PaperBLAST

PaperBLAST Hits for sp|P72158|PURK_PSEAE N5-carboxyaminoimidazole ribonucleotide synthase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=purK PE=3 SV=2 (360 a.a., MKIGVIGGGQ...)

Show query sequence

>sp|P72158|PURK_PSEAE N5-carboxyaminoimidazole ribonucleotide synthase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=purK PE=3 SV=2
MKIGVIGGGQLGRMLALAGTPLGMNFAFLDPAPDACAASLGEHIRADYGDQEHLRQLADE
VDLVTFEFESVPAETVAFLSQFVPVYPNAESLRIARDRWFEKSMFKDLGIPTPDFADVQS
QADLDAAAAAIGLPAVLKTRTLGYDGKGQKVLRQPADVQGAFAELGSVPCILEGFVPFTG
EVSLVAVRARDGETRFYPLVHNTHDSGILKLSVASSGHPLQALAEDYVGRVLARLDYVGV
LAFEFFEVDGGLKANEIAPRVHNSGHWTIEGAECSQFENHLRAVAGLPLGSTAKVGESAM
LNFIGAVPPVAQVVAVADCHLHHYGKAFKNGRKVGHATLRCADRATLQARIAEVEALIEA

Running BLASTp...

Found 138 similar proteins in the literature:

PA5425 phosphoribosylaminoimidazole carboxylase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Massively parallel mutant selection identifies genetic determinants of <i>Pseudomonas aeruginosa</i> colonization of <i>Drosophila melanogaster</i>
  Miles, mSystems 2024
  • “...PA3108 purF Nucleotide metabolism [F] PA4854 purH Nucleotide metabolism [F] PA4855 purD Nucleotide metabolism [F] PA5425 purK Nucleotide metabolism [F] PA4756 carB Nucleotide metabolism [F] PA4758 carA Nucleotide metabolism [F] PA3527 pyrC' Nucleotide metabolism [F] PA0402 pyrB Nucleotide metabolism [F] PA0430 metF Amino acids [E] +...”
• Pseudomonas aeruginosa two-component system CprRS regulates HigBA expression and bacterial cytotoxicity in response to LL-37 stress
  Song, PLoS pathogens 2024
  • “...transcriptional regulatory protein DctD -1.59323 0.027239 PA5497 CIA_05153 Vitamin B12-dependent ribonucleotide reductase NrdJa -1.29239 0.027055 PA5425 CIA_05226 N5-carboxyaminoimidazole ribonucleotide synthase PurK -1.31462 0.000195 PA5413 CIA_05238 Low specificity L-threonine aldolase ltaA -1.29148 0.017305 PA5221 CIA_05439 Probable FAD-dependent monooxygenase -1.12814 0.017697 PA5167 CIA_05495 C4-dicarboxylate-binding periplasmic protein DctP -1.02455...”
• Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa
  Fraser-Pitt, Frontiers in cellular and infection microbiology 2021
  • “...PA3163 cmk Nucleobase-containing small molecule interconversion, pyrimidine nucleotide metabolic process NP_254112.1 phosphoribosylaminoimidazole carboxylase ATPase subunit PA5425 purK IMP biosynthesis via de novo pathway NP_249563.1 phenylalanine 4-monooxygenase PA0872 phhA Tyrosine biosynthesis, L-phenylalanine catabolism NP_253137.1 histidinol-phosphate aminotransferase PA4447 hisC1 L-histidine biosynthesis NP_252221.1 bacterioferritin PA3531 bfrB Intracellular sequestering of...”
• Bacterial fitness in chronic wounds appears to be mediated by the capacity for high-density growth, not virulence or biofilm functions
  Morgan, PLoS pathogens 2019
  • “...17.2 0.006 nt PA4462 rpoN 108 0.7 0.006 nt PA4856 retS 715 4.6 0.006 nt PA5425 purK 767 5.1 0.007 nt PA1550 - 1659 11.1 0.007 <0.01 PA1777 oprF 1685 11.3 0.007 nt PA3014 faoA 1313 8.9 0.007 nt PA5565 gidA 269 1.8 0.007 nt PA1801...”
• Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR
  Okino, Scientific reports 2016
  • “...rpsP 30S ribosomal protein S16 1.569 0.0033692 PA3744 rimM 16S rRNA processing protein 1.568 0.0079584 PA5425 purK phosphoribosylaminoimidazole carboxylase 1.566 0.0264866 PA4854 purH phosphoribosylaminoimidazolecarboxamide formyltransferase 1.566 0.0452696 PA4566 obg GTP-binding protein Obg 1.565 0.0333140 PA3821 secD secretion protein SecD 1.564 0.0070363 PA2404 hypothetical protein 1.561 0.0088869...”

CIA_05226 5-(carboxyamino)imidazole ribonucleotide synthase from Pseudomonas aeruginosa PA14
100% identity, 100% coverage

• Pseudomonas aeruginosa two-component system CprRS regulates HigBA expression and bacterial cytotoxicity in response to LL-37 stress
  Song, PLoS pathogens 2024
  • “...regulatory protein DctD -1.59323 0.027239 PA5497 CIA_05153 Vitamin B12-dependent ribonucleotide reductase NrdJa -1.29239 0.027055 PA5425 CIA_05226 N5-carboxyaminoimidazole ribonucleotide synthase PurK -1.31462 0.000195 PA5413 CIA_05238 Low specificity L-threonine aldolase ltaA -1.29148 0.017305 PA5221 CIA_05439 Probable FAD-dependent monooxygenase -1.12814 0.017697 PA5167 CIA_05495 C4-dicarboxylate-binding periplasmic protein DctP -1.02455 0.004803...”

PFL_6125 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Pseudomonas fluorescens Pf-5
90% identity, 99% coverage

• Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator
  Burlinson, The ISME journal 2013
  • “...PFL_5629 PFL_5651 PFL_5742 PFL_5850 PFL_5877 PFL_5899 PFL_5900 PFL_5919 PFL_6125 PFL_6158 PFL_6226 PFL_6229 PFL_6230 / / / / / 85A12 32F2, 28H5* 7A5 20E8* 10H11...”

PFLU6054 phosphoribosylaminoimidazole carboxylase atpase subunit from Pseudomonas fluorescens SBW25
89% identity, 99% coverage

• Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library
  Ertesvåg, BMC genomics 2017
  • “...PFLU5034 purL 50 1 43 10 70 1 1 3 348 7 0 2 2 PFLU6054 purK 84 4 2 5 113 8 0 4 343 3 1 4 1 PFLU6055 purE 88 7 45 25 87 5 37 5 368 9 0 2 2 PFLU5396...”

ACU12_RS13275 5-(carboxyamino)imidazole ribonucleotide synthase from Xanthomonas oryzae pv. oryzicola
54% identity, 89% coverage

• Antagonistic transcriptome profile reveals potential mechanisms of action on Xanthomonas oryzae pv. oryzicola by the cell-free supernatants of Bacillus velezensis 504, a versatile plant probiotic bacterium
  Zhou, Frontiers in cellular and infection microbiology 2023
  • “...genes involved in nucleotide metabolism, such as ACU12_RS19055 predicted to encode ibonucleotide-diphosphate reductase subunit beta, ACU12_RS13275 predicted to encode 5-(carboxyamino) imidazole ribonucleotide synthase, ACU12_RS02015 predicted to encode phosphomannomutase, and guaA predicted to encode glutamine-hydrolyzing GMP synthase, were down-regulated by treatment with the CFSs of B. velezensis...”

3aw8A / Q5SKY0 Crystal structure of n5-carboxyaminoimidazole ribonucleotide synthetase from thermus thermophilus hb8
53% identity, 96% coverage

• Ligand: adenosine monophosphate (3aw8A)

XHV734_1808 5-(carboxyamino)imidazole ribonucleotide synthase from Xanthomonas hortorum pv. vitians
54% identity, 91% coverage

• A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians
  Morinière, mSystems 2022
  • “...synthase, beta subunit Psyr_0034 RS_RS09965 ATU_RS00090 XHV734_1765 trpA Tryptophan synthase alpha chain Psyr_0033 RS_RS09955 ATU_RS00095 XHV734_1808 purK N5-carboxyaminoimidazole ribonucleotide synthase ATU_RS17455 Dda3937_01683 XHV734_1945 tgt tRNA-guanine transglycosylase RS_RS13575 XHV734_1977 gdh NAD-specific glutamate dehydrogenase ATU_RS13460 XHV734_2148 purM Phosphoribosylaminoimidazole synthetase ATU_RS05630 Dda3937_02515 XHV734_2154 sodA Superoxide dismutase, Mn ATU_RS04315 XHV734_2180...”

FQU82_00036 5-(carboxyamino)imidazole ribonucleotide synthase from Acinetobacter baumannii
47% identity, 92% coverage

• Transcriptomic analysis reveals the regulatory role of quorum sensing in the Acinetobacter baumannii ATCC 19606 via RNA-seq
  Xiong, BMC microbiology 2022
  • “...( ndk ), FQU82_02944 ( purL ), FQU82_02508 ( purH ), FQU82_02833 ( purB ), FQU82_00036, FQU82_01050 ( ureC ), FQU82_01048 ( ureA ), and FQU82_01049, and 2 were upregulated, including FQU82_02113 and FQU82_00719. A key gene in purine metabolism FQU82_00576 ( ndk ), encoding an...”

KZA74_18440 5-(carboxyamino)imidazole ribonucleotide synthase from Acinetobacter baumannii
47% identity, 92% coverage

• DNA damage response coregulator <i>ddrR</i> affects many cellular pathways and processes in <i>Acinetobacter baumannii</i> 17978
  Cook, Frontiers in cellular and infection microbiology 2023
  • “...A1S_0624 NSD NSD KZA74_19065* NA NSD NSD KZA74_19230* A1S_0651 NSD NSD KZA74_01755 A1S_3146 Upreg NSD KZA74_18440 A1S_2963 Upreg NSD NSD = No significant difference from WT expression. * Gene is encoded on pAB3. More than half of the induced genes showed altered basal expression levels in...”

ABUW_3885 5-(carboxyamino)imidazole ribonucleotide synthase from Acinetobacter baumannii
47% identity, 92% coverage

• Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
  Scribano, International journal of molecular sciences 2019
  • “...Rs: 1.000 0.880 0.905 SpI score = 22.2592 Protein fate 0.204 A0A0D5YMJ1 N5-carboxyaminoimidazole ribonucleotide synthase ABUW_3885 purK Sec SP MLCS: 120 [AQA-AL]. Rs: 0.972 0.107 0.239 CYT score = 0.200913 Purines, pyrimidines, nucleosides, and nucleotides 0.323 C5HUY1 Beta-lactamase ABUW_4052 blaGES-11 Sec SP MLCS: 118 [AYA-SE]. Rs:...”

VC0051 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Vibrio cholerae O1 biovar eltor str. N16961
Q9KVT8 N5-carboxyaminoimidazole ribonucleotide synthase from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
41% identity, 95% coverage

• Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR
  Beyhan, Journal of bacteriology 2007
  • “...These genes include the following: VC0051 (purK, phosphoribosylaminoimidazole carboxylase; ATPase subunit), VC0052 (purE, phosphoribosylaminoimidazole...”
• Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1
  Beyhan, Infection and immunity 2006
  • “...1.9-, and 2.0-fold higher expression of VC0051 (purK) phosphoribosylaminoimidazole carboxylase-ATPase subunit, VC2390 (carA) carbamoyl phosphate synthase small...”
• Host-induced epidemic spread of the cholera bacterium
  Merrell, Nature 2002
  • “...expressed in the stool samples are VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350 and VCA0583, all of which were recently identified in a genetic screen...”
• Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.
  Mukherjee, Genomics discovery 2014
  • “...atpI Q9KNG8 Type 4 prepilin-like proteins leader peptide-processing enzyme tcpJ P0C6D9 N5-carboxyaminoimidazole ribonucleotide synthase purK Q9KVT8 Coproporphyrinogen-III oxidase hemF Q9KVT4 Aldehyde dehydrogenase aldA P0C6D7 Putative N-acetylmannosamine-6-phosphate 2-epimerase nanE Q9KR62 N-acetylmannosamine kinase nanK Q9KR61 N-acetylneuraminate epimerase nanM Q9KR69 N5-carboxyaminoimidazole ribonucleotide mutase purE Q9KVT7 Ribosome modulation factor Rmf...”

4mamA / Q5NGE8 The crystal structure of phosphoribosylaminoimidazole carboxylase atpase subunit of francisella tularensis subsp. Tularensis schu s4 in complex with an adp analog, amp-cp
42% identity, 96% coverage

• Ligand: phosphomethylphosphonic acid adenosyl ester (4mamA)

FTA_0422 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Francisella tularensis subsp. holarctica FTA
42% identity, 96% coverage

• Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00
  Barabote, PloS one 2009
  • “...FTA_1565 YH 2 putative permease, YjgP/YjgQ family protein R FTA_0096 VI 3 acetyltransferase protein I FTA_0422 VI 3 phosphoribosylaminoimidazole carboxylase ATPase subunit F FTA_0429 VI 3 2-polyprenylphenol 6-hydroxylase R FTA_0537 VI 3 transposase ISFTu1 L FTA_0711 VI 3 DNA ligase L FTA_1237 VI 3 hypothetical protein...”

ATU_RS17455 5-(carboxyamino)imidazole ribonucleotide synthase from Agrobacterium fabrum str. C58
Atu3755 phosphoribosylaminoimidazole carboxylase ATPase subunit from Agrobacterium tumefaciens str. C58 (Cereon)
46% identity, 91% coverage

• A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians
  Morinière, mSystems 2022
  • “...ATU_RS00090 XHV734_1765 trpA Tryptophan synthase alpha chain Psyr_0033 RS_RS09955 ATU_RS00095 XHV734_1808 purK N5-carboxyaminoimidazole ribonucleotide synthase ATU_RS17455 Dda3937_01683 XHV734_1945 tgt tRNA-guanine transglycosylase RS_RS13575 XHV734_1977 gdh NAD-specific glutamate dehydrogenase ATU_RS13460 XHV734_2148 purM Phosphoribosylaminoimidazole synthetase ATU_RS05630 Dda3937_02515 XHV734_2154 sodA Superoxide dismutase, Mn ATU_RS04315 XHV734_2180 Dihydroorotase ATU_RS06435 XHV734_2250 UDP- N...”
• Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens
  Heindl, Microbiology (Reading, England) 2019
  • “...1.84 + + No Atu1471 rluC Ribosomal large subunit pseudouridine synthase C 1.84 + No Atu3755 purK Phosphoribosylaminoimidazole carboxylase ATPase subunit 1.70 + No Atu3606 ftsE Cell division ATP-binding protein 1.63 + + No Atu1791 ABC transporter, membrane spanning protein (sugar) 1.55 + No Atu3572 XRE...”

A1S_2963 phosphoribosylaminoimidazole carboxylase ATPase subunit from Acinetobacter baumannii ATCC 17978
49% identity, 75% coverage

• DNA damage response coregulator <i>ddrR</i> affects many cellular pathways and processes in <i>Acinetobacter baumannii</i> 17978
  Cook, Frontiers in cellular and infection microbiology 2023
  • “...NSD NSD KZA74_19065* NA NSD NSD KZA74_19230* A1S_0651 NSD NSD KZA74_01755 A1S_3146 Upreg NSD KZA74_18440 A1S_2963 Upreg NSD NSD = No significant difference from WT expression. * Gene is encoded on pAB3. More than half of the induced genes showed altered basal expression levels in the...”
• Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii
  Blaschke, Current microbiology 2021
  • “...surface-associated motility: PurH, PurF, PurM, and PurE. In A. nosocomialis M2, inactivation of purK ( a1s_2963 ) has been previously described to result in a 70% reduction in surface motility [ 26 ]. Mutations in the genes purD , purF , purH , purL , and...”
• A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter
  Peterson, Microbiology (Reading, England) 2020
  • “...F ruvA Holliday junction helicase subunit A L ruvB Holliday junction helicase subunit B L A1S_2963 purK ; phosphoribosylaminoimidazole carboxylase ATPase subunit F A1S_2970 put. glutathione-like synthetase E A1S_2977 cation diffusion facilitator family transporter P A1S_3139 put. signal peptide A1S_3146 mdfA ; Multidrug efflux transport protein...”
• Genome-wide identification of Acinetobacter baumannii genes necessary for persistence in the lung
  Wang, mBio 2014
  • “...in the pulmonary environment. Ten genes involved in purine metabolism (A1S_2189, A1S_2251, A1S_2606, A1S_2585, A1S_2605, A1S_2963, A1S_2964, A1S_3425, A1S_2187, and A1S_2188) were identified as important for the persistence of A.baumannii in the murine pneumonia model. These genes were purF , - D , - N ,...”
• Genetic analysis of surface motility in Acinetobacter baumannii
  Clemmer, Microbiology (Reading, England) 2011
  • “...(data not shown). The EZ : : TN insertion is within A1S_2963, encoding a protein with 39 % identity and 55 % similarity to purK of In an earlier study, in which...”

DR0024 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Deinococcus radiodurans R1
44% identity, 96% coverage

• Expression and mutational analysis of DinB-like protein DR0053 in Deinococcus radiodurans
  Appukuttan, PloS one 2015
  • “...compared with DNase as the positive control. The PCR product of the Deinococcal dr0023 and dr0024 (3 kb) regions was used to test the direct nuclease activity of the DR0053 protein. The purified PCR product in distilled water with 1 mM MgCl 2 was incubated with...”

DDB_G0283987 phosphoribosylaminoimidazole carboxylase from Dictyostelium discoideum AX4
Q54QE4 Bifunctional purine synthesis protein purC/E from Dictyostelium discoideum
38% identity, 34% coverage

• Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity
  Xiong, Cells 2023
  • “...Uncharacterized protein K 18 0.00 25.50 Q54JB0 DDB_G0288187 DDI1 homolog K 55 0.00 24.82 Q54QE4 DDB_G0283987 Bifunctional purine synth. protein purC/E K 234 0.00 24.71 Q8MMQ2 DDB_G0275539 Uncharacterized protein K 86 0.00 24.64 Q54GS9 DDB_G0289933 Uncharacterized protein K 346 0.00 24.30 Q54YL1 DDB_G0278621 Uncharacterized protein K...”
• Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity
  Xiong, Cells 2023
  • “...DDB_G0271028 Uncharacterized protein K 18 0.00 25.50 Q54JB0 DDB_G0288187 DDI1 homolog K 55 0.00 24.82 Q54QE4 DDB_G0283987 Bifunctional purine synth. protein purC/E K 234 0.00 24.71 Q8MMQ2 DDB_G0275539 Uncharacterized protein K 86 0.00 24.64 Q54GS9 DDB_G0289933 Uncharacterized protein K 346 0.00 24.30 Q54YL1 DDB_G0278621 Uncharacterized protein...”

BMEI0295 PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT from Brucella melitensis 16M
43% identity, 91% coverage

• Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M
  Brambila-Tapia, PloS one 2014
  • “...kinase E/R 185 [17] , [18] BMEI0233 purH Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase F 665 [8] BMEI0295 purK Phosphoribosylaminoimidazole carboxylase atpase subunit F 566 [8] BMEI0296 purE Phosphoribosylaminoimidazole carboxylase catalytic subunit F 706 [8] , [13] BMEI1090 BMEI1090 Deoxyguanosinetriphosphate triphosphohydrolase-like protein F 464 [20] BMEI1123 purS Phosphoribosylformylglycinamidine...”
• Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network
  Hur, BMC immunology 2011
  • “...transport and metabolism BMEI0296 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit 11 4 (4) V U (2.00) BMEI0295 purK phosphoribosylaminoimidazole carboxylase ATPase subunit 4 1 (1) CM (7.88) Signal transduction mechanisms BMEI2035 bvrS sensor histidine kinase BvrS, putative 10 3 (1) V CM (10.00) BMEI0190 ptsP phosphoenolpyruvate-protein phosphotransferase...”

BamMC406_2543 phosphoribosylaminoimidazole carboxylase ATPase subunit from Burkholderia ambifaria MC40-6
39% identity, 85% coverage

• Combining functional and structural genomics to sample the essential Burkholderia structome
  Baugh, PloS one 2013
  • “...B. thailandensis BTH_I3304 P06132 48.5, 98.1 Yes BTH_II0675 Aspartate-semialdehyde dehydrogenase 3UW3 B. thailandensis BTH_II0675 Yes BamMC406_2543 Phosphoribosylaminoimidazole carboxylase, ATPase subunit 4E4T B. ambifaria BTH_II0682 Yes BTH_II1941 Agmatinase, putative 4DZ4 B. thailandensis BTH_II1941 Q9BSE5 42.5, 88.8 Yes BTH_II2229 Isochorismatase family protein 3TXY B. thailandensis BTH_II2229 Yes An...”

3r5hA Crystal structure of adp-air complex of purk: n5-carboxyaminoimidazole ribonucleotide synthetase (see paper)
BA0289 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Bacillus anthracis str. Ames
39% identity, 86% coverage

• Ligands: adenosine-5'-diphosphate; 5-aminoimidazole ribonucleotide (3r5hA)
• Gene expression control by Bacillus anthracis purine riboswitches
  Kirchner, RNA (New York, N.Y.) 2017
  • “...1997 ); purE (phosphoribosylaminoimidazole carboxylase BA0288) ( Johansen et al. 2003 ); purK (phosphoribosylaminoimidazole carboxylase BA0289) ( Johansen et al. 2003 ); purB (adenylsuccinate lyase; BA0290); purC (phosphoribosylaminoimidazole succinocarboxamide synthase; BA0291); purS (phosphoribosylformylglycinamidine synthase; BA0292); purQ (phosphoribosylformylglycinamidine synthase; BA0293); purL (phosphoribosylformylglycinamidine synthase; BA0294): purF (glutamine phosphoribosyldiphosphate...”

BC0324 Phosphoribosylaminoimidazole carboxylase ATPase subunit from Bacillus cereus ATCC 14579
39% identity, 86% coverage

• Correction: SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins
  , PloS one 2014
  • “...0.08 8.2E-07 Metabolism BC0297 Guanine-hypoxanthine permease 0.08 9.2E-08 BC0323 PRAI carboxylase catalytic subunit 0.04 2.4E-08 BC0324 PRAI carboxylase ATPase subunit 0.07 2.1E-08 BC0325 Adenylosuccinate lyase 0.07 3.7E-07 BC0326 PRAI-succinocarboxamide synthase 0.04 2.4E-05 BC0327 PRFGA synthetase, PurS component 0.04 4.6E-06 BC0328 PRFGA synthase 0.04 1.9E-06 BC0329 PRFGA...”
• SecDF as part of the Sec-translocase facilitates efficient secretion of Bacillus cereus toxins and cell wall-associated proteins
  Vörös, PloS one 2014
  • “...0.08 8.2E-07 Metabolism BC0297 Guanine-hypoxanthine permease 0.08 9.2E-08 BC0323 PRAI carboxylase catalytic subunit 0.04 2.4E-08 BC0324 PRAI carboxylase ATPase subunit 0.07 2.1E-08 BC0325 Adenylosuccinate lyase 0.07 3.7E-07 BC0326 PRAI-succinocarboxamide synthase 0.04 2.4E-05 BC0327 PRFGA synthetase, PurS component 0.04 4.6E-06 BC0328 PRFGA synthase 0.04 1.9E-06 BC0329 PRFGA...”

BCAL2836 phosphoribosylaminoimidazole carboxylase ATPase subunit from Burkholderia cenocepacia J2315
39% identity, 86% coverage

• Comparative metabolic systems analysis of pathogenic Burkholderia
  Bartell, Journal of bacteriology 2014
  • “...BCAL2388 BCAL2389 BCAL2403 BCAL2759 BCAL2761 BCAL2770 BCAL2836 BCAL2837 BCAL2838 BCAL2912 BCAL2944 BCAL2951 BCAL3012 BCAL3110 BCAL3113 BCAL3133 BCAL3134...”

LMRG_02497 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Listeria monocytogenes 10403S
39% identity, 88% coverage

• Identification of Listeria monocytogenes determinants required for biofilm formation
  Alonso, PloS one 2014
  • “...940.21 1 1 UDP-glucose 4-epimerase lmrg_01771 910.43 9 4 purD lmrg_02507 870.14 1 1 purE lmrg_02497 900.28 1 1 purF lmrg_02503 900.11 2 2 purH lmrg_02506 900.28 2 1 purL lmrg_02502 1000.21 1 1 purN lmrg_02505 1000.57 1 1 Isocitrate dehydrogenase lmrg_01401 1000.38 1 1 2-oxovalerate...”

Q2QJL2 5-(carboxyamino)imidazole ribonucleotide mutase (EC 5.4.99.18) from Acetobacter aceti (see paper)
purK / AAZ04484.1 N5-carboxyaminoimidazole ribonucleotide synthetase from Acetobacter aceti (see paper)
38% identity, 86% coverage

EQB38_RS06240 5-(carboxyamino)imidazole ribonucleotide synthase from Enterococcus faecium
36% identity, 94% coverage

• Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: unraveling the transcriptional dynamics of host-enterococcal interactions
  Stege, FEMS microbes 2024
  • “...clusters. Cluster 93 represents genes that are involved in purine metabolism (EQB38_RS06220, xpt; EQB38_RS06235, purE; EQB38_RS06240, purK ; EQB38_RS06245, purB ; EQB38_RS06265, purC ; EQB38_RS06270, purS ; EQB38_RS06275, purQ ; EQB38_RS06280, purl ; EQB38_RS06285, purF ; EQB38_RS06290, purM ; EQB38_RS06295, purN ; EQB38_RS06300, purH ; EQB38_RS06305,...”

lmo1774 phosphoribosylaminoimidazole carboxylase II from Listeria monocytogenes EGD-e
Q8Y6B7 N5-carboxyaminoimidazole ribonucleotide synthase from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
38% identity, 88% coverage

• Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
  Pinilla, Data in brief 2022
  • “...Q8YA71 lmo0288 lmo0288 Nis Annotation not available Q8YAJ0 lmo0135 lmo0135 Nis Annotation not available Q8Y6B7 lmo1774 purK Nis Phosphoribosylaminoimidazole carboxylase ATPase subunit; catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide and HCO 3 to N5-carboxyaminoimidazole ribonucleotide Q8Y8Q4 lmo0842 lmo0842 Nis Annotation not available Q92CZ4 lmo1028 lmo1028 LNis...”
• Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
  Orsi, BMC evolutionary biology 2008
  • “..., lmo1420 , opuCC ( lmo1426 ), trpD ( lmo1631 ), lmo1693 , purK ( lmo1774 ), lmo1825 , panB ( lmo1902 ), lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487 , lmo0878 , lmo1004 , lmo1011 , cbiH ( lmo1199 ). "x" indicate substitutions...”
• Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
  Pinilla, Data in brief 2022
  • “...GTP Q8YA71 lmo0288 lmo0288 Nis Annotation not available Q8YAJ0 lmo0135 lmo0135 Nis Annotation not available Q8Y6B7 lmo1774 purK Nis Phosphoribosylaminoimidazole carboxylase ATPase subunit; catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide and HCO 3 to N5-carboxyaminoimidazole ribonucleotide Q8Y8Q4 lmo0842 lmo0842 Nis Annotation not available Q92CZ4 lmo1028 lmo1028...”

NP_213168 phosphoribosyl aminoimidazole carboxylase from Aquifex aeolicus VF5
37% identity, 93% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole carboxamide formyltransferase /IMP cyclohydrolase Theam_0328 P. marina sim. 59% YP_002731268 Aquificae / Bacteria 86% YP_004281681 78% WP_022847359 59% YP_002731268 56% YP_001931239 53% YP_003433270 50% YP_007499473 57% WP_008288360...”

lp_2728 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Lactobacillus plantarum WCFS1
39% identity, 91% coverage

• Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays
  Saulnier, Applied and environmental microbiology 2007
  • “...lp_2720 lp_2721 lp_2722 lp_2723 lp_2724 lp_2725 lp_2726 lp_2728 lp_3194 lp_3269 lp_3270 lp_3271 Continued on following page Downloaded from http://aem.asm.org/...”
  • “...and nucleotides lp_1058 lp_2585 lp_2728 lp_3334 Adenylate kinase Nucleotide-disulphide oxidoreductase Phosphoribosylaminoimidazole carboxylase, ATPase...”

BSU06430 phosphoribosylaminoimidazole carboxylase ATPase subunit from Bacillus subtilis subsp. subtilis str. 168
P12045 N5-carboxyaminoimidazole ribonucleotide synthase from Bacillus subtilis (strain 168)
37% identity, 87% coverage

• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...purE BSU06420 No 4.1.1.21 1XMP B. anthracis purK BSU06430 No 4.1.1.21 4DLK B. anthracis Chorismate for aromatic amino acids, menaquinone, and folate aroA Ala,...”
• Cloning and expression of the Lactococcus lactis purDEK genes, required for growth in milk
  Nilsson, Applied and environmental microbiology 1998
  • “...for PurE, P12044, P09028, and P21264; and for PurK, P12045, P09029, and P21264. b The amino acid sequence deduced from L. lactis purK9 is not complete. purDEK...”

LSEI_1755 Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) from Lactobacillus casei ATCC 334
37% identity, 91% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_1749 LSEI_1750 LSEI_1751 LSEI_1752 LSEI_1753 LSEI_1754 LSEI_1755 LSEI_1756 Malolactic enzyme Malate/lactate antiporter ATP synthase C chain (EC 3.6.3.14)...”

B4602_RS05185 5-(carboxyamino)imidazole ribonucleotide synthase from Staphylococcus aureus
33% identity, 93% coverage

• Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus
  Wang, Frontiers in pharmacology 2023
  • “...subunit 0.79 1.16 B4602_RS08185 BCCP WP_001019340.1 Acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 1.03 0.88 B4602_RS05185 purK WP_001010407.1 5-(carboxyamino)imidazole ribonucleotide synthase 0.90 2.44 B4602_RS05935 carB WP_001126265.1 Carbamoyl-phosphate synthase large subunit 2.13 0.78 B4602_RS09915 - WP_000544969.1 Type 1 glutamine amidotransferase 0.16 0.34 Ribosome and protein synthesis B4602_RS14385...”

MW0948 ORFID:MW0948~phosphoribosylaminoimidazole carboxylase carbon dioxide-fixation chain PurK homolog from Staphylococcus aureus subsp. aureus MW2
33% identity, 89% coverage

• The SaeR/S gene regulatory system is essential for innate immune evasion by Staphylococcus aureus
  Voyich, The Journal of infectious diseases 2009
  • “...oxidase polypeptide III QoxC 2.47 ES MW0943 qoxB Quinol oxidase polypeptide I QoxB 2.20 ES MW0948 purK Nucleotide transport and metabolism 2.59 ES MW0949 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 2.54 ES MW0951 purQ phosphoribosylformylglycinamidine synthase I PurQ 1.60 & 2.69 ME & ES MW0952 purL phosphoribosylformylglycinamidine synthetase PurL...”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...SAV0010 SAV2384 MW0010 MW2304 gltT SAV1255 MW1138 codY MW0948 purK MW0476 nupC MW1029 MW1135 uvrC xerC MW0393 hsdS Secretion genes SAV0964 SAV2230 SAV0778...”

3orqA / A0A0H3KFM7 Crystal structure of n5-carboxyaminoimidazole synthetase from staphylococcus aureus complexed with adp (see paper)
33% identity, 90% coverage

• Ligands: magnesium ion; adenosine-5'-diphosphate; pyrophosphate 2- (3orqA)

SAV_RS05745 5-(carboxyamino)imidazole ribonucleotide synthase from Staphylococcus aureus subsp. aureus Mu50
SA0917 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV1065 phosphoribosylaminoimidazole carboxylase carbon dioxide-fixation chain PurK homolog from Staphylococcus aureus subsp. aureus Mu50
33% identity, 93% coverage

• Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus
  Vandecandelaere, PloS one 2017
  • “...Phosphoribosylamine-glycine ligase -2.93 + 0.13 0.00 purC SAV_RS05750 Phosphoribosylaminoimidazole-succinocarboxamide synthase -2.97 + 0.17 0.00 purK SAV_RS05745 Phosphoribosylaminoimidazole carboxylase ATPase subunit -2.98 + 0.16 0.00 purH SAV_RS05785 Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase -3.83 + 0.12 0.00 purF SAV_RS05770 Amidophosphoribosyltransferase -3.91 + 0.15 0.00 purM SAV_RS05775 Phosphoribosylaminoimidazole synthetase -4.08...”
• An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
  Cui, Antimicrobial agents and chemotherapy 2010
  • “...metabolism SA0016 SA0373 SA0374 SA0375 SA0376 SA0468 SA0916 SA0917 Gene 5230 CUI ET AL. ANTIMICROB. AGENTS CHEMOTHER. TABLE 3--Continued Ratio of signal...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...hypothetical protein sa_c6985s6107_a_at * 4.3 2.5 2.5 SA0392 NADH-dependent flavin oxidoreductase sa_c8540s7497_at 3.2 5 stable SA0917 NifU domain-containing protein sa_c2220s1920_a_at * 4.7 2.5 30 SA1514 glycerol-3-phosphate dehydrogenase sa_c5074s4372_a_at 7.1 2.5 2.5 SA2293 NAD/NADP octopine/nopaline dehydrogenase family protein Transport sa_c6427s5598_a_at 3.8 2.5 15 cudT SA2632 osmoprotectant transporter...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...N315 ORF Gene Purine and pyrimidine metabolism SA0373 xprT SA0917 purK purQ purL purF purM purN purH purD pyrR pyrB pyrC pyrAA pyrAB pyrF pyrE ABC...”
• Transcriptomic and functional analysis of an autolysis-deficient, teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus
  Renzoni, Antimicrobial agents and chemotherapy 2006
  • “...0.001 0.05 0.05 NS 0.001 0.05 0.001 SA0922 SA0925 SA0917 SA0921 SA0923 SA0924 SA0920 SA0454 purF purH purK purL purM purN purQ purR Hypothetical protein,...”
• Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
  Seggewiss, Journal of bacteriology 2006
  • “...(comprising purCDEFHKLMNQ) (SA0918, SA0926, SA1048, SA0922, SA0925, SA0917, SA0921, SA0923, SA0924, and SA0920), folD (FolD bifunctional protein, SA0915), and...”
• Genome-wide analysis of the regulatory function mediated by the small regulatory psm-mec RNA of methicillin-resistant Staphylococcus aureus
  Cheung, International journal of medical microbiology : IJMM 2014
  • “...component 16.4 SAV2507 (Mu50) Gluconate operon transcriptional repressor 14.1 SAV1068 (Mu50) Phosphoribosylformylglycinamidine synthase I 11.5 SAV1065 (Mu50) Phosphoribosylaminoimidazole carboxylase 10.1 MSA3407, down-regulated SAV1330 (Mu50) Homoserine kinase 11.6 SAV1329 (Mu50) Threonine synthase 11.3 MRSA252, up-regulated SAV2190 (Mu50) PTS system, lactose-specific IIBC component 10.0 SAV2194 (Mu50) Galactose-6-phosphate isomerase...”
  • “...synthase I 6.4 SAV1073 (Mu50) Bifunctional purine biosynthesis protein 5.9 SAV1074 (Mu50) Phosphoribosylamine-glycine ligase 5.4 SAV1065 (Mu50) Phosphoribosylaminoimidazole carboxylase 5.3 1 The entire list of differentially regulated genes can be accessed using the GEO database (XXX). 2 Gene number according to strain Mu50 ( Kuroda et...”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...MW0200 Nucleotide and nucleic acid metabolism genes SAV1065 SAV0521 DNA replication, recombination, and repair genes SAV1146 SAV1252 SAV0432 SAV2550 MW2471 feoB...”
• Staphylococcus aureus mutants with increased lysostaphin resistance
  Gründling, Journal of bacteriology 2006
  • “...in in in in in in SAV1001 SAV1002 SAV1064 SAV1065 SAV1066 SAV1067 SAV1068 SAV1070 SAV1071 SAV1074 (purE) (purK) (purC) (purS) (purQ) (purF) (purM) (purD) This...”
  • “...genes of the purine biosynthesis cluster (SAV1064, SAV1065, SAV1066, SAV1067, SAV1068, SAV1070, SAV1071, and SAV1074 [Table 1]) generated mutants with...”

A0A0H3KFM7 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) from Staphylococcus aureus (see paper)
BTN44_07450, CH51_RS05425 5-(carboxyamino)imidazole ribonucleotide synthase from Staphylococcus aureus
SAOUHSC_01009 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0967 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1074 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Staphylococcus aureus subsp. aureus COL
33% identity, 93% coverage

• Combined transcriptome and metabolome analysis revealed the antimicrobial mechanism of Griseorhodin C against Methicillin-resistant Staphylococcus aureus
  Liao, Scientific reports 2024
  • “...Ald 1 Down -4.482342678 Alanine dehydrogenase BTN44_15735 Gab T Down -1.072624287 Aspartate aminotransferase family protein BTN44_07450 pur K Up 1.549285893 5-(carboxyamino)imidazole ribonucleotide synthase BTN44_07435 pur Q Up 1.838537906 Phosphoribosylformylglycinamidine synthase I BTN44_07430 pur L Up 1.729881085 Phosphoribosylformylglycinamidine synthase subunit PurL BTN44_07420 pur m Up 1.207319705 Phosphoribosyl...”
• Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
  Shang, Frontiers in microbiology 2020
  • “...0.47 ND Purine metabolism CH51_RS05420 5-(carboxyamino)imidazole ribonucleotide mutase 4.99 ND CH51_RS06845 Polyribonucleotide nucleotidyltransferase 0.35 ND CH51_RS05425 5-(carboxyamino)imidazole ribonucleotide synthase 3.06 ND Iron metabolism CH51_RS00480 Iron-siderophore ABC transporter substrate-binding protein 0.41 ND CH51_RS06060 Iron-regulated surface determinant protein A 0.23 ND CH51_RS06065 Iron-regulated surface determinant protein C 0.44...”
• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...two-component system, cationic antimicrobial peptide (CAMP) resistance, Staphylococcus aureus infection D-alaninepoly (phosphoribitol) ligase subunit 2 SAOUHSC_01009 purK 1.26 Biosynthesis of secondary metabolites, biosynthesis of antibiotics, purine metabolism Phosphoribosylaminoimidazole carboxylase ATPase subunit SAOUHSC_01010 purC 1.32 Biosynthesis of secondary metabolites, biosynthesis of antibiotics, purine metabolism Phosphoribosylaminoimidazole-succinocarboxamide synthase SAOUHSC_01012...”
  • “...ID DEG name Mfe(kcal/mol) DEG ID DEG name Mfe(kcal/mol) SAOUHSC_01018 purD -95.5 SAOUHSC_01626 SA1360 -82.5 SAOUHSC_01009 purK -94.8 SAOUHSC_01821 SA1534 -82.5 SAOUHSC_00707 fruB -93.5 SAOUHSC_01954 lukD -81.7 SAOUHSC_01013 purL -92.9 SAOUHSC_01668 bex -81.6 SAOUHSC_02402 mtlA -92.6 SAOUHSC_02549 modA -81.5 SAOUHSC_00204 SA0231 -90.1 SAOUHSC_00712 SA0658 -80.7 SAOUHSC_01012...”
• 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_2097 SAUSA300_0968 SAUSA300_2568 SAUSA300_1712 SAUSA300_0967 SAUSA300_1713 SAUSA300_1714 SAUSA300_1715 SAUSA300_0966 SAUSA300_0883 SAUSA300_2569...”
• Tea tree oil-induced transcriptional alterations in Staphylococcus aureus
  Cuaron, Phytotherapy research : PTR 2013
  • “...carrier protein ligase SACOL0935 10.1 purF amidophosphoribosyltransferase SACOL1079 9.8 purK phosphoribosylaminoimidazole carboxylase CO 2 -fixation SACOL1074 8.9 rplD 50S ribosomal protein L4 SACOL2238 8.6 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit SACOL1073 8.3 purN phosphoribosylaminoimidazole carboxylase, catalytic subunit SACOL1072 8.0 tenA transcriptional regulator, TenA family SACOL2086 7.9 2.9...”
• Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
  Scherr, Infection and immunity 2013
  • “...Locus Protein description purK SACOL1074 SACOL0240 SACOL0514 Phosphoribosylaminoimidazole carboxylase, ATPase subunit 4-Diphosphocytidyl-2C-methyl-D-erythritol...”
• Global analysis of the Staphylococcus aureus response to mupirocin
  Reiss, Antimicrobial agents and chemotherapy 2012
  • “...SACOL1092 PheT PtsI PurB PurC PurD PurE PurH SACOL1074 SACOL1080 SACOL1077 SACOL1216 SACOL2213 SACOL1274 SACOL2057 SACOL0429 PurK PurM PurQ PyrF RpoA RpsB RsbU...”
• The fusidic acid stimulon of Staphylococcus aureus
  Delgado, The Journal of antimicrobial chemotherapy 2008
  • “...SACOL1005 SACOL1777 SACOL0851 SACOL0921 SACOL1034 SACOL1074 SACOL2461 SACOL0225 SACOL2579 SACOL0922 SACOL2462 SACOL2241 SACOL1115 SACOL0688 SACOL1522 SACOL0781...”
• Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin
  Cirz, Journal of bacteriology 2007
  • “...category SACOL0458 SACOL0460 SACOL0554 SACOL1073 SACOL1074 Lipid biosynthesis Down-regulated ORFs SACOL0987 SACOL0988 SACOL1243 SACOL1244 SACOL1245 SACOL1571...”

UC7_RS13090 5-(carboxyamino)imidazole ribonucleotide synthase from Enterococcus caccae ATCC BAA-1240
37% identity, 89% coverage

• Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus
  Wang, Molecules (Basel, Switzerland) 2017
  • “...UC7_RS14300 GNAT family acetyltransferase 1.6 Transcriptional regulation UC7_RS16190 penicillin-binding protein 2B 1.6 Cell wall synthesis UC7_RS13090 phosphoribosylaminoimidazole carboxylase ATPase subunit 1.6 Purine and pyrimidine ribonucleotide biosynthesis UC7_RS15255 hypothetical protein 1.6 Unknown UC7_RS13120 hypothetical protein 1.6 Unknown UC7_RS13335 chaperone protein ClpB 1.6 Protein folding UC7_RS14685 DNA-binding response...”

K0NB96 N5-carboxyaminoimidazole ribonucleotide synthase from Lacticaseibacillus paracasei
37% identity, 91% coverage

• Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
  Adu, PloS one 2018
  • “...<1% 3.78 Lipoprotein 6 PepC K0NC50 14 37 1.34E-06 <1% -4.24 PepC protein 7 PurK_2 K0NB96 9 78 0.0001214 <1% -5.31 N5-carboxyaminoimidazole ribonucleotide synthase 8 PurD K0MWC4 16 177 0.0002099 <1% -8.14 Phosphoribosylamineglycine ligase 9 PurH K0N634 18 286 1.89E-06 <1% -8.18 Bifunctional purine biosynthesis protein...”

P15567 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Schizosaccharomyces pombe (see paper)
ade6 / RF|NP_588141.1 phosphoribosylaminoimidazole carboxylase Ade6; EC 4.1.1.21 from Schizosaccharomyces pombe (see paper)
SPCC1322.13 phosphoribosylaminoimidazole carboxylase Ade6 from Schizosaccharomyces pombe
34% identity, 61% coverage

• CharProtDB Source (per GeneDB): GeneDB_Spombe
• Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B
  Lera-Ramirez, eLife 2022
  • “...resource Designation Source or reference Identifiers Additional information Gene ( S. pombe ) ade6 Pombase SPCC1322.13 Gene ( S. pombe ) alp7 Pombase SPAC890.02c Gene ( S. pombe ) ark1 Pombase SPCC320.13c Gene ( S. pombe ) ase1 Pombase SPAPB1A10.09 Gene ( S. pombe ) atb2...”
• Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants
  Iben, Nucleic acids research 2011
  • “...2 3E+06 2901509 G T 47 miscRNA T T 3 1E+06 1316977 T A 80 SPCC1322.13 ade6 d C215stop NA A 3 2E+06 1647827 G T 33 * G T 3 2E+06 1862803 A G 48 * A G Mt 1788 1788 C T 9483 rRNA...”
• A novel function of the mitochondrial transcription factor Mtf1 in fission yeast; Mtf1 regulates the nuclear transcription of srk1
  Sun, Nucleic acids research 2011
  • “...1.8 3.3 Mug150 D SPCC1322.08 0.7 18.5 Srk1 chr2.mini.tile157: 4.99 SPCC1322.12c 0.3 0.4 Bub1 D SPCC1322.13 0.4 2.8 Ade6 chr1.2362.1 5.05 SPAC212.11 0.9 0.3 RecQ D SPAC212.09c 1.4 0.9 pseudogene chr1.15s.1 5.92 SPAC1805.09c 0.9 2.4 Fmt1 D SPAC1805.10 N/A N/A orphan chr2.mini.tile179: 5.03 SPBCPT2R1.08c 1 0.4...”

Q5GTP1 N5-carboxyaminoimidazole ribonucleotide synthase from Wolbachia sp. subsp. Brugia malayi (strain TRS)
35% identity, 94% coverage

• Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis
  Sharma, Scientific reports 2016
  • “...1. FDT070 Q5GS61 Outer membrane protein 32. FDT102 Q5GTJ9 Riboflavin synthase alpha chain 2. FDT071 Q5GTP1 N5-carboxyaminoimidazole ribonucleotide synthase 33. FDT103 Q5GTK4 Holo-[acyl-carrier-protein] synthase 3. FDT072 Q5GRP6 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 34. FDT104 Q5GRR7 Ferrochelatase 4. FDT073 Q5GRK8 UDP-N-acetylenolpyruvoylglucosamine reductase 35. FDT105 Q5GTL0 3-polyprenyl-4-hydroxybenzoate decarboxylase 5. FDT074 Q5GSC8...”

TK0835 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Thermococcus kodakaraensis KOD1
37% identity, 88% coverage

• Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis
  Sanders, Frontiers in microbiology 2021
  • “...Phosphoribosyl formylglycinamidine cyclo-ligase Purine metabolism 8.43 TK1356 ATPase, AAA superfamily Unknown, viral region 4 8.41 TK0835 Phosphoribosy laminoimidazole carboxylase, ATPase subunit Purine metabolism 7 60 TK1393 Anaerobic glycerol 3-phosphate dehydrogenase Lipid metabolism 7.40 TK2060 Distant homolog of phosphate transport system regulator PhoU Transport 7.20 TK1391 Molybdopterin...”
• An archaeal histone is required for transformation of Thermococcus kodakarensis
  Čuboňováa, Journal of bacteriology 2012
  • “...TK0194 TK0157 TK0475 TK0268 TK0269 TK0270 TK0271 TK1893 TK0835 TK0204 TK0203 TK1895 TK0010 TK2147 TK1002 TK1287 TK2138 TK1737 TK0766 TK1605 TK1961 TK1459 TK0252...”
  • “...TK0202 TK0203 TK0204 TK0190 TK0191 TK0192 TK0193 TK0194 TK0835 TK0207 TK0603 TK0604 TK1090 TK0561 TK1352 TK1583 TK0418 TK1287 TK0260 TK1895 TK0084 TK0612 TK1923...”

YP_RS04370 5-(carboxyamino)imidazole ribonucleotide synthase from Yersinia pestis biovar Microtus str. 91001
YPO3077 phosphoribosylaminoimidazole carboxylase ATPase subunit PurK from Yersinia pestis CO92
y1102 phosphoribosylaminoimidazole carboxylase, CO(2)-fixing subunit from Yersinia pestis KIM
39% identity, 94% coverage

• Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities
  Xiao, Microorganisms 2023
  • “...purT formate-dependent phosphoribosylglycinamide formyltransferase Purine metabolism YP_RS04375 3.12 4.25 10 46 purE 5-(carboxyamino)imidazole ribonucleotide mutase YP_RS04370 3.01 2.65 10 52 purK 5-(carboxyamino)imidazole ribonucleotide synthase YP_RS16125 2.30 1.50 10 46 purH bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_RS14005 2.29 1.70 10 55 purM phosphoribosylformylglycinamidine cyclo-ligase YP_RS12405 1.98 2.79 10...”
  • “...purT formate-dependent phosphoribosylglycinamide formyltransferase Purine metabolism YP_RS04375 3.76 4.12 10 46 purE 5-(carboxyamino)imidazole ribonucleotide mutase YP_RS04370 3.60 5.14 10 64 purK 5-(carboxyamino)imidazole ribonucleotide synthase YP_RS16125 2.97 1.89 10 64 purH bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_RS13160 2.83 4.37 10 41 purL phosphoribosylformylglycinamidine synthase YP_RS14005 2.76 8.61 10...”
• Generation of Yersinia pestis attenuated strains by signature-tagged mutagenesis in search of novel vaccine candidates
  Flashner, Infection and immunity 2004
  • “...YPCD1.49 YPO3357 y0502 Y0032 y0832 PurH LcrF Pcm 0.002 0.08 YPO3077 YPO3505 y1102 y0679 PurK GreA 0/3 (5) 0/3 (4) 0/3 (3) 0/3 (4) 0/3 (4) 0.035 0.054 0.057...”
• Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue
  Palace, mBio 2014
  • “...l -isoaspartate O -methyltransferase 0.677 2.60E03 brnQ (y0981) Branched-chain amino acid import 0 1.00E05 purK (y1102) Purine biosynthesis 0.298 1.00E05 purE (y1103) Purine biosynthesis 0.261 6.00E04 purL (y1309) Purine biosynthesis 0.168 1.00E05 guaB (y1362) Purine metabolism 0 6.00E04 guaA (y1363) Purine metabolism 0 4.20E03 purN (y1406)...”
• Generation of Yersinia pestis attenuated strains by signature-tagged mutagenesis in search of novel vaccine candidates
  Flashner, Infection and immunity 2004
  • “...YPO3357 y0502 Y0032 y0832 PurH LcrF Pcm 0.002 0.08 YPO3077 YPO3505 y1102 y0679 PurK GreA 0/3 (5) 0/3 (4) 0/3 (3) 0/3 (4) 0/3 (4) 0.035 0.054 0.057 0.15 0.26...”

LGG_01813 phosphoribosylaminoimidazole carboxylase ATPase subunit (AIR carboxylase) (AIRC) from Lactobacillus rhamnosus GG
LGG_01813 5-(carboxyamino)imidazole ribonucleotide synthase from Lacticaseibacillus rhamnosus GG
37% identity, 89% coverage

• Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
  Laakso, Microbial biotechnology 2011
  • “...LGG_01809 purL Phosphoribosylformylglycinamidine synthase II 73 3.8 1.653 LGG_01812 purC Phosphoribosylaminoimidazolesuccinocarboxamide synthase 74 2.5 1.466 LGG_01813 purK Phosphoribosylaminoimidazole carboxylase, ATPase subunit 6 a ,75,76 2.8 1.539 LGG_01968 guaA GMP synthase 77 1.8 1.916 LGG_02466 adk Adenylate kinase 78 1.7 1.865 Pyrimidine metabolism LGG_01175 upp Uracil phosphoribosyltransferase...”

CNE02500 phosphoribosylaminoimidazole carboxylase from Cryptococcus neoformans var. neoformans JEC21
35% identity, 60% coverage

• PRM1 and KAR5 function in cell-cell fusion and karyogamy to drive distinct bisexual and unisexual cycles in the Cryptococcus pathogenic species complex
  Fu, PLoS genetics 2017
  • “...into the intergenic region between CNE02520 and CNE02530, which is downstream of the ADE2 gene (CNE02500). To visualize the cytosol in Cryptococcus , a plasmid encoding the cytosolic mCherry gene and containing a dominant selectable marker ( NEO cassette) was generated. The mCherry coding sequence was...”

YP_003473050 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Thermocrinis albus DSM 14484
37% identity, 94% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole carboxamide formyltransferase /IMP cyclohydrolase Theam_0328 P. marina sim. 59% YP_002731268 Aquificae / Bacteria 86% YP_004281681 78% WP_022847359 59% YP_002731268 56% YP_001931239 53% YP_003433270...”

CNAG_02294 phosphoribosylaminoimidazole carboxylase from Cryptococcus neoformans var. grubii H99
35% identity, 60% coverage

• Transformation of Cryptococcus neoformans by electroporation using a transient CRISPR-Cas9 expression (TRACE) system
  Lin, Fungal genetics and biology : FG & B 2020
  • “...(deletion of the ADE2 gene in H99) Gene locus Primer Sequence (5 to 3) Purpose CNAG_02294 ADE2 P1 CTCCGTGTACCACGCTGC 1 st Round of PCR for 5arm. (pair with P2) P2 CTGGCCGTCGTTTTAC-CCACCGCCTGAGGATG 1 st Round of PCR for 5arm. (pair with PI) Red sequence is overhang complement...”
• Purine Acquisition and Synthesis by Human Fungal Pathogens
  Chitty, Microorganisms 2017
  • “...four enzymatic activities for its conversion to AMP. Deletion of the gene encoding AIR carboxylase (CNAG_02294, ADE2 ) showed the identical phenotype to C. albicans and S. cerevisiae of red pigmentation produced and similarly led to the pathways investigation as a potential antifungal drug target. The...”
• A genomic safe haven for mutant complementation in Cryptococcus neoformans
  Arras, PloS one 2015
  • “...was generated using the Superscript III First-Strand Synthesis System (Invitrogen, USA). Primers for ADE2 ( CNAG_02294 ), the genes flanking ADE2 ( CNAG_02293 and CNAG_02295 ) and the genes flanking the safe haven insertion site ( CNAG_00777 and CNAG_00778 ) were designed to span exonexon boundaries....”

APL_0661 phosphoribosylaminoimidazole carboxylase ATPase subunit from Actinobacillus pleuropneumoniae L20
39% identity, 95% coverage

• Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
  Auger, Infection and immunity 2009
  • “...nucleosides, and nucleotides APL_0148 APL_0593 APL_0147 APL_0255 APL_0661 APL_1172 APL_2018 APL_0834 gpt purK purD purC udk Ribonucleotide reductase, alpha...”

C4J6I7 phosphoribosylaminoimidazole carboxylase from Zea mays
33% identity, 55% coverage

• A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize
  Silva-Sanchez, Frontiers in plant science 2014
  • “...from Zea mays (B6SWN1) 5.78 6.59 71.07 68.68 0.65 1.49 9 3 4 0.00 C C4J6I7 Simillar to Phosphoribosylaminoimidazole carboxylase atpase-subunit, putative from Ricinus communis (B9S7H9) 6.59 68.71 5 7 2 0.00 C 362 Q9ZP62 Glutathione transferase III(A) 6.47 5.96 16.45 23.92 0.67 1.99 3 3...”

Rmet_0506 5-(carboxyamino)imidazole ribonucleotide synthase from Cupriavidus metallidurans CH34
38% identity, 78% coverage

• Linking the transcriptome to physiology: response of the proteome of Cupriavidus metallidurans to changing metal availability
  Galea, Metallomics : integrated biometal science 2024
  • “...b 4.35 0.08 Rmet_1026 iscU 54536 2.30.6 233 172472 659 26.5 AM0+ 3.17 27.9 0.11 Rmet_0506 purK 12524 0.30.6 375 629 1.30.6 46.2 AM0 0.49 b 4.00 0.12 Rmet_0970 ggt 23517 2.30.6 101 373 2.71.1 14.0 AM0 0.16 b 1.14 0.14 Rmet_1026 iscU 50617 40 127...”

UG58_01935 5-(carboxyamino)imidazole ribonucleotide synthase from Escherichia coli O25b:H4-ST131
38% identity, 99% coverage

• Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
  Brochmann, Scientific reports 2018
  • “...two predicted stress inducible genes (Fig. 5c and Supplementary File 8 ). Three genes (UG58_01930, UG58_01935 and UG58_13625) encoding enzymes from the de novo IMP biosynthesis pathway were also notably down-regulated with respect to the control samples in the 90min samples, although the remainder of the...”

SPD_0060 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Streptococcus pneumoniae D39
38% identity, 91% coverage

• Glutamate Dehydrogenase (GdhA) of Streptococcus pneumoniae Is Required for High Temperature Adaptation
  Gazioglu, Infection and immunity 2021 (secret)

1b6sB / P09029 Structure of n5-carboxyaminoimidazole ribonucleotide synthetase (see paper)
38% identity, 99% coverage

• Ligands: magnesium ion; adenosine-5'-diphosphate (1b6sB)

spr0054 Phosphoribosyl glucinamide formyltransferase from Streptococcus pneumoniae R6
38% identity, 86% coverage

• Eukaryotic-type serine/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae
  Sasková, Journal of bacteriology 2007
  • “...1.46 1.54E-05 1.32E-03 4.31 2.75 spr0054 spr1109 spr1128 Adenylosuccinate synthetase (purA) Phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE)...”
• Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors
  Ng, Journal of bacteriology 2003
  • “...spr0046 spr0047 spr0048 spr0049 spr0050 spr0051 spr0052 spr0053 spr0054 spr0055 spr0056 368 NG ET AL. J. BACTERIOL. transcript amounts from many of the genes...”

ECs0584 phosphoribosylaminoimidazole carboxylase from Escherichia coli O157:H7 str. Sakai
38% identity, 99% coverage

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...cyoB 2.01 10 ECs2027 ydcI 3.35 2 ECs0489 bolA 2.10 2 ECs2031 ydcH 2.99 2 ECs0584 purK -2.27 1 ECs2037 ydcN 2.71 2 ECs0585 purE -2.66 1 ECs2083 sfcA -2.18 1 ECs0610 cusC -2.31 1 ECs2182 O157 3.21 2 ECs0611 cusF -2.82 1 ECs2293 ynfE -2.97...”

PurK / b0522 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
purK / P09029 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) from Escherichia coli (strain K12) (see 9 papers)
PURK_ECOLI / P09029 N5-carboxyaminoimidazole ribonucleotide synthase; N5-CAIR synthase; 5-(carboxyamino)imidazole ribonucleotide synthetase; EC 6.3.4.18 from Escherichia coli (strain K12) (see 3 papers)
NP_415055 5-(carboxyamino)imidazole ribonucleotide synthase from Escherichia coli str. K-12 substr. MG1655
b0522 phosphoribosylaminoimidazole carboxylase from Escherichia coli str. K-12 substr. MG1655
38% identity, 99% coverage

• function: Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
  catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + hydrogencarbonate + ATP = 5-carboxyamino-1-(5-phospho-D- ribosyl)imidazole + ADP + phosphate + 2 H(+) (RHEA:19317)
  subunit: Homodimer.
• Interpol review of detection and characterization of explosives and explosives residues 2016-2019
  Klapec, Forensic science international. Synergy 2020
  • “...with a capillary liquid xenon converter coupled to a gaseous photomultiplier J.Instrum. 12 9 2017 P09029 850 Kendziora C. Furstenberg R. Papantonakis M. Nguyen V. McGill R. May). Broadband infrared imaging spectroscopy for standoff detection of trace explosives Proceedings of the International Society for Optics and...”
• Isatins Inhibit N⁵-CAIR Synthetase by a Substrate Depletion Mechanism
  Streeter, Biochemistry 2019
  • “...for financial support. ASSOCIATED CONTENT Accession Codes N 5 -CAIR synthetase ( E. coli ), P09029; N 5 -CAIR synthetase ( A. clavatus , residues 1383), A1CII2; N 5 -CAIR mutase ( E. coli ), P0AG19; SAICAR synthetase ( E. coli ), P0A7D7. The authors declare...”
• Structure of N5-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis
  Tuntland, Acta crystallographica. Section D, Biological crystallography 2011
  • “...atom(s) (of (accession No. EAW10687) and ecPurK (accession No. P09029) showing the conserved residues (red), the Leu269 in chain A and of Leu269 ecPurK deletion...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...(DIGE 4.5-6.5) PurK P09029 Phosphoribosylaminoimidazolesuccinocarboxamide synthase Phosphoribosylamine-glycine ligase Phosphoribosylaminoimidazole carboxylase...”
• Divergence of function in sequence-related groups of Escherichia coli proteins
  Nahum, Genome research 2001
  • “...apo-serine activating enzyme purK purT b0522 b1849 P09029 P33221 CO2 subunit of phosphoribosylaminoimidazole carboxylase GAR transformylase 2 355 391 guaB guaC...”
• Cloning and expression of the Lactococcus lactis purDEK genes, required for growth in milk
  Nilsson, Applied and environmental microbiology 1998
  • “...PurE, P12044, P09028, and P21264; and for PurK, P12045, P09029, and P21264. b The amino acid sequence deduced from L. lactis purK9 is not complete. purDEK OF...”
• Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea
  Dörnte, Fungal biology and biotechnology 2020
  • “...of bifunctional Ade8 Chr_1:2,548,1092,550,858 AIR to CAIR 5-(Carboxyamino)imidazole ribonucleotide synthase+5-(carboxyamino)imidazole ribonucleotide mutase (AIR carboxylase) PurK+PurE, NP_415055, NP_415056 Fused Ade2, P21264 CC1G_11091T0, fused Ade1 Chr_5:473,822471,864 CAIR to SAICAR Phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICARS) PurC, NP_416971 Ade1, NP_009409 CC1G_05887T0 Chr_7:2,536,5702,535,540 SAICAR to AICAR Adenylosuccinate lyase BifunctionalPurB, THI73349 Bifunctional Ade13, NP_013463...”
• Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli.
  Thoden, Biochemistry 2008
  • GeneRIF: Report is given of X-ray structures of N5-carboxyaminoimidazole ribonucleotide synthetase (CAIR) with either magnesium (Mg)ATP or MgADP/inorganic phosphorus (Pi) bound in the enzyme's active site cleft.
• Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway.
  Meyer, Biochemistry 1992 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...+ b0508 hyi 588 9.457 IS04 551087 1 C TGGC ACCGCGTG TGC A 551095 - b0522 purK - b0517 allD 5500 7.934 IS05 567582 2 G TGG TGCAATAC TTGC A 567568 + b0543 emrE + b0544 ybcK 543 10.546 IS06 655861 1 T TGG TAAAGTTT TTGC...”
• Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
  Orth, BMC systems biology 2012
  • “...negative model predictions caused by missing isozymes or alternate pathways Gene Putative Isozyme E-value purK (b0522) purT (b1849) 2.00E-12 gltA (b0720) prpC (b0333) 1.00E-41 aspC (b0928) tyrB (b4054) 4.00E-94 fabH (b1091) none identified pabC (b1096) ilvE (b3770) 7.00E-8 icd (b1136) dmlA (b1800) 3.00E-19 aldA (b1415) gabD...”
• Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli
  Aggarwal, Journal of bacteriology 2011
  • “...purK purE purR purC purN purH cmk b2499 b2312 b2557 b1849 b0522 b0523 b1658 b2476 b2500 b4006 b0910 3.1 (0.5) 4.1 (0.4) 3.1 (0.7) 3.0 (1.5) 2.2 (0.8) 2.2 (1.4)...”
• Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
  Xu, BMC bioinformatics 2009
  • “...b4039, b4040 b4407, s0001 SS MM APM GM MLM PPB genes b0159 b0159 b0175 b0185 b0522, b0523 b2687 b0386 b2585 b1092 b0945, b1062 b2942 b2818 b3018 b1094 b1131, b1281 b3939 b3172 b4041 b2316 b2312, b2476 b4013 b3957 b4160 b2323 b2499, b2507 s0001 b3958 b3255 b2557, b2780...”
• Experimental and computational assessment of conditionally essential genes in Escherichia coli
  Joyce, Journal of bacteriology 2006
  • “...purD (b4005) purE (b0523) purF (b2312) purH (b4006) purK (b0522) purL (b2557) purM (b2499) pyrB (b4245) pyrC (b1062) pyrD (b0945) pyrE (b3642) pyrF (b1281) thyA...”
• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...0.66 0.93 0.48 0.48* 0.91 0.62* 0.75 b0522 purK 1 2.11* 1.24 0.98 b0523 purE 1 Phosphoribosylaminoimidazole carboxylase, CO2-fixing subunit...”
• Divergence of function in sequence-related groups of Escherichia coli proteins
  Nahum, Genome research 2001
  • “...ligase apo-serine activating enzyme purK purT b0522 b1849 P09029 P33221 CO2 subunit of phosphoribosylaminoimidazole carboxylase GAR transformylase 2...”
• Genome-wide expression profiling in Escherichia coli K-12
  Richmond, Nucleic acids research 1999
  • “...b2507 guaA -10.4 -3.3 b0033 carB -10.7 3.2 b0522 purK -10.8 2.0 b2498 upp -11.8 -1.0 Uracil phosphoribosyltransferase b0337 codA -12.0 -1.0 Cytosine deaminase...”

BJK46_008860 5-(carboxyamino)imidazole ribonucleotide synthase from Staphylococcus pseudintermedius
35% identity, 93% coverage

• Erythritol alters gene transcriptome signatures, cell growth, and biofilm formation in Staphylococcus pseudintermedius
  Fujii, BMC veterinary research 2023
  • “...synthase 0.71 GO:0009236 cobalamin biosynthetic process 0.70 GO:0006189 de novo IMP biosynthetic process -3.86 1.28E-235 BJK46_008860 5-(carboxyamino)imidazole ribonucleotide synthase purK 0.61 N5-carboxyaminoimidazole ribonucleotide synthase 0.70 GO:0006189 de novo IMP biosynthetic process -3.8 4.19E-66 BJK46_011905 peptidoglycan-binding protein -3.63 3.78E-181 BJK46_009875 ABC-type cobalamin Fe3+-siderophores transport system periplasmic component...”
  • “...( purL ), BJK46_008845 ( purQ ), BJK46_008850 ( purS ), BJK46_008855 ( purC ), BJK46_008860 ( purK ), and BJK46_008865 ( purE ), were located on a single pur -operon and assigned GO biological process classes predicted to be associated with de novo IMP biosynthetic...”

A8IJJ8 phosphoribosylaminoimidazole carboxylase from Chlamydomonas reinhardtii
36% identity, 53% coverage

• Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii
  Roustan, Frontiers in plant science 2018
  • “...purine metabolism were found to be significantly up-regulated during rapamycin treatment (A8JGY3, A8HPI1, A8IXD1, and A8IJJ8). Finally, we also investigated the 199 other proteins presenting a significant difference in treatment factor, but also with time and interaction factors. Previously published transcriptomics data corroborate a significant decrease...”
  • “...(PUR4 a formylglycinamidine ribonucleotide synthase), A8I6R4 (PUR5 a phosphoribosylformylglycinamidine cyclo-ligase), A8JBQ5 (PUR7 a SAICAR synthetase) A8IJJ8 (AIR carboxylase) A8IVF0 (AICAR transformylase). Additionally, we could confirm the downregulation of pyrimidine metabolism represented by two carbamoyl phosphate synthetases (A8IMN5, A8JIR0) and a translation factor (A8HTK7) (Figure 7 )....”

Dda3937_01683 5-(carboxyamino)imidazole ribonucleotide synthase from Dickeya dadantii 3937
36% identity, 99% coverage

• A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians
  Morinière, mSystems 2022
  • “...XHV734_1765 trpA Tryptophan synthase alpha chain Psyr_0033 RS_RS09955 ATU_RS00095 XHV734_1808 purK N5-carboxyaminoimidazole ribonucleotide synthase ATU_RS17455 Dda3937_01683 XHV734_1945 tgt tRNA-guanine transglycosylase RS_RS13575 XHV734_1977 gdh NAD-specific glutamate dehydrogenase ATU_RS13460 XHV734_2148 purM Phosphoribosylaminoimidazole synthetase ATU_RS05630 Dda3937_02515 XHV734_2154 sodA Superoxide dismutase, Mn ATU_RS04315 XHV734_2180 Dihydroorotase ATU_RS06435 XHV734_2250 UDP- N -acetylmuramyl...”
• Identification by Tn-seq of Dickeya dadantii genes required for survival in chicory plants
  Royet, Molecular plant pathology 2019
  • “...4.27 0.02 N Dda3937_02337 pnp Polynucleotide phosphorylase/polyadenylase GD 50 5 0 105000 3.97 0.00 N Dda3937_01683 purK N5Carboxyaminoimidazole ribonucleotide synthase NE 16 90 0 722000 3.49 0.01 Y purE (5.75) purK (3.49) Dda3937_00689 yrbF (mlaF) Predicted toluene transporter subunit GA 9 1254 114 15962 3.47 0.01...”

Q8F650 N5-carboxyaminoimidazole ribonucleotide synthase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
LA_1462 phosphoribosylaminoimidazole carboxylase ATPase subunit from Leptospira interrogans serovar lai str. 56601
33% identity, 90% coverage

• In silico identification of common putative drug targets in Leptospira interrogans
  Amineni, Journal of chemical biology 2010
  • “...cobA Q8EXQ3 Cob(I)alamin adenosyltransferase purK Q8F650 Phosphoribosylaminoimidazole carboxylase ATPase subunit cheR Q8F4J9 Methylase of chemotaxis...”
• A Novel Pan-Genome Reverse Vaccinology Approach Employing a Negative-Selection Strategy for Screening Surface-Exposed Antigens against leptospirosis
  Zeng, Frontiers in microbiology 2017
  • “...0.6918 LB_279 LIC20214 COG4870O Cysteine protease OMPs 0.6034 LB_280 LIC20215 COG2267I Hypothetical protein ECPs 0.5028 LA_1462 LIC12293 COG1633S Hypothetical protein Unknown 0.5146 * Proteins were confirmed to be reactive with human serum (Lessa-Aquino et al., 2013 ). Osmolarity (in vivo/in vitro), physiologic osmolarity compared with those...”

Q72Q21 N5-carboxyaminoimidazole ribonucleotide synthase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
LIC12293 phosphoribosylaminoimidazole carboxylase atpase subunit protein from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
33% identity, 89% coverage

• In silico identification of common putative drug targets in Leptospira interrogans
  Amineni, Journal of chemical biology 2010
  • “...(porphyrin and chlorophyll metabolism) 55 Q72Q21 Phosphoribosylaminoimidazole carboxylase ATPase subunit (purine metabolism) 56 Q72R77 Chemotaxis protein...”
• A Novel Pan-Genome Reverse Vaccinology Approach Employing a Negative-Selection Strategy for Screening Surface-Exposed Antigens against leptospirosis
  Zeng, Frontiers in microbiology 2017
  • “...LB_279 LIC20214 COG4870O Cysteine protease OMPs 0.6034 LB_280 LIC20215 COG2267I Hypothetical protein ECPs 0.5028 LA_1462 LIC12293 COG1633S Hypothetical protein Unknown 0.5146 * Proteins were confirmed to be reactive with human serum (Lessa-Aquino et al., 2013 ). Osmolarity (in vivo/in vitro), physiologic osmolarity compared with those at...”

SP_0054 phosphoribosylaminoimidazole carboxylase ATPase subunit from Streptococcus pneumoniae TIGR4
37% identity, 91% coverage

• The Two-Component System YesMN Promotes Pneumococcal Host-to-Host Transmission and Regulates Genes Involved in Zinc Homeostasis
  Zafar, Infection and immunity 2023 (secret)
• The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes
  Jamalkandi, BMC microbiology 2020
  • “...module 14 genes are very important in pneumococcal infection. For instance, SP_0050 (purH), SP_0202 (nrdD), SP_0054 (purK) and SP_0205 (nrdG) are early pneumococcal response genes in human lung epithelial cells [ 15 ]. Iron starvation condition up-regulates the expression of nrdD, SP_0204, and SP_0205 genes, whereas...”
  • “...are critical for the infection process based on previous reports. For instance, as mentioned above, SP_0054 is an early response gene in human lung epithelial cells, while SP_0274 is a crucial gene in pulmonary infection [ 8 , 17 ]. Table 3 shows some critical infection-related...”
• Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
  Jiménez-Munguía, PeerJ 2018
  • “...2/2 Downregulated 38469 SP_0024, SP_0025, SP_0026 3/3 Downregulated 38472 SP_0042, SP_0043 2/2 Downregulated 38476 SP_0053, SP_0054, SP_0055 3/4 Downregulated 38486 SP_0119, SP_0120 2/2 Downregulated 38495 SP_0151, SP_0152 2/3 Downregulated 38498 SP_0164, SP_0165 2/2 Downregulated 38510 SP_0220, SP_0221, SP_0222 3/14 Downregulated 38529 SP_0321, SP_0322, SP_0323, SP_0324, SP_0325,...”
• Physiological and molecular characterization of genetic competence in Streptococcus sanguinis
  Rodriguez, Molecular oral microbiology 2011
  • “...clpL SGO_1856 SP_1722 SSA_0456 scrA SGO_1857 --- SSA_0860 SGO_2013 --- --- SGO_2086 --- --- SGO_2088 SP_0054 purK SSA_0040 purK SGO_2089 purK SP_0051 purD SSA_0037 purD SGO_2092 purD --- --- SGO_2093 --- SSA_0036 * SGO_2094 --- --- SGO_2095 comX --- --- SGO_2147 comC a Genes listed on...”

OG1RF_11498 5-(carboxyamino)imidazole ribonucleotide synthase from Enterococcus faecalis OG1RF
35% identity, 93% coverage

• Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections
  Tan, mBio 2024
  • “...purL2 Phosphoribosylformylglycinamidine synthase subunit PurQ 3.03 2.91E-37 2.59E-36 OG1RF_11496 purS Phosphoribosylformylglycinamidine synthase 2.68 7.75E-15 5.12E-14 OG1RF_11498 purK 5-(Carboxyamino)imidazole ribonucleotide synthase 2.15 9.76E-13 5.37E-12 a Complete table can be found in Supplementary file 1 (sheet 1). TABLE 2 E. faecalis purine biosynthesis genes differentially regulated from 8...”
  • “...1.35E-81 OG1RF_11496 purS Phosphoribosylformylglycinamidine synthase 6.35 7.15E-22 2.25E-21 OG1RF_11497 purC Phosphoribosylaminoimidazolesuccinocarboxamide synthase 7.29 6.75E-118 1.28E-116 OG1RF_11498 purK 5-(Carboxyamino)imidazole ribonucleotide synthase 5.37 1.57E-62 1.20E-61 OG1RF_11499 purE 5-(Carboxyamino)imidazole ribonucleotide mutase 5.24 1.24E-75 1.29E-74 a Complete table can be found in Supplementary file 1 (sheet 2). To confirm the...”

PF0426 phosphoribosylaminoimidazole carboxylase from Pyrococcus furiosus DSM 3638
34% identity, 91% coverage

• Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus
  Khatibi, Biotechnology and bioengineering 2017
  • “...and nucleotides PF0421 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5-monophosphate synthetase --- 19 29 PF0422 phosphoribosylamine-glycine ligase --- 13 12 PF0426 phosphoribosylaminoimidazole carboxylase --- 7 8 PF0427 phosphoribosylaminoimidazole carboxylase 2 4 8 PF0430 phosphoribosylglycinamide formyltransferase 2 36 16 PF1516 GMP synthase --- 10 6 Unclassified PF0449 glutamine metabolism 10 --- 10...”
• Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus
  Chou, Applied and environmental microbiology 2007
  • “...Maltose S0 vs maltose 4.1 2.5 2.1 2.3 PF0426 PF1516 PF1517 4.3 2.3 4.8 4.0 2.4 3.1 SAICAR synthase Glutamine phosphoribosylpyrophosphate amidotransferase NCAIR...”

SERP0650 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Staphylococcus epidermidis RP62A
32% identity, 89% coverage

• Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis
  Gonçalves, Frontiers in microbiology 2022
  • “...ID Gene Purine/Nucleotide Metabolism Xanthine phosphoribosyltransferase SERP0067 xpt Adenylate kinase SERP1810 adk N5-carboxyaminoimidazole ribonucleotide synthase SERP0650 purK Phosphoribosylformylglycinamidine synthase subunit PurL SERP0654 purL Phosphoribosylformylglycinamidine cyclo-ligase SERP0656 purM Phosphoribosylaminoimidazole-succinocarboxamide synthase SERP0651 purC Phosphoribosylamine-glycine ligase SERP0659 purD Phosphoribosylformylglycinamidine synthase SERP0653 purQ Amidophosphoribosyltransferase SERP0655 purF Glycolysis/Pyruvate metabolism Glyceraldehyde-3-phosphate dehydrogenase...”

SPRG_11850 hypothetical protein from Saprolegnia parasitica CBS 223.65
38% identity, 63% coverage

• Identification of Growth Inhibitors of the Fish Pathogen Saprolegnia parasitica Using in silico Subtractive Proteomics, Computational Modeling, and Biochemical Validation
  Kumar, Frontiers in microbiology 2020
  • “...proteins from S. parasitica , including two uncharacterized proteins (SPRG_06530, a probable FtsZ protein, and SPRG_11850 and a phosphoribosylaminoimidazole carboxylase), a tryptophan synthase (SPRG_05079) and a cell division protein FtsZ (SPRG_11942). Tryptophan synthase catalyzes the final step of the tryptophan biosynthetic pathway. This enzyme is absent...”

Q4QL53 N5-carboxyaminoimidazole ribonucleotide synthase from Haemophilus influenzae (strain 86-028NP)
NTHI1424 phosphoribosylaminoimidazole carboxylase ATPase subunit from Haemophilus influenzae 86-028NP
35% identity, 98% coverage

• Correction: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism
  , PloS one 2014
  • “...purine biosynthesis protein purH NTHI1051 Q4QM21 -1.98 0.001 Hydrolase Phosphoribosylaminoimidazole carboxylase ATPase subunit purK NTHI1424 Q4QL53 -1.96 0.001 Lyase N5-carboxyaminoimidazole ribonucleotide mutase purE NTHI1425 Q4QL52 -3.70 5E-05 Lyase Phosphoribosylformylglycinamidine cyclo-ligase purM NTHI1704 Q4QKF3 -3.45 9E-05 Ligase Phosphoribosylaminoimidazole-succinocarboxamide synthase purC NTHI2033 Q4QJM1 -2.50 0.0003 Ligase Phosphoribosylglycinamide formyltransferase...”
• Beta- lactam antibiotics stimulate biofilm formation in non-typeable haemophilus influenzae by up-regulating carbohydrate metabolism
  Wu, PloS one 2014
  • “...purine biosynthesis protein purH NTHI1051 Q4QM21 1.98 0.001 Hydrolase Phosphoribosylaminoimidazole carboxylase ATPase subunit purK NTHI1424 Q4QL53 1.96 0.001 Lyase N5-carboxyaminoimidazole ribonucleotide mutase purE NTHI1425 Q4QL52 3.70 5E-05 Lyase Phosphoribosylformylglycinamidine cyclo-ligase purM NTHI1704 Q4QKF3 3.45 9E-05 Ligase Phosphoribosylaminoimidazole-succinocarboxamide synthase purC NTHI2033 Q4QJM1 2.50 0.0003 Ligase Phosphoribosylglycinamide formyltransferase...”
• Correction: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism
  , PloS one 2014
  • “...Bifunctional purine biosynthesis protein purH NTHI1051 Q4QM21 -1.98 0.001 Hydrolase Phosphoribosylaminoimidazole carboxylase ATPase subunit purK NTHI1424 Q4QL53 -1.96 0.001 Lyase N5-carboxyaminoimidazole ribonucleotide mutase purE NTHI1425 Q4QL52 -3.70 5E-05 Lyase Phosphoribosylformylglycinamidine cyclo-ligase purM NTHI1704 Q4QKF3 -3.45 9E-05 Ligase Phosphoribosylaminoimidazole-succinocarboxamide synthase purC NTHI2033 Q4QJM1 -2.50 0.0003 Ligase Phosphoribosylglycinamide...”
• Beta- lactam antibiotics stimulate biofilm formation in non-typeable haemophilus influenzae by up-regulating carbohydrate metabolism
  Wu, PloS one 2014
  • “...Bifunctional purine biosynthesis protein purH NTHI1051 Q4QM21 1.98 0.001 Hydrolase Phosphoribosylaminoimidazole carboxylase ATPase subunit purK NTHI1424 Q4QL53 1.96 0.001 Lyase N5-carboxyaminoimidazole ribonucleotide mutase purE NTHI1425 Q4QL52 3.70 5E-05 Lyase Phosphoribosylformylglycinamidine cyclo-ligase purM NTHI1704 Q4QKF3 3.45 9E-05 Ligase Phosphoribosylaminoimidazole-succinocarboxamide synthase purC NTHI2033 Q4QJM1 2.50 0.0003 Ligase Phosphoribosylglycinamide...”

SCO3060 phosphoribosylaminoimidazole carboxylase ATPase subunit PurK from Streptomyces coelicolor A3(2)
37% identity, 82% coverage

• DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
  Šmídová, Nucleic acids research 2019
  • “...biosynthesis subgroup we found 17 genes (81%)prsA (SCO0782), purB (SCO1254), guaB2 (SCO1461), purE (SCO3059), purK (SCO3060), prsA2 (SCO3123), purA (SCO3629), SCO3677, purQ (SCO4078), purl (SCO4079), purF (SCO4086), purM (SCO4087), adk (SCO723), guaB (SCO4770), SCO4771, purN (SCO4813), purH (SCO4814). In the pyrimidine biosynthesis subgroup we found six...”
• ArgR of Streptomyces coelicolor is a versatile regulator
  Pérez-Redondo, PloS one 2012
  • “...in the argR mutant. They included SCO2015 (encoding a putative secreted nucleotidase), SCO5662 (adenosine deaminase), SCO3060 ( purK , phosphoribosylaminoimidazole carboxylase ATPase), SCO5743 ( thyX, thymidylate synthase), and SCO5868 ( dut , deoxyuridine 5-triphosphate nucleotidohydrolase). Two sets of independent ribonucleotide reductases (RNRs) in Streptomyces are encoded...”
• Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation
  Manteca, Molecular & cellular proteomics : MCP 2010
  • “...SCO1773 SCO1494 SCO5547 SCO4958 SCO0216 SCO5212 SCO2198 SCO1660 SCO3834 SCO5385 SCO1514 SCO3899 SCO3060 SCO4917 6 4 2 4 2 2 6 8 6 6 1 2 8 6 7 6 7 6 2 4 2...”
• Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase
  Cummings, Biochemistry 2010
  • “...with Sco3058. The Sco3058 gene is also adjacent to Pur E (Sco3059) and Pur K (Sco3060) which code for proteins annotated as phosphoribosylaminoimidazole carboxylase catalytic and ATPase subunits, respectively. It is conceivable that Sco3058 could either hydrolyze a molecule such as 4-[( N -succinylamino)carbonyl]-5-aminoimidazole ribonucleotide (SAICAR)...”

LBA_RS07640 5-(carboxyamino)imidazole ribonucleotide synthase from Lactobacillus acidophilus NCFM
LBA1560 phosphoribosylaminoimidazole carboxylase from Lactobacillus acidophilus NCFM
35% identity, 93% coverage

• Metabolomic Analysis of Lactobacillus acidophilus, L. gasseri, L. crispatus, and Lacticaseibacillus rhamnosus Strains in the Presence of Pomegranate Extract
  Chamberlain, Frontiers in microbiology 2022
  • “...ligase (fthf; LBA_RS07650), 5-(carboxyamino) imidazole ribonucleotide mutase (purE; LBA_RS07645), and 5-(carboxyamino) imidazole ribonucleotide synthase (purK; LBA_RS07640). Although fthf is within the operon, it is not required for the production of 5-aminoimidazole-4-carboxamide. The second locus consists of phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC; LBA_RS07635), phosphoribosylformylglycinamidine (pur) synthase subunit purS (LBA_RS07630),...”
• Characterization of a novel bile-inducible operon encoding a two-component regulatory system in Lactobacillus acidophilus
  Pfeiler, Journal of bacteriology 2007
  • “...and the operon involved in purine biosynthesis (LBA1551 to LBA1560). Because of the repression of these groups of genes, growth of NCFM was monitored in the...”

sll0578 phosphoribosyl aminoimidazole carboxylase from Synechocystis sp. PCC 6803
34% identity, 88% coverage

• Isolation of cyanobacterial mutants exhibiting growth defects under microoxic conditions by transposon tagging mutagenesis of Synechocystis sp. PCC 6803
  Terauchi, The Journal of general and applied microbiology 2017 (PubMed)
  • “...locus in T-5. Two open reading frames (sll0577 and sll0578) were partially deleted by the insertion of the kanamycin resistance gene in T-5. A reverse...”
  • “...disrupted. Only the mutants partially lacking an intact sll0578 gene showed growth defects under microoxic conditions, whereas it grew normally under aerobic...”

A8AZX7 N5-carboxyaminoimidazole ribonucleotide synthase from Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)
SGO_2089 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Streptococcus gordonii str. Challis substr. CH1
36% identity, 91% coverage

• Proteomic response in Streptococcus gordonii DL1 biofilm cells during attachment to salivary MUC5B
  Robertsson, Journal of oral microbiology 2021
  • “...metabolism; de novo purine biosynthesis. A8AUA0 Phosphoribosylglycinamide formyltransferase PurN Nucleotide metabolism; de novo purine biosynthesis. A8AZX7 N5-carboxyaminoimidazole ribonucleotide synthase PurK Nucleotide metabolism; de novo purine biosynthesis. A8AUM3 Membrane dipeptidase (amylase binding protein) AbpB Proteolysis. A8AXS5 Multiple sugar metabolism transmembrane permease F MsmF Transmembrane transport permease protein...”
• Physiological and molecular characterization of genetic competence in Streptococcus sanguinis
  Rodriguez, Molecular oral microbiology 2011
  • “...scrA SGO_1857 --- SSA_0860 SGO_2013 --- --- SGO_2086 --- --- SGO_2088 SP_0054 purK SSA_0040 purK SGO_2089 purK SP_0051 purD SSA_0037 purD SGO_2092 purD --- --- SGO_2093 --- SSA_0036 * SGO_2094 --- --- SGO_2095 comX --- --- SGO_2147 comC a Genes listed on the same line are...”

PHATRDRAFT_56626 predicted protein from Phaeodactylum tricornutum CCAP 1055/1
36% identity, 55% coverage

• Examination of metabolic responses to phosphorus limitation via proteomic analyses in the marine diatom Phaeodactylum tricornutum
  Feng, Scientific reports 2015
  • “...were downregulated, such as carbamate kinase (PHATRDRAFT_24238), adenylosuccinate synthetase (PHATRDRAFT_26256) and putative phosphoribosyl aminoimidazole carboxylase (PHATRDRAFT_56626). Carbamate kinase (CKase) is a member of transferases, transferring phosphorus-containing groups with a carboxyl group as an acceptor, which is involved in purine metabolism and other metabolic pathways such as...”
  • “...4.7 310 28.74 - PHATRDRAFT_55192 640 ECHS1 hydratase enyol-CoA hydratase 28912.5 5.6 75 12.26 --- PHATRDRAFT_56626 125 ADE2 putative phosphoribosylaminoimidazole carboxylase 64153.74 6.03 77.2 14.47 --- PSAC_PHATC 899 psaC photosystem I iron-sulfur center 9289.3 5.75 174 55.56 - Locus tag, identification of predicted protein in NCBI,...”

SSA_0040 Phosphoribosylaminoimidazole carboxylase, ATPase subunit, putative from Streptococcus sanguinis SK36
36% identity, 91% coverage

• Physiological and molecular characterization of genetic competence in Streptococcus sanguinis
  Rodriguez, Molecular oral microbiology 2011
  • “...SP_1722 SSA_0456 scrA SGO_1857 --- SSA_0860 SGO_2013 --- --- SGO_2086 --- --- SGO_2088 SP_0054 purK SSA_0040 purK SGO_2089 purK SP_0051 purD SSA_0037 purD SGO_2092 purD --- --- SGO_2093 --- SSA_0036 * SGO_2094 --- --- SGO_2095 comX --- --- SGO_2147 comC a Genes listed on the same...”

YP_003433072 phosphoribosylaminoimidazole carboxylase ATPase subunit from Hydrogenobacter thermophilus TK-6
33% identity, 96% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...YP_002731257 Methanogens /Deltaproteo bacteria 78% YP_004281335 64% WP_022847512 76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole carboxamide formyltransferase /IMP cyclohydrolase Theam_0328 P. marina sim. 59% YP_002731268 Aquificae / Bacteria 86% YP_004281681...”

AT2G37690 phosphoribosylaminoimidazole carboxylase, putative / AIR carboxylase, putative from Arabidopsis thaliana
32% identity, 53% coverage

• Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
  Bellin, Molecules (Basel, Switzerland) 2023
  • “.../Col-0 Col-0 atc#1 Col-0 atc#1 Function AT4G18440 ADSL 1.27 0.98 0.46 1.09 0.50 de novo AT2G37690 AIR carb. 0.69 1.90 1.36 0.88 0.43 de novo AT2G37250 AMK1 1.37 1.56 0.43 de novo AT5G35170 AMK5 0.72 1.14 1.16 0.50 de novo AT3G01820 AMK7 2.97 3.16 0.80 de...”
• Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
  Liebthal, Antioxidants (Basel, Switzerland) 2020
  • “...glutamate synthase 1 (AT5G04140) GDSL esterase/lipase ESM1 (AT3G14210) Myrosinase 2 (AT5G25980) AIR carboxylase like protein (AT2G37690) antioxidants-09-00515-t002_Table 2 Table 2 Overlap between the results of this study and published redox proteomes. Overlap between polypeptides found in our study and ( A ) proteins identified in the...”

D820_RS09285 5-(carboxyamino)imidazole ribonucleotide synthase from Streptococcus mutans ATCC 25175
35% identity, 91% coverage

• Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
  Muehler, Microorganisms 2022
  • “...D820_RS03970, D820_RS03955, D820_RS03950, D820_RS03960, D820_RS03940, D820_RS03930 7.00 10 3 Purine nucleotide biosynthesis D820_RS04105, D820_RS04110, D820_RS04100, D820_RS09285, D820_RS09290, D820_RS09325, D820_RS09250, D820_RS08295, D820_RS09340, D820_RS09355, D820_RS09335, D820_RS09300, D820_RS09345 1.00 10 2 Inosine-5-phosphate biosynthesis D820_RS09285, D820_RS09290, D820_RS09325, D820_RS09250 2.00 10 2 Downregulated Lactose degradation D820_RS02995, D820_RS02980, D820_RS02985, D820_RS03025, D820_RS02990 4.00...”

Q01930 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Ogataea methanolica (see paper)
29% identity, 65% coverage

M28_Spy0031 phosphoribosylaminoimidazole carboxylase ATPase subunit from Streptococcus pyogenes MGAS6180
36% identity, 89% coverage

• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...purD 15.56 9.89 11.31 Phosphoribosylamine-glycine ligase M28_Spy0030 SPy0033 purE 16.52 7.50 11.42 Phosphoribosylaminoimidazole carboxylase carboxyltransferase M28_Spy0031 SPy0034 purK 6.05 11.19 Phosphoribosylaminoimidazole carboxylase NCAIR mutase M28_Spy0064 SPy0074 adk 8.25 Adenylate kinase M28_Spy0134 SPy0160 purA 3.17 Adenylosuccinate synthetase M28_Spy0193 SPy0235 - 2.67 Deoxyuridine 5 -triphosphate nucleotidohydrolase M28_Spy0316 SPy0392...”

ADE2 / P21264 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 3 papers)
PUR6_YEAST / P21264 Phosphoribosylaminoimidazole carboxylase; AIR carboxylase; AIRC; EC 4.1.1.21 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
P21264 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Saccharomyces cerevisiae (see paper)
YOR128C Ade2p from Saccharomyces cerevisiae
31% identity, 61% coverage

• catalytic activity: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + H(+) = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + CO2 (RHEA:10792)
• Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea
  Dörnte, Fungal biology and biotechnology 2020
  • “...AIR to CAIR 5-(Carboxyamino)imidazole ribonucleotide synthase+5-(carboxyamino)imidazole ribonucleotide mutase (AIR carboxylase) PurK+PurE, NP_415055, NP_415056 Fused Ade2, P21264 CC1G_11091T0, fused Ade1 Chr_5:473,822471,864 CAIR to SAICAR Phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICARS) PurC, NP_416971 Ade1, NP_009409 CC1G_05887T0 Chr_7:2,536,5702,535,540 SAICAR to AICAR Adenylosuccinate lyase BifunctionalPurB, THI73349 Bifunctional Ade13, NP_013463 CC1G_08733T0, bifunctional Ade5 Chr_10:936,450934,462...”
• Response mechanism of Saccharomyces cerevisiae under benzoic acid stress in ethanol fermentation
  Xiu-Feng, Scientific reports 2024
  • “...metabolism pathways under benzoic acid stress. Gene ID Gene name Log 2 FC Gene description YOR128C ADE2 2.35 Phosphoribose aminoimidazole carboxylase catalyzes de novo purine nucleotide biosynthesis YMR120C ADE17 2.67 Purine biosynthesis de novo enzymes YNL220W ADE12 1.04 Catalyze the synthesis of adenosine monophosphate from inosine...”
• Yeast to Study Human Purine Metabolism Diseases
  Daignan-Fornier, Cells 2019
  • “...Ade16 YLR028C AICAR transformylase and IMP cyclohydrolase Ade17 YMR120C AICAR transformylase and IMP cyclohydrolase Ade2 YOR128C Phosphoribosylaminoimidazole carboxylase Ade4 YMR300C Phosphoribosylpyrophosphate amidotransferase Ade5,7 YGL234W Aminoimidazole ribonucleotide synthetase and glycinamide ribotide synthetase Ade6 YGR061C Formylglycinamidine-ribonucleotide synthetase Ade8 YDR408C Phosphoribosyl-glycinamide transformylase Adk1 YDR226W Adenylate kinase Adk2 YER170W Adenylate...”
• Identification and Functional Testing of Novel Interacting Protein Partners for the Stress Sensors Wsc1p and Mid2p of Saccharomyces cerevisiae
  Santiago-Cartagena, G3 (Bethesda, Md.) 2019
  • “...homolog of HIP-55 (hematopoietic progenitor kinase 1 [HPK1]-interacting protein of 55 kD) viable ADE2 (37) YOR128C WSC1 Phosphoribosylaminoimidazole carboxylase; catalyzes a step in the de novo purine nucleotide biosynthetic pathway; red pigment accumulates in mutant cells deprived of adenine viable ATX1 YNL259C MID2 Cytosolic copper metallochaperone;...”
• Yeast screen for modifiers of C9orf72 poly(glycine-arginine) dipeptide repeat toxicity
  Chai, FEMS yeast research 2018
  • “...pathway (7/133, P = 3.488e-5) ade1 YAR015W ade2 YOR128C ade4 YMR300C ade5, 7 YGL234W ade6 S000003293 ade8 YDR408C bas1 YKR099W Human ortholog(s) Function part...”
• Multiplexed precision genome editing with trackable genomic barcodes in yeast
  Roy, Nature biotechnology 2018
  • “...principle, we designed a guide-donor plasmid to introduce a PTC into the ADE2 ORF ( YOR128C ). Disruption of ADE2 results in accumulation of red pigment, enabling direct visual identification of edited colonies 6 . First we tested three different Pol III promoters ( RPR1 ,...”
• Decoding the chromatin proteome of a single genomic locus by DNA sequencing
  Korthout, PLoS biology 2018
  • “...expression of the barcoded ADE2 locus. (A) NatMX6 (pink) was inserted downstream of the ADE2 (YOR128C) coding sequence (orange), after which 15 bp barcodes were inserted 57 bp downstream of the start codon of ADE2 by template-directed repair of a CRISPR/Cas9-induced break. The zoom-in visualizes the...”
• Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
  Chen, Biotechnology for biofuels 2016
  • “...YDR502C, YER043C, YER070W, YFL045C, YGR209C, YGR281W, YKR080W, YLR043C, YLR180W, YLR231C, YMR120C, YMR300C, YNL112W, YNL220W, YOL086C, YOR128C, YOR153W, YOR184W, YOR328W, YPL036W, YPL058C YCR021C , YDR502C, YGR043C, YGR256W, YKL151C, YLR249W, YMR105C, YOR128C, YPL036W YBL022C, YCR021C , YDL055C, YDR011W, YDR135C, YDR214W, YDR502C, YEL039C, YER043C, YFL037W, YGR043C, YGR209C, YGR256W, YGR281W,...”
• Improved Gene Targeting through Cell Cycle Synchronization
  Tsakraklides, PloS one 2015
  • “...39 bp 40 bp 6% (96) 48% (96) 1.68 x 10 11 S . cerevisiae YOR128C nat 50 bp 50 bp 6% (639) 17% (258) 4.04 x 10 07 P . pastoris PAS_chr3_0085 nat 50 bp 50 bp 1.6% (374) 5.4% (279) 5.01 x 10 3...”
• More

B9S7H9 phosphoribosylaminoimidazole carboxylase from Ricinus communis
32% identity, 54% coverage

• A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize
  Silva-Sanchez, Frontiers in plant science 2014
  • “...9 3 4 0.00 C C4J6I7 Simillar to Phosphoribosylaminoimidazole carboxylase atpase-subunit, putative from Ricinus communis (B9S7H9) 6.59 68.71 5 7 2 0.00 C 362 Q9ZP62 Glutathione transferase III(A) 6.47 5.96 16.45 23.92 0.67 1.99 3 3 1 0.31 Bouov et al., 2011 B4FY73 Simillar to Rhicadhesin...”

PURK_MYCTU / P9WHL9 N5-carboxyaminoimidazole ribonucleotide synthase; N5-CAIR synthase; 5-(carboxyamino)imidazole ribonucleotide synthetase; EC 6.3.4.18 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Rv3276c phosphoribosylaminoimidazole carboxylase from Mycobacterium tuberculosis H37Rv
35% identity, 81% coverage

• function: Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
  catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + hydrogencarbonate + ATP = 5-carboxyamino-1-(5-phospho-D- ribosyl)imidazole + ADP + phosphate + 2 H(+) (RHEA:19317)
  subunit: Homodimer.
• Identification and Quantification of S-Sulfenylation Proteome of Mycobacterium tuberculosis under Oxidative Stress
  Lu, Microbiology spectrum 2023
  • “...Rv0957 ) with increased SOH modification levels have strong interaction with PurK ( P9WHL9 , Rv3276c ), and IlvC ( P9WKJ7 , Rv3001c ) with decreased SOH modification levels. Interestingly, the modified long-chain fatty acyl-CoA thioesterase FcoT ( P9WM67 , Rv0098 ), which is essential for...”
• Assessment of closely related Mycobacterium tuberculosis variants with different transmission success and in vitro infection dynamics
  Abascal, Scientific reports 2021
  • “...protein 2142832 C>T >0.9 Rv1895 21425212143675 + Non-essential 384 Synonymous Possible dehydrogenase 3659433 G>A >0.9 Rv3276c (purK) 36586353659924 Non-essential 429 Synonymous Phosphoribosylaminoimidazole carboxylase ATPase subunit 4314130 T>C >0.9 IG3905 (Rv3840-Rv3841) 43139814314177 a Allele frequency in all secondary cases was>0.9. dnaA encodes a key protein for triggering...”
• Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study
  Sinha, BMC bioinformatics 2020
  • “...3.1.3.7 (3(2),5-biphosphate nucleotidase) Rv2131c 2.7.1.25 (Adenylyl-sulfate kinase) Rv1286 4.1.1.21(Phosphoribosylaminoimidazole carboxylase/purine metabolism) 6.3.4.18 (5-(carboxyamino)imidazole ribonucleotide synthase) Rv3276c 5.4.99.18 (5-(carboxyamino)imidazole ribonucleotide mutase Rv3275c 5.4.99.61(Precorrin isomerase/porphyrin and chlorophyll metabolism) 6.3.5.9 (Hydrogenobyrinic acid a,c-diamide synthase) Rv2847c 2.1.1.132 (Precorrin-6 methyltransferase) Rv2072c 6.2.1.28 (DHCA-CoA ligase) 1.2.1.3 (Aldehyde dehydrogenase (NAD(+)) Rv0458 2.3.1.16 (Acyl...”
• Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex
  Chiner-Oms, Science advances 2019
  • “...), Rv3910, Rv0166 ( fadD5 ), Rv0874c, Rv1152, Rv1678, Rv1951c, Rv2584c ( apt ), Rv3026c, Rv3276c ( purK ), Rv3370, Rv3759c ( proX ), and Rv3900c were under a stronger negative selective pressure following speciation. Many of them are annotated as hypothetical conserved proteins. On the...”
• Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region
  Weiner, PloS one 2012
  • “...helicase rhlE Rv3247c thymidylate kinase tmk Rv3263 DNA methylase Rv3275c phosphoribosylaminoimidazole carboxylase catalytic subunit purE Rv3276c phosphoribosylaminoimidazole carboxylase ATPase subunit purK Rv3297 endonuclease VIII nei Rv3307 purine nucleoside phosphorylase deoD Rv3309c uracil phosphoribosyltransferase upp Rv3313c adenosine deaminase add Rv3314c thymidine phosphorylase deoA Rv3315c cytidine deaminase cdd...”
• Identification and Quantification of S-Sulfenylation Proteome of Mycobacterium tuberculosis under Oxidative Stress
  Lu, Microbiology spectrum 2023
  • “...P9WHM7 , Rv0957 ) with increased SOH modification levels have strong interaction with PurK ( P9WHL9 , Rv3276c ), and IlvC ( P9WKJ7 , Rv3001c ) with decreased SOH modification levels. Interestingly, the modified long-chain fatty acyl-CoA thioesterase FcoT ( P9WM67 , Rv0098 ), which is...”

gbs0044 Unknown from Streptococcus agalactiae NEM316
35% identity, 93% coverage

• Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid
  Sitkiewicz, PloS one 2009
  • “...formyltransferase gbs0042 purD 36.4 30.0 Phosphoribosylamine-glycine ligase gbs0043 purE 49.0 47.5 Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit gbs0044 purK 34.9 27.2 Phosphoribosylaminoimidazole carboxylase NCAIR mutase subunit gbs0047 purB 3.0 3.6 Adenylosuccinate lyase gbs0106 - 12.0 CTP synthase (EC 6.3.4.2) gbs0553 pyrD 6.5 3.5 7.1 Dihydroorotate dehydrogenase (EC 1.3.3.1)...”

Q92210 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Candida albicans (see paper)
ADE2 phosphoribosylaminoimadazole carboxylase from Candida albicans (see 8 papers)
30% identity, 62% coverage

• CharProtDB CGD description: Phosphoribosylaminoimadazole carboxylase; enzyme of adenine biosynthesis; required for wild-type growth and virulence in immunosuppressed mouse systemic infection; not induced during GCN response, in contrast to S. cerevisiae ortholog

Saci_1191 phosphoribosylaminoimidazole carboxylase ATPase from Sulfolobus acidocaldarius DSM 639
34% identity, 95% coverage

• The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius
  Couturier, Frontiers in microbiology 2018
  • “...and transport ( 11 ) Saci_0798 * F: Nucleotide metabolism and transport ( 6 ) Saci_1191 INFORMATION STORAGE AND PROCESSING K: Transcription ( 2 ) Saci_0102; ( 3 ) Saci_0800; ( 14 ) Saci_0942; ( 16 ) Saci_1012; ( 5 ) Saci_1107; ( 8 ) Saci_1341;...”

Q49WI9 N5-carboxyaminoimidazole ribonucleotide synthase from Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)
31% identity, 89% coverage

• Staphylococcus saprophyticus Proteomic Analyses Elucidate Differences in the Protein Repertories among Clinical Strains Related to Virulence and Persistence
  Silva, Pathogens (Basel, Switzerland) 2020
  • “...Urease accessory protein UreG 0.416 0.936 1.352 0.464 0.038 0.003 De Novo Purine Biosynthetic Pathway Q49WI9 N5-carboxyaminoimidazole ribonucleotide synthase PurK 2.377 2.377 0.000 0.000 0.000 1.000 Q49WJ0 Phosphoribosylaminoimidazole-succinocarboxamide synthase PurC 2.184 2.184 0.000 0.000 0.000 1.000 Q49WJ1 Phosphoribosylformylglycinamidine synthase subunit PurS 1.035 1.035 0.000 0.000 0.000...”

SPy0034 phosphoribosylaminoimidazole carboxylase II from Streptococcus pyogenes M1 GAS
35% identity, 91% coverage

• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...15.56 9.89 11.31 Phosphoribosylamine-glycine ligase M28_Spy0030 SPy0033 purE 16.52 7.50 11.42 Phosphoribosylaminoimidazole carboxylase carboxyltransferase M28_Spy0031 SPy0034 purK 6.05 11.19 Phosphoribosylaminoimidazole carboxylase NCAIR mutase M28_Spy0064 SPy0074 adk 8.25 Adenylate kinase M28_Spy0134 SPy0160 purA 3.17 Adenylosuccinate synthetase M28_Spy0193 SPy0235 - 2.67 Deoxyuridine 5 -triphosphate nucleotidohydrolase M28_Spy0316 SPy0392 upp...”

Q6T7F1 phosphoribosylaminoimidazole carboxylase (Fragment) from Nicotiana tabacum
32% identity, 55% coverage

• Characterization of Proteins Involved in Chloroplast Targeting Disturbed by Rice Stripe Virus by Novel Protoplast⁻Chloroplast Proteomics
  Zhao, International journal of molecular sciences 2019
  • “...glucan phosphorylase GO:0005737; GO:0005980; GO:0008184; GO:0030170 K4BLP5 Uncharacterized protein E5LBC4 Prephenate aminotransferase GO:0008483; GO:0009058; GO:0030170 Q6T7F1 Phosphoribosylaminoimidazole carboxylase GO:0004638; GO:0005524; GO:0006189; GO:0046872 K4C5B9 Uroporphyrinogen decarboxylase GO:0004853; GO:0005829; GO:0006782; GO:0006783; GO:0009570; GO:0009735; GO:0009941 K4BJL2 Uncharacterized protein GO:0003735; GO:0005840; GO:0006412 K4CPX9 Uncharacterized protein GO:0000027; GO:0003735; GO:0005762; GO:0006412; GO:0019843...”

ADE2 / AAA96380.1 phosphoribosylaminoimidazole carboxylase from Schwanniomyces occidentalis (see paper)
29% identity, 63% coverage

Q9UVE6 phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) from Zygosaccharomyces rouxii (see paper)
30% identity, 61% coverage

Teth39_1803 phosphoribosylaminoimidazole carboxylase ATPase subunit from Thermoanaerobacter ethanolicus ATCC 33223
32% identity, 88% coverage

• A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E
  Clarkson, Biotechnology for biofuels 2014
  • “...0.018 Teth39_1323 2.46 DNA-directed RNA polymerase, omega subunit 0.005 Teth39_1713 2.12 Phosphoribosylformylglycinamidine synthase II 0.006 Teth39_1803 36.39 Phosphoribosylaminoimidazole carboxylase, ATPase subunit 0.000 Teth39_1828 2.76 Cytidine deaminase 0.009 Teth39_1832 2.14 ABC transporter related 0.004 Redox proteins Teth39_0646 3.61 FAD-dependent pyridine nucleotide disulfide oxidoreductase 0.005 Teth39_0720 3.77 4Fe-4S...”
  • “...of nucleotide-related genes were also upregulated, including two de novo purine biosynthesis genes (Teth39_1713 and Teth39_1803) and two genes involved in nucleoside degradation (Teth39_1828 and Teth39_1832). Additionally, Teth39_1216, predicted to be involved in isoprenoid biosynthesis, and Teth39_0175, predicted to function in cell wall turnover, are downregulated...”

PMM0683 phosphoribosylaminoimidazole carboxylase from Prochlorococcus marinus sp. MED4
31% identity, 85% coverage

• Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection
  Stazic, Nucleic acids research 2011
  • “...is organized as a polycistron extending into two upstream genes, ssrS (6S RNA, Yfr7) and PMM0683 ( purK ), and one downstream gene, yfr3 ( Figure 2 A and B). In total, the polycistronic region encompasses 3kb from nucleotide position 651 956654 987, as determined from...”

CLUG_04693 phosphoribosylaminoimidazole carboxylase from Clavispora lusitaniae
31% identity, 61% coverage

• Development of a CRISPR-Cas9 System for Efficient Genome Editing of Candida lusitaniae
  Norton, mSphere 2017
  • “...with different 20-bp protospacers were used to target sites within the C.lusitaniae ADE2 gene ( CLUG_04693 ). We targeted ADE2 since mutants lacking this gene develop a distinctive red-colony phenotype instead of the normal white phenotype, providing a visual readout of loss of function. To test...”

CPAR2_805940 uncharacterized protein from Candida parapsilosis
29% identity, 60% coverage

• A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets
  Viana, Genes 2022
  • “...URA4 CAD 3.5.2.3 CPAR2_405900 ERG24 TM7SF2 1.3.1.70 CPAR2_806200 IPP1 PPA2 3.6.1.1 ERG4 ERG4 - 1.3.1.71 CPAR2_805940 ADE2 PAICS 4.1.1.21 CPAR2_206550 TMP1 TYMS 2.1.1.45 URA3 URA3 UMPS 4.1.1.23 CPAR2_202250 ADE17 ATIC 2.1.2.3 CPAR2_109530 MVD1 MVD 4.1.1.33 CPAR2_203160 URA2 CAD 2.1.3.2 CPAR2_800750 CAB3 PPCDC 4.1.1.36 CPAR2_203160 URA2 CAD...”
• Identification and Characterization of a Neutral Locus for Knock-in Purposes in C. parapsilosis
  Nemeth, Frontiers in microbiology 2020
  • “...create pNRVL-L-GFP and pNRVL-S-GFP. The reintegration of ADE2 gene was carried out by amplifying the CPAR2_805940 ORF along with 1 kb upstream and 500 bp downstream regions with the primer pair CPAR2_805940RIXhoIF CPAR2_805940RIMluIR from C. parapsilosis CLIB214 genomic DNA. The amplicon was digested with Xho I/...”
  • “...the maximum LDH release (positive control) to determine cytotoxicity percentage. Deletion and Reintegration of ADE2 (CPAR2_805940) The CPAR2_805940 knock-out mutant was generated according to the double auxotrophy complementation method developed by Holland et al. (2014) . Briefly, C. maltosa LEU2 and C. dubliniensis HIS1 markers were...”

purK / CAA73603.1 purK from Saccharolobus solfataricus (see paper)
29% identity, 95% coverage

3k5hA / A1CII2 Crystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus clavatus complexed with atp (see paper)
30% identity, 86% coverage

• Ligands: adenosine-5'-triphosphate; magnesium ion (3k5hA)

A1CII2 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) from Aspergillus clavatus (see paper)
30% identity, 57% coverage

3ax6A / Q9WYS8 Crystal structure of n5-carboxyaminoimidazole ribonucleotide synthetase from thermotoga maritima
31% identity, 93% coverage

• Ligand: adenosine-5'-diphosphate (3ax6A)

AFUA_4G12600 phosphoribosyl-aminoimidazole carboxylase from Aspergillus fumigatus Af293
31% identity, 57% coverage

• Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach
  Kaltdorf, Frontiers in molecular biosciences 2016
  • “...synthase AFUA_4G12990 0.000 1.271 0.000 1416 Thioredoxin reductase AFUA_2G11290 0.452 0.573 0.000 Orotate phosphoribosyltransferase 1 AFUA_4G12600 0.000 0.294 2.812 Phosphoribosylaminoimidazole carboxylase AFUA_3G05650 0.000 0.474 1.158 17 Trehalose-phosphatase AFUA_7G01220 0.000 1.010 1.083 Squalene synthase AFUA_5G10680 0.000 0.203 0.000 Phosphomevalonate kinase AFUA_3G05730 0.000 0.024 0.000 Nicotinate mononucleotide pyrophosphorylase...”

CSP5_0498 5-(carboxyamino)imidazole ribonucleotide synthase from Cuniculiplasma divulgatum
30% identity, 96% coverage

• Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum
  Bargiela, Microorganisms 2020
  • “...Nucleotide transport and metabolism category-related proteins were nucleoside-triphosphatase THEP1 (CSP5_1184) and phosphoribosylaminoimidazole carboxylase (NCAIR synthetase; CSP5_0498). In the category Coenzyme transport and metabolism, GTP:adenosylcobinamide-phosphate guanylyltransferase (CSP5_1294), archaeal CTP-dependent riboflavin kinase (CSP5_1177) (Flavin biosynthesis II in archaea) and FMN-dependent dehydrogenase/L-lactate dehydrogenase/type II isopentenyl diphosphate isomerase (CSP5_0048) were...”

EF2362 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Enterococcus faecalis V583
OG1RF_11796 5-(carboxyamino)imidazole ribonucleotide synthase from Enterococcus faecalis OG1RF
27% identity, 89% coverage

• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...EF0225 EF0226 EF0970 EF1694 EF2395 EF2397 EF2473 EF2474 EF2679 EF2731 EF3070 EF0285 EF1714 EF1718 EF2362 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...”
• Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation
  Willett, mBio 2021
  • “...Group 2 glycosyl transferase 9.53E05 1.71 1 1803231 OG1RF_11722 Hypothetical protein 2.01E06 1.37 1 1893517 OG1RF_11796 Phosphoribosylaminoimidazole carboxylase ATPase subunit PurK 8.09E13 2.04 1 1894091 OG1RF_11796 Phosphoribosylaminoimidazole carboxylase ATPase subunit PurK 5.64E09 1.03 1 1894392 OG1RF_11796 Phosphoribosylaminoimidazole carboxylase ATPase subunit PurK 4.10E09 1.33 1 2099505 OG1RF_11987...”

AN3626 phosphoribosyl-aminoimidazole carboxylase (AFU_orthologue; AFUA_4G12600) from Emericella nidulans (see paper)
29% identity, 58% coverage

• CharProtDB Description: Putative phosphoribosylamino-imidazole-carboxylase with a predicted role in purine metabolism; Source:AspGD

VC1228 phosphoribosylglycinamide formyltransferase 2 from Vibrio cholerae O1 biovar eltor str. N16961
30% identity, 77% coverage

• Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR
  Beyhan, Journal of bacteriology 2007
  • “...VC1126 (purB, adenylosuccinate lyase), VC1228 (purT, phosphoribosylglycinamide formyltransferase II), VC2183 (prsA, ribose-phosphate pyrophosphokinase),...”

lp_1141 phosphoribosylaminoimidazole carboxylase, ATPase subunit from Lactobacillus plantarum WCFS1
28% identity, 74% coverage

• Selection and characterization of conditionally active promoters in Lactobacillus plantarum, using alanine racemase as a promoter probe
  Bron, Applied and environmental microbiology 2004
  • “...0.5 1.8 2.4 a b c ORF in insertc lp_1141 (purK2) lp_1320 lp_1101 (ldhl2) lp_2937 lp_1430 lp_2109 (urvC) lp_0464 lp_3392 lp_0525 (kupI) lp_3418 (pck) lp_1144...”

MMP0123 Phosphoribosylglycinamide formyltransferase 2 from Methanococcus maripaludis S2
26% identity, 87% coverage

• Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
  Hendrickson, Journal of bacteriology 2004
  • “...but it does have the alternative enzyme purT (Mmp0123) (74). As with certain other Archaea and Bacteria, M. maripaludis encodes a two-subunit...”

BPSL1111 phosphoribosylglycinamide formyltransferase 2 from Burkholderia pseudomallei K96243
29% identity, 71% coverage

• Identification of Burkholderia pseudomallei genes required for the intracellular life cycle and in vivo virulence
  Pilatz, Infection and immunity 2006
  • “...due to an intact purT homologue in B. pseudomallei (BPSL1111), which might also be capable of catalyzing the third step in the purine biosynthetic pathway, as...”

swp_4077 Phosphoribosylglycinamide formyltransferase 2 from Shewanella piezotolerans WP3
26% identity, 86% coverage

• Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
  Ding, Genetics research 2021
  • “...05 Pyruvate metabolism swp_1380, swp_5027, swp_4752, swp_4333, swp_3528, swp_2388, swp_2216, swp_2215, swp_2213, swp_2053, swp_1378, swp_1379, swp_4077, swp_0481, swp_0360 2 12 0.56 1.56 E 04 Ribosome swp_2008, swp_2030, swp_4802, swp_3049, swp_2027, swp_2028, swp_2025, swp_2007, swp_0208, swp_1998, swp_0427, swp_1556 3 9 0.64 2.84 E 04 Peptidoglycan biosynthesis swp_2592,...”

FTN_1745 phosphoribosylglycinamide formyltransferase 2 from Francisella tularensis subsp. novicida U112
27% identity, 77% coverage

• Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
  Akimana, Frontiers in microbiology 2011
  • “...kdpA FTN_1719 NAD-dependent formate dehydrogenase, fragment FTN_1733 Conserved hypothetical membrane, pseudogene FTN_1743 Chaperone ClpB clpB FTN_1745 Phosphoribosylglycinamide formyltransferase 2 purT FTN_1750 Acyltransferase FTN_1753 Oxidase-like protein, pseudogene FTN_1762 ABC transporter, ATP-binding protein yjjK FTN_1763 Major facilitator superfamily (MFS) transport protein FTN_1776 Anthranilate synthase component II, pseudogene trpG1...”
• Reciprocal analysis of Francisella novicida infections of a Drosophila melanogaster model reveal host-pathogen conflicts mediated by reactive oxygen and imd-regulated innate immune response
  Moule, PLoS pathogens 2010
  • “...x FTN_1715 FTT1736c two component sensor protein kdpD x FTN_1753 FTT1759c Oxidase-like protein, pseudogene x FTN_1745 FTT1767c phosphoribosylglycinamide formyltransferase 2 purT x FTN_1762 FTT1782c ABC transporter, ATP-binding protein yjjK x x Confirmation of negatively selected mutants To confirm the results of the TraSH screen, we tested...”
• Working toward the future: insights into Francisella tularensis pathogenesis and vaccine development
  Pechous, Microbiology and molecular biology reviews : MMBR 2009
  • “...FTN_1699 FTN_1700 FTN_1715 FTN_1726 FTN_1731 FTN_1743 FTN_1744 FTN_1745 FTN_1753 FTN_1756 FTN_1760 FTN_1778 Cells/animals in which mutant strain is attenuatedb...”

EAMY_2052 phosphoribosylglycinamide formyltransferase 2 from Erwinia amylovora CFBP1430
30% identity, 76% coverage

• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “...EAMY_2567 guaA , GMP synthase 1.66 9.06 EAMY_2859 guaC , GMP reductase 1.55 8.44 IMP EAMY_2052 purT , phosphoribosylglycinamide formyltransferase II 1.79 9.79 EAMY_2542 purM , phosphoribosylformylglycinamidine cyclo-ligase 1.74 10.49 EAMY_2610 purl , FGAM synthase 1.5 10.89 EAMY_2529 purC , SAICAR synthase 1.4 9.8 EAMY_0262 purH...”

Rmet_1820 formate-dependent phosphoribosylglycinamide formyltransferase from Cupriavidus metallidurans CH34
Rmet_1820 phosphoribosylglycinamide formyltransferase 2 from Ralstonia metallidurans CH34
28% identity, 88% coverage

• The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
  Janssen, PloS one 2010
  • “...and linkage between individual ones is blurred. These genes are folB (Rmet_0183), folD (Rmet_1192), purT (Rmet_1820), folP (Rmet_2187), folC (Rmet_2463), folA (Rmet_2569), purN (Rmet_2878), folK (Rmet_2915), trpG (Rmet_3179), and a putative folE (Rmet_3990). We failed to identify a hydrolase gene for converting 7,8-dihydroneopterin triphosphate into 7,8-dihydro-D-neopterin....”

BSU02230 phosphoribosylglycinamide formyltransferase 2 from Bacillus subtilis subsp. subtilis str. 168
25% identity, 89% coverage

• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...0.3885 79 yeaC BSU06330 0.893 15 243578 243734 forward BSU02170 ybfB -5370 0.363 236 purT BSU02230 0.89 16 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889 17 2376780 2376936 forward BSU22510 ypjC -15199 0.4395 16564 ypzI BSU22869 0.888 18 748205 748361 forward BSU06780...”
  • “...0.3885 79 yeaC BSU06330 0.893 8 243578 243734 forward BSU02170 ybfB -5370 0.363 236 purT BSU02230 0.89 9 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889 10 3421066 3421222 reverse BSU33340 sspJ -320 0.3312 79 lysP BSU33330 0.885 11 1493630 1493786 forward BSU14230...”

E8X9F0 phosphoribosylglycinamide formyltransferase 2 (EC 6.3.1.21) from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
27% identity, 76% coverage

GW13_PRO0295 formate-dependent phosphoribosylglycinamide formyltransferase from Salmonella enterica subsp. enterica serovar Cerro
27% identity, 76% coverage

• Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB
  He, Scientific reports 2015
  • “...motif is located in upstream regions, 200bp prior to the start codon, of eleven genesGW13_PRO0283, GW13_PRO0295, GW13_PRO0296, GW13_PRO0509, GW13_PRO0798, GW13_PRO2418, GW13_PRO2485, GW13_PRO2826, GW13_PRO3447, GW13_PRO3539 and GW13_PRO4223. Among them, only GW13_PRO3447, encoding DndB protein, harbors two 5-TACGN 10 CGTA-3 motifs in the promoter region. The other ten...”

B5XQ21 Formate-dependent phosphoribosylglycinamide formyltransferase from Klebsiella pneumoniae (strain 342)
28% identity, 76% coverage

• Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
  Yang, PloS one 2019
  • “...81 Exodeoxyribonuclease 7 small subunit xseB B5Y0W9 DNA processing Control 82 Formate-dependent phosphoribosylglycinamide formyltransferase purT B5XQ21 Purine metabolism Control 83 Fructose-6-phosphate aldolase fsa A6TGD7 Carbohydrate metabolism Control 84 Gamma-glutamyl phosphate reductase proA A6T561 Protein biosynthesis Control 85 Glucans biosynthesis protein D mdoD B5XWS2 Glycan metabolism Control...”

Entcl_1941 formate-dependent phosphoribosylglycinamide formyltransferase from [Enterobacter] lignolyticus SCF1
29% identity, 76% coverage

• Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
  Deangelis, Frontiers in microbiology 2013
  • “...ABC transporters 2.410 1.035 Entcl_3614 2-oxo-acid dehydrogenase E1 subunit, homodimeric type (complement(3877006..3879669)) Glycolysis/Gluconeogenesis 2.500 0.229 Entcl_1941 Phosphoribosylglycinamide formyltransferase 2 (complement(2053388..2054566)) Purine metabolism 2.080 0.779 Entcl_1559 Cytidine deaminase (complement(1657176..1658060)) Pyrimidine metabolism 3.710 1.169 Entcl_0641 Cys/Met metabolism pyridoxal-phosphate-dependent protein (complement(670311..671459)) None given 2.000 1.757 Entcl_3443 Taurine dioxygenase (complement(3672816..3673664))...”

Theam_1211 formate-dependent phosphoribosylglycinamide formyltransferase from Thermovibrio ammonificans HB-1
26% identity, 73% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...- - - - 70% WP_008287030 65% NP_214247 - phosphori bosylglycina mide formyl transferase 2 Theam_1211 P. marina sim. 76% YP_002731257 Methanogens /Deltaproteo bacteria 78% YP_004281335 64% WP_022847512 76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. -...”
  • “...Assuming low substrate specificity, other candidate enzymes with similar substrate requirements are the phosphoribosylglycinamide formyltransferase (Theam_1211) or phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (Theam_0328), which could catalyze the synthesis of formyl-THF, albeit with sub-optimal kinetics. While all four enzymes were detected in the proteomic analysis ( Figure 3 ),...”

purT / Q58881 phosphoribosylglycinamide formyltransferase monomer (EC 6.3.1.21) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see paper)
26% identity, 91% coverage

LSEI_1119 Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) from Lactobacillus casei ATCC 334
27% identity, 75% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...transport and metabolism LSEI_1557 LSEI_1118 LSEI_1119 LSEI_1120 LSEI_1286 LSEI_1746 LSEI_1747 LSEI_1748 LSEI_1749 LSEI_1750 LSEI_1751 LSEI_1752 LSEI_1753...”

WP_022847512 formate-dependent phosphoribosylglycinamide formyltransferase from Desulfurobacterium sp. TC5-1
25% identity, 85% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...formyl transferase 2 Theam_1211 P. marina sim. 76% YP_002731257 Methanogens /Deltaproteo bacteria 78% YP_004281335 64% WP_022847512 76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole carboxamide formyltransferase /IMP cyclohydrolase Theam_0328 P. marina...”

YP_RS08450 formate-dependent phosphoribosylglycinamide formyltransferase from Yersinia pestis biovar Microtus str. 91001
27% identity, 76% coverage

• Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities
  Xiao, Microorganisms 2023
  • “...C. Locus Tag * Log 2 FC p -Adjust Gene Name Gene Description Pathway Name YP_RS08450 3.92 5.23 10 120 purT formate-dependent phosphoribosylglycinamide formyltransferase Purine metabolism YP_RS04375 3.12 4.25 10 46 purE 5-(carboxyamino)imidazole ribonucleotide mutase YP_RS04370 3.01 2.65 10 52 purK 5-(carboxyamino)imidazole ribonucleotide synthase YP_RS16125 2.30...”
  • “...37 C. Locus Tag * Log 2 FC p -Adjust Gene Name Gene Description KEGG YP_RS08450 4.18 1.68 10 95 purT formate-dependent phosphoribosylglycinamide formyltransferase Purine metabolism YP_RS04375 3.76 4.12 10 46 purE 5-(carboxyamino)imidazole ribonucleotide mutase YP_RS04370 3.60 5.14 10 64 purK 5-(carboxyamino)imidazole ribonucleotide synthase YP_RS16125 2.97...”

Avin_39610 Phosphoribosylglycinamide formyltransferase from Azotobacter vinelandii AvOP
27% identity, 90% coverage

• The Azotobacter vinelandii AlgU regulon during vegetative growth and encysting conditions: A proteomic approach
  Chowdhury-Paul, PloS one 2023
  • “...septum site-determining protein MinD minD 0.1 Avin_35120 Motif GAACTGgggcgaggccgtgcacaTCcaC 0.81 13 Phosphoribosylglycinamide formyltransferase purT 0.3 Avin_39610 Motif GGACGTacgcatgttgaaggaaaTCcc 0.81 14 Fe-S protein assembly chaperone HscA hscA 0 Avin_40360 TU hit GAGCTTttatggcccgctccgg.TCgaA 0.81 15 Transport-associated protein 0 Avin_43670 Motif GAACTTaccaagtcccgagggagTCcaT 0.9 16 Quinone NAD(PH:oxidoreductase MdaB mdaB 0...”

BCAL2415 phosphoribosylglycinamide formyltransferase 2 from Burkholderia cenocepacia J2315
27% identity, 71% coverage

• DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility
  Vandenbussche, mSphere 2020
  • “...of both strain backgrounds: BCAL1515, BCAL2465, and BCAM0820 were upregulated in BCAL3494, whereas genes BCAL0079, BCAL2415, and BCAM1362 were upregulated in BCAM0992. Four additional genes were upregulated in K56-2 mutants only: BCAL0423, BCAM2738, and BCAS0223 were upregulated in BCAL3494, and BCAL1556 was upregulated in BCAM0992. Subsequently,...”
  • “...0.171 1.690 0.006 RpiA ribose-5-phosphate isomerase A BCAL2406 1.693 0.273 1.009 0.938 WabR putative glycosyltransferase BCAL2415 2.819 0.006 6.029 0.001 PurT phosphoribosylglycinamide formyltransferase 2 BCAL2701 0.613 0.076 1.519 0.170 A r gD acetylornithine transaminase protein BCAL2942 1.143 0.474 1.451 0.274 CysM cysteine synthase B BCAM0076 1.630...”

PA3751 5'-phosphoribosylglycinamide transformylase from Pseudomonas aeruginosa PAO1
27% identity, 86% coverage

• Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
  Yung, NPJ biofilms and microbiomes 2019
  • “...carboxykinase NR NR NR NR PhhA PA0872 Phenylalanine 4-monooxygenase NR NR NR NR NR PurT PA3751 Phosphoribosylglycinamide formyltransferase NR NR o NR NR RplL PA4271 50S ribosomal protein L7/L12 NR NR NR NR o RplM PA4433 50S ribosomal protein L13 NR NR NR NR RplT PA2741...”
• Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms
  Amini, PLoS pathogens 2011
  • “...SAH127 (PA1723, pscJ ), SAH128 (PA3222), SAH129 (PA3966), SAH130 (PA5207), SAH318 (PA1946, rbsB ), SAH320 (PA3751, purT ), and SAH328 (PA4175). NPN (final concentration of 50 M) and tobramycin (final concentration of 8 g/ml) were added after 60 and 180 seconds, respectively. Error bars show the...”

Gmet_3193 Phosphoribosylglycinamide formyltransferase 2 from Geobacter metallireducens GS-15
28% identity, 76% coverage

• The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens
  Aklujkar, BMC microbiology 2009
  • “...sulfurreducens has evidently lost the purT gene product of G. metallireducens and several other Geobacteraceae (Gmet_3193, 58% identical to the E. coli enzyme [ 73 ]), which incorporates formate directly into purine nucleotides instead of using the folate-dependent purN gene product (Gmet_1845 = GSU1759, 46% identical...”

ECs2559 phosphoribosylglycinamide formyltransferase 2 from Escherichia coli O157:H7 str. Sakai
26% identity, 76% coverage

• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...1.03 2.13 0.90 Purines, pyrimidines, and nucleotides ECs1476 ECs2559 ECs3117 ECs4947 ECs5191 tmk purT nrdA O157 cpdB 1.52 1.02 1.37 1.17 0.76 Regulatory...”

S1925 phosphoribosylglycinamide formyltransferase 2 from Shigella flexneri 2a str. 2457T
26% identity, 76% coverage

• Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella
  Gao, Microorganisms 2022
  • “...Kottbus 216 UofLaval6 S494 Lockleaze 192 UofLaval22 S238 Mbandaka 201 UofLaval13 S1395 Mississippi 207 UofLaval2 S1925 Muenchen 218 UofLaval15 S206 Muenchen 215 UofLaval27 S317 Ohio 203 UofLaval28 S307 Poona 197 UofLaval21 S212 Stanley 223 UofLaval18 S761 Stanleyville 218 UofLaval26 S193 Thompson 210 UofLaval34 S164 Typhimurium 226...”

YP_001931730 phosphoribosylglycinamide formyltransferase 2 from Sulfurihydrogenibium sp. YO3AOP1
25% identity, 73% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...P. marina sim. 76% YP_002731257 Methanogens /Deltaproteo bacteria 78% YP_004281335 64% WP_022847512 76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole carboxamide formyltransferase /IMP cyclohydrolase Theam_0328 P. marina sim. 59% YP_002731268 Aquificae...”

PP1457 phosphoribosylglycinamide formyltransferase 2 from Pseudomonas putida KT2440
27% identity, 76% coverage

• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

PurT / b1849 phosphoribosylglycinamide formyltransferase 2 (EC 2.7.2.15; EC 2.7.2.1) from Escherichia coli K-12 substr. MG1655 (see 10 papers)
purT / P33221 phosphoribosylglycinamide formyltransferase 2 (EC 6.3.1.21; EC 2.7.2.15) from Escherichia coli (strain K12) (see 8 papers)
PURT_ECOLI / P33221 Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; GAR transformylase T; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 6.3.1.21 from Escherichia coli (strain K12) (see 6 papers)
P33221 phosphoribosylglycinamide formyltransferase 2 (EC 6.3.1.21) from Escherichia coli (see 5 papers)
NP_416363 phosphoribosylglycinamide formyltransferase 2 from Escherichia coli str. K-12 substr. MG1655
b1849 phosphoribosylglycinamide formyltransferase 2 from Escherichia coli str. K-12 substr. MG1655
26% identity, 76% coverage

• function: Involved in the de novo purine biosynthesis (PubMed:8117714, PubMed:8501063, PubMed:9184151). Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N- formylglycinamide (FGAR) (PubMed:8117714, PubMed:8501063, PubMed:9184151). Formate is provided by PurU via hydrolysis of 10- formyl-tetrahydrofolate (PubMed:8226647). PurT is also able to cleave acetyl phosphate and carbamoyl phosphate to produce ATP with acetate and carbamate, respectively (PubMed:8117714, PubMed:9184151).
  catalytic activity: N(1)-(5-phospho-beta-D-ribosyl)glycinamide + formate + ATP = N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + ADP + phosphate + H(+) (RHEA:24829)
  catalytic activity: acetate + ATP = acetyl phosphate + ADP (RHEA:11352)
  catalytic activity: carbamate + ATP = carbamoyl phosphate + ADP (RHEA:30755)
  subunit: Homodimer.
  disruption phenotype: Mutant defective in both purN and purT requires an exogenous purine source for growth.
• Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea
  Dörnte, Fungal biology and biotechnology 2020
  • “...(GART) PurN, P08179 Ade8, NP_010696 CC1G_04353T0, potentially Ade4 Chr_1:715,850716,603 [Bacterial alternative: formate-dependent phosphoribosylglycinamide formyltransferase] PurT, NP_416363 FGAR to FGAM Phosphoribosylformylglycinamidine synthase (FGAMS) PurL, THH53207 Ade6, NP_011575 CC1G_11804T0, potentially Ade4 Chr_6:3,409,0973,413,188 FGAM to AIR Aminoimidazole ribonucleotide synthase (AIRS) PurM, THH44093 C-terminal domain of bifunctional Ade5,7, NP_011280 CC1G_01782T0,...”
• Simultaneous presence of fhs and purT genes is disadvantageous for the fitness of Escherichia coli growth.
  Aluri, FEMS microbiology letters 2015 (PubMed)
  • GeneRIF: Studies revealed that a simultaneous presence of both the genes fhs and purT confers growth disadvantage compared to when present in single
• Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli.
  Marolewski, Biochemistry 1994 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• Divergence of function in sequence-related groups of Escherichia coli proteins
  Nahum, Genome research 2001
  • “...activating enzyme purK purT b0522 b1849 P09029 P33221 CO2 subunit of phosphoribosylaminoimidazole carboxylase GAR transformylase 2 355 391 guaB guaC b2508...”
• FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
  Hassani, Microbial cell factories 2024
  • “...PFK 1.28 33.69 b0825, b3946, b3916, b1723 Triple ACKr, GLCpts, PYK 0.56 54.88 b2296, b3115, b1849, b1819, b2415, b2416, b1621, b1101, b2417, b1817, b1818, b1854, b1676 DHAPT, GART, PPAKr Quadruple ACKr, ARGDC, GLCpts, PYK 0.56 64.72 b2296, b3115, b1849, b2938, b4117, b1819, b2415, b2416, b1621, b1101,...”
• Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
  Hamilton, Biophysical journal 2013
  • “...Lethal Lethal Lethal Lethal Worse in TMFA b1849 purT Nonlethal Nonlethal Lethal Lethal Nonlethal Nonlethal b2500 purN Nonlethal Nonlethal Lethal Lethal...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
  Orth, BMC systems biology 2012
  • “...predictions caused by missing isozymes or alternate pathways Gene Putative Isozyme E-value purK (b0522) purT (b1849) 2.00E-12 gltA (b0720) prpC (b0333) 1.00E-41 aspC (b0928) tyrB (b4054) 4.00E-94 fabH (b1091) none identified pabC (b1096) ilvE (b3770) 7.00E-8 icd (b1136) dmlA (b1800) 3.00E-19 aldA (b1415) gabD (b2661) 1.00E-90...”
• Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli
  Aggarwal, Journal of bacteriology 2011
  • “...purT purK purE purR purC purN purH cmk b2499 b2312 b2557 b1849 b0522 b0523 b1658 b2476 b2500 b4006 b0910 3.1 (0.5) 4.1 (0.4) 3.1 (0.7) 3.0 (1.5) 2.2 (0.8) 2.2...”
• Genome-scale gene/reaction essentiality and synthetic lethality analysis
  Suthers, Molecular systems biology 2009
  • “...a single member (i.e. k =1). For example, by maintaining only the activity of purT (b1849) in cluster K or the activity of either purU (b1232) or purN (b2500) in cluster L, we can prevent lethality. Unlike clusters K and L, cluster M has fourteen alternative...”
  • “...Arginine aroL (b0388), aroK (b3390) Disjoint pair Lobner-Olesen et al (1992) Aromatic amino acids purT (b1849), purN (b2500) Cluster A Nygaard and Smith (1993) Purine SLs with indirect evidence ubiX (b2311), ubiD (b3843) Disjoint pair Meganathan (2001) and Gulmezian et al (2001) metC (b3008), malY (b1622)...”
• A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli
  Ernst, PLoS computational biology 2008
  • “...araF 1 Fur b1452, yncE 1 Yes Evidence from microarray expression of mutant [65] PurR b1849, purT 1 Yes LacZ reporter with mutant evidence [66] CysB b2762, cysH 1 1 Confirmed with direct binding evidence in Salmonella typhimurium [67] PhoB b4068, yjcH 1 NagC b2677, proV...”
• Divergence of function in sequence-related groups of Escherichia coli proteins
  Nahum, Genome research 2001
  • “...ligase apo-serine activating enzyme purK purT b0522 b1849 P09029 P33221 CO2 subunit of phosphoribosylaminoimidazole carboxylase GAR transformylase 2 355 391...”

alr1299 phosphoribosylglycinamide formyltransferase 2 from Nostoc sp. PCC 7120
25% identity, 83% coverage

• Current Understanding of the Structure and Function of Pentapeptide Repeat Proteins
  Zhang, Biomolecules 2021
  • “...linked to thylakoid biogenesis and membrane synthesis. Alr1297 was annotated as an ABC transport system. Alr1299 was predicted to be involved in purine metabolism, metabolic pathways and biosynthesis of secondary metabolites. The other genes were unannotated. Given the proximity of the alr1298 gene to an annotated...”
• The First Proteomics Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation
  Koksharova, Toxins 2020
  • “...6 EC:2.7.4.6 nucleoside diphosphate kinase alr3402 transferring phosphorus-containing groups 0.75 0.004 7 EC:2.1.2.2 phosphoribosylglycinamide formyltransferase-2 alr1299 purine metabolism 2.14 0.05 8 EC:2.1.2.3 3.5.4.10 | purH; bifunctional purine biosynthesis protein all3093 purine metabolism 0.71 0.08 9 EC:1.1.1.205 inosine 5-monophosphate dehydrogenase alr0051 purine metabolism 1.75 0.00013 Secondary metabolites...”
• The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box
  Oliveira, Life (Basel, Switzerland) 2015
  • “...NH 4 + Energy metabolism Anabaena Alr1080 Acetylornithine aminotransferase N 2 Amino acid biosynthesis - Alr1299 Phosphoribosylglycinamide formyltransferase 2 N 2 Purines, pyrimidines, nucleosides, and nucleotides - Alr1310 Alr1310 protein NH 4 + Conserved hypothetical protein - Alr1313 3-isopropylmalate dehydrogenase NH 4 + Amino acid biosynthesis...”
  • “...including nucleic acids, along with interconversion and salvage of nucleosides (All3791, Alr0069, Alr7261, Alr3402, Alr0051, Alr1299, Alr1520), degradation of proteins and peptides, as well as processes regarding amino acid biosynthesis and processing (All2533, Alr0237, Alr0880, Alr0996, Alr1381, All4287, Alr1742, Alr4853, All2315, Alr1004, Alr1313, Alr2771, Alr0608, Alr1080,...”

1eyzA / P33221 Structure of escherichia coli purt-encoded glycinamide ribonucleotide transformylase complexed with mg and amppnp (see paper)
26% identity, 77% coverage

• Ligands: magnesium ion; phosphoaminophosphonic acid-adenylate ester (1eyzA)

YP_002731257 phosphoribosylglycinamide formyltransferase 2 from Persephonella marina EX-H1
25% identity, 73% coverage

• Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
  Giovannelli, eLife 2017
  • “...WP_008287030 65% NP_214247 - phosphori bosylglycina mide formyl transferase 2 Theam_1211 P. marina sim. 76% YP_002731257 Methanogens /Deltaproteo bacteria 78% YP_004281335 64% WP_022847512 76% YP_002731257 73% YP_001931730 f.e. - 28% YP_003433072 67% YP_007499479 74% WP_008288476 f.e. - 25% YP_003473050 f.e. - 30% NP_213168 phosphori bosylaminoi midazole...”

PF0430 phosphoribosylglycinamide formyltransferase 2 from Pyrococcus furiosus DSM 3638
28% identity, 67% coverage

• Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus
  Khatibi, Biotechnology and bioengineering 2017
  • “...--- 13 12 PF0426 phosphoribosylaminoimidazole carboxylase --- 7 8 PF0427 phosphoribosylaminoimidazole carboxylase 2 4 8 PF0430 phosphoribosylglycinamide formyltransferase 2 36 16 PF1516 GMP synthase --- 10 6 Unclassified PF0449 glutamine metabolism 10 --- 10 CONTINUOUS (D4) VS. BATCH (0.45 hr 1 ) CONTRASTS D4 vs. E...”

TK0207 formate-dependent phosphoribosylglycinamide formyltransferase from Thermococcus kodakaraensis KOD1
29% identity, 67% coverage

• Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis
  Sanders, Frontiers in microbiology 2021
  • “...7.20 TK1391 Molybdopterin oxidoreductase, 4Fe-4S cluster-binding subunit Central metabolsim 6.81 TK1023 Hypothetical protein Unknown 6.64 TK0207 Format-dependent hosphoribosylglycinamide formyltransferase Purine metabolism 6.42 TK1960 Replication factor A complex, RPA14 subunit Replication/recombi nation/repair 6.42 TK0201 Phosphoribosy lformylglycinamidine synthase I Purine metabolism 6.26 TK1464 Hypothetical protein Unknown 6.05 TK0599...”
• An archaeal histone is required for transformation of Thermococcus kodakarensis
  Čuboňováa, Journal of bacteriology 2012
  • “...TK0203 TK0204 TK0190 TK0191 TK0192 TK0193 TK0194 TK0835 TK0207 TK0603 TK0604 TK1090 TK0561 TK1352 TK1583 TK0418 TK1287 TK0260 TK1895 TK0084 TK0612 TK1923 TK2180...”

Saci_0214 phosphoribosylglycinamide formyltransferase 2 from Sulfolobus acidocaldarius DSM 639
25% identity, 57% coverage

• Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A
  Huang, Frontiers in microbiology 2020
  • “...purC/Saci_1607, purS / Saci_1608 , and purL/Saci_1610 ) and a putative purine transporter gene ( Saci_0214 ) were transcriptionally down-regulated in response to UV in S. acidocaldarius ( Hoffmann et al., 2017 ; Schult et al., 2018 ). These changes suggested that nucleotide synthesis and uptake...”
  • “...this, the transcripts of the gene cluster ( Saci_1607-Saci_1613 ) and the uptake gene ( Saci_0214 ) have been shown to be higher in S-phase, where a large number of DNA replication events occur ( Lundgren and Bernander, 2007 ). Our results suggest that purine biosynthesis...”
• Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response
  Schult, Nucleic acids research 2018
  • “...with the archaellum regulatory network ( 68 ). Several genes involved in purine biosynthesis (e.g. Saci_0214, formate-dependent phosphoribosylglycinamide formyl-transferase ( purT )); Saci_1607, purC , phosphoribosylaminoimidazolesuccinocarboxamide synthase and Saci_1608 and Saci_1610, which encode the PurS and the PurL domains of the phosphoribosylformylglycinamidine synthase complex) were also...”
  • “...the amount of transcripts of the pyrimidine synthesis gene cluster (Saci_1607-Saci_1613) and the uptake system (Saci_0214) have been shown to be coordinately increased in the chromosome replication stage of the cell cycle (S-phase), where high amounts of DNA building blocks are required ( 29 ). Our...”

2dwcB / O58056 Crystal structure of probable phosphoribosylglycinamide formyl transferase from pyrococcus horikoshii ot3 complexed with adp
28% identity, 70% coverage

• Ligand: adenosine-5'-diphosphate (2dwcB)

CV_4341 D-alanine--D-alanine ligase from Chromobacterium violaceum ATCC 12472
35% identity, 20% coverage

• Guava leaf extract inhibits quorum-sensing and Chromobacterium violaceum induced lysis of human hepatoma cells: whole transcriptome analysis reveals differential gene expression
  Ghosh, PloS one 2014
  • “...protein 61.92 7.3 3.08 9.58E-005 CV_4340 ftsQ cell division transmembrane protein 41.07 1.13 5.19 0 CV_4341 ddlB D-alanine-D-alanine ligase, Peptidoglycan biosynthesis 41.07 1.13 5.19 0 CV_4344 ftsW cell division protein 25.93 3.05 3.09 0 CV_4345 murD Peptidoglycan biosynthesis 25.93 3.05 3.09 0 CV_4346 mraY Peptidoglycan biosynthesis...”

MAP3871 PurT from Mycobacterium avium subsp. paratuberculosis str. k10
25% identity, 68% coverage

• Iron Acquisition in Mycobacterium avium subsp. paratuberculosis
  Wang, Journal of bacteriology 2015
  • “...14 MAP3770 Cobalamin synthesis protein MAP3775c ABC transporter, ATP-binding protein 15 MAP3834 Sugar transport protein MAP3871 Phosphoribosylglycinamide formyltransferase 2 MAP3883c Beta-lactamase MAP3884 F420-dependent glucose-6-phosphate dehydrogenase MAP4076 Glycosylhydrolase family protein a Genes identified to be enriched (5 median) in the presence of mycobactin J in two independent...”

A9HEX0 Biotin carboxylase from Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5)
25% identity, 50% coverage

• Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
  Dos, PeerJ 2020
  • “...insertional mutants of G. diazotrophicus PAl5, defective in production of the proteins EttA (A9H4G2), AccC (A9HEX0), and Zwf (A9H326) were obtained from the G. diazotrophicus PAl5 mutant library of the Laboratrio de BiotecnologiaUENF ( Intorne et al., 2009 ). Such a mutant library was obtained by...”
  • “...4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) ispG 6.00 1,571.93 3.00 A9GZU8 Conserved protein GDI0061 7.00 1,962.62 3.04 A9HEX0 acetyl-CoA carboxylase biotin carboxylase subunit accC 13.00 4,423.06 3.52 A9HS02 Elongation factor G fusA 31.00 10,183.21 3.93 A9H932 TonB-dependent receptor GDI0667 14.00 2,074.37 4.10 ILVC Ketol-acid reductoisomerase (NADP(+)) ilvC 5.00...”

RLV_1849 acetyl-CoA carboxylase biotin carboxylase subunit family protein from Rhizobium leguminosarum bv. viciae
27% identity, 42% coverage

• Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells
  Durán, Molecular & cellular proteomics : MCP 2021
  • “...0 RLV_1846 pRlvC D-alanine-- ligase 3.77 111 42 RLV_1848 pRlvC Glutamyl-tRNA reductase 2.88 128 64 RLV_1849 pRlvC putative urea amidolyase 2.66 76 35 RLV_1887 pRlvC putative glutamate dehydrogenase 2.35 81 56 RLV_1889 pRlvC TlpA like family protein 2.12 44 13 RLV_1961 pRlvC Uptake hydrogenase large subunit...”

PG0530 carbamoyl-phosphate synthase, large subunit from Porphyromonas gingivalis W83
26% identity, 21% coverage

• Arginine deiminase inhibits Porphyromonas gingivalis surface attachment
  Cugini, Microbiology (Reading, England) 2013
  • “...carbamoyl-phosphate synthase small and large subunits (PG0529 and PG0530, respectively) (Lewis et al., 2009; Nelson et al., 2003; Xu et al., 2007)....”

New Search

Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.