PaperBLAST
PaperBLAST Hits for sp|P20574|TRPD_PSEAE Anthranilate phosphoribosyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=trpD PE=3 SV=1 (349 a.a., MDIKGALNRI...)
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>sp|P20574|TRPD_PSEAE Anthranilate phosphoribosyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=trpD PE=3 SV=1
MDIKGALNRIVNQLDLTTEEMQAVMRQIMTGQCTDAQIGAFLMGMRMKSETIDEIVGAVA
VMRELADGVQLPTLKHVVDVVGTGGDGANIFNVSSAASFVVAAAGGKVAKHGNRAVSGKS
GSADLLEAAGIYLELTSEQVARCIDTVGVGFMFAQVHHKAMKYAAGPRRELGLRTLFNML
GPLTNPAGVRHQVVGVFTQELCKPLAEVLKRLGSEHVLVVHSRDGLDEFSLAAATHIAEL
KDGEVREYEVRPEDFGIKSQTLMGLEVDSPQASLELIRDALGRRKTEAGQKAAELIVMNA
GPALYAADLATSLHEGIQLAHDALHTGLAREKMDELVAFTAVYREENAQ
Running BLASTp...
Found 153 similar proteins in the literature:
BWR11_03465 anthranilate phosphoribosyltransferase from Pseudomonas aeruginosa
PA14_08350 anthranilate phosphoribosyltransferase from Pseudomonas aeruginosa UCBPP-PA14
PA0650 anthranilate phosphoribosyltransferase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed (Phragmites australis)
Wu, Frontiers in microbiology 2018 - “...genes clustered at various chromosomal locations, including trpAB ( BWR11_00180 and BWR11_00185 ), trpDC ( BWR11_03465 and BWR11_03470 ), trpE (two copies: BWR11_22230 and BWR11_03280 ), trpF ( BWR11_10025 ), and trpG (two copies: BWR11_03460 and BWR11_22225 ). Moreover, we detected two clusters of genes involved...”
- “...genes clustered at various chromosomal locations, including trpAB ( BWR11_00180 and BWR11_00185 ), trpDC ( BWR11_03465 and BWR11_03470 ), trpE (two copies: BWR11_22230 and BWR11_03280 ), trpF ( BWR11_10025 ), and trpG (two copies: BWR11_03460 and BWR11_22225 ). Tryptophan biosynthetic genes are involved in IAA synthesis...”
- Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Panayidou, Scientific reports 2020 - “...the wild type PA14 in all the above assays 25 PA14_08360 ( trpC ) 26 PA14_08350 ( trpD ) 27 PA14_23850 ( trpF ) 28 PA14_66600 ( aroB ) 29 Valine, leucine and isoleucine biosynthesis (pau00290) PA14_62130 ( ilvC ) 30 PA14_04630 ( ilvD ) 31...”
- Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
Kwon, Journal of proteome research 2014 - “...PA1642 fatty acid biosynthesis 0.014 PA1609, PA1610, PA2965, PA3645 phenylalanine, tyrosine, and tryptophan biosynthesis 0.040 PA0650, PA0870, PA0872 phenylalanine metabolism 0.004 PA0865, PA0870,PA0872, PA5304 pyrimidine metabolism 0.020 PA0849 , PA1532, PA1816 , PA3625, PA3654 a A hypergeometric test was used to evaluate significance of enrichment with...”
- Involvement of the lon protease in the SOS response triggered by ciprofloxacin in Pseudomonas aeruginosa PAO1
Breidenstein, Antimicrobial agents and chemotherapy 2012 - “...phase PA no. PA0069 PA0610 PA0611 PA0625 PA0649 PA0650 PA0651 PA0669 PA0670 PA0671 PA0865 PA0872 PA0922 PA2008 PA2009 PA2288 PA3007 PA3413 PA3414 PA3616 PA4761...”
- Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach
Nalca, Antimicrobial agents and chemotherapy 2006 - “...name PA0044b PA0263c PA0409 PA0422 PA0456 PA0555 PA0649 PA0650 PA0651 PA0805 PA0943 PA0996 PA1440 PA1493d PA1494 PA1564 PA1696b PA1706 b,d PA1707b PA1708b...”
Psyr_4580 Anthranilate phosphoribosyl transferase from Pseudomonas syringae pv. syringae B728a
82% identity, 98% coverage
PP0421, PP_0421 anthranilate phosphoribosyltransferase from Pseudomonas putida KT2440
80% identity, 99% coverage
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
Verhoef, Applied microbiology and biotechnology 2010 - “...component II ( trpG ) PP0420 4.2 10.3 2.9 2.7 Anthranilate phosphoribosyltransferase ( trpD ) PP0421 4.4 7.8 Indole-3-glycerol phosphate synthase ( trpC ) PP0422 2.6 5.6 4.0 DAHP synthase, class I ( aroF1 ) PP2324 2.5 2.6 DAHP synthase, class I ( aroF2 ) PP3080...”
- Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440
Molina-Henares, Microbial biotechnology 2009 - “...and Aux3 was located in the geneencoding PP0422 (32nd codon after the first ATG) and PP0421 (184th codon after the first ATG). blast analysis indicated that PP0082 exhibited high similarity to the tryptophan synthase alphasubunit ( trpA ) gene, whereas PP0421 encoded anthranilate phosphoryl transferase (...”
- A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Nogales, BMC systems biology 2008 - “...Tryptophan PP_0082 trpA TRPS1r, TRPS3r (-/-) PP_0083 trpB TRPS2, TRPS1r (-/-) PP_0422 trpC IGPS (-/-) PP_0421 trpD ANPRT (-/-) PP_0417 trpE ANS (-/-) PP_1995 trpF PRAI (-/-) PP_0420 trpG ANS (-/-) The comparison of the in silico gene essentiality and experimental P. aeruginosa data are shown...”
- Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production
Wierckx, Journal of bacteriology 2008 - “...Indole-3-glycerol phosphate synthase (trpC) PP0417 PP0420 PP0421 PP0422 8.6 6.8 6.3 5.9 Aromatic degradation 4-Hydroxybenzoate transporter (pcaK)...”
PFL_5622 anthranilate phosphoribosyltransferase from Pseudomonas fluorescens Pf-5
80% identity, 99% coverage
ELZ14_28395 anthranilate phosphoribosyltransferase from Pseudomonas brassicacearum
79% identity, 99% coverage
PFLU5559 anthranilate phosphoribosyltransferase (ec 2.4.2.18) from Pseudomonas fluorescens SBW25
79% identity, 99% coverage
P00500 anthranilate synthase (subunit 1/2) (EC 4.1.3.27) from Serratia marcescens (see paper)
60% identity, 99% coverage
4yi7A / P00500 Anthranilate bound at active site of anthranilate phosphoribosyl transferase from acinetobacter (anprt; trpd)
57% identity, 99% coverage
- Ligand: 2-aminobenzoic acid (4yi7A)
A1S_2359 anthranilate phosphoribosyltransferase from Acinetobacter baumannii ATCC 17978
59% identity, 88% coverage
WP_027788472 anthranilate phosphoribosyltransferase from Burkholderia contaminans
51% identity, 97% coverage
trpD / BAC65124.1 anthranilate phosphoribosyltransferase from Burkholderia multivorans (see paper)
50% identity, 97% coverage
Bxe_A0459 anthranilate phosphoribosyltransferase from Paraburkholderia xenovorans LB400
49% identity, 97% coverage
Bxe_A0459 anthranilate phosphoribosyltransferase from Burkholderia xenovorans LB400
49% identity, 97% coverage
RSc2884 PROBABLE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE PROTEIN from Ralstonia solanacearum GMI1000
51% identity, 97% coverage
L5014_35350 anthranilate phosphoribosyltransferase from Paraburkholderia tagetis
50% identity, 97% coverage
BP3262 anthranilate phosphoribosyltransferase from Bordetella pertussis Tohama I
47% identity, 97% coverage
J0661_17720 anthranilate phosphoribosyltransferase from Stenotrophomonas maltophilia
47% identity, 96% coverage
TRPD_XANCP / Q8PD71 Anthranilate phosphoribosyltransferase; EC 2.4.2.18 from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
50% identity, 96% coverage
- function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA).
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+) (Binds 2 magnesium ions per monomer.)
subunit: Homodimer.
XHV734_0640 anthranilate phosphoribosyltransferase from Xanthomonas hortorum pv. vitians
50% identity, 96% coverage
J0657_01675 anthranilate phosphoribosyltransferase from Stenotrophomonas indicatrix
48% identity, 96% coverage
MLD56_14610 anthranilate phosphoribosyltransferase from Paenibacillus peoriae
43% identity, 97% coverage
RL2493 putative anthranilate phosphoribosyltransferase from Rhizobium leguminosarum bv. viciae 3841
44% identity, 97% coverage
LGG_RS00500 anthranilate phosphoribosyltransferase from Lacticaseibacillus rhamnosus GG
43% identity, 98% coverage
- Ribosome Profiling Reveals Genome-Wide Cellular Translational Regulation in Lacticaseibacillus rhamnosus ATCC 53103 under Acid Stress
Fan, Foods (Basel, Switzerland) 2022 - “...43.02 2.67 0.0396827 LGG_RS00155 -- 0.67 4.93 2.88 0.0153195 LGG_RS00490 trpF 0.28 13.15 5.55 0.0303543 LGG_RS00500 trpD 0.61 41.48 6.09 2.95 10 6 LGG_RS00715 TTE1650 0.01 0.07 2.81 0.0409188 LGG_RS02170 -- 0.01 1.7 7.41 1.666 10 9 LGG_RS02790 TTE1650 0.01 0.07 2.81 0.0409188 LGG_RS03170 HSP17.6C 0.01...”
- “...carA , pyrC , pyrB , pyrR1 ko00400 Phenylalanine, tyrosine, and tryptophan biosynthesis 0.008 LGG_RS00490, LGG_RS00500 trpF , trpD ko00999 Biosynthesis of secondary metabolitesunclassified 0.029 LGG_RS10200 acpP ko01110 Biosynthesis of secondary metabolites 0.057 LGG_RS00490, LGG_RS00500, LGG_RS13475 trpF , trpD , argH ko01100 Metabolic pathways 0.068 LGG_RS00490,...”
trpD / AAB39009.1 anthranilate phosphoribosyltransferase from Bradyrhizobium japonicum (see paper)
43% identity, 97% coverage
AFE_3243 anthranilate phosphoribosyltransferase from Acidithiobacillus ferrooxidans ATCC 23270
45% identity, 98% coverage
LSEI_0078 Anthranilate phosphoribosyltransferase from Lactobacillus casei ATCC 334
44% identity, 97% coverage
YDYSG_32680 anthranilate phosphoribosyltransferase from Paenibacillus tyrfis
43% identity, 97% coverage
ATCR1_02965 anthranilate phosphoribosyltransferase from Agrobacterium tumefaciens CCNWGS0286
43% identity, 97% coverage
ATU_RS08260 anthranilate phosphoribosyltransferase from Agrobacterium fabrum str. C58
43% identity, 97% coverage
Elgi_45140 anthranilate phosphoribosyltransferase from Paenibacillus elgii
43% identity, 97% coverage
DET1483 anthranilate phosphoribosyltransferase from Dehalococcoides ethenogenes 195
43% identity, 97% coverage
P17170 Anthranilate phosphoribosyltransferase from Lacticaseibacillus casei
43% identity, 97% coverage
SMc00235 PROBABLE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE PROTEIN from Sinorhizobium meliloti 1021
43% identity, 97% coverage
WP_003245959 anthranilate phosphoribosyltransferase from Bacillus subtilis
42% identity, 95% coverage
Rumal_1716 bifunctional anthranilate synthase component II/anthranilate phosphoribosyltransferase from Ruminococcus albus 7 = DSM 20455
41% identity, 62% coverage
- Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis
Christopherson, BMC genomics 2014 - “...finding was further verified using reverse transcription quantitative PCR (RT-qPCR) of the tryptophan biosynthetic gene, Rumal_1716, normalized to 16S rRNA, which was found to be expressed 7.2 fold higher on cellulose, relative to cellobiose. Despite the highly regulated nature of this pathway, induction of the tryptophan...”
- “...according to the manufacturers protocol (Biorad, USA). The resulting cDNA was used to quantify the Rumal_1716 and 16S rRNA genes by amplification using the iQ Sybr Green Supermix according to the manufacturers protocol (Biorad, USA) on a BioRad CSX-Connect qPCR machine. Amplification of Rumal_1716 and 16S...”
RHOM_RS06425 anthranilate phosphoribosyltransferase from Roseburia hominis A2-183
42% identity, 93% coverage
- Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183
Bhattacharya, Microorganisms 2022 - “...h. The putative function of the target genes RHOM_RS11135, RHOM_RS11140, RHOM_RS11145, RHOM_RS11160, RHOM_RS11175, RHOM_RS14610, RHOM_RS15885, RHOM_RS06425, and RHOM_RS13400 was functionally predicted as -mannoside phosphorylase ( Rh MOP130A), mannosylglucose phosphorylase ( Rh MGP130), epimerase ( Rh Mep), ABC substrate-binding protein ( Rh MosBP), -galactosidase ( Rh Gal36A),...”
R3M60_07680 anthranilate phosphoribosyltransferase from Bacillus subtilis
42% identity, 95% coverage
WP_134981823 anthranilate phosphoribosyltransferase from Bacillus subtilis
42% identity, 95% coverage
CAC3161 Anthranilate phosphoribosyltransferase from Clostridium acetobutylicum ATCC 824
43% identity, 96% coverage
- Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum
Amador-Noguez, Applied and environmental microbiology 2011 - “...tyrosine, and tryptophan biosynthesis, cac3162, cac3163, cac3161, cac3159, cac3162, cac3163; and glutamate dehydrogenase, cac0737. The gray bars indicate...”
- Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
Senger, Biotechnology and bioengineering 2008 - “...CAC0819/CAC3221. List 9: CAC0936, CAC0943, CAC0942, CAC0940, CAC0939, CAC0938, CAC1369, CAC2727, CAC0937. List 10: CAC3162/CAC3163, CAC3161, CAC3159, CAC3160, CAC3157/CAC3158. List 11: CAC1234, CAC0893, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832. List 12: CAC1234, CAC0217, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832. List 13 (also shown in Fig. 5 ): CAC2391/CAC3020, CAC2388, CAC2389, CAC2390. Figure 5 Proposed pathway of...”
A6A40_04650 anthranilate phosphoribosyltransferase from Azospirillum humicireducens
43% identity, 97% coverage
MJ920_11020 anthranilate phosphoribosyltransferase from Bacillus velezensis
43% identity, 95% coverage
RBIBE_21160 anthranilate phosphoribosyltransferase from Bacillus velezensis
43% identity, 95% coverage
- Complete genome sequence data of chitin-degrading Bacillus velezensis RB.IBE29
Tran, Data in brief 2023 - “...Tryptophan synthase alpha chain RBIBE_21120 Tryptophan synthase beta chain RBIBE_21130 Tryptophan-tRNA ligase RBIBE_10890 Anthranilate phosphoribosyltransferase RBIBE_21160 Anthranilate synthase component 1 RBIBE_21170 Aminodeoxychorismate/anthranilate synthase component 2 RBIBE_00760 Indole-3-glycerol phosphate synthase RBIBE_21150 Chorismate mutase RBIBE_21180 3-dehydroquinate synthase RBIBE_21190 Chorismate synthase RBIBE_21200 Nitrate transport and reduction Nitrate reductase-like protein...”
P18261 Anthranilate phosphoribosyltransferase from Bacillus pumilus
41% identity, 97% coverage
R5D67_06200 anthranilate phosphoribosyltransferase from Bacillus velezensis
42% identity, 95% coverage
lp_1654 anthranilate phosphoribosyltransferase from Lactobacillus plantarum WCFS1
Q88WI3 Anthranilate phosphoribosyltransferase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_1654 anthranilate phosphoribosyltransferase from Lactiplantibacillus plantarum WCFS1
42% identity, 96% coverage
- Butanol Tolerance of Lactiplantibacillus plantarum: A Transcriptome Study
Petrov, Genes 2021 - “...trpE Anthranilate synthase component I 2.31 NC lp_1653, trpG Anthranilate synthase component II 3.25 2.07 lp_1654, trpD Anthranilate phosphoribosyltransferase 2.49 NC lp_1656, trpF Phosphoribosylanthranilate isomerase 2.33 NC lp_1658, trpB Tryptophan synthase subunit 2.26 NC lp_1657, trpA Tryptophan synthase subunit 2.11 NC * The difference in gene...”
- Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis.
Zhai, Scientific reports 2017 - “...ligase; glutathione synthetase 1.50 F9UR58 oahS; O-acetylhomoserine sulfhydrylase 2.44 Other Q88UT5 glyA; glycine hydroxymethyltransferase 1.53 Q88WI3 trpD; anthranilate phosphoribosyltransferase 4.58 Nucleic acid metabolism F9UT41 ndk; nucleoside-diphosphate kinase 1.72 F9UM77 gmk2; guanylate kinase 1.64 F9URN3 lp_2762; phosphohydrolase 1.87 F9US18 nrdD; anaerobic ribonucleoside-triphosphate reductase 2.16 P71479 pyrR1; pyrimidine...”
RSp0681 PROBABLE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE (GLYCOSYLTRANSFERASE) PROTEIN from Ralstonia solanacearum GMI1000
40% identity, 97% coverage
BMEI0844 ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE from Brucella melitensis 16M
41% identity, 97% coverage
BAB1_1163 Glycosyl transferase, family 3:Anthranilate phosphoribosyl transferase from Brucella melitensis biovar Abortus 2308
41% identity, 97% coverage
- ChIP-seq analysis of Brucella reveals transcriptional regulation of GntR
Li, Journal of basic microbiology 2020 (PubMed)- “...we performed chromatin immunoprecipitation of GntR10 followed by next-generation sequencing (ChIP-seq). We selected target gene BAB1_1163 directly regulated by GntR10 and created the mutant (2308 1163) from virulent Brucella abortus 2308 (S2308). 2308 1163 strain survival capability in murine macrophages (RAW 264.7) was detected and the levels of...”
Q71Z37 Anthranilate phosphoribosyltransferase from Listeria monocytogenes serotype 4b (strain F2365)
37% identity, 95% coverage
- Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
Srivastava, International journal of peptide research and therapeutics 2021 - “...1.001 Non-allergen 34 Q71XF3 0.951 Non-allergen 35 Q71VR5 0.589 Non-allergen 36 Q71WI0 0.766 Non-allergen 37 Q71Z37 0.698 Non-allergen 38 Q71XR3 1.167 Non-allergen 39 Q720G2 0.776 Non-allergen 40 Q71Y82 1.037 Non-allergen 41 Q71XV6 1.471 Non-allergen 42 Q724M3 0.608 Non-allergen 43 Q724B0 1.957 Non-allergen 44 Q724I1 0.449 Non-allergen...”
- “...LIFNTILPK 65.3 1.134 Antigen Q71WI0 DRB1_0101 FALHYPYEL 1003.9 1.4132 Antigen DRB1_0701 FALHYPYEL 319.5 1.4132 Antigen Q71Z37 DRB1_0101 FLFAPHVHP 425 1.8183 Antigen DRB1_0101 IAFLFAPHV 125 1.9413 Antigen DRB1_0101 LYTLRPEDV 1060.8 1.3501 Antigen Q71XV6 DRB1_0701 FSMVLSLVF 100 1.4972 Antigen DRB1_0701 ASRSKSNRL 302 1.1981 Antigen DRB1_0701 YIMALHFGI 307 1.9206...”
trpD / AAD09118.1 anthranilate phosphoribosyltransferase from Rhodobacter sphaeroides (see paper)
44% identity, 77% coverage
lmo1631 highly similar to anthranilate phosphoribosyltransferase from Listeria monocytogenes EGD-e
Q8Y6Q3 Anthranilate phosphoribosyltransferase from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
37% identity, 95% coverage
- Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures
Balogh, RSC chemical biology 2022 - “...Q8Y7A2 Putative pyrrolysine-5-carboxylate reductase a lmo1475 ( hrcA ) P0DJM4 HrcA (heat-inducable transcription repressor A) lmo1631 ( trpD ) Q8Y6Q3 Anthranilate phosphoribosyltransferase lmo1713 ( mreB ) Q8Y6H3 Cell shape-determining protein MreB lmo1813 Q8Y684 l -Serine deaminase lmo1881 Q8Y621 Putative 5-3-exonuclease a lmo2267 ( addA ) Q8Y511...”
- Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
Orsi, BMC evolutionary biology 2008 - “..., smbA ( lmo1313 ), lmo1401 , lmo1420 , opuCC ( lmo1426 ), trpD ( lmo1631 ), lmo1693 , purK ( lmo1774 ), lmo1825 , panB ( lmo1902 ), lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487 , lmo0878 , lmo1004 , lmo1011 , cbiH...”
- Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures
Balogh, RSC chemical biology 2022 - “...a lmo1475 ( hrcA ) P0DJM4 HrcA (heat-inducable transcription repressor A) lmo1631 ( trpD ) Q8Y6Q3 Anthranilate phosphoribosyltransferase lmo1713 ( mreB ) Q8Y6H3 Cell shape-determining protein MreB lmo1813 Q8Y684 l -Serine deaminase lmo1881 Q8Y621 Putative 5-3-exonuclease a lmo2267 ( addA ) Q8Y511 ATP-dependent helicase/nuclease subunit A...”
HWX41_RS17800 anthranilate phosphoribosyltransferase from Bacillus paramycoides
39% identity, 97% coverage
- Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits
Adeleke, Plants (Basel, Switzerland) 2021 - “...synthase subunit beta HWX41_RS17785 trpC indole-3-glycerol phosphate synthase Trp C HWX41_RS17795 trp D anthranilate phosphoribosyltransferase HWX41_RS17800 trp E anthranilate synthase component I HWX41_RS17810 trp S TryptophantRNA ligase HWX41_RS18055 IAA production, IPA pathway dha S aldehyde dehydrogenase Dha S HWX41_RS06485 dha aldehyde dehydrogenase HWX41_RS25615 dha acetaldehyde dehydrogenase...”
MXAN_6062 anthranilate phosphoribosyltransferase from Myxococcus xanthus DK 1622
44% identity, 97% coverage
Fisuc_0138 anthranilate phosphoribosyltransferase from Fibrobacter succinogenes subsp. succinogenes S85
39% identity, 63% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...(Fisuc_1188), putative transcription regulators Fisuc_0335, Fisuc_0933 and Fisuc_1186, a diguanylate cyclase Fisuc_2957, and genes Fisuc_0137, Fisuc_0138 and Fisuc_2558, which are involved in tryptophan metabolism. A gene ontology enrichment analysis was performed on differentially expressed genes. Among the up-regulated genes in the pH 5.65 samples, category V:...”
bll2049 anthranilate phosphoribosyltransferase from Bradyrhizobium japonicum USDA 110
36% identity, 97% coverage
- Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency
Nicoud, mSystems 2021 - “...HemN1 ( bll2007 ), and, to a lesser extent, an anthranilate phosphoribosyltransferase (TrpD, encoded by bll2049 ), was overexpressed in soybean nodules. USDA110 transcriptomics data in the perspective of previously described regulons and stimulons. USDA110 is one of the best-characterized rhizobial strains in terms of transcriptomic...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...2223 were also induced beyond 2.8-fold by SSE at 12 hpi, but only three genes bll2049, bll2065, and bll2067 have functions as anthranilate phosphoribosyltransferase ( trpD ), carbonic anhydrase, and nodulate formation efficiency C protein ( nfeC ), respectively. Clones covering a large genes cluster, nifDKENX-fer3-nifS-fixU-nifB-frxA-nifZ-nifH-...”
VF_1031 anthranilate phosphoribosyltransferase from Aliivibrio fischeri ES114
VF_1031 anthranilate phosphoribosyltransferase from Vibrio fischeri ES114
36% identity, 96% coverage
SPO2150 anthranilate phosphoribosyltransferase from Ruegeria pomeroyi DSS-3
40% identity, 93% coverage
- A mutant fitness assay identifies bacterial interactions in a model ocean hot spot
Schreier, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...metH Methionine 3.9 SPO1973 3-dehydroquinate dehydratase, type II ( aroQ ) Aromatic amino acids 3.9 SPO2150 anthranilate phosphoribosyltransferase ( trpD ) Tryptophan 3.6 2.3 SPO2151 indole-3-glycerol phosphate synthase ( trpC ) Tryptophan 4.4 SPO3768 glutamate synthase ( gltB ) Glutamate 0.9 0.75 SPO2634 sulfite reductase Amino...”
SNE_A10180 anthranilate phosphoribosyltransferase from Simkania negevensis Z
38% identity, 97% coverage
1kgzB / Q8VP84 Crystal structure analysis of the anthranilate phosphoribosyltransferase from erwinia carotovora (current name, pectobacterium carotovorum) (see paper)
38% identity, 95% coverage
- Ligands: manganese (ii) ion; 1-o-pyrophosphono-5-o-phosphono-alpha-d-ribofuranose (1kgzB)
LLNZ_05325 anthranilate phosphoribosyltransferase from Lactococcus cremoris subsp. cremoris NZ9000
37% identity, 96% coverage
- Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Gupta, Scientific reports 2020 - “...transport system, periplasmic component Quorum sensing 12 LLNZ_05120 Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferaseIMP cyclohydrolase Purine metabolism 13 LLNZ_05325 Anthranilate phosphoribosyltransferase Phenylalanine, tyrosine and tryptophan biosynthesis 14 LLNZ_01920 Dipeptide transport ATP-binding protein dppD ABC transporters 15 LLNZ_11520 Galactokinase Galactose metabolism 16 LLNZ_05020 Amidophosphoribosyltransferase Purine metabolism 17 LLNZ_01800 Putative cobalt...”
- “...5.7 Arginine biosynthesis 2 LLNZ_10425 ABC-type oligopeptide transport system, periplasmic component 5.12 Peptide uptake 3 LLNZ_05325 Anthranilate phosphoribosyltransferase 4.98 Phenylalanine, tyrosine and tryptophan biosynthesis 4 LLNZ_05020 Amidophosphoribosyltransferase 4.77 Alanine, aspartate and glutamate metabolism 5 LLNZ_05715 Dihydroorotate dehydrogenase electron transfer subunit 4.29 Pyrimidine metabolism 6 LLNZ_05720 Dihydroorotate...”
NTHI1764 anthranilate phosphoribosyltransferase from Haemophilus influenzae 86-028NP
40% identity, 80% coverage
SPRG_08603 anthranilate phosphoribosyltransferase from Saprolegnia parasitica CBS 223.65
40% identity, 97% coverage
- Analysis of Saprolegnia parasitica Transcriptome following Treatment with Copper Sulfate
Hu, PloS one 2016 - “...biological pathways, the expression of certain genes (such as SPRG_05378, SPRG_01336, SPRG_00691, SPRG_19437, SPRG_17560, SPRG_13611, SPRG_08603, SPRG_09764, and SPRG_01617) were upregulated, while SPRG_11730, SPRG_04491, SPRG_10490, SPRG_12259, SPRG_04186, SPRG_18377, SPRG_18063, SPRG_06771, SPRG_16261, and SPRG_02541 genes were downregulated after copper sulfate treatment. These findings were consistent with the...”
spr1635 Anthranilate phosphoribosyltransferase from Streptococcus pneumoniae R6
SP_1815 anthranilate phosphoribosyltransferase from Streptococcus pneumoniae TIGR4
SPD_1600 anthranilate phosphoribosyltransferase from Streptococcus pneumoniae D39
39% identity, 91% coverage
TRPD_SACS2 / P50384 Anthranilate phosphoribosyltransferase; EC 2.4.2.18 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see 4 papers)
P50384 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Saccharolobus solfataricus (see 7 papers)
2gvqD / P50384 Anthranilate phosphoribosyl-transferase (trpd) from s. Solfataricus in complex with anthranilate (see paper)
WP_009992305 anthranilate phosphoribosyltransferase from Saccharolobus solfataricus
35% identity, 97% coverage
HI1389 anthanilate phosphoribosyltransferase (trpD) from Haemophilus influenzae Rd KW20
39% identity, 80% coverage
- Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis
Wong, Frontiers in cellular and infection microbiology 2012 - “...a HI1387 trpE Anthranilate synthase component I a HI1388 trpG Anthranilate synthase component II a HI1389 trpD Anthranilate phosphoribosyltransferase a HI1389.1 trpC Bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase a HI1431 trpB Tryptophan synthase subunit beta a HI1432 trpA Tryptophan synthase subunit alpha a HI1290 tyrA Bifunctional chorismate...”
- Identification of a siderophore utilization locus in nontypeable Haemophilus influenzae
Morton, BMC microbiology 2010 - “...ten strains were positive for the presence of at least four genes, and one strain (HI1389) was consistently positive for the presence of three genes. Four of the total 21 biotype III strains tested were consistently negative for the presence of all five genes. Negative results...”
- “...Yes Yes Yes Yes No HI1387 (nt) EAR 42 III Yes Yes Yes Yes No HI1389 (nt) EAR 44 III Yes Yes Yes No No HI1390 (nt) BLD 45 III Yes Yes Yes Yes No HI1397 (nt) EAR 57 III Yes Yes Yes Yes No HI1399...”
- Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage
Hendrix, Proceedings of the National Academy of Sciences of the United States of America 1999 - “...on one side and trpE, trpD, and trpC (HI1388, HI1389, and HI1389.1, respectively) on the other (Fig. 3). This entire region contains '40 genes, including...”
Q8F708 Anthranilate phosphoribosyltransferase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
34% identity, 97% coverage
SCO3212 probable anthranilate phosphoribotransferase from Streptomyces coelicolor A3(2)
41% identity, 93% coverage
Q72PD0 Anthranilate phosphoribosyltransferase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
34% identity, 97% coverage
EAMY_1917 anthranilate phosphoribosyltransferase / anthranilate synthase component II from Erwinia amylovora CFBP1430
42% identity, 83% coverage
Ssal_00459 anthranilate phosphoribosyltransferase from Streptococcus salivarius 57.I
36% identity, 94% coverage
CF0439 anthranilate phosphoribosyltransferase from Chlamydia felis Fe/C-56
CF0439 anthranilate phosphoribosyltransferase from Chlamydophila felis Fe/C-56
35% identity, 96% coverage
PMI1345 anthranilate synthase component (anthranilate phosphoribosyltransferase) from Proteus mirabilis HI4320
41% identity, 80% coverage
- Editorial: Quorum Network (Sensing/Quenching) in Multidrug-Resistant Pathogens
García-Contreras, Frontiers in cellular and infection microbiology 2019 - “...Proteus mirabilis . The authors identified new proteins involved in the QS of this pathogen PMI1345, GltB, PMI3678, and RcsC, which could be used as new targets to develop of new treatments for Proteus mirabilis . Current efforts in quorum quenching (QQ) research are dedicated to...”
- In silico Identification of the Indispensable Quorum Sensing Proteins of Multidrug Resistant Proteus mirabilis
Pawar, Frontiers in cellular and infection microbiology 2018 - “...be important for AIPL (Table 1 ). Others like QSPO, QSPH, and QSPV have YajC, PMI1345, OppA, RpoS, flagellar proteins of the flh and fli operon and some other two-component systems proteins like CheY and KdpE as important rankers. The functions of these proteins are mentioned...”
- “...TrmA MnmC, LuxS, MtnN, ThrA , MetH PMI3678 , ThrA , MetH, PMI0028, PMI0626 QSPO PMI1345, PMI1344, TrpE , PabA, PabB YajC, PMI1345, GadC, RibD , PMI2708 PMI1345, PMI1344, TrpE , PabA, PabB KdpE, Hfq , FlhD, FlhC, PMI1345 QSPH PMI1345, GadC, TrpE , FlhD, FlhC...”
AT5G17990 TRP1 (tryptophan biosynthesis 1); anthranilate phosphoribosyltransferase from Arabidopsis thaliana
37% identity, 75% coverage
- Genome-wide association studies from spoken phenotypic descriptions: a proof of concept from maize field studies
Yanarella, G3 (Bethesda, Md.) 2024 - “...9-154188566 (157067037) 9-154188566 (157067037) 35 Total Zm00001d048461 blue fluorescent1 (bf1) GO:0009684 Indoleacetic acid biosynthetic process AT5G17990 + 14 unrelated a Only shown if any are apparently relevant to plant height trait. b See Supplementary Table 4 for full list of Gene IDs and GO terms c...”
- Proteome Analysis of the ROF-FKBP Mutants Reveals Functional Relations among Heat Stress Responses, Plant Development, and Protein Quality Control during Heat Acclimation in Arabidopsis thaliana
Lefa, ACS omega 2024 - “...AT1G52560 CHLD AT1G08520 psbH ATCG00710 5-METHYLT HIORIBOSE AT2G05830 HSP70-3 AT3G09440 XTH24 AT4G30270 HSP81-2 AT5G56030 PAT1 AT5G17990 HSP90-1 AT5G52640 CBBY AT3G48420 LEA7 AT1G52690 BGLU34 AT1G47600 MBF1C AT3G24500 cox2 ATMG00160 PAP1 AT4G04020 PDX12 AT3G16050 AT5G53140 3.5 Heat Stress Response The heat response pathway in the WT and ROF...”
- Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole
Abu-Zaitoon, Plants (Basel, Switzerland) 2023 - “...is the conversion of anthranilate to phosphoribosyl anthranilate via phosphoribosyl anthranilate transferase ( TRP1 ; At5g17990, TRP2 ; At1g70570). Analysis of microarray data revealed that unlike INS , TSA is strongly coexpressed with phosphoribosyl anthranilate transferase1 ( TRP1 ) in all platforms, under general and specific...”
- “...TSB1 At5g54810 ASB2 At5g57890 TSB2 At4g27070 ASB (putative) At1g24807 At1g24909 At1g25083 At1g25155 TSB3 At5g38530 TRP1 At5g17990; At1g70570 TSB4 At5g28237 PAI1 At1g07780 INS At4g02610 PAI2 At5g05590 plants-12-01687-t002_Table 2 Table 2 Coexpression of TSA with TSB1 , TSB2 , TSB3 , and TSB4 under general and specific conditions....”
- Diversification of JAZ-MYC signaling function in immune metabolism
Johnson, The New phytologist 2023 - “...JAZ13 (AT3G22275), MYC2 (AT1G32640), MYC3 (AT5G46760), MYC4 (AT4G17880), MYC5 (AT5G46830), TSA1 (AT3G54640), ASA1 (AT5G05730), TRP1 (AT5G17990), PDF1.2 (AT5G44420), PP2A (AT1G13320), VSP2 (AT5G24770), ORA59 (AT1G06160), and ACT (AT5G61160). Results MYC3 and MYC4 promote resistance to 5-methyl tryptophan As a prelude to investigating the contribution of JAZ and...”
- Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening
Nilo-Poyanco, BMC genomics 2021 - “...2 Qualit_O1 Glutamate dehydrogenase 2 AT5G07440 Prupe.5G171400 0.998 2 Up_O1 Anthranilate phosphoribosyltransferase / Phosphoribosyl-anthranilate pyrophosphorylase AT5G17990 Prupe.6G249100 0.999 1 Up_O1 Diaminopimelate epimerase, chloroplastic AT3G53580 Prupe.8G013600 1 2 Up_O1 ATP phosphoribosyltransferase / Phosphoribosyl-ATP pyrophosphorylase AT1G09795 Carbohydrate Metabolism/Abiotic Stress Response Prupe.3G289900 1 2 Qualit_O1 GALACTINOL--SUCROSE GALACTOSYLTRANSFERASE 5-RELATED AT5G40390...”
- First Come, First Served: Sui Generis Features of the First Intron
Zalabák, Plants (Basel, Switzerland) 2020 - “...to ATG Function Organism Reference IME UBQ10 (At4g05320) downstream IME Arabidopsis [ 80 ] PAT1/TRP1 (At5g17990) downstream IME Arabidopsis [ 72 ] ADH1 (GRMZM2G442658) downstream IME maize [ 55 ] Sh1 (GRMZM2G089713) downstream IME, splicing-dependent maize [ 56 , 68 ] PRF1 (At2g19760) downstream IME Arabidopsis...”
- Co-regulation of indole glucosinolates and camalexin biosynthesis by CPK5/CPK6 and MPK3/MPK6 signaling pathways
Yang, Journal of integrative plant biology 2020 - “...database under the following accession numbers: CPK5 (At4g35310), CPK6 (At2g17290), ASA (AT5G05730), ASB (AT1G25220), PAT (AT5G17990), IGPS (At2g04400), TSA (AT3G54640), TSB (AT5G54810), CYP79B2 (At4g39950), CYP79B3 (At2g22330), CYP81F2 (AT5G57220), IGMT1 (At1g21100), IGMT2 (At1g21120), CYP71A13 (AT2G30770), CYP71A12 (AT2G30750), PAD3 (AT3G26830), CYP83B1 (AT4G31500), UGT74B1 (AT1G24100), ST5a (AT1G74100), PDR12 (AT1G15520),...”
- An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana
Gallegos, Scientific reports 2019 - “...Arabidopsis Genome Initiative or EMBL/GenBank data libraries under the following accession numbers: COR15a (At2g42540), TRP1 (At5g17990), and UBQ10 (At4g05320). All materials and strains are available upon request. Competing Interests The authors declare no competing interests. References 1. Butler JE Kadonaga JT The RNA polymerase II core...”
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STER_1552, STER_RS07630, T303_08780 anthranilate phosphoribosyltransferase from Streptococcus thermophilus ASCC 1275
35% identity, 94% coverage
- Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome
Henry, Frontiers in microbiology 2019 - “...acid ABC transporter ATP-binding protein YP_820506.1 WP_011681207.1 STER_1117 STER_RS05525 TrpD Anthranilate phosphoribosyl transferase YP_820900.1 WP_011681519.1 STER_1552 STER_RS07630 AroG1 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase YP_821042.1 WP_002947699.1 STER_1703 STER_RS08325 GlnA Glutamine synthetase YP_821087.1 WP_011681641.1 STER_1751 STER_RS08555 Carbohydrate metabolism and transport Pgi Glucose-6-phosphate isomerase YP_820037.1 WP_011680683.1 STER_0241 STER_RS01180 Tkt Transketolase...”
- “...ABC transporter ATP-binding protein YP_820506.1 WP_011681207.1 STER_1117 STER_RS05525 TrpD Anthranilate phosphoribosyl transferase YP_820900.1 WP_011681519.1 STER_1552 STER_RS07630 AroG1 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase YP_821042.1 WP_002947699.1 STER_1703 STER_RS08325 GlnA Glutamine synthetase YP_821087.1 WP_011681641.1 STER_1751 STER_RS08555 Carbohydrate metabolism and transport Pgi Glucose-6-phosphate isomerase YP_820037.1 WP_011680683.1 STER_0241 STER_RS01180 Tkt Transketolase YP_819848.1...”
- Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275
Padmanabhan, Frontiers in microbiology 2018 - “...genes were significantly downregulated in M17-G. Genes responsible for tryptophan synthesis (T303_08760, T303_08765, T303_08770, T303_08775 T303_08780, T303_08785, T303_08790), arginine biosynthesis (T303_00020, T303_00025) and valine/leucine/isoleucine biosynthesis (T303_06860, T303_06865, T303_06875, T303_06880) were significantly upregulated in L5h when compared to other two sugars. FIGURE 8 Changes in expression of...”
PITG_17032 anthranilate phosphoribosyltransferase, putative from Phytophthora infestans T30-4
D0NUM7 Anthranilate phosphoribosyltransferase, putative from Phytophthora infestans (strain T30-4)
36% identity, 95% coverage
- Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity
Resjö, Molecular & cellular proteomics : MCP 2017 - “...to encode anthranilate phosphoribosyltransferase (PITG_17032), serine hydroxymethyltransferase (PITG_06427), asparagine synthetase (PITG_13399),...”
- “...metabolism D0NUM7 Anthranilate phosphoribosyltransferase, putative PITG_17032 Amino acid metabolism D0MSJ4# Putative uncharacterized protein PITG_01131 Cell...”
- Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization
Ah-Fong, BMC genomics 2017 - “...were as follows: a, anthranilate synthase (PITG_01711 and PYU1_G005607) in late tubers. b, anthranilate phosphoribosyltransferase (PITG_17032, PYU1_G006488) in late tubers. c, 20GFe(II) oxygenase (PITG_00237, PYU1_G003898) from early tubers. d, 12-oxophytodienoate reductase (PITG_08491, PYU1_G007433) from early pea. e, 20GFe(II)oxygenase (PITG_08301, PYU1_G002215) from early pea. f, carboxypeptidase (PITG_00756,...”
- Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity
Resjö, Molecular & cellular proteomics : MCP 2017 - “...putative PITG_16076 Amino acid metabolism D0NUM7 Anthranilate phosphoribosyltransferase, putative PITG_17032 Amino acid metabolism D0MSJ4# Putative...”
VC1172 anthranilate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
39% identity, 81% coverage
- Substrate-dependent activation of the Vibrio cholerae vexAB RND efflux system requires vexR
Taylor, PloS one 2015 - “...resulting from cellular byproducts inhibiting the luciferase reporter [ 43 ]. Three mutants were identified (VC1172, VC1579, and VCA1046) that resulted in a >2-fold increase in vexRAB expression ( S1 Table ). VC1172 encodes TrpD which functions in tryptophan biosynthesis; VC1579 encodes AlmE which is a...”
- “...tryptophan biosynthetic pathway. Disruption of the tryptophan biosynthetic pathway affects vexRAB expression Mutation of trpD (VC1172) resulted in the strongest induction of vexRAB expression suggesting that tryptophan biosynthesis intermediates may function as inducers of the vexRAB operon. To investigate this we examined vexRAB expression in six...”
SCO2147 anthranilate phosphoribosyltransferase from Streptomyces coelicolor A3(2)
O68608 Anthranilate phosphoribosyltransferase 1 from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
37% identity, 94% coverage
DKG71_12405 anthranilate phosphoribosyltransferase from Streptomyces sp. NEAU-S7GS2
37% identity, 95% coverage
Q9YGB4 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Thermococcus kodakarensis (see paper)
5nofA / Q9YGB4 Anthranilate phosphoribosyltransferase from thermococcus kodakaraensis (see paper)
TK0253 anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis KOD1
37% identity, 96% coverage
LBDG_36740 anthranilate phosphoribosyltransferase from Leptolyngbya boryana dg5
37% identity, 95% coverage
PF1710 anthranilate phosphoribosyltransferase from Pyrococcus furiosus DSM 3638
36% identity, 96% coverage
Q72EV1 Anthranilate phosphoribosyltransferase from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU0467 anthranilate phosphoribosyltransferase from Desulfovibrio vulgaris Hildenborough
38% identity, 94% coverage
- Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors.
Fida, Frontiers in microbiology 2018 - “...Q72F29, Q72EN0, Q72FN6, Q729Q3, and Q72CP5), tryptophan synthase (Q72EU7, Q72EU8, and Q72FX8), anthranilate synthase (Q72EV0, Q72EV1, Q72EV2, and Q72EV3), and antibiotic resistance proteins such as the small multidrug resistance family (Q729L9) and the metallo-beta-lactamase family proteins (Q727Q1). Decreased expression of genes involved in ribosome activity and...”
- Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris
Zhou, The ISME journal 2015 - “...another clone bearing six mutations in DVU0281, DVU0467, DVU1530, DVU2287b, DVU2802 and DVU3045 went extinct (<a href="#f2">Figure 2a</a>). In contrast, under...”
- Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough
Zhou, Applied and environmental microbiology 2012 - “...Amino acid transport and metabolism DVU0465 DVU0466 DVU0467 DVU0468 DVU0469 DVU0470 DVU0471 DVU0386 Log2 R (mutant/wild type)a Annotation JW9007 JW9009 JW9011...”
- Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough
Bender, Applied and environmental microbiology 2007 - “...DVU0459 DVU0465 DVU0466 NA trpE trpG ND ND ND DVU0467 DVU0468 DVU0469 DVU0470 2 DVU0471 2 DVU2449 trpD trpC trpF1 trpB2 trpA metK Hypothetical protein...”
- Response of Desulfovibrio vulgaris to alkaline stress
Stolyar, Journal of bacteriology 2007 - “...DVU0460 DVU0461 DVU0462 DVU0463 DVU0464 DVU0465 DVU0466 DVU0467 DVU0468 DVU0469 DVU0470 DVU0471 DVU0663 DVU0890 DVU1466 DVU1585 DVU1609 DVU1610 DVU2981 DVU2982...”
TRPGD_SALTY / P00905 Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
NP_460683 anthranilate synthase, component II from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM1724 anthranilate synthase, component II, bifunctional: glutamine amidotransferase and phosphoribosylanthranilate transferase from Salmonella typhimurium LT2
40% identity, 53% coverage
- function: Part of a heterotetrameric complex that catalyzes the two- step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine-binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia. In addition to synthesizing anthranilate, it also catalyzes the second step of the pathway, the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate.
catalytic activity: chorismate + L-glutamine = anthranilate + pyruvate + L- glutamate + H(+) (RHEA:21732)
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
subunit: Monomer. Heterotetramer consisting of two non-identical subunits: a beta subunit (TrpG) and a large alpha subunit (TrpE) (Probable). - PurF-independent phosphoribosyl amine formation in yjgF mutants of Salmonella enterica utilizes the tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase.
Browne, Journal of bacteriology 2006 - GeneRIF: The tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase, composed of the TrpD and TrpE proteins, was shown to be essential for phosphoribosyl amine formation in strains lacking both yjgF and purF.
- Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
Han, Heliyon 2020 - “...subunit 1.8 0.004 trpC STM1725 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase 2.0 0.002 1.0 0.006 trpD STM1724 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase 3.0 0.002 1.8 0.005 trpE STM1723 anthranilate synthase component I 3.1 0.002 2.0 0.003 ilvA SSTM3905 Threonine dehydratase 3.4 0.008 [P] Inorganic ion transport and metabolism...”
- The transcriptional programme of Salmonella enterica serovar Typhimurium reveals a key role for tryptophan metabolism in biofilms
Hamilton, BMC genomics 2009 - “...flowing conditions. Gene name Description Identifier Fold-induction P -value a trpD Anthranilate synthase, component II STM1724 5 3E-03 trpC Tryptophan biosynthesis protein TRPCF, bifunctional STM1725 11 4E-04 trpB Tryptophan synthase beta protein STM1726 8 6E-05 trpA Tryptophan synthase alpha chain STM1727 7 7E-05 trpS2 Putative tryptophanyl-tRNA...”
- Media ion composition controls regulatory and virulence response of Salmonella in spaceflight
Wilson, PloS one 2008 - “...transport protein STM1374 1.84 x ynhA putative SufE protein probably involved in Fe-S center assembly STM1724 1.96 x trpD anthranilate synthase, component II, bifunctional STM2665 2.53 x yfiA ribosome associated factor, stabilizes ribosomes against dissociation STM2924 2.55 rpoS sigma S (sigma 38) factor of RNA polymerase...”
Entcl_2524 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from [Enterobacter] lignolyticus SCF1
38% identity, 63% coverage
CCA00563 phosphoribosylanthranilate transferase from Chlamydophila caviae GPIC
34% identity, 96% coverage
STM14_2087 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
40% identity, 53% coverage
TrpD / b1263 anthranilate synthase subunit TrpD (EC 2.4.2.18; EC 4.1.3.27) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
trpD / P00904 anthranilate synthase subunit TrpD (EC 2.4.2.18) from Escherichia coli (strain K12) (see 2 papers)
TRPGD_ECOLI / P00904 Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 from Escherichia coli (strain K12) (see 3 papers)
NP_415779 anthranilate synthase subunit TrpD from Escherichia coli str. K-12 substr. MG1655
b1263 bifunctional indole-3-glycerol-phosphate synthase/anthranilate phosphoribosyltransferase from Escherichia coli str. K-12 substr. MG1655
41% identity, 53% coverage
- function: Part of a heterotetrameric complex that catalyzes the two- step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine-binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia. In addition to synthesizing anthranilate, it also catalyzes the second step of the pathway, the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate.
catalytic activity: chorismate + L-glutamine = anthranilate + pyruvate + L- glutamate + H(+) (RHEA:21732)
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
subunit: Heterotetramer consisting of two non-identical subunits: a beta subunit (TrpG) and a large alpha subunit (TrpE). - The Role of Propionate-Induced Rearrangement of Membrane Proteins in the Formation of the Virulent Phenotype of Crohn's Disease-Associated Adherent-Invasive Escherichia coli
Pobeguts, International journal of molecular sciences 2024 - “...OmpX 89 0.26 0.03 Amino acid biosynthesis P2566 5-methyltetrahydropteroyltriglutamate homocysteine methyltransferase MetE 192 0.78 0.10 P00904 Bifunctional Protein TrpGD 52 0.65 0.08 P0A912 peptidoglycan-associated outer membrane lipoprotein Pal 46 0.34 0.04 P0ABT2 DNA starvation/stationary phase protection protein Dps 56 0.42 0.05 ijms-25-10118-t001_Table 2 Table 2 (...”
- Proteome-level responses of Escherichia coli to long-chain fatty acids and use of fatty acid inducible promoter in protein production
Han, Journal of biomedicine & biotechnology 2008 - “...flavoprotein subunit 22 OppA Gel match P23843 5.93/56.1 Periplasmic oligopeptide-binding protein 23 TrpD Gel match P00904 6.08/55.9 Anthranilate synthase component II; Anthranilate 24 GuaB (GuaR) Gel match P06981 6.01/55.0 Inosine- 5 -monophosphate dehydrogenase 25 AtpA Gel match P00822 5.84/53.1 ATP synthase alpha chain 26 DppA Gel...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...Tryptophan synthase beta chain 5.71/42,851.82 TrpD P00904 6.05/56,738.75 TrpS P00954 TrxA P0AA25 Anthranilate synthase component II Tryptophanyl-tRNA synthetase...”
- Engineering Escherichia coli for increased productivity of serine-rich proteins based on proteome profiling
Han, Applied and environmental microbiology 2003 - “...5.74/63.7 21 OppA Gel match P23843 5.93/56.1 22 TrpD Gel match P00904 6.08/55.9 23 GuaB or GuaR Gel match P06981 6.01/55.0 24 25 26 AtpA LpdA or Lpd DppA Gel...”
- Structural homology of the glutamine amidotransferase subunits of the anthranilate synthetases of Escherichia coli, Salmonella typhimurium and Serratia marcescens.
Li, Nature 1974 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level
Razaghi-Moghadam, Bioinformatics (Oxford, England) 2021 - “...OptReg. In comparison, the reactions proposed by GeneReg to be upregulated involve three genes b1262, b1263 and b1264, which participate in no other reactions (see Supplementary Table S5 ). Taking a closer look at the list of reactions to downregulate shows that the strategy devised by...”
- Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
Metris, Applied and environmental microbiology 2014 - “...b0565 b1243 b0903 b0688 b2502 b0243 b2679 b0636 b3296 b4200 b2533 b1261 b1264 b1263 b4058 4.5 5 2 2 4.5 4.5 4.5 4.5 5 2 5 4.5 2 2 4.5 4.5 2 2 2 4.5 4.5 4.5 4.5...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...TTPM TIM genes b0639 b0720 b0907 b0908, b1260 b0914 b1098 b1136 b1261, b1262 s0001 b2827 b1263, b1264 b3648 b1693, b2329 s0001 b2599, b2600 b3389 SS AAM FM ACM HM CM genes b0928 b1415 b1415 b2019, b2020 b2750, b2751 b3941 b3608 b2021, b2022 b2752, b2762 b2023, b2024...”
- Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
White-Ziegler, Journal of bacteriology 2007 - “...I; also functions as protease I trpD b1263 Anthranilate synthase component II L-asparaginase ybiK b0828 yecC b1917 Putative ATP-binding component of...”
- Experimental and computational assessment of conditionally essential genes in Escherichia coli
Joyce, Journal of bacteriology 2006 - “...(b0004) trpA (b1260) trpB (b1261) trpC (b1262) trpD (b1263) trpE (b1264) tyrA (b2600) Group 8262 JOYCE ET AL. J. BACTERIOL. two experimentally defined essential...”
- Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
Gyaneshwar, Journal of bacteriology 2005 - “...b2310), three trp biosynthetic genes (b1260, b1261, and b1263), and six arg biosynthetic genes (b2818, b3958 to b3960, b3172, and b3359) (Fig. 2). Regulation...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...csgC hdeB b3524 b2601 b1261 b1264 b1493 b3517 b3320 b1263 b2600 b1260 b1973 b1262 b3340 b1779 b3321 b3308 b3304 b3616 b3339 b2155 b3829 b3317 b3296 b2913 b0631...”
- “...b1004 b0179 b2600 b1260 b3509 b1261 b2342 b2800 b3460 b3458 b1263 b1783 b0907 b0461 b2464 b0812 b0903 b1262 b0126 b4015 b2674 0.06 0.07 0.07 0.08 0.10 0.11 0.13...”
- More
c1729 Anthranilate synthase component II from Escherichia coli CFT073
41% identity, 53% coverage
FTN_1776 anthranilate phosphoribosyltransferase from Francisella tularensis subsp. novicida U112
37% identity, 83% coverage
TRPD2_NOSS1 / Q8YXQ9 Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
alr1153 anthranilate phosphoribosyltransferase from Nostoc sp. PCC 7120
35% identity, 92% coverage
- function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA).
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+) (Binds 2 magnesium ions per monomer.)
subunit: Homodimer. - Open reading frame all0601 from Anabaena sp. strain PCC 7120 represents a novel gene, cnaT, required for expression of the nitrate assimilation nir operon
Frías, Journal of bacteriology 2003 - “...that are more likely to represent true trpD genes, alr1153 and alr0409, the latter of which is located in a putative tryptophan biosynthesis gene cluster (23)....”
- “...exhibits 26% identity to the Rhodobacter TrpD protein, the alr1153 and alr0409 products exhibit 39 and 41% identity, respectively, to this TrpD protein. ORFs of...”
GM298_00220 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from Enterobacter sp. HSTU-ASh6
41% identity, 53% coverage
LMH90_000735 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from Enterobacter hormaechei
40% identity, 53% coverage
- Genome Assembly of a Putative Plant Growth-Stimulating Bacterial Sweet Pepper Fruit Isolate, Enterobacter hormaechei SRU4.4
Mamphogoro, Microbiology resource announcements 2023 - “...trpB LMH90_000725 Tryptophan synthase subunit beta trpCF LMH90_000730 Bifunctional indole-3-glycerol-phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF trpD LMH90_000735 Anthranilate phosphoribosyltransferase TrpD aldA LMH90_002155 Aldehyde dehydrogenase trpS LMH90_010130 Tryptophan-tRNA ligase Cytokinin miaA LMH90_010760 Adenosine(37)- N 6-dimethylallyltransferase MiaA miaB LMH90_013275 N 6-Isopentenyl adenosine(37)- C 2-methylthiotransferase MiaB Ammonia production nadE LMH90_014565...”
FTA_2078 anthranilate phosphoribosyltransferase from Francisella tularensis subsp. holarctica FTA
36% identity, 84% coverage
- Francisella tularensis metabolism and its relation to virulence
Meibom, Frontiers in microbiology 2010 - “...is absent in the Schu S4 and LVS strains but present in the subsp. novicida (FTA_2078). TyrA*, the gene is absent in the Schu S4 strain but present in both LVS (FTL_048) and subsp. novicida (FTN_0055). Bruce Stocker's pioneer work on the genetics of Salmonella enterica...”
FPV33_RS10200 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from Klebsiella aerogenes
40% identity, 53% coverage
- Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions
Chen, Frontiers in microbiology 2024 - “...FPV33_RS05525 gshA Glutamate--cysteine ligase 1.74 FPV33_RS10040 astD Succinylglutamate-semialdehyde dehydrogenase 1.37 FPV33_RS19730 proB Glutamate 5-kinase 1.22 FPV33_RS10200 trpD Bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD 1.08 FPV33_RS19735 proA Glutamate-5-semialdehyde dehydrogenase 1.01 FPV33_RS00465 gltS Sodium/glutamate symporter 1.14 FPV33_RS09905 gapA Glyceraldehyde-3-phosphate dehydrogenase 2.84 FPV33_RS06275 fdx ISC system...”
WP_101962912 anthranilate phosphoribosyltransferase from Micrococcus yunnanensis
34% identity, 93% coverage
Q31LB6 Anthranilate phosphoribosyltransferase from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
38% identity, 95% coverage
NR795_07870 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD from Pseudescherichia sp. L3
37% identity, 63% coverage
WP_016875302 anthranilate phosphoribosyltransferase from Chlorogloeopsis fritschii PCC 9212
34% identity, 91% coverage
DET0126 anthranilate phosphoribosyltransferase from Dehalococcoides ethenogenes 195
36% identity, 89% coverage
G5S_1087 anthranilate phosphoribosyltransferase from Chlamydia pecorum E58
32% identity, 97% coverage
TRPD_THETH / P83827 Anthranilate phosphoribosyltransferase; EC 2.4.2.18 from Thermus thermophilus
TRPD_THET8 / Q5SH88 Anthranilate phosphoribosyltransferase; EC 2.4.2.18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Q72HJ6 Anthranilate phosphoribosyltransferase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
TTC1491 No description from Thermus thermophilus HB27
41% identity, 91% coverage
- function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA).
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+) (Binds 2 magnesium ions per monomer.)
subunit: Homodimer. - function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA).
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+) (Binds 2 magnesium ions per monomer.)
subunit: Homodimer. - Thermus thermophilus nucleoside phosphorylases active in the synthesis of nucleoside analogues
Almendros, Applied and environmental microbiology 2012 - “...Q72L73), TTC1185 (UniProt Q72IE7), and TTC1491 (UniProt Q72HJ6)-- had NP-like domains and were selected for cloning. Cloning, expression, and purification of...”
- Thermus thermophilus nucleoside phosphorylases active in the synthesis of nucleoside analogues
Almendros, Applied and environmental microbiology 2012 - “...TTC0188 (UniProt Q72L73), TTC1185 (UniProt Q72IE7), and TTC1491 (UniProt Q72HJ6)-- had NP-like domains and were selected for cloning. Cloning, expression, and...”
- “...proteins remained soluble in the case of TTC0188 and TTC1491. The purity of the thermostable proteins in the heat-purified fractions was estimated to be ca. 40%...”
TRPD_MYCTU / P9WFX5 Anthranilate phosphoribosyltransferase; EC 2.4.2.18 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
A5U4M0 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Mycobacterium tuberculosis (see paper)
P9WFX5 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Mycobacterium tuberculosis (see 3 papers)
Rv2192c anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis H37Rv
NP_216708 anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis H37Rv
DPM14_10670, TBPG_RS21255 anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis W-148
39% identity, 90% coverage
- function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA)
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+) (Binds 2 magnesium ions per monomer. {ECO:0000255|HAMAP- Rule:MF_00211, ECO:0000269|PubMed:16337227, ECO:0000269|PubMed:23363292, ECO:0000269|Ref.4, ECO:0000269|Ref.)5}
subunit: Homodimer. - Genomic analysis of Mycobacterium brumae sustains its nonpathogenic and immunogenic phenotype
Renau-Mínguez, Frontiers in microbiology 2022 - “...Proteasome-associated protein 87.7 100 Rv2136c Rv2136c 2,396,008 2,396,838 Reverse Oxidative and nitrosative stresses 74.7 100 Rv2192c trpD 2,455,631 2,456,743 Reverse Other virulence factors 72.8 92.7 Rv2220 glnA1 2,487,615 2,489,051 Forward Other virulence factors 83.1 100 Rv2246 kasB 2,519,396 2,520,712 Forward Lipids and Fatty Acids Metabolism 74...”
- The rate and role of pseudogenes of the Mycobacterium tuberculosis complex
Soler-Camargo, Microbial genomics 2022 - “...deleted in M. bovis and M. africanum strains [ 71, 72 ]. The trpD gene (Rv2192c; the sole representative of the tryptophan synthesis category) is pseudogenized in representatives of all MTBC ecotypes and is intact in M. canettii genomes. The putative glycosyltransferases 3 ( gtf3 )...”
- Low-cost anti-mycobacterial drug discovery using engineered E. coli
Bongaerts, Nature communications 2022 - “.... Four additional Mtb target sequences of interest dapB (Rv2773c), asd (Rv3708c), cysH (Rv2392), trpD (Rv2192c) were taken from the same Mtb genome. A complete list of plasmids created for this study is provided in Supplementary Table 2 . Plasmid DNA sequences are available as a...”
- The tryptophan biosynthetic pathway is essential for Mycobacterium tuberculosis to cause disease
Lott, Biochemical Society transactions 2020 - “...biosynthetic pathway [ 19 ]. The predicted TrpA (Rv1613), TrpB (Rv1612), TrpC (Rv1611) and TrpD (Rv2192c) proteins have all been heterologously expressed and characterised, and demonstrate the expected biochemical activities in vitro [ 2024 ], and all the enzymes in the pathway have been structurally characterised...”
- “...TrpB: 2o2e, 2o2j TrpC Rv1611 Indole-3-glycerol phosphate synthase 3qja, 3t40, 3t44, 3t55, 3t78, 4fb7 TrpD Rv2192c Anthranilate phosphoribosyl transferase 1zvw, 2bpq, 3r88, 3twp, 3uu1, 4ij1, 4giu, 4gkm, 4m0r, 4n5v, 4n8q, 4n93, 4owu, 4owv, 4owm, 4own, 4owo, 4owq, 4ows, 5byt, 5bne, 5c1r, 5c2l, 5c7s TrpE Rv1609 Anthranilate...”
- Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis
Rahman, mBio 2014 - “...ATCC 13950. A few other examples include the genes Rv0069c (EC 4.3.1.17), Rv1905c (EC 1.4.3.3), Rv2192c (EC 2.4.2.18), Rv2006 (EC 3.2.1.28), Rv3393 (EC 3.2.2.1), and Rv0091 (EC 3.2.2.9), which are present in M. tuberculosis but absent in M. indicus pranii and M. intracellulare ATCC 13950. These...”
- targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
Raman, BMC systems biology 2008 - “...step is best used at the post-identification analysis stage. For example, proteins such as TrpD (Rv2192c), AroA (Rv3227), RibC (Rv1412) do not appear to be expressed in any of the experiments considered. Comparison with Anti-targets An ideal target should not only have specific recognition to the...”
- “...auxotroph has vaccine potential [ 90 ]; suggested as potential target [ 91 ] TrpD (Rv2192c) -do- X X LeuA (Rv3710) Suggested as potential target [ 92 ] DapB (Rv2773c) Suggested as potential target [ 93 ] X X X AroB (Rv2538c) Shikimate pathway suggested as...”
- Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
Jamshidi, BMC systems biology 2007 - “...86 4 FadD32 Rv3801c 86 4 AccD5 Rv3280 78 2 LeuD Rv2987c 14 2 TrpD Rv2192c 10 4 DapB Rv2773c 2 3 AroA Rv3227 20 3 AroC Rv2540c 20 3 AroE Rv2537c 11 4 AroG Rv2178c 11 4 AroQ Rv2537c 11 4 ilvG (acetolactate synthase) Rv1820...”
- Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence
Smith, Clinical microbiology reviews 2003 - “...TrpD (Rv2192c, trpD) ..............................................................................................................................482 (iii)...”
- “...or in human macrophages (12). (ii) TrpD (Rv2192c, trpD). TrpD is anthranilate phosphoribosyl transferase, which is involved in the tryptophan biosynthetic...”
- Anthranilate phosphoribosyltransferase: Binding determinants for 5'-phospho-alpha-d-ribosyl-1'-pyrophosphate (PRPP) and the implications for inhibitor design.
Evans, Biochimica et biophysica acta. Proteins and proteomics 2018 (PubMed)- GeneRIF: The AnPRT structures presented herein indicated that PRPP binds a surface cleft and becomes enclosed due to re-positioning of two mobile loops.
- Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site.
Cookson, Biochemistry 2015 (PubMed)- GeneRIF: Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site.
- Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis.
Cookson, The Biochemical journal 2014 (PubMed)- GeneRIF: AnPRT exhibits a broad substrate tolerance. Analysis of the crystal structures of the enzyme in complex with alternative substrates illuminates some details of the reaction mechanism.
- The substrate capture mechanism of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase provides a mode for inhibition.
Castell, Biochemistry 2013 (PubMed)- GeneRIF: PRPP is bound at the base of a deep cleft in anthranilate phosphoribosyltransferase and predicts two anthranilate binding sites along the tunnel leading to the PRPP binding site.
- The crystal structure of TrpD, a metabolic enzyme essential for lung colonization by Mycobacterium tuberculosis, in complex with its substrate phosphoribosylpyrophosphate.
Lee, Journal of molecular biology 2006 (PubMed)- GeneRIF: structure of TrpD from M.tuberculosis was solved by X-ray crystallography, at 1.9 A resolution for the native enzyme (R = 0.191, Rfree = 0.230) and at 2.3 A resolution for the complex with its substrate phosphoribosylpyrophosphate (PRPP)[TrpD]
- System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Bespyatykh, Scientific reports 2019 - “...pseudogene TBPG_RS21255 in W-148 by using H37Rv annotation, do belong to the TrpD anthranilate phosphoribosyltransferase (DPM14_10670) in RUS_B0. Withal, LTSAGDDAERSDEEER and RLTSAGDDAER peptides have been previously identified only after six-frame translation as GSSPs. In the RUS_B0 annotation, the corresponding peptides were identified for the DUF3000 domain-containing...”
- “...example, the peptides AASSLSGGADTLEALGVR and IDLGPDLVAR, previously identified as parts of the of the pseudogene TBPG_RS21255 in W-148 by using H37Rv annotation, do belong to the TrpD anthranilate phosphoribosyltransferase (DPM14_10670) in RUS_B0. Withal, LTSAGDDAERSDEEER and RLTSAGDDAER peptides have been previously identified only after six-frame translation as...”
5c2lA / P9WFX5 Magnesium soaked into the active site of mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
39% identity, 95% coverage
- Ligand: magnesium ion (5c2lA)
BIF_01409 anthranilate phosphoribosyltransferase from Bifidobacterium animalis subsp. lactis BB-12
35% identity, 96% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...Intergenic(+50/+8) BIF_00866 / BIF_00684 1903558 34bp73bp Intergenic(+2/+61) BIF_00971 / BIF_01033 1913433 CT Intergenic(+33/+59) BIF_02085 / BIF_01409 1914632 + AAGGGGCGCCG Coding(60/1,200nt) BIF_01409 1914636 AG V19A(G T AG C A) BIF_01409 1932289 +G Intergenic(+61/+53) BIF_02266 / BIF_00333 1932291 +T Intergenic(+63/+51) BIF_02266 / BIF_00333 1932292 +G Intergenic(+64/+50) BIF_02266 /...”
Ddes_1591 anthranilate phosphoribosyltransferase from Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774
38% identity, 61% coverage
- Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide
Cadby, Scientific reports 2017 - “...Tryptophan synthase, subunit 3.98 3.36e-5 Ddes_1589 Phosphoribosylanthranilate isomerase 2.87 6.69e-5 Ddes_1590 Indole-3-glycerol-phosphate synthase 3.15 3.32e-7 Ddes_1591 Anthranilate phosphoribosyltransferase 2.43 0.000678 Ddes_1668 4Fe-4S ferredoxin NADH-dependent dehydrogenase 4.16 6.11e-9 Ddes_1669 NADH-quinone oxidoreductase large subunit 2.1 0.00277 Ddes_1671 NADH-ubiquinone oxidoreductase 20kDa subunit 3.23 2.99e-6 Ddes_1672 NADH dehydrogenase subunit 1...”
HP1280 anthranilate synthase component II from Helicobacter pylori 26695
P56737 Anthranilate phosphoribosyltransferase from Helicobacter pylori (strain ATCC 700392 / 26695)
35% identity, 93% coverage
- Study of Helicobacter pylori Isolated from a High-Gastric-Cancer-Risk Population: Unveiling the Comprehensive Analysis of Virulence-Associated Genes including Secretion Systems, and Genome-Wide Association Study
Saruuljavkhlan, Cancers 2023 - “...least known genes in terms of thorough functional explanations of H. pylori virulence, encompassing HP0452, HP1280 (genes encoding hypothetical proteins), HP1547 ( leuS encoding leucyl-tRNA synthase), and HP1220 ( yhcG encoding ABC transporter ATP-binding protein associated with multidrug-efflux proteins). In addition, three SNPs from all nine...”
- “...hyp a 469,160 405 G T 2.8/33.3 Glu135Asp (McrB family protein) SNP 5.39 10 7 HP1280 hyp a 1,355,874 808 C T 2.8/33.3 Thr270Val (Anthranilate phosphoribosyltransferase) SNP 5.39 10 7 HP1547 leuS a 1,625,904 2014 C T 2.8/33.3 Ala672Thr Leuci-tRNA ligase k-mer 3.62 10 9 HP1220...”
- Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
Thiele, Journal of bacteriology 2005 - “...PRAIi), HP1280 (ANPRT) TYRt2r...”
- Acid-induced gene expression in Helicobacter pylori: study in genomic scale by microarray
Ang, Infection and immunity 2001 - “...HP0744 HP0857 HP0903 HP0904 HP0922 HP1007 HP1194 HP1198 HP1280 HP1353 HP1369 HP1417 HP1460 HP1500 HP1522 Hp1528 HP1536 HP1538 HP1589 a ORFs that were less...”
- Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping
Fujibuchi, Nucleic acids research 2000 - “...names in parentheses are alternative names, except for HP1280 which contains a frameshift (no amino acid sequence). Eco, Escherichia coli; Hin, Haemophilus...”
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25121 dxs 369 O25549 ruvA 370 P56104 adk 371 O25293 ychF 372 O25595 alr 373 P56737 trpD 374 O26103 pdxA 375 P56137 purA 376 P56452 alaS 377 P94842 ybgC 378 O24885 gmd 379 O24864 CheV 380 P56184 prs 381 O25475 secA 382 O25477 HP_0788 383 O24973...”
Q84PB1 Putative phosphoribosylanthranilate transferase (Fragment) from Oryza sativa subsp. japonica
36% identity, 89% coverage
- Combining Proteomics and Metabolomics to Analyze the Effects of Spaceflight on Rice Progeny
Zeng, Frontiers in plant science 2022 - “...transferase 0.78 1.4128E-02 B9FFK4 Anthranilate synthase component 0.78 4.0609E-02 B9FHA5 Serine O -acetyltransferase 0.77 4.0609E-02 Q84PB1 Phosphoribosyl anthranilate transferase 0.77 9.2369E-05 Q6K6Q1 Phenylalanine ammonia-lyase 1.35 5.9680E-03 Q0JFF8 Hydroxy pyruvate reductase HPR3 1.27 4.8507E-03 B8AGS8 Acetylornithine deacetylase 1.27 3.2391E-03 A0A0P0W7B4 Amidase At4g34880 1.26 9.8779E-03 B9G099 Indole-3-glycerol phosphate...”
all0409 anthranilate phosphoribosyltransferase from Nostoc sp. PCC 7120
34% identity, 93% coverage
MAP1931c TrpD from Mycobacterium avium subsp. paratuberculosis str. k10
37% identity, 91% coverage
- Amino Acids As Mediators of Metabolic Cross Talk between Host and Pathogen
Ren, Frontiers in immunology 2018 - “...subunit beta, MAP1306), trpC (indole-3-glycerol-phosphate synthase, MAP1305), hisA (phosphoribosyl isomerase A, MAP1297), trpD (anthranilate phosphoribosyltransferase, MAP1931c), and trpE (anthranilate synthase component I, MAP1303), which are all involved in the biosynthesis of l -tryptophan ( 83 ). Collectively, tryptophan is required for both host and pathogen and...”
- Indoleamine 2,3-dioxygenase, tryptophan catabolism, and Mycobacterium avium subsp. paratuberculosis: a model for chronic mycobacterial infections
Plain, Infection and immunity 2011 - “...isomerase A, MAP1297), trpD (anthranilate phosphoribosyltransferase, MAP1931c), and trpE (anthranilate synthase component I, MAP1303), which are involved in...”
- Profiling bovine antibody responses to Mycobacterium avium subsp. paratuberculosis infection by using protein arrays
Bannantine, Infection and immunity 2008 - “...MAP1417c MAP1609c MAP1636c MAP1643 MAP1655c MAP1730c MAP1931c MAP2077c MAP2116c MAP2121c MAP2121c-His MAP2151 MAP2155 MAP2156 MAP2157 MAP2158 MAP2182c MAP2231...”
- “...MAP2380 MAP3840 MAP0389 MAP3129 MAP0855 MAP3833c MAP0866 MAP1931c MAP2657 MAP2751 MAP2753 MAP3531c MAP4207c MAP2151 MAP0736 283.71e 146.74 266.55 21.71 75.99...”
- Early antibody response against Mycobacterium avium subspecies paratuberculosis antigens in subclinical cattle
Bannantine, Proteome science 2008 - “...[beta] module MAP1655c 0.93 381 126 hypothetical protein MAP1730c 0.26 1023 340 putative ATP/GTP-binding protein MAP1931c 0.32 1104 367 anthranilate phosphoribosyltransferase MAP2077c 1.66 330 109 hypothetical protein MAP2116c 0.27 1269 422 cell invasion protein MAP2121c 7.14 887 295/307 major membrane protein I MAP2121c-his 0.99 924 307...”
- “...0 2.049 0 0 G6 MAP1730c 1.147 29.831 43.872 52.35 0 12.272 57.799 57.47 B10 MAP1931c 0 2.917 0 2.217 0.511 2.886 2.077 3.339 H5 MAP2077c 3.833 0 2.784 9.443 1.385 0 3.63 9.221 D11 MAP2116c 1.418 29.88 33.215 42.633 0.568 11.24 51.336 47.918 F4 MAP2121c...”
CJJ81176_0370 anthranilate synthase component II from Campylobacter jejuni subsp. jejuni 81-176
34% identity, 61% coverage
- Campylobacter jejuni Virulence Factors Identified by Modulating Their Synthesis on Ribosomes With Altered rRNA Methylation
Sałamaszyńska-Guz, Frontiers in cellular and infection microbiology 2021 - “...protein, MlaD CJJ81176_1639 Uncharacterized protein, Cjp27 CJJ81176_pVir0026 OstA family protein, LptA CJJ81176_0677 Anthranilate phosphoribosyltransferase, TrpD CJJ81176_0370 ABC transporter, permease protein, MlaE CJJ81176_1637 Uncharacterized protein CJJ81176_1429 Hydrogenase, (NiFe)/(NiFeSe) small subunit family CJJ81176_1398 UDP-N-acetylglucosamine 4,6-dehydratase, FlmA CJJ81176_1310 Tryptophan synthase beta-chain, TrpB CJJ81176_0372 Putative imidazole glycerol phosphate synthase subunit,...”
Cj0346 anthranilate synthase component II from Campylobacter jejuni subsp. jejuni NCTC 11168
34% identity, 61% coverage
- The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts
Clark, BMC microbiology 2014 - “...1.271.08 Anthranilate synthesis Anthranilate synthase component I Cj0345 gi|121612335 0.800.75 0.870.71 Anthranilate synthase component II Cj0346 gi|121612640 0.670.60 0.600.46 N-(5phosphoribosyl)anthranilate isomerase Cj0347 gi|157414644 1.000.53 0.830.65 Chemotaxis Methyl-accepting chemotaxis protein Cj1189c gi|121613242 0.701.10 0.070.06 Methyl-accepting chemotaxis protein Cj1506c gi|121613017 2.01.31 3.232.40 Methionine biosynthesis 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE Cj1201...”
- Adaptive mechanisms of Campylobacter jejuni to erythromycin treatment
Xia, BMC microbiology 2013 - “...genes in this category included trpB , trpD , trpA , trpE ( cj0348 , cj0346 , cj0349 , cj0345 ) encoding tryptophan synthase and anthranilate synthase subunits, two genes ( cj1017c , cj1019c ) encoding a branched-chain amino-acid ABC transport system permease and a periplasmic...”
- AI-2 does not function as a quorum sensing molecule in Campylobacter jejuni during exponential growth in vitro
Holmes, BMC microbiology 2009 - “...[ fabD ], Cj0441 [ acpP ], Cj1400 [ fabI ]), and amino acid biosynthesis (Cj0346 [ trpD ], Cj0347 [ trpF ], Cj0348 [ trpB ], Cj0349 [ trpA ], Cj0405 [ aroE ], Cj0891 [ serA ], Cj1599 [ hisB ], Cj1600 [ hisF...”
- Culture of Campylobacter jejuni with sodium deoxycholate induces virulence gene expression
Malik-Kale, Journal of bacteriology 2008 - “...Cj0246c Cj0247c Cj0295 Cj0301c Cj0309c Cj0323 Cj0324 Cj0346 Cj0352 Cj0356c Cj0365c Cj0366c Cj0367c Cj0381c Cj0382c Cj0395c Cj0397c Cj0413 Cj0484 Cj0512 Cj0526c...”
CNA07880 anthranilate phosphoribosyltransferase from Cryptococcus neoformans var. neoformans JEC21
32% identity, 72% coverage
- Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets
Tezcan, Frontiers in bioinformatics 2023 - “...Metabolism CND01510, CND06120, CNB01460, CNA07220, CNH01620, CNB03030 Histidine Metabolism CNA07990 Phenylalanine Metabolism CNB01990, CNH02650, CNI00560, CNA07880, CNF03410, CNM00820 Phenylalanine, Tyrosine and Tryptophan Biosynthesis CNG04250 Glycerophospholipid Metabolism Further on this issue, the double-gene deletion analysis and comparison with the human genes in the Recon3D model revealed eight...”
- “...albicans Chorismate Flavin mononucleotide Streptococcus pneumoniae, Helicobacter pylori 1,3--glucan Ibrexafungerp, Anidulafungin, Caspofungin, Micafungin Aspergillus niger CNA07880 5-O-phosphono-alpha-D-ribofuranosyl diphosphate Erwinia carotovora CNF01260 Flavin adenine dinucleotide, Azelaic acid Escherichia coli, Staphylococcus aureus CNN02320 Ibrexafungerp, Anidulafungin, Caspofungin, Micafungin Aspergillus niger CNH01520 alpha-Ketoisovalerate Mycobacterium tuberculosis CNA07120 Dihydroorotic Acid, Orotic acid,...”
BBMN68_312 anthranilate phosphoribosyltransferase from Bifidobacterium longum subsp. longum BBMN68
35% identity, 96% coverage
CA265_RS05010 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Pedobacter sp. GW460-11-11-14-LB5
30% identity, 96% coverage
- mutant phenotype: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01245.
ZMO0200 anthranilate phosphoribosyltransferase from Zymomonas mobilis subsp. mobilis ZM4
31% identity, 94% coverage
SAOUHSC_01368 anthranilate phosphoribosyltransferase from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1264 anthranilate phosphoribosyltransferase from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1281 anthranilate phosphoribosyltransferase from Staphylococcus aureus subsp. aureus str. Newman
SACOL1405 anthranilate phosphoribosyltransferase from Staphylococcus aureus subsp. aureus COL
34% identity, 76% coverage
- Stenotrophomonas maltophilia affects the gene expression profiles of the major pathogens Pseudomonas aeruginosa and Staphylococcus aureus in an in vitro multispecies biofilm model
Alio, Microbiology spectrum 2023 - “...toxin called YoeB [SAOUHSC_02691 ( F3 )] and the tryptophane biosynthesis [SAOUHSC_01369 ( F4 ), SAOUHSC_01368 ( F5 ), SAOUHSC_01371 ( F6 ), SAOUHSC_01372 ( F7 )]. ( G ) SH1000 + K279a + SC5314: regulated genes of SH1000 are a serine/threonine exchange transporter [SAOUHSC_01450 (...”
- “...( G2 )], and the tryptophane biosynthesis [SAOUHSC_01371 ( G3 ), SAOUHSC_01372 ( G4 ), SAOUHSC_01368 ( G5 ), SAOUHSC_01369 ( G6 )]. ( H ) PAO1 + K279a: regulated genes of PAO1 are a thioestherase [PA1019a ( H1 )], type 2 [PA2676 ( H2 )],...”
- Interaction analyses based on growth parameters of GWAS between Escherichia coli and Staphylococcus aureus
Liang, AMB Express 2021 - “...transcriptional activator RclR S. aureus SAOUHSC_00299 scdA 313,151 CG AGCACC Cell wall biosynthesis protein ScdA SAOUHSC_01368 trpD 1,313,228 TA TCCACC Anthranilate phosphoribosyltransferase SAOUHSC_00545 sdrD 554,869 CT GACGAT Fibrinogen-binding protein SdrD SAOUHSC_01219 - 1,169,344 GC GATCAT Cell wall hydrolase Analyses of significant genes in S. aureus Meanwhile,...”
- Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus
Norambuena, PLoS pathogens 2023 - “...= UMP Upp SAUSA300_2066 Anthranilate phosphoribosyltransferase Anthranilate + PRPP = N-(5-phospho-D-ribosyl)-anthranilate + PP i TrpD SAUSA300_1264 Orotate phosphoribosyltransferase Orotate + PRPP = orotidine 5-phosphate + PP i PyrE SAUSA300_1098 Amidophosphoribosyltransferase PRPP + H 2 O + glutamine = 5-phospho--D-ribosylamine + diphosphate + glutamate PurF SAUSA300_0972 Xanthine...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_1819 SAUSA300_0808 SAUSA300_0077 SAUSA300_1569 SAUSA300_1264 SAUSA300_2561 SAUSA300_2080 SAUSA300_2014 SAUSA300_2534 SAUSA300_0359 SAUSA300_2384...”
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...NWMN_1241 NWMN_1245 NWMN_1277 NWMN_1279 NWMN_1280 NWMN_1281 NWMN_1282 NWMN_1283 NWMN_1284 NWMN_1304 NWMN_1305 NWMN_1306 NWMN_1307 NWMN_1308 NWMN_1311 NWMN_1348...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...trpE Anthranilate synthase component I 6.0 (1.4) SACOL1404 trpG Anthranilate synthase component II 6.4 (1.5) SACOL1405 trpD Anthranilate phosphoribosyltransferase 8.6 (1.6) 6.5 (1.1) SACOL1406 trpC Indole-3-glycerol-phosphage synthase 13.7 (1.5) 7.7 (1.2) SACOL1407 trpF N-(5-phosphoribosyl)anthranilate isomerase 21.9 (1.5) 10.0 (1.3) SACOL1408 trpB Tryptophan synthase subunit 18.4 (1.7)...”
SA1201 anthranilate phosphoribosyltransferase from Staphylococcus aureus subsp. aureus N315
33% identity, 76% coverage
UH47_02030 anthranilate phosphoribosyltransferase from Staphylococcus pseudintermedius
31% identity, 94% coverage
NCgl2929 anthranilate phosphoribosyltransferase from Corynebacterium glutamicum ATCC 13032
cg3361 anthranilate phosphoribosyltransferase from Corynebacterium glutamicum ATCC 13032
34% identity, 92% coverage
- CRISPR-Driven Genome Engineering for Chorismate- and Anthranilate-Accumulating Corynebacterium Cell Factories
Kim, Journal of microbiology and biotechnology 2023 - “...cultivation ( Fig. 2A ). ANT is metabolized in subsequent steps by ANT phosphoribosyltransferase TrpD (NCgl2929), so we constructed a strain capable of accumulating ANT by removing TrpD in Inha304, a shikimate-producing strain compensating for AroK, and naming it Inha350 ( Figs. S3B and S3C )....”
- 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 - “...cg2893 cg1410 cg2391 cg3359 cg2894 cg1612 cg3362 cg2565 cg3361 cg1419 cg2610 cg3360 cg2837 cg2137 cg2836 cg0303 cg3047 cg2138 cg2559 cg2136 cg0961 cg3096 cg3022...”
- 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 - “...lysA (2) Diaminopimelate decarboxylase Lysine biosynthesis [102] 46 Tryptophan cg3364 , cg3363 , cg3362 , cg3361 , cg3359 , cg3360 trpA (5) , trpB (11) , trpCF (10) , trpD (9), trpE (6), trpG (2) Tryptophan synthase alpha chain, Tryptophan synthase beta chain, Indole-3-glycerol-phosphate synthase/phosphoribosylanthranilate isomerase,...”
CNAG_00811 anthranilate phosphoribosyltransferase from Cryptococcus neoformans var. grubii H99
33% identity, 72% coverage
- Expanding the Toolbox for Functional Genomics in Fonsecaea pedrosoi: The Use of Split-Marker and Biolistic Transformation for Inactivation of Tryptophan Synthase (trpB) Gene
Favilla, Journal of fungi (Basel, Switzerland) 2023 - “...YKL211C Trp3 CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Anthranilate phosphoribosyl transferase [EC:2.4.2.18] Trp4 YDR354W Trp4 CNAG_00811 TrpD Afu4g11980 TrpDZ517_01180 -KIW85788 63.84 Phosphoribosylanthranilate isomerase [EC:5.3.1.24] Trp1 YDR007W Trp3 CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Tryptophan synthase [EC:4.2.1.20] Trp5 YGL026C Trp5 CNAG_00649 TrpB Afu2g13250 TrpBZ517_07968 -KIW78135 78.39 a...”
- Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans
Kelliher, PLoS genetics 2016 - “...PRC1, PSR1, PYC1, PYC2, ROD1, SCP160, SEY1, SMC3, SMC4, VAC14, VBA1, YBR053C, CNAG_00320, CNAG_00498, CNAG_00770, CNAG_00811, CNAG_00991, CNAG_01055, CNAG_01167, CNAG_01372, CNAG_01461, CNAG_01566, CNAG_01622, CNAG_01750, CNAG_01844, CNAG_02022, CNAG_02154, CNAG_02229, CNAG_02447, CNAG_02506, CNAG_02793, CNAG_02927, CNAG_03395, CNAG_03453, CNAG_03743, CNAG_03845, CNAG_04033, CNAG_04168, CNAG_04170, CNAG_04900, CNAG_04961, CNAG_05003, CNAG_05144, CNAG_05934, CNAG_05977, CNAG_06087,...”
BT0530 anthranilate phosphoribosyltransferase (EC 2.4.2.18) from Bacteroides thetaiotaomicron VPI-5482
29% identity, 96% coverage
- mutant phenotype: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01245.
SXYL_01501 anthranilate phosphoribosyltransferase from Staphylococcus xylosus
31% identity, 95% coverage
7dsjA / P07285 Anthranilate phosphoribosyltransferase from saccharomyces cerevisiae in complex with prpp and mg (see paper)
30% identity, 83% coverage
- Ligands: 1-o-pyrophosphono-5-o-phosphono-alpha-d-ribofuranose; magnesium ion (7dsjA)
TRPD_YEAST / P07285 Anthranilate phosphoribosyltransferase; PRtransferase; EC 2.4.2.18 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
YDR354W Anthranilate phosphoribosyl transferase of the tryptophan biosynthetic pathway, catalyzes the phosphoribosylation of anthranilate, subject to the general control system of amino acid biosynthesis from Saccharomyces cerevisiae
30% identity, 79% coverage
- function: Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'- phosphoribosyl)-anthranilate (PRA), the second step in tryptophan biosynthesis.
catalytic activity: N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5- phospho-alpha-D-ribose 1-diphosphate + anthranilate (RHEA:11768)
cofactor: Mg(2+)
subunit: Homodimer. - Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes
Zheng, Nucleic acids research 2023 - “...YBR248C YBR249C YCL030C YCR005C YDL131W YDL182W YDR127W YDR354W YDR379C-A YDR380W YER052C YER055C YER069W YER175C YFL026W YGL032C YGL117W YGL186C YGL202W...”
- “...YCL030C YCR005C YDL025C YDL131W YDL182W YDL198C YDR127W YDR354W YDR379C-A YDR380W YER052C YER053C YER055C YER175C YFL014W YFL026W YGL032C YGL117W YGL186C...”
- Expanding the Toolbox for Functional Genomics in Fonsecaea pedrosoi: The Use of Split-Marker and Biolistic Transformation for Inactivation of Tryptophan Synthase (trpB) Gene
Favilla, Journal of fungi (Basel, Switzerland) 2023 - “...4.1.1.48] Trp3 YKL211C Trp3 CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Anthranilate phosphoribosyl transferase [EC:2.4.2.18] Trp4 YDR354W Trp4 CNAG_00811 TrpD Afu4g11980 TrpDZ517_01180 -KIW85788 63.84 Phosphoribosylanthranilate isomerase [EC:5.3.1.24] Trp1 YDR007W Trp3 CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Tryptophan synthase [EC:4.2.1.20] Trp5 YGL026C Trp5 CNAG_00649 TrpB Afu2g13250 TrpBZ517_07968 -KIW78135...”
- A simplified and easy-to-use HIP HOP assay provides insights into chalcone antifungal mechanisms of action
Prescott, FEBS letters 2022 - “...Y24835 Membrane disruption LEM3 HOP Benzethonium, gefitinib YNL323w Y31121 Membrane disruption TRP4 HOP Dyclonine, fenpropimorph YDR354w Y34191 Vacuolar ATPases VMA4 HIP Leucanicidin, bafilomycin A1, concanamycin A, hygrolidin YOR332w Y21629 Vacuolar ATPases RAV2 HOP Leucanicidin, bafilomycin A1, concanamycin A, hygrolidin YDR202c Y36970 Mitochondria TOM40 HIP Ethidium bromide,...”
- A novel ER membrane protein Ehg1/May24 plays a critical role in maintaining multiple nutrient permeases in yeast under high-pressure perturbation
Kurosaka, Scientific reports 2019 - “...0.80.1 1.10.4 0.70.1 ARO1 YDR127W 3.80.2 0.10.0 0.50.0 2.40.2 0.20.0 0.30.1 0.60.0 1.10.1 0.80.2 TRP4 YDR354W 4.40.1 0.40.1 0.90.4 4.00.3 0.30.1 0.80.3 0.90.1 0.70.2 0.90.1 TRP5 YGL026C 4.30.2 0.40.1 0.50.2 4.00.2 0.30.0 0.50.2 0.90.1 0.70.1 1.00.2 TRP2 YER090W 4.30.3 0.40.0 1.10.1 3.50.4 0.30.1 0.70.2 0.80.1 0.70.1...”
- A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells
Alver, G3 (Bethesda, Md.) 2013 - “...YKL187C YKL187c CAR1 YPL111w PAR32 YDL173w TPO2 YGR138c YLR125W YLR125w COT1 YOR316c PDC5 YLR134w TRP4 YDR354w YLR225C YLR225c CUE2 YKL090w PDR12 YPL058c TUM1 YOR251c YML053C YML053c CYC7 YEL039c PFA4 YOL003c UBC11 YOR339c YML089C YML089c DFG5 YMR238w PIR3 YKL163w UTR2 YEL040w YMR010W YMR010w DGR2 YKL121w PLB1 YMR008c...”
- Global screening of genes essential for growth in high-pressure and cold environments: searching for basic adaptive strategies using a yeast deletion library
Abe, Genetics 2008 - “...THR4 ARO2 0.3 0.4 0.5 0.6 1.2 0.3 6 0.1 4.9 6 0.2 YDR354W TRP4 0.2 0.7 0.1 0.5 0.4 0.3 6 0.1 4.7 6 0.6 4.1 4.3 5.2 4.4 4.6 2.2 6 0.2 5.0 6 0.1 Systematic...”
- Global response of Saccharomyces cerevisiae to an alkylating agent
Jelinsky, Proceedings of the National Academy of Sciences of the United States of America 1999 - “...synthase YFL030W -- 5.0 Transaminases\ YDR354W TRP4 4.8 Anthranilate phosphoribosyltransferase YDR035W ARO3 4.7 2-Dehydro-3-deoxyphosphoheptonate YER090W TRP2...”
AFUA_4G11980, Afu4g11980 anthranilate phosphoribosyltransferase, putative from Aspergillus fumigatus Af293
36% identity, 43% coverage
- Expanding the Toolbox for Functional Genomics in Fonsecaea pedrosoi: The Use of Split-Marker and Biolistic Transformation for Inactivation of Tryptophan Synthase (trpB) Gene
Favilla, Journal of fungi (Basel, Switzerland) 2023 - “...CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Anthranilate phosphoribosyl transferase [EC:2.4.2.18] Trp4 YDR354W Trp4 CNAG_00811 TrpD Afu4g11980 TrpDZ517_01180 -KIW85788 63.84 Phosphoribosylanthranilate isomerase [EC:5.3.1.24] Trp1 YDR007W Trp3 CNAG_04501 TrpC Afu1g13090 TrpCZ517_05805 -KIW79193 66.49 Tryptophan synthase [EC:4.2.1.20] Trp5 YGL026C Trp5 CNAG_00649 TrpB Afu2g13250 TrpBZ517_07968 -KIW78135 78.39 a Sequence ID...”
- A Multifaceted Role of Tryptophan Metabolism and Indoleamine 2,3-Dioxygenase Activity in Aspergillus fumigatus-Host Interactions
Choera, Frontiers in immunology 2017 - “...Aromatic amino acid (AAA) biosynthesis TrpE Trp2 Afu6g12580 Anthranilate synthase TrpC Trp3 Afu1g13090 TrpD Trp4 Afu4g11980 Anthranilate phosphoribosyltransferase TrpC Trp1 Afu1g13090 Phosphoribosylanthranilate isomerase TrpB Trp5 Afu2g13250 Trp synthase IcsA Afu6g12110 Isochorismate synthase AroC Aro7 Afu5g13130 Chorismate mutase PheA Pha2 Afu5g05690 Prephenate dehydratase TyrA Tyr1 Afu2g10450 Prephenate...”
- Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach
Kaltdorf, Frontiers in molecular biosciences 2016 - “...AFUA_5G05820 13 105 66 39 25.362 Homoserine kinase AFUA_4G04030 14 109 70 39 14.660 Histidinol-phosphatase AFUA_4G11980 15 114 63 51 33.665 DOWN Anthranilate phosphoribosyltransferase AFUA_6G12400 16 140 101 39 0.513 1,3-beta-glucan synthase catalytic subunit FksP AFUA_4G13680 17 167 117 50 5000.000 DOWN Phosphatidylserine synthase List of...”
- “...AFUA_5G05820 0.000 2.065 1.107 AA_s Homoserine kinase (THR1) AFUA_4G04030 0.000 NA 0.000 AA_HIS Histidinol-phosphatase (HIS2) AFUA_4G11980 0.000 0.083 0.000 AA_a Anthranilate phosphoribosyltransferase (TRP4) * AFUA_6G12400 0.000 0.031 1.568 GLU 6 1,3-beta-glucan synthase catalytic subunit FksP AFUA_4G13680 0.000 0.112 0.000 AA_s Phosphatidylserine synthase Sup2 AFUA_6G11390 0.926 0.459...”
- TrpE feedback mutants reveal roadblocks and conduits toward increasing secondary metabolism in Aspergillus fumigatus
Wang, Fungal genetics and biology : FG & B 2016 - “...synthase (EC:2.5.1.19); AroB (Afu1g06940), chorismate synthase (EC:4.2.3.5); TrpC (Afu1g13090), TrpE (Afu6g12580), anthranilate synthase (EC:4.1.3.27); TrpD (Afu4g11980), anthranilate phosphoribosyltransferase (EC:2.4.2.18); TrpC (Afu1g13090), phosphoribosylanthranilate isomerase (EC:5.3.1.24), indole-3-glycerol-phosphate synthase (EC:4.1.1.48); TrpB (Afu2g13250), tryptophan synthase (EC:4.2.1.20); PabaA (Afu6g04820), ADC synthetase (EC:2.6.1.85); PabaB (Afu2g01650), ADC lyase (4.1.3.38); AroC (Afu5g13130), chorismate mutase...”
- “...XM_745350 4.2.3.5 Chorismate synthase Afu6g12580 TrpE Trp2 XM_746043 4.1.3.27 Anthranilate synthase Afu1g13090 TrpC Trp3 XM_747586 Afu4g11980 TrpD Trp4 XM_746540 2.4.2.18 Anthranilate phosphoribosyltransferase Afu1g13090 TrpC Trp1 XM_747586 5.3.1.24 Phosphoribosylanthranilate isomerase Afu1g13090 TrpC Trp3 XM_747586 4.1.1.48 Indoyl-glycerolphosphate synthase Afu2g13250 TrpB Trp5 XM_750564 4.2.1.20 Tryptophan synthase Chorismate branch Afu6g04820...”
- Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus
Lind, G3 (Bethesda, Md.) 2016 - “...Afu4g11270 , Afu4g11280 , Afu4g11290 , Afu4g11300 Inglis et al. (2013) Cluster 19 Not known Afu4g11980 , Afu4g11990 , Afu4g12000 , Afu4g12010 , Afu4g12020 , Afu4g12030 , Afu4g12040 , Afu4g12050 , Afu4g12060 , Afu4g12070 Inglis et al. (2013) Cluster 20 Trypacidin Afu4g14460 , Afu4g14480 , Afu4g14470...”
- RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
Irmer, BMC genomics 2015 - “...especially tryptophan production, a highly energy consuming pathway [ 57 ]: AFUA_1G13090 (multifunctional anthranilate synthase), AFUA_4G11980 (anthranilate phosphoribosyltransferase), AFUA_2G13250 (bifunctional tryptophan synthase TrpB). In the category C-compound and carbohydrate metabolism several of the down-regulated genes, are predicted to be involved in sugar, glucoside, polyol and carboxylate...”
- Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae
Inglis, BMC microbiology 2013 - “...- Afu4g11170 - Afu4g11300 - n/a n/a No PKS or NRPS backbone 2 n/a - Afu4g11980 - Afu4g12070 - n/a n/a No PKS or NRPS backbone 3 n/a - Afu5g00100 - Afu5g04130 - n/a n/a No PKS or NRPS backbone 4 n/a - Afu7g00230 -Afu7g00350 Afu5g00100...”
AN3634 anthranilate phosphoribosyltransferase, hypothetical (Eurofung) from Emericella nidulans (see paper)
33% identity, 49% coverage
- CharProtDB Description: Putative anthranilate phosphoribosyltransferase with a predicted role in aromatic amino acid biosynthesis; Source:AspGD
PADG_01789 anthranilate phosphoribosyltransferase from Paracoccidioides brasiliensis Pb18
28% identity, 68% coverage
BMD_2992 glycosyl transferase family protein from Bacillus megaterium DSM319
25% identity, 89% coverage
YDYSG_26220 anthranilate phosphoribosyltransferase from Paenibacillus tyrfis
27% identity, 92% coverage
Elgi_57810 anthranilate phosphoribosyltransferase from Paenibacillus elgii
26% identity, 92% coverage
HVO_2226 anthranilate phosphoribosyltransferase from Haloferax volcanii DS2
24% identity, 90% coverage
tll1358 ORF_ID:tll1358~probable glycosyl transferase from Thermosynechococcus elongatus BP-1
25% identity, 92% coverage
Q9HNW7 Phosphoribosyl transferase from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
24% identity, 92% coverage
KZA74_06170 glycosyl transferase family protein from Acinetobacter baumannii
26% identity, 88% coverage
SYNW2492 glutamine amidotransferase-phosphoribosyl anthranilate transferase from Synechococcus sp. WH 8102
26% identity, 91% coverage
all0601 hypothetical protein from Nostoc sp. PCC 7120
23% identity, 93% coverage
- Hfq is required for optimal nitrate assimilation in the Cyanobacterium Anabaena sp. strain PCC 7120
Puerta-Fernández, Journal of bacteriology 2011 - “...NtcA and NtcB transcription factors (19). Also, genes all0601 and all0605, encoding CnaT and NirB, respectively, are involved in this regulation (18, 21). NtcA,...”
- “...activation (19, 20). CnaT and NirB, encoded by genes all0601 and all0605, respectively, are also involved in this regulation (18, 21). Since Anabaena hfq mutant...”
- Open reading frame all0601 from Anabaena sp. strain PCC 7120 represents a novel gene, cnaT, required for expression of the nitrate assimilation nir operon
Frías, Journal of bacteriology 2003 - “...Rights Reserved. Vol. 185, No. 17 Open Reading Frame all0601 from Anabaena sp. Strain PCC 7120 Represents a Novel Gene, cnaT, Required for Expression of the...”
- “...of ntcB, there is an open reading frame, all0601 (previously designated orf356 and now designated the cnaT gene), that putatively encodes a protein similar...”
sll1634 unknown protein from Synechocystis sp. PCC 6803
P73453 Sll1634 protein from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)
29% identity, 52% coverage
- A novel gene (narM) required for expression of nitrate reductase activity in the cyanobacterium Synechococcus elongatus strain PCC7942
Maeda, Journal of bacteriology 2004 - “...homologous to the internal part of the Synechocystis Sll1634 gene product, suggesting that the flanking sequences were discontiguous, due to loss of a PstI-PstI...”
- “...and ORF161 were 51 and 49% identical, respectively, to Sll1634 and Sll1455 of the Synechocystis gene products of unknown function (15). The 2110 MAEDA AND OMATA...”
- Open reading frame all0601 from Anabaena sp. strain PCC 7120 represents a novel gene, cnaT, required for expression of the nitrate assimilation nir operon
Frías, Journal of bacteriology 2003 - “...the amino acid level) is just downstream of ntcB, sll1634 of Synechocystis sp. strain PCC 6803 (encoding a product with 54.9% identity to CnaT) is just upstream...”
- ANLN promotes head and neck squamous cell carcinoma progression by upregulating PD-L1 via the ERK-MAPK pathway.
Wang, iScience 2025
PP3997 glycosyl transferase, putative from Pseudomonas putida KT2440
26% identity, 67% coverage
PH1598 pyrimidine-nucleoside phosphorylase from Pyrococcus horikoshii OT3
25% identity, 27% coverage
4ga6A / Q5JCX3 Crystal structure of amp phosphorylasE C-terminal deletion mutant in complex with substrates (see paper)
27% identity, 27% coverage
- Ligand: adenosine monophosphate (4ga6A)
deoA / Q5JCX3 AMP phosphorylase (EC 2.4.2.57) from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (see 2 papers)
AMPPA_THEKO / Q5JCX3 AMP phosphorylase; AMPpase; Nucleoside monophosphate phosphorylase; NMP phosphorylase; EC 2.4.2.57 from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) (see 3 papers)
Q5JCX3 AMP phosphorylase (EC 2.4.2.57) from Thermococcus kodakarensis (see 3 papers)
TK0352 Thymidine phosphorylase from Thermococcus kodakaraensis KOD1
27% identity, 27% coverage
- function: Catalyzes the conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO.
catalytic activity: AMP + phosphate = alpha-D-ribose 1,5-bisphosphate + adenine (RHEA:36975)
catalytic activity: CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate (RHEA:36987)
catalytic activity: UMP + phosphate = alpha-D-ribose 1,5-bisphosphate + uracil (RHEA:36991)
subunit: Forms an exceptionally large macromolecular structure (>40- mers) in solution. - A non-carboxylating pentose bisphosphate pathway in halophilic archaea
Sato, Communications biology 2022 - “.... T. kodakarensis also harbors a unique nucleoside-5-monophosphate phosphorylase (NMP phosphorylase, previously designated AMP phosphorylase; TK0352) that catalyzes the phosphorolysis of AMP, CMP, and UMP 14 , 15 . This allows the direct conversion of NMPs to R15P, as well as the conversion of nucleosides to...”
- Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
Maruyama, Frontiers in microbiology 2020 - “...Type 2 DNA topoisomerase 6 subunit B 64.2 top6B TK0799 Q5JCX3 AMP phosphorylase 53.7 deoA TK0352 Q5JIR2 V-type ATP synthase beta chain 52.4 atpB TK1603 Q5JFZ4 Elongation factor 1-alpha 47.5 tuf TK0308 Q5JE34 DNA-directed RNA polymerase subunit A 43.7 rpoA2 TK1081 Q5JGA2 Uncharacterized protein 40.8 TK0462...”
- An archaeal histone is required for transformation of Thermococcus kodakarensis
Čuboňováa, Journal of bacteriology 2012 - “...TK1046 TK1624 TK0560 TK1245 TK2048 TK0136 TK0307 TK2268 TK0352 TK2035 TK1539 TK0878 TK1500 TK0465 TK1534 TK1295 TK0308 TK1469 TK1174 Fold difference Proline...”
- Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
Fukui, Genome research 2005 - “...phosphorylase (TK1479). Along with thymidine phosphorylase DeoA (TK0352) and probable purine nucleoside phosphorylases (TK1482 and TK1895), these enzymes are...”
- Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
Maruyama, Frontiers in microbiology 2020 - “...enzyme 72.1 TK0752 TK0752 Q5JH81 Type 2 DNA topoisomerase 6 subunit B 64.2 top6B TK0799 Q5JCX3 AMP phosphorylase 53.7 deoA TK0352 Q5JIR2 V-type ATP synthase beta chain 52.4 atpB TK1603 Q5JFZ4 Elongation factor 1-alpha 47.5 tuf TK0308 Q5JE34 DNA-directed RNA polymerase subunit A 43.7 rpoA2 TK1081...”
MJ0667 thymidine phosphorylase (deoA) from Methanocaldococcus jannaschii DSM 2661
27% identity, 28% coverage
PF1607 thymidine phosphorylase from Pyrococcus furiosus DSM 3638
26% identity, 27% coverage
MA3242 thymidine phosphorylase from Methanosarcina acetivorans C2A
25% identity, 29% coverage
Pnuc_1003 glycosyl transferase family protein from Polynucleobacter sp. QLW-P1DMWA-1
22% identity, 69% coverage
TON_1062 Thymidine phosphorylase from Thermococcus onnurineus NA1
23% identity, 29% coverage
- Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus
Ergal, Microorganisms 2020 - “...(TON_0742), fructose bisphosphatase (TON_1497), ribose-5-phosphate isomerase (TON_0168), adenine phosphoribosyl transferase (TON_0120), AMP phosphorylase homolog DeoA (TON_1062), and 3-hexulose-6-phosphate synthase/6-phospho-3-hexuloisomerase (HPS/PHI) (TON_0336) were upregulated during growth on formate in T. onnurineus [ 56 ]. It was also demonstrated that gluconeogenesis and the PP pathway products, such as...”
- Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1
Moon, International journal of molecular sciences 2015 - “...]. As shown in Supplementary Table S1 , RBPI homolog (TON_1296) and AMP phosphorylase (DeoA, TON_1062), two major enzymes of AMP recycling pathway, were also detected in our proteomic analysis. However, RBPI (TON_1296) was up-regulated in cells grown on sulfur, and the induction level of DeoA...”
- “...may be a suitable substrate for the type III RuBisCO (TON_1234), which together with DeoA (TON_1062) and RBPI (TON_1296) replenish the 3-phosphoglycerate used in gluconeogenesis. Therefore, it may potentially be metabolically favorable to fix CO 2 and channel some of the fixed carbon into carbohydrate synthesis...”
- Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions
Moon, Molecular & cellular proteomics : MCP 2012 - “...2.22 1.19 0.70 S 2.44 1.64 TON_0120 TON_0168 TON_0336 TON_1062 TON_1234 TON_1296 TON_1403 TON_0192 TON_0583 1.92 S 1.04 0.56 S 2.27 F 0.87 0.48 1.59 0.58 0.70...”
- “...adenine phosphoribosyltransferase (TON_0120), AMP phosphorylase homolog DeoA (TON_1062), and HPS/PHI (TON_0336), were induced in response to formate (Fig. 1 and...”
- The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism
Lee, Journal of bacteriology 2008 - “...NA1 harbors both homologs for AMP phosphorylase (TON_1062) and ribose-1,5-bisphosphate isomerase (TON_1296), enzymes required to supply the RuBisCO substrate....”
MG_051 thymidine phosphorylase from Mycoplasma genitalium G37
28% identity, 34% coverage
PAB1982 thymidine phosphorylase from Pyrococcus abyssi GE5
25% identity, 26% coverage
Q3XXR6 Pyrimidine-nucleoside phosphorylase from Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
29% identity, 30% coverage
- Proteomic characterization of persisters in Enterococcus faecium
Pont, BMC microbiology 2024 - “...1.51 erpQ Q3XZG3 ErpQ protein 1.54 cspA I3U0N2 Cold shock protein Csp 1.57 -6.12 pdp Q3XXR6 Pyrimidine-nucleoside phosphorylase 1.59 accA Q3Y0R8 Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha 1.68 2.74 glpF Q3XYL4 Glycerol MIP family major intrinsic protein channel protein 1.74 2.59 10,691 Q3Y16 Flavin reductase...”
Q5FVR2 Thymidine phosphorylase from Rattus norvegicus
28% identity, 28% coverage
- iTRAQ-based quantitative proteomics analysis of the hepatoprotective effect of melatonin on ANIT-induced cholestasis in rats.
Wang, Experimental and therapeutic medicine 2021 - “...0.0756 Q4KLZ6 Triokinase and FMN cyclase (TKFC) 2.2275 0.0849 Q5BJY9 Keratin 18 (KRT18) 0.5850 0.0080 Q5FVR2 Thymidine phosphorylase (TYMP) 2.0643 0.0869 Q5HZE3 Thyroid hormone responsive (THRSP) 1.7476 0.0140 Q5I0M4 Aldo-keto reductase family 1, member C13 (AKR1C13) 1.5343 0.1205 Q5RJP0 Aldo-keto reductase family 1, member B7 (AKR1B7)...”
- iTRAQ-Based Identification of Proteins Related to Muscle Growth in the Pacific Abalone, Haliotis discus hannai.
Huang, International journal of molecular sciences 2017 - “...domain-containing protein 1 (GDPD1; Accession Number: Q8N9F7) Bladder cancer - thymidine phosphorylase (Tymp; Accession Number: Q5FVR2), EGFR, GDPD1 Apoptosis actin A1, actin-2, actin, myophilin (Accession Number: Q24799) CTSC, GDPD1, CTSB Thyroid hormone signaling pathway actin A1, actin-2, actin, solute carrier family 2 facilitated glucose transporter member...”
- Antioxidant, antiapoptotic and amino acid balance regulating activities of 1,7-dihydroxy-3,4,8-trimethoxyxanthone against dimethylnitrosamine-induced liver fibrosis.
Zheng, PloS one 2017 - “...Q07523 Hydroxyacid oxidase 2 0.48 4.23 Q07936 Annexin A2 4.12 0.31 Q0D2L3 Agmatinase 0.37 2.57 Q5FVR2 Thymidine phosphorylase 0.29 10.84 Q641W2 UPF0160 protein MYG1 2.70 0.46 Q64648 Cytochrome P450 2C12 7.86 0.12 Q68G41 Enoyl-CoA delta isomerase 1 0.45 2.18 Q6AYC4 Macrophage-capping protein 4.65 0.30 Q6IMY6 Lysosomal...”
PAP_04670 AMP phosphorylase from Palaeococcus pacificus DY20341
27% identity, 26% coverage
- Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments
Zeng, International journal of molecular sciences 2020 - “...carboxylase (Rubisco, PAP_06885) [ 17 ]. Palaeococcus pacificus harbors both homologs for AMP phosphorylase (DeoA, PAP_04670) and ribose-1, 5-bisphosphate isomerase (RBPI, PAP_04815), enzymes required to supply the RuBisCO substrate, ribulose-1,5-bisphosphate, from AMP and phosphate. In this pathway, adenine is released from AMP and the phosphoribose moiety...”
SYNPCC7002_A1618 glycosyl transferase family protein from Synechococcus sp. PCC 7002
22% identity, 88% coverage
- An organic acid based counter selection system for cyanobacteria
Begemann, PloS one 2013 - “...8.85E-06 SYNPCC7002_A0793 AhpC/TSA family protein 2.29 0 hliA high light/nutrient deprived stress response 2.28 8.32E-03 SYNPCC7002_A1618 glycosyl transferase family 2.26 7.11E-14 rplE 50S ribosomal protein L5 2.24 0 SYNPCC7002_A2607 probable Rieske iron-sulfur protein 2.24 6.43E-04 SYNPCC7002_A1619 conserved hypothetical protein 2.21 6.11E-14 SYNPCC7002_A2241 conserved hypothetical protein 2.21...”
MM0087 Pyrimidine-nucleoside phosphorylase from Methanosarcina mazei Goe1
23% identity, 29% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory