dehydro-3-deoxyheptonate aldolase from Glycine max
77% identity, 98% coverage
LOC123205490 phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic-like from Mangifera indica
78% identity, 96% coverage
A0A0D5ZBC4 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) from Gossypium hirsutum (see paper)
75% identity, 97% coverage
M1BC24 Phospho-2-dehydro-3-deoxyheptonate aldolase from Solanum tuberosum
80% identity, 95% coverage
- Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease
Xiao, BMC genomics 2020 - “...reductase 1.23 0.00 A9LMM9 Dehydroascorbate reductase 1.22 0.00 P31212 Threonine dehydratase biosynthetic (Fragment) 1.31 0.00 M1BC24 Phospho-2-dehydro-3-deoxyheptonate aldolase 1.24 0.02 G9IHI3 Apoplastic invertase 0.80 0.00 F2Q9V9 Glyceraldehyde-3-phosphate dehydrogenase 0.82 0.01 M1ALJ6 Phosphotransferase 0.83 0.03 M1BQC2 Pectinesterase 0.82 0.00 Q38JH8 S-adenosylmethionine synthase 2 0.73 0.00 M1CD27 Methylthioribose-1-phosphate...”
- “...were positively induced, but we focused on two proteins threonine dehydratase (P31212) and Phospho-2-dihydro-3-deoxyheptonate aldolase (M1BC24) related to the shikimate pathway. Threonine dehydratase is the first enzyme in L-isoleucine biosynthesis, catalyzing deamination and dehydration of threonine to produce 2-ketobutyrate and ammonia. One report indicates that this...”
F6H0X2 Phospho-2-dehydro-3-deoxyheptonate aldolase from Vitis vinifera
75% identity, 95% coverage
O24051 Phospho-2-dehydro-3-deoxyheptonate aldolase from Morinda citrifolia
78% identity, 93% coverage
- Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor.
Zamboni, BMC genomics 2009 - “...WRKY transcription factor-b Q5DJU0 TC55553 x Effector genes Phe biosynthesis CLU083 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase precursor O24051 TC74975 x 1611211_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase precursor O24046 TC57386 x 1614440_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase Q6YH16 TC54321 x 1619357_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase O24046 TC57642 x 1621405_at Plastidic 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2...”
Q9SK84 Phospho-2-dehydro-3-deoxyheptonate aldolase from Arabidopsis thaliana
AT1G22410 2-dehydro-3-deoxyphosphoheptonate aldolase, putative / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, putative / DAHP synthetase, putative from Arabidopsis thaliana
77% identity, 99% coverage
- Insights into the function of NADPH thioredoxin reductase C (NTRC) based on identification of NTRC-interacting proteins in vivo
González, Journal of experimental botany 2019 - “...2.6 7 (6) x Q9LPR4 At1g18500 IPMS1, 2-Isopropylmalate synthase 1 C 3 2.4 9 (9) Q9SK84 At1g22410 Class-II DAHP synthase-like protein C 2 6.45 7 (7) x Q9FVP6 At1g48860 EPSPS, 5-Enolpyruvylshikimate-3-phosphate synthase C 2 14.77 10 (9) D7MUW5 At5g54810 TRPB, Tryptophan synthase beta-subunit C, M 2...”
- Photosynthetic Electron Flows and Networks of Metabolite Trafficking to Sustain Metabolism in Photosynthetic Systems
Fakhimi, Plants (Basel, Switzerland) 2024 - “...three DAHPS genes: At DAHPS 1 (AT4G39980), At DAHPS 2 (At4g33510), and At DAHPS 3 (At1g22410). Based on homology to Arabidopsis DAHPS, we identified a single putative DAHPS locus (Cre17.g726750_4532) on the Chlamydomonas genome. The Chlamydomonas protein has ~57% amino acid identity to its Arabidopsis homologue...”
- Beneficial Effects of Phosphite in Arabidopsis thaliana Mediated by Activation of ABA, SA, and JA Biosynthesis and Signaling Pathways
Pérez-Zavala, Plants (Basel, Switzerland) 2024 - “...processes. SA biosynthesis involves six enzymatic reactions carried out by 3-deoxy-7-phosphoheptulonate synthase (DHS1/AT4G39980, DHS2/AT4G33510, and AT1G22410), 3-dehydroquinate synthase (AT5G66120), 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase (MEE32/AT3G06350), shikimate kinase (SK1/AT2G21940 and SK2/AT4G39540), and 3-phosphoshikimate 1-carboxyvinyltransferase (EPSP/AT2G45300 and AT1G48860), to synthesize the SA precursor, chorismate, and isochorismate synthase (ICS1/AT1G74710, ICS2/AT1G8870) that...”
- Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes
Yu, BMC biology 2023 - “...BnaA09G0210400ZS 0.1702 0.0111 0.219 0.0025 BnaAnng07300D AT5G46880 HDG5 HD-ZIP BnaA09G0461900ZS 0.2985 0 0.3258 0 BnaA09g30660D AT1G22410 BnaC01G0103400ZS 0.2117 0.0054 0.1911 0.0217 BnaC01g09920D AT4G28500 NAC073 NAC BnaC01G0446100ZS 0.1675 0.0043 0.3083 0 BnaC01g37520D AT1G55210 DIR20 BnaC02G0432700ZS 0.1501 0.0097 0.1364 0.0304 AT2G02080 IDD4 C2H2 BnaC03G0110800ZS 0.1675 0.0115 0.1438 0.0449...”
- “...AT5G62500 EB1B BnaC04G0035900ZS 0.2249 0.0041 0.3451 0 BnaC04g52650D AT2G42860 BnaC05G0194900ZS 0.3038 0 0.351 0 BnaC05g17710D AT1G22410 BnaC08G0026700ZS 0.1598 0.0058 0.1663 0.0087 BnaCnng77910D AT1G07120 BnaC08G0027400ZS 0.1466 0.0116 0.175 0.0057 BnaC08g02000D AT1G07120 BnaC08G0169300ZS 0.2199 0.0002 0.3051 0 BnaC08g12180D AT4G26420 GAMT1 BnaC08G0442600ZS 0.1663 0.0041 0.1395 0.0268 BnaC04g35160D AT2G22640 BRK1...”
- Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress
Soltani, PloS one 2023 - “...ALDH7B4 ), jasmonate-Zim-domain protein 1 ( JAZ1 ), and some genes with unknown function including AT1G22410 , AT1G06550 , AT5G58950 , and AT1G68300 were identified. In addition, a total of 12 down-regulated DEGs including metallothionein 3 ( MT3 ), silent information regulator ( SIR ), ATP-binding...”
- “...apurinic/apyrimidinic endodeoxyribonuclease 1 ( APE1 ) as well as some genes with unknown function including AT1G22410 , AT3G15810 , AT2G21180 , and AT4G09890 were identified. Gene enrichment analysis of DEGs Finally, 1232 biotic DEGs and 308 hormonal DEGs were studied by GO analysis (Figs 3 and...”
- AP1G2 Affects Mitotic Cycles of Female and Male Gametophytes in Arabidopsis
Zhou, Frontiers in plant science 2022 - “...In this study, we characterized AP1G2 in female and male gametogenesis. We identified three loci, At1g22410, At1g22730, and At1g23900 after mapping the causal mutation of a female sterile mutant obtained by EMS mutagenesis, and then screening and annotation of candidate SNPs showed that suppression of recombination...”
- “...lines of AP1G2 , SALK_032500 ( ap1g2-1 ), SALK_137129 ( ap1g2-3 ), and lines of At1g22410 and At1g22730 in Supplementary Table 2 were obtained from the Arabidopsis Biological Resource Center (ABRC). The pAKV:H2B-YFP marker line was kindly provided by W.C. Yang at Academician of the Chinese...”
- Point mutations that boost aromatic amino acid production and CO2 assimilation in plants
Yokoyama, Science advances 2022 - “...F 2 progenies identified high-frequency missense mutations from all eight lines in At4g39980, At4g33510, or At1g22410, which are the three loci encoding 3-deoxy- d - arabino -heptulosonate 7-phosphate synthase (DAHP synthase or DHS) isoforms (fig. S3 and table S1). DHS catalyzes the first reaction in the...”
- The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation
Yokoyama, The Plant cell 2021 - “...type II DHS enzymes, AthDHS1, 2, and 3, which are encoded by AT4G39980, AT4G33510, and AT1G22410, respectively ( Supplemental Figure S1 ; Entus et al., 2002 ; Richards et al., 2006 ; Tohge et al., 2013 ). AthDHS1 has been biochemically characterized as recombinant protein and...”
- “...under standard growth condition. (A) Schematic structural models of AthDHS1 (AT4G39980), AthDHS2 (AT4G33510), and AthDHS3 (AT1G22410) genes, with exons and introns shown in gray boxes and solid lines, respectively. The positions of the T-DNA insertion are indicated by triangles for dhs1 (SALK_055360), dhs2 (SALK_033389), and dhs3...”
- Barley Root Proteome and Metabolome in Response to Cytokinin and Abiotic Stimuli
Berka, Frontiers in plant science 2020 - “...acid metabolism HORVU5Hr1G104700 Glutamate dehydrogenase 1 N/A NR NR NR NR HORVU2Hr1G029870 Phospho-2-dehydro-3-deoxyheptonate aldolase 2 AT1G22410 NR NR Biosynthesis of secondary metabolites HORVU3Hr1G015640 Alkenal reductase AT5G16990 NR NR NR NR HORVU6Hr1G035420 Cinnamyl alcohol dehydrogenase 5 AT3G19450 NR NR NR HORVU7Hr1G082280 O-Methyltransferase 1 AT5G54160 NR NR NR...”
- More
Q75LR2 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic from Oryza sativa subsp. japonica
74% identity, 94% coverage
- Drought Stress Induces Morpho-Physiological and Proteome Changes of Pandanus amaryllifolius.
Amnan, Plants (Basel, Switzerland) 2022 - “...2, chloroplastic Thiamine biosynthesis Transferase 3 Q9LN49 3-ketoacyl-CoA synthase 4 Acyltransferase Fatty acid biosynthesis 3 Q75LR2 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic Amino acid biosynthesis Transferase 3 O82627 Granule-bound starch synthase 1, chloroplastic/amyloplastic Starch biosynthesis Glycosyltransferase 3 Q8W0A1 Beta-galactosidase 2 Carbohydrate metabolism Glycosidase 3 O23787 Thiamine thiazole synthase,...”
Q0D4J5 Phospho-2-dehydro-3-deoxyheptonate aldolase from Oryza sativa subsp. japonica
80% identity, 88% coverage
AROG1_PETHY / A0A067XH53 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1; DAHP synthase 1; PhDAHP1; Phospho-2-keto-3-deoxyheptonate aldolase 1; EC 2.5.1.54 from Petunia hybrida (Petunia) (see 2 papers)
75% identity, 98% coverage
- function: Involved in the production of volatile organic compounds (VOCs), including floral volatile benzenoids and phenylpropanoids (FVBP), in flowers of fragrant cultivars (e.g. cv. Mitchell and cv. V26), scent attracting pollinators (e.g. the night-active hawkmoth pollinator Manduca sexta) (PubMed:24815009). Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7- phosphate (DAH7P) and inorganic phosphate (By similarity).
catalytic activity: D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7- phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate (RHEA:14717)
cofactor: Mn(2+) (Binds 1 divalent metal cation per subunit that could be manganese.)
subunit: Homodimer.
disruption phenotype: Reduced floral volatile benzenoids and phenylpropanoids (FVBP) emission.
LOC107867463 phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic from Capsicum annuum
79% identity, 90% coverage
O22407 Phospho-2-dehydro-3-deoxyheptonate aldolase from Petroselinum crispum
77% identity, 88% coverage
- Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor.
Zamboni, BMC genomics 2009 - “...TC54321 x 1619357_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase O24046 TC57642 x 1621405_at Plastidic 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2 O22407 TC51974 x 1609646_at 3-Dehydroquinate synthase-like protein Q9FKX0 TC56854 x 1609932_at Prephenate dehydratase Q6JJ29 TC53641 x 1621307_at Prephenate dehydratase Q6JJ29 TC53641 x 1611895_at Putative chorismate mutase Q5JN19 TC62307 x General phenylpropanoid...”
Q75W16 Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic from Oryza sativa subsp. japonica
80% identity, 88% coverage
- Physiological and Proteomic Analysis of Various Priming on Rice Seed under Chilling Stress
Zhang, Plants (Basel, Switzerland) 2024 - “...and amino acid synthesis, regulating the upregulation of 60S ribosomal protein (B7F845) and phospho-2-dehydro-3-deoxyheptanate aldolase (Q75W16) expression. The 60S ribosomal protein, a component of the large subunit in plant cells responsible for protein synthesis, plays a crucial role under low-temperature stress by participating in the biosynthesis...”
- “...Os03g0192700 O64437 Inositol-3-phosphate synthase 7.191 7.754 UP Os02g0626100 P14717 Phenylalanine ammonia-lyase 6.882 9.259 UP Os07g0622200 Q75W16 Phospho-2-dehydro-3-deoxyheptonate aldolase 5.189 4.498 UP Os10g0517500 Q7XCS3 Cys/Met metabolism PLP-dependent enzyme family protein 2.799 3.545 UP Os07g0681400 Q7XHW4 Probable calcium-binding protein 3.629 3.103 UP Os02g0169900 Q6H6B9 Inositol-1-monophosphatase 0.010 0.010 Down...”
- ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...38 65.85 1.82 Q6K6Q1 Phenylalanine ammonia-lyase 23 30.08 4.02 P14717 Phenylalanine ammonia-lyase 44 55.35 2.88 Q75W16 Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic 14 25.60 2.42 A0A0P0WP33 Phosphoglycerate kinase 41 68.18 2.27 Q6Z8F4 Phosphoribulokinase 27 57.32 1.53 Q8LMR0 Phosphoserine aminotransferase 10 26.76 1.77 P0C355 Photosystem I P700 chlorophyll a...”
- “...44 55.35 2.70 Q6K6Q1 Phenylalanine ammonia-lyase 23 30.08 3.98 Q0DZE0 Phenylalanine ammonia-lyase 22 27.91 5.86 Q75W16 Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic 14 25.60 2.49 A0A0P0WP33 Phosphoglycerate kinase 41 68.18 1.92 P0C355 Photosystem I P700 chlorophyll a apoprotein A1 19 16.80 1.56 P0C358 Photosystem I P700 chlorophyll a...”
P21357 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic from Solanum tuberosum
84% identity, 84% coverage
- Physiological and differential protein expression analyses of the calcium stress response in the Drynaria roosii rhizome.
Wu, Heliyon 2024 - “...prchiA 5.181 0.019 Q9LVD2 Cytochrome P450 71B10 CYP71B10 1.747 0.016 Secondary metabolism ( 7 ) P21357 Phospho-2-dehydro-3-deoxyheptonate aldolase 1 SHKA 42.900 0.000 P23281 3-phosphoshikimate 1-carboxyvinyltransferase 2 EPSPS-2 2.601 0.039 Q9SSE7 Arogenate dehydratase/prephenate dehydratase 2 ADT2 2.848 0.002 W5XMH0 Cinnamate 4-hydroxylase C4H 2.225 0.008 B9VV87 Cinnamate 4-hydroxylase...”
- “...) Q6Z6S1 Apoptosis inhibitor 5-like protein API5 API5 0.561 0.030 Secondary metabolism ( 5 ) P21357 Phospho-2-dehydro-3-deoxyheptonate aldolase 1 SHKA 0.026 0.001 P50303 S-adenosylmethionine synthase 3 SAM3 0.219 0.006 A9NYY0 S-adenosylmethionine synthase 2 METK2 0.270 0.011 Q9LQ04 Bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/dTDP-4-dehydrorhamnose reductase NRS/ER 0.233 0.033 A0A6C0VZT6 REF1...”
- Comparative proteomics analysis of proteins expressed in the I-1 and I-2 internodes of strawberry stolons
Fang, Proteome science 2011 - “...Q9ZWB7 acyltransferase activity Arabidopsis thaliana 52.3/6.6 16.4/6.6 57 15 8/32 66 Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic P21357 3-deoxy-7-phosphoheptulonate synthase activity Solanum tuberosum 60.0/8.9 27.9/7.3 62 31 11/71 87 Molybdenum cofactor sulfurase Q655R6 lyase activity Oryza sativa 92.9/7.1 27.2/5.2 60 12 6/22 136 Probable beta-1,3-galactosyltransferase 18 Q8RX55 galactosyltransferase...”
AT4G33510 DHS2 (3-deoxy-d-arabino-heptulosonate 7-phosphate synthase); 3-deoxy-7-phosphoheptulonate synthase from Arabidopsis thaliana
Q00218 Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic from Arabidopsis thaliana
79% identity, 92% coverage
- Photosynthetic Electron Flows and Networks of Metabolite Trafficking to Sustain Metabolism in Photosynthetic Systems
Fakhimi, Plants (Basel, Switzerland) 2024 - “...]. The Arabidopsis genome contains three DAHPS genes: At DAHPS 1 (AT4G39980), At DAHPS 2 (At4g33510), and At DAHPS 3 (At1g22410). Based on homology to Arabidopsis DAHPS, we identified a single putative DAHPS locus (Cre17.g726750_4532) on the Chlamydomonas genome. The Chlamydomonas protein has ~57% amino acid...”
- Point mutations that boost aromatic amino acid production and CO2 assimilation in plants
Yokoyama, Science advances 2022 - “...sota -like F 2 progenies identified high-frequency missense mutations from all eight lines in At4g39980, At4g33510, or At1g22410, which are the three loci encoding 3-deoxy- d - arabino -heptulosonate 7-phosphate synthase (DAHP synthase or DHS) isoforms (fig. S3 and table S1). DHS catalyzes the first reaction...”
- The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings
Koskimäki, Tree physiology 2022 - “...chorismic acid pathway were differentially expressed. BX677095 similar with 3-deoxy- d -arabino-heptulosonate-7-phosphate 2 (DAHP2) ( AT4G33510 ) had increased expression by 0.56 logFC ( P <0.01) (see Table S1 available as Supplementary data at Tree Physiology Online). BX681579 similar with 3-deoxy- d -arabino-heptulosonate 7-phosphate synthase (DHS2)...”
- The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation
Yokoyama, The Plant cell 2021 - “...has three type II DHS enzymes, AthDHS1, 2, and 3, which are encoded by AT4G39980, AT4G33510, and AT1G22410, respectively ( Supplemental Figure S1 ; Entus et al., 2002 ; Richards et al., 2006 ; Tohge et al., 2013 ). AthDHS1 has been biochemically characterized as recombinant...”
- “...exhibited drastic phenotypes under standard growth condition. (A) Schematic structural models of AthDHS1 (AT4G39980), AthDHS2 (AT4G33510), and AthDHS3 (AT1G22410) genes, with exons and introns shown in gray boxes and solid lines, respectively. The positions of the T-DNA insertion are indicated by triangles for dhs1 (SALK_055360), dhs2...”
- SNPeffect: identifying functional roles of SNPs using metabolic networks
Sarkar, The Plant journal : for cell and molecular biology 2020 - “...associated ( P value=2.67e5) with vegetative growth rate and the inactivating SNP at 16121370 in AT4G33510 (encoding DAHP synthase) was previously found to be significantly associated ( P value=9.71e5) with flowering time (Atwell et al. , 2010 ). This is possibly because amino acid metabolism is...”
- Photoprotective Acclimation of the Arabidopsis thaliana Leaf Proteome to Fluctuating Light
Niedermaier, Frontiers in genetics 2020 - “...(FL/CL) Peptides Q94AG1 AT3G07470 putative transmembrane protein (DUF538) 1.06 0.19 1.06 0.88 5 Q00218; F4JIZ3 AT4G33510 DHS2 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2 0.27 0.38 0.58 0.54 14 Q94A68 AT1G06690 NAD(P)-linked oxidoreductase superfamily protein, chloroplastic 0.33 0.31 0.40 0.40 10 Q2V2S7 AT4G37925 NDHM NDH-like complex subunit M 0.34...”
- Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
Liebthal, Antioxidants (Basel, Switzerland) 2020 - “...(AT1G64510) MECDP synthase (AT1G63970) Acyl-ACP thioesterase ATL3 (AT1G68260) HTPA synthase 1 (AT3G60880) DAHP synthase 2 (AT4G33510) Elongation factor 1 alpha (AT4G20360) TRAF-like family protein (AT3G28220) HTPA reductase 1 (AT2G44040) Adenylosuccinate synthetase (AT3G57610) CDPME kinase (AT2G26930) Ferredoxin--NADP reductase (AT1G20020) 50S ribosomal protein L27 (AT5G40950) Allene oxide synthase...”
- Ectopic RING zinc finger gene from hot pepper induces totally different genes in lettuce and tobacco
Kesawat, Molecular breeding : new strategies in plant improvement 2018 - “...protein s4 (rps4a) 2.32 At1g02780 60s ribosomal protein 3.31 At5g13650 Elongation factor family protein 2.38 At4g33510 3-Deoxy-D-arabino-heptulosonate-7-phosphate 2 (dahp2) 2.58 At5g64680 Uncharacterized gene 2.23 At5g36070 Uncharacterized gene 5.56 At3g43684 Uncharacterized gene 2.58 At2g36885 Uncharacterized gene 4.09 At2g05752 Uncharacterized gene 4.38 At5g02240 Uncharacterized gene 3.00 At1g67700 Uncharacterized...”
- More
- Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
Liebthal, Antioxidants (Basel, Switzerland) 2020 - “...3-oxoacyl-[acyl-carrier-protein] synthase 1 P52410 * Thylakoid lumenal 19 kDa protein P82658 * Phospho-2-dehydro-3-deoxyheptonate aldolase 2 Q00218 * Glutathione S-transferase F8 Q96266 * 2-Cys peroxiredoxin B Q9C5R8 * Photosystem II repair protein PSB27-H1 Q9LR64 * Peroxiredoxin Q Q9LU86 * Soluble inorganic pyrophosphatase 6 Q9LXC9 * 50 S...”
- Photoprotective Acclimation of the Arabidopsis thaliana Leaf Proteome to Fluctuating Light
Niedermaier, Frontiers in genetics 2020 - “...log 2 (FL/CL) Peptides Q94AG1 AT3G07470 putative transmembrane protein (DUF538) 1.06 0.19 1.06 0.88 5 Q00218; F4JIZ3 AT4G33510 DHS2 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2 0.27 0.38 0.58 0.54 14 Q94A68 AT1G06690 NAD(P)-linked oxidoreductase superfamily protein, chloroplastic 0.33 0.31 0.40 0.40 10 Q2V2S7 AT4G37925 NDHM NDH-like complex subunit...”
Sb01g033590 No description from Sorghum bicolor
85% identity, 81% coverage
- Shikimate and phenylalanine biosynthesis in the green lineage
Tohge, Frontiers in plant science 2013 - “...10 BD 11 OS 12 OSindica DHS Cr17g06460 Mrcc02g07760 Ot06g03510 Sb01g028770 Zm02g39200 Bd1g21330 Os03g27230 Osi07g35030 Sb01G033590 Zm04g31550 Bd1g60750 Os07g42960 Osi08g36090 Sb02G039660 Zm05g06990 Bd3g33650 Os08g37790 Osi10g31830 Sb07G029080 Bd3g38670 Os10g41480 DQS Cr08g02240 Mrcc01g05190 Ot05g01830 Sb02G031240 Zm02g34320 Bd4g36507 Os09g36800 Osi09g29080 DHQD Cr08g04550 Mrcc01g03580 Ot12g02660 Sb08G016970 Zm03g17940 Bd4g05897 Os12g34874 Osi12g23310...”
A0A3Q7H097 Phospho-2-dehydro-3-deoxyheptonate aldolase from Solanum lycopersicum
78% identity, 89% coverage
Sb02g039660 No description from Sorghum bicolor
77% identity, 89% coverage
- Shikimate and phenylalanine biosynthesis in the green lineage
Tohge, Frontiers in plant science 2013 - “...OSindica DHS Cr17g06460 Mrcc02g07760 Ot06g03510 Sb01g028770 Zm02g39200 Bd1g21330 Os03g27230 Osi07g35030 Sb01G033590 Zm04g31550 Bd1g60750 Os07g42960 Osi08g36090 Sb02G039660 Zm05g06990 Bd3g33650 Os08g37790 Osi10g31830 Sb07G029080 Bd3g38670 Os10g41480 DQS Cr08g02240 Mrcc01g05190 Ot05g01830 Sb02G031240 Zm02g34320 Bd4g36507 Os09g36800 Osi09g29080 DHQD Cr08g04550 Mrcc01g03580 Ot12g02660 Sb08G016970 Zm03g17940 Bd4g05897 Os12g34874 Osi12g23310 Zm10g05140 SK Cr10g04010 Mrcc13g02500 Ot14g03180...”
F2D2N1 Phospho-2-dehydro-3-deoxyheptonate aldolase from Hordeum vulgare subsp. vulgare
84% identity, 85% coverage
GRMZM2G365160 uncharacterized protein LOC100501272 from Zea mays
76% identity, 90% coverage
- Transcriptional analyses of natural leaf senescence in maize
Zhang, PloS one 2014 - “...phospho-2-dehydro-3-deoxyheptonate aldolase 2 chloroplast, thylakoid GRMZM2G161337 1.39 0.84 AT2G29690 ASA2 anthranilate synthase component I-2 chloroplast GRMZM2G365160 2.04 2.13 AT1G22410 \ 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...”
AROG2_PETHY / A0A067XGX8 Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 from Petunia hybrida (Petunia) (see paper)
78% identity, 92% coverage
- function: Involved in the production of volatile organic compounds (VOCs) (PubMed:24815009). Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) and inorganic phosphate (By similarity).
catalytic activity: D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7- phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate (RHEA:14717)
cofactor: Mn(2+) (Binds 1 divalent metal cation per subunit that could be manganese.)
subunit: Homodimer.
disruption phenotype: Normal floral volatile benzenoids and phenylpropanoids (FVBP) emission.
D0VBC1 Phospho-2-dehydro-3-deoxyheptonate aldolase from Vitis vinifera
80% identity, 88% coverage
A0A0A0L679 Phospho-2-dehydro-3-deoxyheptonate aldolase from Cucumis sativus
79% identity, 86% coverage
GRMZM2G396212 uncharacterized protein LOC100274492 from Zea mays
74% identity, 86% coverage
PA2843 probable aldolase from Pseudomonas aeruginosa PAO1
62% identity, 85% coverage
- Pseudomonas aeruginosa Citrate Synthase GltA Influences Antibiotic Tolerance and the Type III Secretion System through the Stringent Response
Chen, Microbiology spectrum 2023 - “..., and the glycerol-3-phosphate dehydrogenase gene gpsA decreased cytotoxicity, whereas mutation in the aldolase gene PA2843 increased cytotoxicity ( 38 ). Further studies are needed to elucidate the interrelationship between metabolism, the stringent response, cAMP, and the T3SS. Overall, our results demonstrated that a PA14 gltA...”
- A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
Glanville, mSystems 2021 - “...PA1758 ]), and several within the AroBCDEFG operon ( aroG1 [ PA1750 ], aroG2 [ PA2843 ], and again PhzH [ PA0051 ]) ( 85 ) ( Fig.S4 ; TableS1A to C ). Also noteworthy, Met-Seq identified two enriched Tn insertions within the vanillin synthesis operon...”
- TpiA is a Key Metabolic Enzyme That Affects Virulence and Resistance to Aminoglycoside Antibiotics through CrcZ in Pseudomonas aeruginosa
Xia, mBio 2020 - “...genes displayed reduced cytotoxicity toward the human alveolar epithelial cell A549, whereas the gltA and PA2843 mutants displayed enhanced cytotoxicity (see Fig.S1 in the supplemental material). Meanwhile, mutants of gltA , fumC1 , pykF , and lpd3 were less susceptible to tobramycin, while the zwf and...”
- A Pseudoisostructural Type II DAH7PS Enzyme from Pseudomonas aeruginosa: Alternative Evolutionary Strategies to Control Shikimate Pathway Flux
Sterritt, Biochemistry 2018 (PubMed) (secret) - Sensitizing bacterial cells to antibiotics by shape recovery triggered biofilm dispersion
Lee, Acta biomaterialia 2018 - “...are related to ATP or metabolic activities ( Fig. 5a ). Among these genes, cynT, PA2843, mdlC, katB, phnW, hisD, and PA5312 were up-regulated and PA2550 , acsA , hdhA , and glpK were down-regulated. For ATP-related genes, nirQ was up-regulated by 3.1-fold, while kdpB was...”
- Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass
Sterritt, Bioscience reports 2018 - “...The type II DAH7PSs are encoded by the ORFs PA1901 (and duplicated as PA4212) and PA2843 ( Pae DAH7PS PA1901 and Pae DAH7PS PA2843 respectively). The structure and properties of Pae DAH7PS PA2843 have recently been reported [ 33 ] and show that Pae DAH7PS PA2843...”
- “...Mtu DAH7PS or Cgl DAH7PS. Although the quaternary assemblies of Mtu DAH7PS and Pae DAH7PS PA2843 resemble each other, there are some differences in orientation of the extra-barrel elements within the tetramer, such that Pae DAH7PS PA2843 is inhibited by only Trp and is unaffected by...”
5uxmA / Q9I000 Type ii dah7ps from pseudomonas aeruginosa with trp bound (see paper)
62% identity, 85% coverage
- Ligands: phosphoenolpyruvate; tryptophan; phosphate ion; cobalt (ii) ion (5uxmA)
B7FRJ9 Phospho-2-dehydro-3-deoxyheptonate aldolase from Phaeodactylum tricornutum (strain CCAP 1055/1)
59% identity, 86% coverage
PflSS101_1729 class II 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas lactis
60% identity, 84% coverage
- Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP
Song, BMC microbiology 2015 - “...1.27 PflSS101_1626 short-chain alcohol dehydrogenase family protein 1.53 1.23 PflSS101_1652 cmk cytidylate kinase 1.35 1.36 PflSS101_1729 3-deoxy-7-phosphoheptulonate synthase 1.28 2 PflSS101_2196 AP endonuclease, family 2 1.65 2.12 PflSS101_3195 cold shock domain protein CspD 2.14 3.15 PflSS101_3348 bkdA2 2-oxoisovalerate dehydrogenase E1 component, beta subunit 1.26 1.23 PflSS101_3776...”
PP1866 phospho-2-dehydro-3-deoxyheptonate aldolase, class II from Pseudomonas putida KT2440
61% identity, 85% coverage
XP_024399688 phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic-like isoform X3 from Physcomitrium patens
67% identity, 78% coverage
- Connecting moss lipid droplets to patchoulol biosynthesis
Peramuna, PloS one 2020 - “...DN26229 (D) XP_024400099 copper chaperone for superoxide dismutase DN26375 (U) XP_024382195 uncharacterized protein DN27466 (D) XP_024399688 phospho-2-dehydro-3-deoxyheptonate aldolase 2 DN29028 (N) N/A uncharacterized protein DN29463 (D) NP_904206.1 PSII 44 kD protein DN30687 (D) N/A uncharacterized protein DN32215 (U) PNR26297 UDP-glycosyltransferase 83A1-like DN32629 (N) N/A uncharacterized protein...”
Q4K8T7 Phospho-2-dehydro-3-deoxyheptonate aldolase from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
60% identity, 84% coverage
- Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5
McKew, MicrobiologyOpen 2021 - “...to ketoglutarate (Wootton, 1983 ); Damino acid dehydrogenase (Q4K3T7, p =0.007), 3deoxy7phosphoheptulonate synthase class II (Q4K8T7, p =0.028), glycine dehydrogenase aminomethyltransferring protein (Q4K416, p =0.018); urocanate hydratase (Q4KJN8, p =0.010) involved in histidine degradation; a Fe(II)containing nonheme oxygenase (4hydroxyphenylpyruvate dioxygenase, Q4KB91, p =0.001) involved in tyrosine...”
M217_RS0108615 class II 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas chlororaphis HT66
60% identity, 84% coverage
CC2300 phospho-2-dehydro-3-deoxyheptonate aldolase, class II from Caulobacter crescentus CB15
57% identity, 86% coverage
- Global regulation of gene expression and cell differentiation in Caulobacter crescentus in response to nutrient availability
England, Journal of bacteriology 2010 - “...fatty acid-CoA ligase CC0094 dichloro-cyclohexadiene dehydrogenase CC2300 aldolase, class II CC1201 aldolase, class II CC0337 succinyl-CoA synthetase CC1726...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...amino acid and histidine synthesis CC2300, phospho-2-dehydro-3-deoxyheptonate aldolase, aroG CC2534, histidinol-phosphate aminotransferase, hisC 0.34 3.99 0.33...”
- “...tryptophan, tyrosine, and phenylalanine, only CC2300 (encoding 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, the first enzyme of the chorismate pathway)...”
BMEI0971 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE from Brucella melitensis 16M
61% identity, 85% coverage
- Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis
Halling, Journal of bacteriology 2005 - “...Homologs of B. melitensis 16 M loci BMEI0888, BMEI0943, BMEI0971, BMEI1055, BMEI1331, and BMEI919 missing in B. abortus S2308 were also missing in B. abortus...”
- “...sequence of B. abortus 9-941, namely BMEI0943, BMEI0971, BMEI1055, BMEII25, BMEI1331, BMEI1380, and BME1919. Evolutionary and genomic analyses. SNPs were...”
- Molecular characterization of Brucella abortus chromosome II recombination
Tsoktouridis, Journal of bacteriology 2003 - “...II II I I BMEI0888 BMEI0929 BMEI0943 BMEI0971 BMEI1055 BMEI1125 BMEI1331 BMEI1380 BMEI1661 BMEI1661 BMEI1919 BMEI1921 BMEI1921 BMEII0292 BMEII0717 BMEII0722...”
BruAb1_1018 Dhs, phospho-2-dehydro-3-deoxyheptonate aldolase, class II from Brucella abortus biovar 1 str. 9-941
61% identity, 85% coverage
jhp0122 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE from Helicobacter pylori J99
Q9ZMU5 Phospho-2-dehydro-3-deoxyheptonate aldolase from Helicobacter pylori (strain J99 / ATCC 700824)
55% identity, 85% coverage
HP0134 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (dhs1) from Helicobacter pylori 26695
O24947 Phospho-2-dehydro-3-deoxyheptonate aldolase from Helicobacter pylori (strain ATCC 700392 / 26695)
55% identity, 84% coverage
F4JIZ3 Phospho-2-dehydro-3-deoxyheptonate aldolase from Arabidopsis thaliana
76% identity, 62% coverage
Cj0716 putative phospho-2-dehydro-3-deoxyheptonate aldolase from Campylobacter jejuni subsp. jejuni NCTC 11168
54% identity, 85% coverage
- Chicken Juice Enhances C. jejuni NCTC 11168 Biofilm Formation with Distinct Morphological Features and Altered Protein Expression
Sung, Foods (Basel, Switzerland) 2024 - “...2.94 Cj0604 ppk-2 Polyphosphate kinase S 1.28 Cj0709 ffh Signal recognition particle protein U 2.15 Cj0716 Phospho-2-dehydro-3-deoxyheptonate aldolase E 1.11 Cj0732 ABC transporter ATP-binding protein P 24.90 Cj0882c flhA Flagellar biosynthesis protein N 3.48 Cj0996 ribA GTP cyclohydrolase II F 23.69 Cj1014c livF ABC transporter ATP-binding...”
- Genome-wide insights into population structure and host specificity of Campylobacter jejuni
Epping, Scientific reports 2021 - “...family protein 678,288 P Inorganic ion transport and metabolism 26 56 90 255 63 V Cj0716 Aro F Putative phospho-2-dehydro-3-deoxyhep-tonate aldolase 678,951 E Amino acid transport and metabolism 26 56 90 255 63 V Cj0715 ura H Transthyretin-like periplasmic protein 676,514 S Function unknown 26 56...”
- EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
Magoc, Evolutionary bioinformatics online 2013 - “...genes. Our 20 genes include these 17 genes as well as 3 additional genes ( Cj0716 , Cj0044c , Cj1004 ). The 3 additional genes had the smallest change in expression; if we used a threshold of 5-fold rather than 4-fold, we would identify precisely the...”
- “...below the threshold for reporting a change in the Chaudhuri et al study. 15 Only Cj0716 , which had a 2-fold change in Chaudhuri et al, was well below their threshold. Sixteen of the 17 downregulated genes were also reported as significantly downregulated in a separate...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj0435, cj0437, cj0443, cj0453, cj0490, cj0541, cj0542, cj0559, cj0576, cj0580c, cj0585, cj0589, cj0638c, cj0647, cj0699c, cj0716, cj0764c, cj0766c, cj0767c, cj0795c, cj0798c, cj0806, cj0813, cj0821, cj0822, cj0847, cj0853c, cj0858c, cj0862c, cj0891c, cj0905c, cj0918c, cj0932c, cj0947c, cj0949c, cj0955c, cj0992c, cj0995c, cj1039, cj1044c, cj1046c, cj1048c, cj1067, cj1080c, cj1081c, cj1088c,...”
D6A8C0 Phospho-2-dehydro-3-deoxyheptonate aldolase from Streptomyces viridosporus (strain ATCC 14672 / DSM 40746 / JCM 4963 / KCTC 9882 / NRRL B-12104 / FH 1290)
54% identity, 84% coverage
CF54_24340 class II 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. Tu 6176
54% identity, 84% coverage
- Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937
Losada, Microbial biotechnology 2017 - “...by sequence homology, together with their orthologues from nataxazol producer Streptomyces sp. T6176, natAL and CF54_24340 (located outside nataxazole biosynthetic cluster). Protein sequence alignments show that CbxF presents higher identity to CbxF (62%) and NatAL (46%) than to CbxF (42%). Besides, CbxF is 91% identical to...”
- “...an enzyme required for primary metabolism as the first dedicated step in the chorismate pathway, CF54_24340 and cbxF might fulfil this role in their respective strains, which leaves out cbxF as the putative paralogue of cbxF for caboxamycin biosynthesis. Nevertheless, a double mutant strain cbxF/F is...”
P80574 Phospho-2-dehydro-3-deoxyheptonate aldolase from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SCO2115 2-dehydro-3-deoxyphosphoheptonate aldolase from Streptomyces coelicolor A3(2)
54% identity, 84% coverage
- Evidence for a novel class of microbial 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase in Streptomyces coelicolor A3(2), Streptomyces rimosus and Neurospora crassa
Walker, Microbiology (Reading, England) 1996 (PubMed) (secret) - Biosynthesis of Tropolones in Streptomyces spp.: Interweaving Biosynthesis and Degradation of Phenylacetic Acid and Hydroxylations on the Tropone Ring
Chen, Applied and environmental microbiology 2018 - “...and utilization of chorismate, i.e., DAHP synthase (SCO2115), prephenate dehydratase (SCO3962), and chorismate mutase (SCO1762, SCO2019, and SCO4784), which are...”
- New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures
Hesketh, BMC genomics 2007 - “...were apparently unaffected, with the exceptions of aromatic amino acid biosynthesis (SCO1496, chorismate synthase; and SCO2115, one of two aroH -like genes for the first step) and biotin biosynthesis (SCO1244, 1246); and among the central pathways of primary carbon metabolism (glycolysis, the pentose phosphate pathway, the...”
- “...1 peptidyl-prolyl cis-trans isomerase CypH Positive correlation in set B SCO1212 100 1 putative ligase SCO2115 100 1 putative 2-dehydro-3-deoxyphosphoheptonate aldolase AroH SCO2539 100 1 Era-like GTP-binding protein SCO3801 100 1 putative aminopeptidase SCO3907 100 1 single strand DNA-binding protein ssb SCO4809 100 1 succinyl CoA...”
WP_031081129 class II 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. NRRL WC-3549
54% identity, 84% coverage
DT87_05590 class II 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. NTK 937
53% identity, 84% coverage
Q6YH16 Phospho-2-dehydro-3-deoxyheptonate aldolase (Fragment) from Vitis vinifera
86% identity, 49% coverage
- Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor
Zamboni, BMC genomics 2009 - “...O24051 TC74975 x 1611211_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase precursor O24046 TC57386 x 1614440_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase Q6YH16 TC54321 x 1619357_at 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase O24046 TC57642 x 1621405_at Plastidic 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2 O22407 TC51974 x 1609646_at 3-Dehydroquinate synthase-like protein Q9FKX0 TC56854 x 1609932_at Prephenate dehydratase Q6JJ29 TC53641...”
B488_07360, B488_RS03555 3-deoxy-7-phosphoheptulonate synthase class II from Liberibacter crescens BT-1
49% identity, 85% coverage
- A synthetic 'essentialome' for axenic culturing of 'Candidatus Liberibacter asiaticus'
Cai, BMC research notes 2022 - “...B488_RS03185 (YqcI/YcgG family protein); B488_RS03190 (dTDP-sugar isomerase, biosynthesis of L-rhamnose); B488_RS03535 (ATP synthase subunit B); B488_RS03555 (3-deoxy-7-phosphoheptulonate synthase; aromatic amino acid biosynthesis); B488_RS03865 (dihydroneopterin aldolase, folate biosynthesis); B488_RS04330 (RNase H fold-containing effector); B488_RS05025 (DUF1134 domain-containing protein); B488_RS05105 (GAF domain containing protein); B488_RS05600 (porin family); B488_RS05940 (DUF4164...”
- 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 - “...L. crescens genome codes for 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...”
SACE_2874 phospho-2-dehydro-3-deoxyheptonate aldolase from Saccharopolyspora erythraea NRRL 2338
52% identity, 83% coverage
WP_118914924 class II 3-deoxy-7-phosphoheptulonate synthase from Dermacoccus abyssi
50% identity, 83% coverage
ZMO0187 3-deoxy-7-phosphoheptulonate synthase from Zymomonas mobilis subsp. mobilis ZM4
48% identity, 83% coverage
SCO3210 2-dehydro-3-deoxyheptonate aldolase from Streptomyces coelicolor A3(2)
46% identity, 92% coverage
- The Inhibition of Antibiotic Production in Streptomyces coelicolor Over-Expressing the TetR Regulator SCO3201 IS Correlated With Changes in the Lipidome of the Strain
Zhang, Frontiers in microbiology 2020 - “...1.243 sco6204 Putative catalase 0 1.179 Aromatic amino acids biosynthesis sco1859 Putative aminotransferase 1.243 0 sco3210 Putative 2-dehydro-3-deoxyheptonate aldolase 1.470 1.906 sco3211 Putative indoleglycerol phosphate synthase 1.850 2.150 sco3212 Probable anthranilate phosphoribotransferase 1.892 1.414 sco3213 Probable anthranilate synthase component II 2.142 0 sco3214 Probable anthranilate synthase...”
- “...sco3201 . The expression of 35 among the 39 genes of the CDA cluster ( sco3210 - sco3249 ) was down-regulated at 24 and 36 h ( Figure 3 and Supplementary Data ), whereas the level of expression of the transcriptional activator CdaR ( sco3217 )...”
- Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon
Bekiesch, PloS one 2016 - “...has similarities to cation-transporting ATPases involved in Mg-transport, and the operon spanning from sco3215 to sco3210 . The latter genes are organized in one operon with maximum 3 bp intergenic region between each gene and are predicted to be involved in tryptophan synthesis. Sco3210 has similarities...”
- “...when fed with tyrosine or casamino acids. As a putative member of the RokB regulon Sco3210 is one of two DAHP synthetases found in S . coelicolor . Sco3215 to Sco3211 are probably involved in tryptophan synthesis. Further putative RokB regulated genes are sco6114 sco6110 ,...”
- A terD domain-encoding gene (SCO2368) is involved in calcium homeostasis and participates in calcium regulation of a DosR-like regulon in Streptomyces coelicolor
Daigle, Journal of bacteriology 2015 - “...the gene cluster responsible for calcium-dependent antibiotic production (SCO3210 to SCO3222 and SCO3227 to SCO3249) and two conserved operons (cvn7 and cvn9)...”
- Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
Alam, BMC genomics 2010 - “...the middle 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...”
- Role of phosphopantetheinyl transferase genes in antibiotic production by Streptomyces coelicolor
Lu, Journal of bacteriology 2008 - “...metabolism genes (for example, the CDA gene cluster is SCO3210 to SCO3249) (1). We have constructed SCO6673 and redU single mutants as well as the corresponding...”
- The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)
Hesketh, Genome biology 2007 - “...hopanoids ( SCO6759 - 71 ), eicosapentaenoic acid ( SCO0124 - 29 ), CDA ( SCO3210 - 49 ), an unknown deoxysugar/glycosyltransferase product ( SCO0381 - 0401 ), and an unknown type I polyketide synthase product ( SCO6273 - 88 ) were affected, as illustrated in...”
SACE_1708 phospho-2-dehydro-3-deoxyheptonate aldolase from Saccharopolyspora erythraea NRRL 2338
49% identity, 82% coverage
O68903 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) from Actinosynnema pretiosum subsp. auranticum (see paper)
49% identity, 82% coverage
PAAG_03237 phospho-2-dehydro-3-deoxyheptonate aldolase from Paracoccidioides lutzii Pb01
48% identity, 84% coverage
- Transcriptional profile of Paracoccidioides spp. in response to itraconazole
da, BMC genomics 2014 - “...genome locus e-value Number of occurrences a 1h 2h Metabolism/Energy 3-deoxy-7-phosphoheptulonate synthase ( DAHP ) PAAG_03237 9.2e-29 +2 Cysteine desulfurase ( CYSD ) PAAG_05850 2.2e-58 +22 Betaine aldehyde dehydrogenase ( BADH ) PAAG_05392 2.1e-19 +2 NADP-specific glutamate dehydrogenase ( GDH ) PAAG_07689 1.6e-26 +1 NAD dependent...”
MMAR_1854 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG_1 from Mycobacterium marinum M
49% identity, 82% coverage
MMAR_3222 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG from Mycobacterium marinum M
49% identity, 82% coverage
AROG_MYCTU / O53512 Phospho-2-dehydro-3-deoxyheptonate aldolase AroG; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase; DAHP synthase; Phospho-2-keto-3-deoxyheptonate aldolase; EC 2.5.1.54 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
O53512 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) from Mycobacterium tuberculosis (see 3 papers)
Rv2178c Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible) from Mycobacterium tuberculosis H37Rv
NP_216694 phospho-2-dehydro-3-deoxyheptonate aldolase AroG from Mycobacterium tuberculosis H37Rv
48% identity, 82% coverage
- function: Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) and inorganic phosphate.
catalytic activity: D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7- phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate (RHEA:14717)
cofactor: Mn(2+) Co(2+) Cd(2+) (Binds 1 divalent cation per subunit. The enzyme is active with manganese, cobalt or cadmium ions.)
subunit: Homodimer. Interacts with Rv0948c. - Evaluation of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase (DAHPS) as a Vulnerable Target in Mycobacterium tuberculosis
Galina, Microbiology spectrum 2022 - “...for M. tuberculosis to target different regions inside the coding sequence of the aroG gene (Rv2178c for M. tuberculosis and MSMEG_4244 for M. smegmatis ), where three different PAM (protospacer adjacent motif) sequences were located ( Fig.1 ). PAM sequences selected for M. smegmatis were 5-NNGGAAC-3,...”
- Two interacting ATPases protect Mycobacterium tuberculosis from glycerol and nitric oxide toxicity
Whitaker, Journal of bacteriology 2020 (secret) - A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis
Jiao, The Journal of biological chemistry 2020 (secret) - Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance
Fahrig-Kamarauskait, The Journal of biological chemistry 2020 - “..., aroQ ) has evolved to transiently interact with DS (MtDS, a tetramer encoded by Rv2178c , aroG ) to form a heterooctameric complex ( Fig. 1 B ). Only the complexed, but not the free dimeric MtCM, is responsive to feedback regulation by Phe and...”
- Remote Control by Inter-Enzyme Allostery: A Novel Paradigm for Regulation of the Shikimate Pathway
Munack, Journal of molecular biology 2016 (PubMed)- “...the first enzyme of the pathway, DAHP synthase (MtDS; Rv2178c), through formation of a non-covalent MtCMMtDS complex. Here, we show how MtDS serves as an...”
- “...complex Mycobacterium tuberculosis Rv2178c and Rv0948c X-ray crystal structure...”
- Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
Anand, Scientific reports 2014 - “...syndrome. Colchicin (DB01394;LOC) 0.57 Rv0032; Rv0474; Rv0570; Rv0732; Rv1181; Rv1296; Rv1300; Rv1380; Rv1655; Rv2113; Rv2156c; Rv2178c; Rv2281; Rv2524c; Rv3037c; Rv3712; Rv3882c; Rv3886c; For treatment and relief of pain in attacks of acute gouty arthritis. Podofilox (DB01179;POD) 0.56 Rv0474; Rv0570; Rv0732; Rv0904c; Rv1181; Rv1296; Rv1300; Rv1550; Rv1650;...”
- Withdrawn
, Infectious disorders drug targets 2012 - “...is not present in mammals and is necessary in Mtb [ 95 ]. Chorismate mutase (Rv2178c) The Mtb enzyme chorismate mutase (CM), an AroQ type CM enzyme that is part of both the phenylalanine and tyrosine biosynthetic pathways, catalyzes the rearrangement of chorismate to prephenate [...”
- A novel noncovalent complex of chorismate mutase and DAHP synthase from Mycobacterium tuberculosis: protein purification, crystallization and X-ray diffraction analysis
Okvist, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - “...complex with another shikimatepathway enzyme, DAHP synthase (MtDS; Rv2178c; 472 amino-acid residues; 52 kDa), which has been shown to enhance the catalytic...”
- “...residues upon the addition of DAHP synthase (MtDS; Rv2178c; Sasso et al., 2009). Here, we report the production, purification and crystallization of MtCM as...”
- More
- Remote Control by Inter-Enzyme Allostery: A Novel Paradigm for Regulation of the Shikimate Pathway.
Munack, Journal of molecular biology 2016 (PubMed)- GeneRIF: Here, the authors show how DAHP synthase serves as an allosteric platform for feedback regulation of both enzymes, DAHP synthase and chorismate mutase.
- Three sites and you are out: ternary synergistic allostery controls aromatic amino acid biosynthesis in Mycobacterium tuberculosis.
Blackmore, Journal of molecular biology 2013 (PubMed)- GeneRIF: Synergistic inhibition of aroG by a combination of tryptophan and phenylalanine can be significantly augmented by the addition of tyrosine.
- Structure and function of a complex between chorismate mutase and DAHP synthase: efficiency boost for the junior partner.
Sasso, The EMBO journal 2009 - GeneRIF: The intracellular chorismate mutase of Mycobacterium tuberculosis (MtCM; Rv0948c) has poor activity and lacks prominent active-site residues. However, its catalytic efficiency increases >100-fold on addition of DAHP synthase (MtDS; Rv2178c).
- A novel noncovalent complex of chorismate mutase and DAHP synthase from Mycobacterium tuberculosis: protein purification, crystallization and X-ray diffraction analysis.
Okvist, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: MtCM was crystallized alone and in complex with MtDS. The crystals diffracted to 1.6 and 2.2 A resolution, respectively.
- DAHP synthase from Mycobacterium tuberculosis H37Rv: cloning, expression, and purification of functional enzyme.
Rizzi, Protein expression and purification 2005 (PubMed)- GeneRIF: Cloning, expression, and purification of DAHP synthase.
- The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes.
Webby, Journal of molecular biology 2005 (PubMed)- GeneRIF: crystal structure in complex with phosphoenolpyruvate and Mn(2+) reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The arrangement of residues in the active site, and the binding modes of PEP and Mn(2+) match those of the type I enzymes
MUL_3533 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG_1 from Mycobacterium ulcerans Agy99
49% identity, 82% coverage
3nv8B / O53512 The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free) (see paper)
48% identity, 82% coverage
- Ligands: manganese (ii) ion; phosphate ion (3nv8B)
B1MP18 Phospho-2-dehydro-3-deoxyheptonate aldolase from Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)
MAB_1987 Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG from Mycobacterium abscessus ATCC 19977
48% identity, 82% coverage
MSMEG_4244 3-deoxy-7-phosphoheptulonate synthase from Mycobacterium smegmatis str. MC2 155
48% identity, 82% coverage
- Evaluation of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase (DAHPS) as a Vulnerable Target in Mycobacterium tuberculosis
Galina, Microbiology spectrum 2022 - “...DAHPS) whereas in M. smegmatis this enzyme ( Msg DAHPS) is encoded by the ortholog MSMEG_4244 . According to a pairwise alignment ( 6 ), M. tuberculosis and M. smegmatis share 87.3% identity and 94.0% of similarity between the protein sequences, suggesting a high conservation between...”
- “...be targeted by three different sgRNAs ( Fig.1A ). FIG1 Location of PAM sequences inside MSMEG_4244 and aroG locus used in this study. (A) From left to right: 5-NNAGGAC-3, 5-NNGGAAC-3, 5-NNAGCAG-3. (B) From left to right: 5-NNGGAAG-3, 5-NNAGCAG-3, and 5-NNGGCAG-3. The repression strength of each PAM...”
- Elimination of PknL and MSMEG_4242 in Mycobacterium smegmatis alters the character of the outer cell envelope and selects for mutations in Lsr2
Báez-Ramírez, Cell surface (Amsterdam, Netherlands) 2021 - “...1500bp fragments, one containing MSMEG_4241 and MSMEG_4243 ( pknL ) and the other MSMEG_4242 and MSMEG_4244 ( Fig. 1 Ba) were amplified from an M. smegmatis boiled lysate with primers 1KOFw4242-1KORv4242, 2KOFw4242-2KORv4242 and 1KOFw4243-1KORv4243, 2KOFw4243-2KORv4243 ( Table S1 ). The amplified fragments containing MSMEG_4242 were cut...”
PADG_03114 3-deoxy-7-phosphoheptulonate synthase from Paracoccidioides brasiliensis Pb18
47% identity, 84% coverage
5hudD / Q8NNL5 Non-covalent complex of and dahp synthase and chorismate mutase from corynebacterium glutamicum with bound transition state analog (see paper)
48% identity, 82% coverage
- Ligands: manganese (ii) ion; tryptophan (5hudD)
NCgl2098 class II 3-deoxy-7-phosphoheptulonate synthase from Corynebacterium glutamicum ATCC 13032
cg2391 phospho-2-dehydro-3-deoxyheptonate aldolase from Corynebacterium glutamicum ATCC 13032
48% identity, 82% coverage
- Metabolic engineering with adaptive laboratory evolution for phenylalanine production by Corynebacterium glutamicum
Tachikawa, Journal of bioscience and bioengineering 2024 (PubMed)- “...from the 4FP-resistant mutants revealed that the mutations in the open reading frames of aroG (NCgl2098), pheA (NCgl2799) and aroP (NCgl1062) encoding 3-deoxy-d-arabino-heptulosonate-7-phosphate, prephenate dehydratase, and aromatic amino acid transporter are responsible for 4FP resistance and higher concentration of aromatic amino acids in their culture supernatants...”
- Artificial cell factory design for shikimate production in Escherichia coli
Lee, Journal of industrial microbiology & biotechnology 2021 - “...highest shikimate productivity after E. coli . After constructing the genetic modules of the aroG (NCgl2098), aroB (NCgl1559), aroD (NCgl0408), and aroE (NCgl1567) genes based on the selected RBS libraries, C. glutamicum RES167 aroK carrying an efficient genetic module produced 7.4 and 11.3 g/l of shikimate...”
- Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities
Sato, Frontiers in bioengineering and biotechnology 2020 - “...Key genes located on the C. glutamicum chromosome are DAHP synthase, encoded by aroG (cg2391, NCgl2098); DHQ synthase, encoded by aroB (cg1827, NCgl1559); DHS synthase, encoded by qsuC (cg0503, NCgl0408); shikimate dehydrogenase, encoded by aroE1 (cg1283, NCgl1087); and aroE3 (cg1835, NCgl1567). Although C. glutamicum carries the...”
- Ribosome binding site libraries and pathway modules for shikimic acid synthesis with Corynebacterium glutamicum
Zhang, Microbial cell factories 2015 - “...SA pathway that are regulated by a same Ptac promoter. Firstly, aro genes [ aroG (NCgl2098), aroB (NCgl1559), aroD (NCgl0408) and aroE (NCgl1567)] from Corynebacterium glutamicum and ribosome binding site (RBS) libraries that were tailored for the above genes were obtained, and the strength of each...”
- Genetic and biochemical identification of the chorismate mutase from Corynebacterium glutamicum
Li, Microbiology (Reading, England) 2009 (PubMed)- “...synthases (DS0950 and DS2098, formerly NCgl0950 and NCgl2098) had been previously identified from C. glutamicum. CM0819 significantly stimulated DAHP synthase...”
- “...(DAHP) synthases (DS0950 and DS2098, formerly NCgl0950 and NCgl2098) had been previously identified from C. glutamicum. CM0819 interacted with DS2098 from C....”
- Corynebacterium glutamicum contains 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that display novel biochemical features
Liu, Applied and environmental microbiology 2008 - “...ATCC 13032, two chromosomal genes, NCgl0950 (aroF) and NCgl2098 (aroG), were located that encode two putative DAHP synthases. The deletion of NCgl2098 resulted...”
- “...and mutants of C. glutamicum RES167 indicated that NCgl2098, rather than NCgl0950, was involved in the biosynthesis of aromatic amino acids. Cloning and...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...NCgl1342 NCgl1343 NCgl1344 NCgl1345 NCgl1346 NCgl1347 NCgl1446 NCgl2098 NCgl2528 cg0104 cg0113 cg0114 cg0115 cg0116 cg0117 cg0118 cg0119 cg0229 cg0230 cg1256...”
- A 4-hydroxybenzoate 3-hydroxylase mutant enables 4-amino-3-hydroxybenzoic acid production from glucose in Corynebacterium glutamicum
Nonaka, Microbial cell factories 2023 - “...(cg1996), cglIR (cg1997), cglIIR (cg1998) [ 62 ] KC265 HT23 derivate; P tuf _ aroG (cg2391) This study KC282 KC265 derivate; P tuf _ aroE3 (cg1835) This study KC300 KC282 derivate; P tuf _ aroB (cg1827) This study KC314 KC300 derivate; P tuf _ aroA (cg0873)...”
- Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities
Sato, Frontiers in bioengineering and biotechnology 2020 - “...). Key genes located on the C. glutamicum chromosome are DAHP synthase, encoded by aroG (cg2391, NCgl2098); DHQ synthase, encoded by aroB (cg1827, NCgl1559); DHS synthase, encoded by qsuC (cg0503, NCgl0408); shikimate dehydrogenase, encoded by aroE1 (cg1283, NCgl1087); and aroE3 (cg1835, NCgl1567). Although C. glutamicum carries...”
- “...slightly increased compared with those of SA-2 ( Figure 6C ), suggesting that a gene cg2391 deletion had little influence on aroG transcription level ( Figure 4D ). Alternatively, in the case of the SA-7 strain, in which aroG and aroB are integrated under the control...”
- Physiological Response of Corynebacterium glutamicum to Indole
Walter, Microorganisms 2020 - “...cg1635 putative membrane protein 1.51 cg1710 bacA undecaprenol kinase 1.77 cg2096 putative membrane protein 1.59 cg2391 aroG 3-deoxy-7-phosphoheptulonate synthase 1.54 cg2500 putative transcriptional regulator. ArsR-family 1.59 cg2559 aceB malate synthase 1.79 cg2560 aceA isocitrate lyase 2.34 cg2719 putative enterochelin esterase 1.6 cg2836 sucD succinate-CoA ligase (ADP-forming),...”
- Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum
Lubitz, BMC microbiology 2016 - “...0.003 cg0712 - Putative secreted protein 1.08 0.014 cg3106 - Conserved hypothetical protein 1.03 0.029 cg2391 aroG 3-Deoxy-7-phosphoheptulonate synthase -1.26 0.022 cg0203 iolE Putative myo-inosose-2 dehydratase -1.25 0.009 cg1342 narJ Respiratory nitrate reductase 2, delta chain -1.13 0.041 cg2378 mraZ Putative MraZ protein -1.13 0.023 cg2118...”
- The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum
Brune, Journal of bacteriology 2007 - “...cg1413 cg1412 cg1658 cg1453 cg1411 cg1129 cg2893 cg1410 cg2391 cg3359 cg2894 cg1612 cg3362 cg2565 cg3361 cg1419 cg2610 cg3360 cg2837 cg2137 cg2836 cg0303 cg3047...”
- “...sequences present upstream of the cg1412 (rbsC), cg1486, cg1617, cg2391 (aroG), and cg2545 genes were used (Fig. 4B). The specificity of the DNA band shift with...”
- Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway
Mormann, BMC genomics 2006 - “...biosynthesis [93] f 5 Arginine cg1586 argG (1) Argininosuccinate synthase Arginine biosynthesis [94] 6 Phenylalanine cg2391 cg3207 aroG (2) pheA (4) Phospho-2-dehydro-3deoxyheptonate aldolase, Prephenate dehydratase Phenylalanine biosynthesis [95] [96] 16 Histidine cg2299 , cg2303 , cg2305 , cg1699 , cg2297 , cg1698 , cg2296, cg0910 hisA...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg1580 cg1581 cg1582 cg1583 cg1584 cg1585 cg1586 cg1588 cg1697 cg2391 cg2900 codAb ureA ureB ureC ureE ureF ureG ureD gltB gltD dapD glnA leuA aroA aroF argS...”
DIP1616 class II 3-deoxy-7-phosphoheptulonate synthase from Corynebacterium diphtheriae NCTC 13129
49% identity, 82% coverage
Pc18g02920 uncharacterized protein from Penicillium rubens
47% identity, 84% coverage
- A Penicillium rubens platform strain for secondary metabolite production
Pohl, Scientific reports 2020 - “...4xKO strain. The entry reaction into the shikimate pathway is mediated by the 3-deoxy-7-phosphoheptulonate synthase (Pc18g02920, log2 FC 0.5) and subsequent enzymes showed also increased expression such as the anthranilate synthase (Pc13g12290, log2 FC 0.4). Further, the fate of aromatic amino acids differs, as the expression...”
MicB006_3510 class II 3-deoxy-7-phosphoheptulonate synthase from Micromonospora sp. B006
47% identity, 83% coverage
DKG71_31600 3-deoxy-7-phosphoheptulonate synthase class II from Streptomyces sp. NEAU-S7GS2
44% identity, 81% coverage
- Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2
Liu, Frontiers in microbiology 2019 - “...The missing phzA (DKG71_22560) was detected to be far away from phzGFEDB , and phzC (DKG71_31600) were detected to be adjacent to phzGFEDB by BLASTp analysis. In addition, there are some genes encoding peptide synthases (DKG71_31585, DKG71_31630, DKG71_31620), the genes related to shikimate pathway (DKG71_08835, DKG71_08840,...”
Sare_1254 3-deoxy-7-phosphoheptulonate synthase from Salinispora arenicola CNS205
40% identity, 88% coverage
N0CZ35 Phospho-2-dehydro-3-deoxyheptonate aldolase from Streptomyces microflavus DSM 40593
38% identity, 81% coverage
MicB006_2892 3-deoxy-7-phosphoheptulonate synthase from Micromonospora sp. B006
36% identity, 80% coverage
- Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes
Braesel, Journal of natural products 2019 - “...synthase 57/77 daqH StrepF001_25945 MicB006_2898 isochorismatase 58/75 daqI StrepF001_25940 MicB006_2899 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase 62/85 daqJ StrepF001_25935 MicB006_2892 DAHP synthase 48/71 daqK StrepF001_25930 MicB006_2930 transposase 43/68 daqL StrepF001_25925 - NAD-dependent epimerase/dehydratase - daqM StrepF001_25920 MicB006_2928 TetR family transcriptional regulator 59/83 daqN StrepF001_25915 MicB006_2931 ketoacyl-ACP synthase III 65/88 daqO...”
- Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete
Braesel, Journal of natural products 2018 - “...(amino-3-deoxy-D-arabinoheptulosonate 7-phosphate synthase) homologs were identified outside the predicted borders of cluster 10: MicB006_3510 and MicB006_2892 . The latter one is part of the diazepinomicin biosynthetic gene cluster. No RifI homolog was found. The gene rifI encodes an aminoshikimate dehydrogenase that has been shown to be...”
DT87_23865 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. NTK 937
37% identity, 81% coverage
- Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937
Losada, Microbial biotechnology 2017 - “...isochorismatase (DT87_23875 and DT87_29880) for the biosynthesis of 3HAA, as well as a DAHP synthase (DT87_23865 and DT87_29890) that would favour the biosynthesis of the chorismate precursor 3deoxyDarabinohept2ulosonate7phosphate (DAHP) (Tables 1 and 2 ). For SA, two possible biosynthetic pathways were evaluated: a direct conversion from...”
- “...close vicinity to one of the DAHP synthase, 2,3dihydro2,3dihydroxybenzoate dehydrogenase, isochorismatase and anthranilate synthase clusters (DT87_23865 to DT87_23880) previously mentioned (Fig. 2 A and Table 1 ). The whole set of genes was recognized by antiSMASH analysis, which includes the putative genes as part of a...”
G3XCJ9 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) from Pseudomonas aeruginosa (see paper)
PA4212 phenazine biosynthesis protein PhzC from Pseudomonas aeruginosa PAO1
PA1901 phenazine biosynthesis protein PhzC from Pseudomonas aeruginosa PAO1
38% identity, 80% coverage
- Inhibition of Pseudomonas aeruginosa quorum sensing by chemical induction of the MexEF-oprN efflux pump
Kristensen, Antimicrobial agents and chemotherapy 2024 - “...8.54E-13 PA4210 phzA1 Phenazines Oxidative stress -6 1.08E-09 PA4111 phzB1 Phenazines Oxidative stress 26 4.70E-92 PA4212 phzC1 Phenazines Oxidative stress 20 1.14E-75 PA4213 phzD1 Phenazines Oxidative stress -4 0.38 PA4214 phzE1 Phenazines Oxidative stress -3 0.31 PA4215 phzF1 Phenazines Oxidative stress -7 0.33 PA4216 phzG1 Phenazines...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...PA4210 phzA1* Probable phenazine biosynthesis protein 9.52 5.52 PA4211 phzB1* Probable phenazine biosynthesis protein 6.41 PA4212 phzC1* Phenazine biosynthesis protein PhzC 13.16 PA4213 phzD1* Phenazine biosynthesis protein PhzD 19.61 PA4214 phzE1* Phenazine biosynthesis protein PhzE 19.61 PA4215 phzF1* Probable phenazine biosynthesis protein 21.74 PA4216 phzG1* Probable...”
- Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Shen, Microorganisms 2021 - “...1.66 PA4210 phzA1 Phenazine biosynthesis protein 2.62 PA4211 phzB1 Phenazine biosynthesis protein phzB 1 1.95 PA4212 phzC Phenazine biosynthesis protein PhzC 1.16 PA4815 Integral membrane protein 1.78 PA4944 hfq RNA-binding protein Hfq 1.06...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...2.2 + Probable phenazine biosynthesis protein PA4211 phzB1 5.8 4.9 + Probable phenazine biosynthesis protein PA4212 phzC1 2.9 3.7 + Phenazine biosynthesis protein PhzC PA4213 phzD1 4 4 + Phenazine biosynthesis protein PhzD PA4214 phzE1 3.9 3.5 + Phenazine biosynthesis protein PhzE PA4215 phzF1 3.7 3.5...”
- Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
Coleman, mSystems 2020 - “...-mannose pyrophosphorylase 1.82 1.3E03 PA3724 lasB Elastase 1.64 1.7E07 PA4175 piv Protease IV 1.86 1.7E05 PA4212 phzC1 Phenazine biosynthesis protein 1.44 4.5E03 PA4213 phzD1 Phenazine biosynthesis protein 1.20 1.4E03 PA4214 phzE1 Phenazine biosynthesis protein 1.24 7.2E04 a Categories of interest include regulators, multidrug efflux, motility, type...”
- Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa
Bricio-Moreno, Nature communications 2018 - “...PA4214 3.93 0.001208844 Pyridoxal 5-phosphate synthase phzG1 PA4216 2.98 0.01260054 Phospho-2-dehydro-3-deoxyheptonate aldolase phzC1 phzC2 PA1901 PA4212 6.89 0.000837624 RND multidrug efflux membrane fusion protein MexE* mexE PA2493 5.39 0.029669765 Anthranilate--CoA ligase pqsA PA0996 2.82 0.040457292 BfmS bfmS PA4102 3.79 0.020754134 LPS modification 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD arnD...”
- Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass
Sterritt, Bioscience reports 2018 - “...II DAH7PSs. The type II DAH7PSs are encoded by the ORFs PA1901 (and duplicated as PA4212) and PA2843 ( Pae DAH7PS PA1901 and Pae DAH7PS PA2843 respectively). The structure and properties of Pae DAH7PS PA2843 have recently been reported [ 33 ] and show that Pae...”
- The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence
Kaihami, Infection and immunity 2017 - “...PA4214 phzE1 5.88 PA14_09450 PA4213 phzD1 6.38 PA14_09460 PA4212 phzC1 9.14 PA14_09470 PA4211 phzB1 9.95 PA14_09480 PA4210 phzA1 6.11 PA14_09490 PA4209 phzM...”
- More
- Inhibition of Pseudomonas aeruginosa quorum sensing by chemical induction of the MexEF-oprN efflux pump
Kristensen, Antimicrobial agents and chemotherapy 2024 - “...3.04E-71 PA1899 phzA2 Phenazines Oxidative stress 39 5.15E-35 PA1900 phzB2 Phenazines Oxidative stress 78 1.39E-139 PA1901 phzC2 Phenazines Oxidative stress 46 3.04E-71 PA1902 phzD2 Phenazines Oxidative stress 12 0.06 PA1903 phzE2 Phenazines Oxidative stress 15 0.05 PA1904 phzF2 Phenazines Oxidative stress 12 0.08 PA1905 phzG2 Phenazines...”
- A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839
Wiehlmann, Frontiers in cellular and infection microbiology 2023 - “...Hypothetical protein 8.3 PA1892 Hypothetical protein 10.6 PA1894 Hypothetical protein 14.5 PA1897 Hypothetical protein 22.6 PA1901 Phenazine biosynthesis protein PhzC2 115.4 PA1902 Phenazine biosynthesis protein PhzD2 17.0 PA1903 Phenazine biosynthesis protein PhzE2 7.9 PA1951 fapF, amyloid outer membrane transporter FabF 27.2 PA2068 Probable MFS transporter 11.3...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...PA1899 phzA2* Probable phenazine biosynthesis protein 16.39 8.77 PA1900 phzB2* Probable phenazine biosynthesis protein 37.04 PA1901 phzC2* Phenazine biosynthesis protein PhzC 16.39 PA1902 phzD2* Phenazine biosynthesis protein PhzD 17.24 PA1903 phzE2* Phenazine biosynthesis protein PhzE 19.23 PA1904 phzF2* Probable phenazine biosynthesis protein 21.28 PA1905 phzG2* Probable...”
- Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Shen, Microorganisms 2021 - “...PA1303 lepB Signal peptidase 13.23 PA1432 lasI Acyl-homoserine-lactone synthase 1.05 PA1871 lasA Protease LasA 2.28 PA1901 phzC Phenazine biosynthesis protein PhzC 1.14 PA2570 lecA PA-I galactophilic lectin 1.24 PA3478 Rhamnosyltransferase subunit B 1.38 PA3724 lasB Elastase LasB 1.08 PA4206 mdtA Resistance-nodulation-cell division (RND) efflux membrane Fusion...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...phzA2 2.1 2.8 Probable phenazine biosynthesis protein PA1900 phzB2 3.2 5.6 Probable phenazine biosynthesis protein PA1901 phzC2 2.8 3.7 + Phenazine biosynthesis protein PhzC PA1902 phzD2 4 4 + Phenazine biosynthesis protein PhzD PA1903 phzE2 3.9 3.5 + Phenazine biosynthesis protein PhzE PA1904 phzF2 3.7 3.5...”
- Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations
Azimi, The ISME journal 2020 - “...1, while the frequency of nonsynonymous SNPs in phzC2 (PA1901) and pvdD (PA2399) fluctuated between 0.4 and 0.5 in different rounds of selection. We detected a...”
- Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
Coleman, mSystems 2020 - “...phenazine biosynthesis protein 1.70 2.6E08 PA1900 phzB2 Probable phenazine biosynthesis protein 1.95 3.0E10 1.25 4.3E02 PA1901 phzC2 Phenazine biosynthesis protein 1.85 2.2E06 1.44 4.5E03 PA1903 phzE2 Phenazine biosynthesis protein 1.24 7.2E04 PA1905 phzG2 Probable pyridoxamine 5-phosphate oxidase 1.53 2.7E05 1.16 9.7E03 PA2231 pslA Undecaprenyl-phosphate glucose phosphotransferase...”
- Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa
Bricio-Moreno, Nature communications 2018 - “...PA1903 PA4214 3.93 0.001208844 Pyridoxal 5-phosphate synthase phzG1 PA4216 2.98 0.01260054 Phospho-2-dehydro-3-deoxyheptonate aldolase phzC1 phzC2 PA1901 PA4212 6.89 0.000837624 RND multidrug efflux membrane fusion protein MexE* mexE PA2493 5.39 0.029669765 Anthranilate--CoA ligase pqsA PA0996 2.82 0.040457292 BfmS bfmS PA4102 3.79 0.020754134 LPS modification 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD...”
- More
PA14_39945 phenazine biosynthesis protein PhzC from Pseudomonas aeruginosa UCBPP-PA14
38% identity, 80% coverage
PA14_09460 phenazine biosynthesis protein PhzC from Pseudomonas aeruginosa UCBPP-PA14
38% identity, 80% coverage
6bmcA / G3XCJ9 The structure of a dimeric type ii dah7ps associated with pyocyanin biosynthesis in pseudomonas aeruginosa (see paper)
38% identity, 80% coverage
- Ligands: phosphoenolpyruvate; cobalt (ii) ion (6bmcA)
SSHG_05330 3-deoxy-7-phosphoheptulonate synthase from Streptomyces albidoflavus
36% identity, 86% coverage
B1MFJ4 Phospho-2-dehydro-3-deoxyheptonate aldolase from Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)
MAB_0295 Putative phenazine biosynthesis protein PhzC from Mycobacterium abscessus ATCC 19977
36% identity, 81% coverage
- Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach.
Shanmugham, PloS one 2013 - “...ID Choke point Protein Virulence Factor * COG ID 1 MAB_0295 putative phenazine 393 mab00400 B1MFJ4 YES NO COG3200E biosynthesis protein PhzC 2 MAB_1987 3-deoxy-D-arabino- 462 mab00400 B1MP18 YES NO COG3200E heptulosonate 7- phosphate synthase AroG 3 MAB_0054c cyanate hydratase 156 mab00910 CYNS YES NO COG1513P...”
- Exploring the Role of a Putative Secondary Metabolite Biosynthesis Pathway in Mycobacterium abscessus Pathogenesis Using a Xenopus laevis Tadpole Model
Miller, Microorganisms 2024 (PubMed)- “...pathways, producing the secondary metabolites streptonigrin and nybomycin. We constructed an in-frame deletion of the MAB_0295 (phzC) gene and tested it in our Xenopus laevis animal model. We have previously shown that X. laevis tadpoles, which have functional lungs and T cells, can serve as a...”
- Exploring the Role of a Putative Secondary Metabolite Biosynthesis Pathway in Mycobacterium abscessus Pathogenesis Using a Xenopus laevis Tadpole Model
, Microorganisms 2024 - “...pathways, producing the secondary metabolites streptonigrin and nybomycin. We constructed an in-frame deletion of the MAB_0295 ( phzC ) gene and tested it in our Xenopus laevis animal model. We have previously shown that X. laevis tadpoles, which have functional lungs and T cells, can serve...”
- “...pathway genes ( stnG to stnL ), as shown below the Mab cluster. MAB_0290 and MAB_0295 to MAB_0298 are also syntenic with the streptonigrin genes, except that they are inverted in Mab and include two additional genes, a transcriptional regulator (MAB_0291, cdaR ) and a putative...”
- Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach
Shanmugham, PloS one 2013 - “...Definition Length(aa) Associated Pathway UniProt ID Choke point Protein Virulence Factor * COG ID 1 MAB_0295 putative phenazine 393 mab00400 B1MFJ4 YES NO COG3200E biosynthesis protein PhzC 2 MAB_1987 3-deoxy-D-arabino- 462 mab00400 B1MP18 YES NO COG3200E heptulosonate 7- phosphate synthase AroG 3 MAB_0054c cyanate hydratase 156...”
- “...targets. Target No KEGG ID Subcellular Localization Broad Spectrum Property Interactors Function Prediction Druggability 1 MAB_0295 Cytoplasmic No(52) 6 Not required Novel 2 MAB_1987 Cytoplasmic No (51) 4 Not required Novel 3 MAB_0054c Cytoplasmic No (37) 8 Not required Novel 4 MAB_1028c Cytoplasmic No (36) 6...”
lpg0063 phospho-2-dehydro-3-deoxyheptonate aldolase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
34% identity, 81% coverage
DT87_29890 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. NTK 937
37% identity, 81% coverage
- Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937
Losada, Microbial biotechnology 2017 - “...and DT87_29880) for the biosynthesis of 3HAA, as well as a DAHP synthase (DT87_23865 and DT87_29890) that would favour the biosynthesis of the chorismate precursor 3deoxyDarabinohept2ulosonate7phosphate (DAHP) (Tables 1 and 2 ). For SA, two possible biosynthetic pathways were evaluated: a direct conversion from chorismate performed...”
- “...to cancel out caboxamycin production in the cbxF mutant, DAHP synthase paralogues, cbxF , cbxF (DT87_29890) and cbxF (DT87_05590), were analysed by sequence homology, together with their orthologues from nataxazol producer Streptomyces sp. T6176, natAL and CF54_24340 (located outside nataxazole biosynthetic cluster). Protein sequence alignments show...”
M217_RS0112890 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas chlororaphis HT66
34% identity, 80% coverage
Pchl3084_4953 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas chlororaphis subsp. aureofaciens 30-84
34% identity, 80% coverage
CXP47_RS25520 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas chlororaphis
34% identity, 80% coverage
- Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity
Li, Genome announcements 2018 - “...and phzI , phzR , phzA through phzG , and phzO (CXP47_RS25500, CXP47_RS25505, CXP47_RS25510, CXP47_RS25515, CXP47_RS25520, CXP47_RS25525, CXP47_RS25530, CXP47_RS25535, CXP47_RS25540, and CXP47_RS25545) coding for phenazine, were found ( 3 ). Meanwhile, as nitrogen-containing pigments, phenazine and its derivatives also have many biotechnological applications, such as colorimetric...”
WP_028443630 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. SID4912
37% identity, 81% coverage
EY04_RS25725 3-deoxy-7-phosphoheptulonate synthase from Pseudomonas chlororaphis
34% identity, 80% coverage
StrepF001_25935 3-deoxy-7-phosphoheptulonate synthase from Streptomyces sp. F001
37% identity, 80% coverage
- Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes
Braesel, Journal of natural products 2019 - “...anthranilate synthase 57/77 daqH StrepF001_25945 MicB006_2898 isochorismatase 58/75 daqI StrepF001_25940 MicB006_2899 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase 62/85 daqJ StrepF001_25935 MicB006_2892 DAHP synthase 48/71 daqK StrepF001_25930 MicB006_2930 transposase 43/68 daqL StrepF001_25925 - NAD-dependent epimerase/dehydratase - daqM StrepF001_25920 MicB006_2928 TetR family transcriptional regulator 59/83 daqN StrepF001_25915 MicB006_2931 ketoacyl-ACP synthase III 65/88...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory