PaperBLAST
PaperBLAST Hits for sp|P42807|HEM1_PSEAE Glutamyl-tRNA reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=hemA PE=3 SV=3 (422 a.a., MAFIALGINH...)
Show query sequence
>sp|P42807|HEM1_PSEAE Glutamyl-tRNA reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=hemA PE=3 SV=3
MAFIALGINHKTASVAVRERVAFTPEQMVEALQQLCRLTTSREAAILSTCNRSELYLEID
HPTADDVLAWLADYHRLTLDELRACAYVHQDEDAVRHMMRVASGLDSMVLGEPQILGQMK
SAYAVAREAGTVGPLLGRLFQATFSTAKTVRTDTAIGENPVSVAFAAVSLAKQIFSDLHR
SQALLIGAGETITLVARHLFEQGVKRIVVANRTLERASLLAEQFGAHAVLLSEIPEELAN
SDIVISSTASQLPILGKGAVERALKQRKHKPMFMVDIAVPRDIEPEVGELDDVYLYSVDD
LHEVVAENLKSRQGAAQAAEELVGSGVAEFMQRLRELAAVDVLRAYRQQAERLRDEELGK
AQRQLANGADPAEVMAQLARGLTNKLLHAPSVQMKKMSAEGRIDALALAQELFALDEGAP
RH
Running BLASTp...
Found 100 similar proteins in the literature:
PA4666 glutamyl-tRNA reductase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
Glanville, mSystems 2021 - “...35 Synthesis (of HemB) gltX PA3134 Glutamyl-tRNA synthetase 151 hemA ALA synthase NA 1 hemA PA4666 Glu-tRNA reductase 152 hemL1 PA3977 Glutamate-1-semialdehyde 2,1-aminomutase 1 hemL2 PA4088 Glutamate-1-semialdehyde 2,1-aminomutase 1 hemL3 PA5523 Glutamate-1-semialdehyde 2,1-aminomutase 2, 1 c 1 hemB PA5243 PBG synthase 1 hemC PA5260 HMB synthase...”
- A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
Xu, PloS one 2013 - “...cysD ), PA4450( murA ),PA4457( KdsD ),PA4524( nadC ),PA4529( coaE ), PA4561( ribF ),PA4655( hemH ),PA4666( hemA ),PA4670( prs ), PA4729( panB ),PA4730( panC ),PA4749( glmM ),PA4750( folP ), PA4759( dapB ),PA4847( accB ),PA4848( accC ),PA4854( purH ), PA4920( nadE ),PA4938( purA ),PA4988( waaA ),PA4996( rfaE...”
- A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence
Storbeck, Archaea (Vancouver, B.C.) 2010 - “...MG1655 B1210 0154 0369 3805 3804 3368 3368 + + 60 61 Pseudomonas aeruginosa PAO1 PA4666 3977 5243 5260 5259 0510 f 2611 0515 f 0512 f 0511 f + + + + 61 62 Desulfovibrio vulgaris Hildenborough DVU1461 3168 0856 1890 0734 0734 1463 0854...”
PP0732 glutamyl-tRNA reductase from Pseudomonas putida KT2440
87% identity, 99% coverage
VC2180 glutamyl-tRNA reductase from Vibrio cholerae O1 biovar eltor str. N16961
53% identity, 99% coverage
VF_0767 glutamyl-tRNA reductase from Vibrio fischeri ES114
52% identity, 99% coverage
SO_3834 glutamyl-tRNA reductase from Shewanella oneidensis MR-1
53% identity, 99% coverage
- Investigation of a spontaneous mutant reveals novel features of iron uptake in Shewanella oneidensis
Dong, Scientific reports 2017 - “...glutamyl-tRNA to protoporphyrin IX 39 . Genes in heme synthesis are conditionally inducible include hemA (SO_3834), hemL (SO_1300), hemB (SO_2587), hemN (SO_4730), hemF (SO_0038), and hemH (SO_2019) 38 , 40 , 41 . To explore which steps are affected in putA WC cells, we monitored abundance...”
- Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation
Barchinger, Applied and environmental microbiology 2016 - “...Heme biosynthesis SO_0027 SO_0038 SO_1300 SO_2019 SO_2587 SO_3720 SO_3834 SO_4208 SO_4314 SO_4730 SO_4613 SO_4614 hemG hemE hemL hemH hemB hemG hemA hemB hemD...”
- Reduced heme levels underlie the exponential growth defect of the Shewanella oneidensis hfq mutant
Brennan, PloS one 2014 - “...then ligated to Bam HI and Xho I-restricted pBBR1-MCS2. To construct plasmid vectors expressing gtrA (So_3834) alone, hemL (So_1300) alone, or both gtrA and hemL from S. oneidensis under control of an arabinose-inducible promoter, the appropriate open reading frame(s) was/were PCR amplified and cloned into pBBAD-SP....”
CBU_1966 glutamyl-tRNA reductase from Coxiella burnetii RSA 493
51% identity, 98% coverage
c1668 glutamyl-tRNA reductase from Escherichia coli CFT073
51% identity, 99% coverage
EC958_1478 glutamyl-tRNA reductase from Escherichia coli O25b:H4-ST131
51% identity, 99% coverage
Q3Z0S8 Glutamyl-tRNA reductase from Shigella sonnei (strain Ss046)
51% identity, 99% coverage
- Proteome based mapping and molecular docking revealed DnaA as a potential drug target against Shigella sonnei
Shahid, Saudi journal of biological sciences 2022 - “...acid metabolism Metabolic pathways Biotin metabolism Biosynthesis of secondary metabolites Biosynthesis of antibiotics Glutamyl-tRNA reductase (Q3Z0S8) ssn00860 ssn01100 ssn01110 ssn01120 Porphyrin and chlorophyll metabolism Metabolic pathways Biosynthesis of secondary metabolites Microbial metabolism in diverse environments Glutamate--tRNA ligase (Q3YZD6) ssn00860 ssn00970 ssn01100 ssn01110 ssn01120 Porphyrin and chlorophyll...”
GtrA / b1210 glutamyl-tRNA reductase (EC 1.2.1.70) from Escherichia coli K-12 substr. MG1655 (see 11 papers)
hemA / P0A6X1 glutamyl-tRNA reductase (EC 1.2.1.70) from Escherichia coli (strain K12) (see 8 papers)
HEM1_ECOLI / P0A6X1 Glutamyl-tRNA reductase; GluTR; EC 1.2.1.70 from Escherichia coli (strain K12) (see 3 papers)
P0A6X1 glutamyl-tRNA reductase (EC 1.2.1.70) from Escherichia coli (see paper)
hemA / MB|P0A6X1 glutamyl-tRNA reductase; EC 1.2.1.70 from Escherichia coli K12 (see 12 papers)
NP_415728 glutamyl-tRNA reductase from Escherichia coli str. K-12 substr. MG1655
b1210 glutamyl-tRNA reductase from Escherichia coli str. K-12 substr. MG1655
ECs1715 glutamyl-tRNA reductase from Escherichia coli O157:H7 str. Sakai
51% identity, 99% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). In the absence of NADPH, exhibits substrate esterase activity, leading to the release of glutamate from tRNA.
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Homodimer. Interacts with glutamate-1-semialdehyde 2,1- aminomutase (GSA-AM), which forms a metabolic channeling between both enzymes to protect the reactive aldehyde species GSA. - A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli.
Hubbard, Microbiology (Reading, England) 2021 (PubMed)- GeneRIF: A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli.
- Complex formation between glutamyl-tRNA reductase and glutamate-1-semialdehyde 2,1-aminomutase in Escherichia coli during the initial reactions of porphyrin biosynthesis.
Lüer, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: analysis of glutamyl-tRNA reductase and glutamate-1-semialdehyde 2,1-aminomutase complex formation in Escherichia coli during the initial reactions of porphyrin biosynthesis
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...b1861 ECs3536 ECs4256 b2673 b3414 ECs1715 ECs3045 ECs0502 b1210 b2153 b0448 ECs4194 ECs3393 ECs3306 ECs4898 ECs1752 b2435 b3967 b1252 b3343 b2527 ECs1853...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0420, b0421, b0423 b3774 b0954 b0915 b3359 b0475, b0750, b0907 b1093 b0918 b3433 b1096, b1208, b1210 b1094 b1094 b3809 b1277, b1662, b1740 b1288 b1215 s0001 b1812, b2103, b2153 b2323 b3198 b2315, b2320, b2400 b3176 b3633 b2515, b2530, b2564 b3189 b2574, b2615, b2746 b3729 b2747, b2763, b2764...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...and biogenesis ECs2571 b1861 ECs3536 ECs4256 b2673 b3414 ECs1715 ECs3045 ECs0502 b1210 b2153 b0448 ECs4194 ECs3393 ECs3306 ECs4898 ECs1752 b2435 b3967 b1252...”
NP_460733 glutamyl tRNA reductase from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
51% identity, 99% coverage
A7MKC0 Glutamyl-tRNA reductase from Cronobacter sakazakii (strain ATCC BAA-894)
51% identity, 95% coverage
BB0383 glutamyl-tRNA reductase from Bordetella bronchiseptica RB50
51% identity, 97% coverage
- Multifunctional and Redundant Roles of Borrelia burgdorferi Outer Surface Proteins in Tissue Adhesion, Colonization, and Complement Evasion
Caine, Frontiers in immunology 2016 - “...mammalian infection Lmp1 bb0210 Chondroitin-6-sulfate ( 53 ) Not determined ( 53 55 ) BmpA bb0383 Laminin ( 56 ) Joint persistence ( 57 ) BmpC bb0384 Not determined Not determined ( 49 ) Bgp bb0588 Heparin, dermatan sulfate, GAGs, and aggrecan ( 58 60 )...”
- Diversity of antibody responses to Borrelia burgdorferi in experimentally infected beagle dogs
Baum, Clinical and vaccine immunology : CVI 2014 - “...The second array also contained purified BB0279, BB0283, BB0383 (P39 or BmpA), BB0774 (P83 antigen), BBA25, BBK07, BBK12, and BBK19, full-length VlsE of strain...”
- The HtrA protease of Borrelia burgdorferi degrades outer membrane protein BmpD and chemotaxis phosphatase CheX
Coleman, Molecular microbiology 2013 - “...proteolytic substrates (Meltzer et al ., 2009 ). BmpD (BB0385) is closely related to BmpA (BB0383), BmpB (BB0382) and BmpC (BB0384) and to the TmpC of T. pallidum , and is present in all species of the B. burgdorferi sensu lato complex (Ramamoorthy et al .,...”
NGFG_01515 glutamyl-tRNA reductase from Neisseria gonorrhoeae MS11
49% identity, 99% coverage
Q2KZZ5 Glutamyl-tRNA reductase from Bordetella avium (strain 197N)
50% identity, 97% coverage
- New Insights about Antibiotic Production by Pseudomonas aeruginosa: A Gene Expression Analysis.
Gionco, Frontiers in chemistry 2017 - “...Access Description Access Description Access Description BAV0296 WP_012415998.1 Glutamyl-tRNA reductase IPR000343 Tetrapyrrole biosynthesis, glutamyl-tRNA reductase Q2KZZ5 Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA) PF00745 Glutamyl-tRNAGlu reductase, N-terminal domain JFBC01000420.1 Hypothetical protein BC89_12120 None predicted A0A136QJ84 Uncharacterized protein We did not find any Pfam-A...”
B0U5Z2 Glutamyl-tRNA reductase from Xylella fastidiosa (strain M12)
47% identity, 97% coverage
- Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction
Xue, International journal of molecular sciences 2010 - “..., C2 region of RNase E is flanked by disordered regions. The same segment in B0U5Z2 and Q65I31 shows are located in short disordered regions which has only about 25 residues in B0U5Z2 and about 40 residues in Q65I31. Hence, the RNaseE-C2-like segments in both B0U5Z2...”
- “...C Yes Q65S31 Mannheimia succiniciproducens CafA protein Yes C1 --- --- --- --- C2 --- B0U5Z2 Xylella fastidiosa Glutamyl-tRNA reductase Yes Q65I31 Bacillus licheniformis Anthranilate synthaseTrpE Yes C3 --- A5UA75 Haemophilus influenzae Hydroxyethylthiazole kinase Yes A4NVQ3 Haemophilus influenzae rRNA pseudouridylate synthase C No Q65S31 Mannheimia succiniciproducens...”
APJL_0425 glutamyl-tRNA reductase from Actinobacillus pleuropneumoniae serovar 3 str. JL03
44% identity, 96% coverage
B2FQ15 Glutamyl-tRNA reductase from Stenotrophomonas maltophilia (strain K279a)
47% identity, 98% coverage
- Subtractive genomics and molecular docking approach to identify drug targets against Stenotrophomonas maltophilia
Saleem, PloS one 2021 - “...sml01200- Carbon metabolism sml01212-Fatty acid metabolism sml00640- Propanoate metabolism sml00620- Pyruvate metabolism 14 Glutamyl-tRNA reductase (B2FQ15) sml01110-Biosynthesis of secondary metabolites sml01100-Metabolic pathways sml01120-Microbial metabolism in diverse environments Sml01240 -Biosynthesis of cofactors Sml00860- Porphyrin and chlorophyll metabolism 15 3-Methyl-2-oxobutanoate hydroxymethyltransferase (B2FL67) sml01110-Biosynthesis of secondary metabolites Sml00770- Pantothenate...”
GSU3284 glutamyl-tRNA reductase from Geobacter sulfurreducens PCA
41% identity, 97% coverage
- Competitive advantage of oxygen-tolerant bioanodes of Geobacter sulfurreducens in bioelectrochemical systems
Speers, Biofilm 2021 - “...stress. Oxt2, on the other hand, carried the Tn 5 insertion in the glutamyl-tRNA reductase (GSU3284, HemA) that catalyzes the first committed step in heme biosynthesis [ 19 ]. Bacteria tightly regulate hemA expression to modulate heme biosynthesis under anaerobic (high levels) and aerobic (low levels)...”
- “...1 Strain Locus tag Gene annotation oxt1 GSU0466 Cytochrome c 551 peroxidase CcpA-1 (MacA) oxt2 GSU3284 Glutamyl-tRNA reductase (HemA) oxt3 GSU2093 ABC transporter, ATP-binding protein oxt4 GSU1572 RibD domain-containing protein oxt5 GSU0710 Hypothetical protein oxt6 GSU3173 Type VI secretion system needle sheath protein (TssC) oxt7 GSU2912...”
Glov_0503 glutamyl-tRNA reductase from Geobacter lovleyi SZ
42% identity, 97% coverage
HMPREF0010_01335 glutamyl-tRNA reductase from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
41% identity, 93% coverage
B7J8J0 glutamyl-tRNA reductase (EC 1.2.1.70) from Acidithiobacillus ferrooxidans (see paper)
42% identity, 94% coverage
BSU28170 glutamyl-tRNA reductase from Bacillus subtilis subsp. subtilis str. 168
36% identity, 93% coverage
- Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data
Faria, Frontiers in microbiology 2016 - “...BSU28140 Hydrogen peroxide 0.905 hemC, BSU28150 Hydrogen peroxide 0.906 hemX, BSU28160 Hydrogen peroxide 0.893 hemA, BSU28170 Hydrogen peroxide 0.804 Stimuli and average Pearson correlation coefficient (PCC) among members of the AR are shown for each gene (Gene names and B. subtilis specific BSU numbers provided) in...”
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...3BS8 1W5Q B. subtilis P. aeruginosa BSU28140 BSU28150 BSU28160 BSU28170 BSU37670 No No No No No 4.2.1.75 2.5.1.61 4MLQ Bacillus megaterium 4N7R 1T0T A. thaliana...”
- Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...0.3885 236 ypzJ BSU23328 0.843 65 2879134 2879290 reverse BSU28190 engB -669 0.4013 79 hemA BSU28170 0.842 66 1533806 1533962 forward BSU14610 pdhD -445 0.3503 236 ykzW BSU14629 0.841 67 368137 368293 forward BSU03360 yciC -802 0.3312 1021 yckC BSU03390 0.841 68 447000 447156 forward BSU03930...”
- “...nt 2879134 2879333 reverse BSU28190 engB -649 -38.80 - 0.2800 126.4779968 - 0.4100 99 hemA BSU28170 0.8852627277 200 nt 3907615 3907814 reverse BSU38100 ywcH -2588 -46.12 - 0.2950 123.9560013 - 0.3600 399 ywcI BSU38080 0.8837128878 200 nt 1248822 1249021 reverse BSU11740 cotZ -521 -54.90 - 0.5300...”
DVU1461 glutamyl-tRNA reductase from Desulfovibrio vulgaris Hildenborough
41% identity, 94% coverage
hemA / CAD48144.1 glutamyl-tRNA-reductase from Bacillus megaterium (see paper)
36% identity, 93% coverage
T479_RS15785 glutamyl-tRNA reductase from Lysinibacillus varians
35% identity, 92% coverage
- Cysteine-Mediated Extracellular Electron Transfer of Lysinibacillus varians GY32
Kong, Microbiology spectrum 2022 - “...hemE Uroporphyrinogen decarboxylase 3.98 0.00 0.25 0.45 T479_RS19380 hemL Glutamate-1-semialdehyde aminotransferase 2.29 0.00 0.07 0.64 T479_RS15785 hemA Glutamyl-tRNA reductase 1.92 0.00 1.11 0.63 T479_RS14675 hemN Coproporphyrinogen III oxidase 3.44 0.00 0.06 0.06 T479_RS06590 c -type cytochrome 2.60 0.00 0.88 0.01 T479_RS20980 class I cytochrome c 5.61...”
Ava_3699 Glutamyl-tRNA reductase from Anabaena variabilis ATCC 29413
38% identity, 98% coverage
FTA_1825 glutamyl-tRNA reductase from Francisella tularensis subsp. holarctica FTA
35% identity, 99% coverage
Fphi_1071 Glutamyl-tRNA reductase from Francisella philomiragia subsp. philomiragia ATCC 25017
35% identity, 99% coverage
- Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources
Siddaramappa, BMC genomics 2012 - “...309 aa, 56%, 4e-86 Fphi_0945 (344 aa) Uroporphyrinogen decarboxylase (HemE) Rmag_1026, 347 aa, 50%, 1e-97 Fphi_1071 (414 aa) Glutamyl-tRNA reductase (HemA) PSPA7_5315, 422 aa, 35%, 2e-70 Fphi_1313 (252 aa) Uroporphyrinogen-III synthase (HemD) PSM_A0104, 613 aa, 31%, 1e-08 Fphi_1400 (400 aa) Protoporphyrinogen oxidase (HemY/HemG) Cphamn1_2137, 396 aa,...”
SXYL_01194 glutamyl-tRNA reductase from Staphylococcus xylosus
36% identity, 94% coverage
- Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro
Leroy, Microorganisms 2021 - “...SXYL_01097-100 ribDEBAH Riboflavin biosynthesis 2.8 * 3.7 * SXYL_00734-35 ecfA2T Energy-coupling factor transporter 2.2 * SXYL_01194 hemA Glutamyl-tRNA reductase 2.0 SXYL_01196 hemC Porphobilinogen deaminase 2.5 SXYL_02635 cobA Uroporphyrin-III C-methyltransferase 2.0 2.9 SXYL_00839 thiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase 2.0 SXYL_01231 HesA/MoeB/ThiF family protein 2.1 2.0 SXYL_01893 menF Isochorismate synthase...”
Caur_2593 glutamyl-tRNA reductase from Chloroflexus aurantiacus J-10-fl
39% identity, 96% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...Heme biosynthesis hemA , hemC , hemD , hemB , hemE , hemL , hemF (Caur_2593 - 2599), hemN (Caur_0209 and Caur_0644), hemG/Y (Caur_0645), protoheme IX farnesyltransferase (Caur_0029) Chlorophyll biosynthesis bchI (Caur_0117, Caur_0419, Caur_1255), bchU (Caur_0137), bchK (Caur_0138), bchF (Caur_0415), bchC (Caur_0416), bchX (Caur_0417), bchD (Caur_0420),...”
- “...2144), COX I (Caur_2426) and COX II (Caur_2425 and Caur_2582) (b) Heme The heme operon (Caur_2593 to Caur_2599: hemA , hemC, hemD , hemB , hemE , hemL and hemF ) is downstream of the cobalamin operon (Caur_2560 to Caur_2580). Except for hemF , other genes...”
NWMN_1566 glutamyl-tRNA reductase from Staphylococcus aureus subsp. aureus str. Newman
SA1496 glutamyl-tRNA reductase from Staphylococcus aureus subsp. aureus N315
SAUSA300_RS08825 glutamyl-tRNA reductase from Staphylococcus aureus subsp. aureus USA300_FPR3757
37% identity, 94% coverage
SAOUHSC_01776 glutamyl-tRNA reductase from Staphylococcus aureus subsp. aureus NCTC 8325
37% identity, 94% coverage
SAR1752 glutamyl-tRNA reductase from Staphylococcus aureus subsp. aureus MRSA252
37% identity, 94% coverage
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...1.32E-02 SAR0649 tagB teichoic acid biosynthesis protein 2.50 4.41E-04 SAR1143 putative carbamate kinase 2.27 6.79E-03 SAR1752 hemA glutamyl-tRNA reductase 2.27 3.93E-02 SAR1807 putative transglycosylase 2.04 8.78E-04 SAR2472 gltT putative proton/sodium-glutamate symport protein 2.04 2.97E-02 SAR2621 cidA holin-like protein 2.27 1.18E-02 SAR2669 putative dihydroorotate dehydrogenase 2.86 3.75E-03...”
- “...down-regulation of SAR2669 encoding a putative dihydroorotate dehydrogenase, SAR0228 encoding a putative glutamine amidotransferase and SAR1752 ( hemA ), in concert, would maintain glutamate levels within the cell. SAR2269 , a putative alanine racemase, was up-regulated thereby increasing synthesis of D-alanine by isomerising L-alanine. The microarray...”
SH1255 glutamyl-tRNA reductase from Staphylococcus haemolyticus JCSC1435
38% identity, 94% coverage
- Planctomycetes as Novel Source of Bioactive Molecules
Graça, Frontiers in microbiology 2016 - “...their bioactive potential. Donadio et al. ( 2007 ) analyzed the genome of Rhodopirellula baltica SH1255 and verified the presence of two small NRPSs, two monomodular PKSs, and a bimodular NRPS-PKS which may be involved in the synthesis of five different, unknown products. In Antarctic sediments,...”
Synpcc7942_0504 glutamyl-tRNA reductase from Synechococcus elongatus PCC 7942
39% identity, 95% coverage
- Promoting Heme and Phycocyanin Biosynthesis in Synechocystis sp. PCC 6803 by Overexpression of Porphyrin Pathway Genes with Genetic Engineering
Cao, Marine drugs 2023 - “...using primers 2udPT-F and 2udPT-R. The 8 heme genes of strain PCC 7942, including hemA-syf (Synpcc7942_0504), hemB-syf (Synpcc7942_1792), hemC-syf (Synpcc7942_0967), hemE-syf (Synpcc7942_1086), hemF-syf (Synpcc7942_0674), hemH-syf (Synpcc7942_0137), hemJ-syf (Synpcc7942_0849), and hemL-syf (Synpcc7942_0645), were homologously recombined to obtain the overexpression plasmids of strain PCC 7942 heme synthesis genes....”
SERP1236 glutamyl-tRNA reductase from Staphylococcus epidermidis RP62A
36% identity, 94% coverage
HEM1_CHLP8 / P28462 Glutamyl-tRNA reductase; GluTR; EC 1.2.1.70 from Chlorobaculum parvum (strain DSM 263 / NCIMB 8327) (Chlorobium vibrioforme subsp. thiosulfatophilum) (see paper)
P28462 glutamyl-tRNA reductase (EC 1.2.1.70) from Prosthecochloris vibrioformis (see paper)
34% identity, 98% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA).
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Homodimer.
lmo1557 highly similar to glutamyl-tRNA reductase from Listeria monocytogenes EGD-e
33% identity, 92% coverage
hemA / AAA27289.1 transfer RNA-Gln reductase from Synechocystis sp (see paper)
slr1808 glutamyl-tRNA reductase from Synechocystis sp. PCC 6803
36% identity, 97% coverage
- A Non-functional γ-Aminobutyric Acid Shunt Pathway in Cyanobacterium Synechocystis sp. PCC 6803 Enhances δ-Aminolevulinic Acid Accumulation under Modified Nutrient Conditions
Kanwal, International journal of molecular sciences 2023 - “...gltX , hemA , hemL and hemB , with the respective gene IDs: sll0179 , slr1808 , sll0017 and sll1994 ( http://genome.microbedb.jp/cyanobase/GCA_000009725.1 (accessed on 7 April 2022)). On the other hand, glutamate (a precursor metabolite in the ALA pathway) is also a chief substrate for an...”
- “...for Gts 190 R-gts CCCCGTCTCGCTTAGATAAT Reverse primer used in the qPCR reaction for Gts F-gtr slr1808 AAGCGCTAACCCATCTGC Forward primer used in the qPCR reaction for Gtr 152 R-gtr GGGAATATTGCCAGTTTCAGA Reverse primer used in the qPCR reaction for Gtr F-gsa sll0017 CTATGGTGGTCGGGAAGAA Forward primer used in the...”
- Promoting Heme and Phycocyanin Biosynthesis in Synechocystis sp. PCC 6803 by Overexpression of Porphyrin Pathway Genes with Genetic Engineering
Cao, Marine drugs 2023 - “...2UD+Cm and 1UD+Gm, respectively. The 10 endogenous heme genes of strain PCC 6803, including hemA-syn (slr1808), hemB-syn (sll1994), hemC-syn (slr1887), hemE-syn (slr0536), hemF-syn (sll1185), hemH-syn (slr0839), hemJ-syn (slr1790), hemL-syn (sll0017), hemN-syn (sll1876), and glbn (slr2097), were amplified by PCR, and the promoter Pcpc560 (P) was connected...”
- A novel "oxygen-induced" greening process in a cyanobacterial mutant lacking the transcriptional activator ChlR involved in low-oxygen adaptation of tetrapyrrole biosynthesis
Aoki, The Journal of biological chemistry 2014 - “...primer for gltX (sll0179) Forward primer for hemA (slr1808) Reverse primer for hemA (slr1808) Forward primer for hemL (sll0017) Reverse primer for hemL...”
- Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light
Huang, Journal of bacteriology 2002 - “...hemF ho pntA trxA slr1055 slr0749 sll1091 slr0772 slr0750 slr1808 sll1185 sll1184 slr1239 slr0623 0.82 0.16 0.27 0.06 0.42 0.13 0.46 0.09 0.45 0.19 0.69 0.2...”
- “...sll1463 5.3 2.7 3.4 1.3 2.0 0.4 2.55 hemA slr1808 0.30 0.15 0.26 rbcL slr0009 0.26 0.15 0.13 a For explanation of treated/control ratio, see Materials and...”
- Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns
De, Genome research 2002 - “...clpP 0.0400 slr0739 crtE 0.0400 slr2075 groES 0.0400 slr1808 hemA 0.0400 sll1599 mntA 0.0400 sll1600 mntB 0.0400 sll0622 nadA 0.0400 slr2034 ycf 0.0400 slr2073...”
DR_2547 glutamyl-tRNA reductase from Deinococcus radiodurans R1
41% identity, 76% coverage
SYNPCC7002_A1302 glutamyl-tRNA reductase from Synechococcus sp. PCC 7002
36% identity, 98% coverage
Q9FPR7 Glutamyl-tRNA reductase from Chlamydomonas reinhardtii
37% identity, 80% coverage
HEM1_METTM / P42809 Glutamyl-tRNA reductase; GluTR; EC 1.2.1.70 from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (see paper)
37% identity, 98% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA).
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Homodimer.
Amuc_0091 glutamyl-tRNA reductase from Akkermansia muciniphila ATCC BAA-835
37% identity, 78% coverage
- Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains
Kirmiz, Applied and environmental microbiology 2020 - “...genomes contained most of the genes associated with the upstream (tetrapyrrole precursor biosynthesis, e.g., Amuc_0090, Amuc_0091, Amuc_0417, Amuc_0896, and Amuc_1730) and downstream (nucleotide loop assembly, e.g., Amuc_1678 to Amuc_1683) stages of vitamin B 12 biosynthesis ( 28 ). Genes annotated as a TonB-dependent transporter (e.g., Amuc_1684)...”
LOC107840125 glutamyl-tRNA reductase 1, chloroplastic from Capsicum annuum
33% identity, 75% coverage
- Pigment Biosynthesis and Molecular Genetics of Fruit Color in Pepper
Wang, Plants (Basel, Switzerland) 2023 - “...pepper. Short Name Enzyme Name Chromosome Location Gene ID GluTR Glutamyl-tRNA reductase 4 LOC107867325 8 LOC107840125 GSA-AM Glutamate-1-semialdehyde 2,1-aminomutase 5 LOC107863035 PBGS (ALAD) Porphobilinogen synthase (5-Aminolevulinate dehydratase) 1 LOC107856090 PBGD Porphobilinogen deaminase (Hydroxymethylbilane synthase) 7 LOC107878895 UROS Uroporphyrinogen III synthase (Uroporphyrinogen III co-synthase) 4 LOC107867127 UROD...”
SYNW1117 Possible glutamyl-tRNA reductase from Synechococcus sp. WH 8102
35% identity, 97% coverage
cce_3976 transfer RNA-Gln reductase from Cyanothece sp. ATCC 51142
35% identity, 97% coverage
AF1975 glutamyl-tRNA reductase (hemA) from Archaeoglobus fulgidus DSM 4304
33% identity, 91% coverage
MM_1741 Glutamyl-tRNA reductase from Methanosarcina mazei Goe1
34% identity, 87% coverage
HEMA1 / P42804 glutamyl-tRNA reductase (EC 1.2.1.70) from Arabidopsis thaliana (see 3 papers)
HEM11_ARATH / P42804 Glutamyl-tRNA reductase 1, chloroplastic; GluTR; EC 1.2.1.70 from Arabidopsis thaliana (Mouse-ear cress) (see 9 papers)
P42804 glutamyl-tRNA reductase (EC 1.2.1.70) from Arabidopsis thaliana (see 3 papers)
AT1G58290 HEMA1; glutamyl-tRNA reductase from Arabidopsis thaliana
NP_176125 Glutamyl-tRNA reductase family protein from Arabidopsis thaliana
33% identity, 76% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). Probably involved in the tetrapyrrole synthesis required for the chlorophyll biosynthesis.
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Part of the FLU-containing chloroplast membrane complex composed of FLU, CRD1, PORB, PORC, CHLP and HEMA1. Interacts (via C- terminus) with FLU, only in the absence of light. Interacts with GLUTRBP and forms a heterotetramer of two GLUTRBP and two HEMA1 subunits. Interacts with CLPF (PubMed:26419670). - Anionic lipids facilitate membrane development and protochlorophyllide biosynthesis in etioplasts
Yoshihara, Plant physiology 2024 - “...SQD2 (AT5G01220), ACT8 (AT1G49240), UBQ11 (AT4G05050), CHLH (AT5G13630), CHLD (AT1G08520), CHLI1 (AT4G18480), GUN4 (AT3G59400), HEMA1 (AT1G58290), CHLM (AT4G25080), CHL27 (AT3G56940), PORA (AT5G54190), and PORB (AT4G27440). Supplementary Material kiad604_Supplementary_Data Acknowledgments We thank Tatsuru Masuda (Graduate School of Arts and Sciences, The University of Tokyo) for providing antibody...”
- “...AT1G08520 CHLI1 Gramene: AT4G18480 CHLI1 Araport: AT4G18480 GUN4 Gramene: AT3G59400 GUN4 Araport: AT3G59400 HEMA1 Gramene: AT1G58290 HEMA1 Araport: AT1G58290 CHLM Gramene: AT4G25080 CHLM Araport: AT4G25080 CHL27 Gramene: AT3G56940 CHL27 Araport: AT3G56940 PORA Gramene: AT5G54190 PORA Araport: AT5G54190 PORB Gramene: AT4G27440 PORB Araport: AT4G27440 References Aoki M...”
- BPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling
Tachibana, Nature communications 2024 - “...BPG4/RPGE2/PEL (AT3G55240), BGH1/RPGE3 (AT3G28990), BGH2/RPGE1 (AT5G02580), BGH3/RPGE4 (AT1G10657), ACT2 (AT3G18780), GAPDH (AT1G13440), eIF4a (AT3G13920), HEMA1 (AT1G58290), GUN4 (AT3G59440), CHLH (AT5G13630), PORB (AT4G27440), CAO (AT1G44446), CHLG (AT3G51820), HEMG1 (AT4G01690), DVR/BPG1 (AT5G18660), LHCB1.2 (AT1G29910), LHCB6 (AT1G15820), LHCA1 (AT3G54890), PAO (AT3G44880), rbcS (AT1G67090), psbA (ATCG00020), HY5 (AT5G11260), COP1 (AT2G32950),...”
- Phenylalanine suppresses cell death caused by loss of fumarylacetoacetate hydrolase in Arabidopsis
Jiang, Scientific reports 2022 - “...5 ' -ACCTGCTTCTTCTCAGCCAT-3 ' BAP1 (AT3G61190) 5 ' -ATCGGATCCCACCAGAGATTACGG-3 ' 5 ' -AATCTCGGCCTCCACAAACCAG-3 ' HEMA1 (AT1G58290) 5 ' -GTTGCTGCCAACAAAGAAGA-3 ' 5 ' -AATCCCTCCATGCTTCAAAC-3 ' PAL1 (AT2G37040) 5 ' -TTTTGGTGCTACTTCTCATCG-3 ' 5 ' -CTTGTTTCTTTCGTGCTTCC-3 ' PAL2 (AT2G37040) 5 ' -GTGCTACTTCTCACCGGAGA-3 ' 5 ' -TATTCCGGCGTTCAAAAATC-3 ' PAL3 (AT5G04230)...”
- Chloroplast-localized PITP7 is essential for plant growth and photosynthetic function in Arabidopsis
Kim, Physiologia plantarum 2022 - “...VTE1 (At4g32770), VTE2 (At2g18950), VTE3 (At3g63410), VTE4 (At1g64970), ZDS (At3g04870), DVR (At5g18660), HCAR (At1g04620), HEMA1 (At1g58290), HEMA2 (At1g09940), NOL (At5g04900), NYC1 (At4g13250), PorA (At5g54190), and PorB (At4g27440). Supporting information Figure S1. Molecular phylogenetic analysis of Sec14like proteins in Arabidopsis and other plant species using the maximumlikelihood...”
- Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis
Hsieh, RNA biology 2022 - “...OPT3, At4g16370; IRT3, At1g60960; BTS, At3g18290; CGLD27, At5g67370; ENH1, At5g17170; YSL1, At4g24120; COPT2, At3g46900; HEMA1, At1g58290; NYC1, At4g13250; NEET, At5g51720; LOX2, At3g45140; LOX3, At1g17420; LOX4, At1g72520; AOS, At5g42650; AOC3, At3g25780; OPR3, At2g06050; JAR1, At2g46370; MYC2, At1g32640; JMT, At1g19640; IAR3, At1g51760; ILL5, At1g51780; ILL6, At1g44350; JAZ1, At1g19180;...”
- Review: the effect of light on the key pigment compounds of photosensitive etiolated tea plant
Yue, Botanical studies 2021 - “...chlorophyll biosynthesis in plant Code Enzyme Abbreviation Gene Gene annotation 1 Glutamyl-tRNA reductase GluTR HEMA1 At1g58290 HEMA2 At1g09940 HEMA3 At2g31250 2 Glutamate-1-semialdehyde-2,1-aminomutase GSA-AM GSA1 At5g63570 GSA2 At3g48730 3 -Aminolevulinic acid dehydratase ALAD HEMB1 At1g69740 HEMB2 At1g44318 4 Porphobilinogen deaminase PBGD HEMC At5g08280 5 Uroporphyrinogen III synthase...”
- TaClpS1, negatively regulates wheat resistance against Puccinia striiformis f. sp. tritici
Yang, BMC plant biology 2020 - “...interacts with TaHEMA1 by yeast two-hybrid assay In Arabidopsis , GluTR, encoded by gene HEMA1 (AT1G58290), was identified as a candidate substrate of AtClpS1 [ 17 ]. To confirm whether glutamyl-tRNA reductase is a substrate of TaClpS1 in wheat, yeast two-hybrid (Y2H) technique was used. Firstly,...”
- PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana
Park, Plant signaling & behavior 2020 (secret) - More
- The GluTR-binding protein is the heme-binding factor for feedback control of glutamyl-tRNA reductase.
Richter, eLife 2019 - GeneRIF: binding of heme to the GluTR-binding protein (GBP) inhibits interaction of GBP with the N-terminal regulatory domain of GluTR1, thus making it accessible to the Clp protease.[GluTR1]
- Production of 5-aminolevulinic acid from glutamate by overexpressing HemA1 and pgr7 from Arabidopsis thaliana in Escherichia coli.
Aiguo, World journal of microbiology & biotechnology 2019 (PubMed)- GeneRIF: HemA1 and pgr7 genes from the higher plant Arabidopsis thaliana into recombinant Escherichia coli to overproduce extracellular 5-aminolevulinic acid via the C5 pathway.
- The Arabidopsis glutamyl-tRNA reductase (GluTR) forms a ternary complex with FLU and GluTR-binding protein.
Fang, Scientific reports 2016 - GeneRIF: a ternary complex composed of the C-terminal tetratricopepetide-repeat domain of FLU, GBP, and GluTR, is reported
- Posttranslational Control of ALA Synthesis Includes GluTR Degradation by Clp Protease and Stabilization by GluTR-Binding Protein.
Apitz, Plant physiology 2016 - GeneRIF: the proteolytic activity of Clp protease counteracts GBP binding to assure the appropriate content of GluTR and the adequate amino levulinic acid synthesis for chlorophyll and heme in higher plants.
- The Non-canonical Tetratricopeptide Repeat (TPR) Domain of Fluorescent (FLU) Mediates Complex Formation with Glutamyl-tRNA Reductase.
Zhang, The Journal of biological chemistry 2015 - GeneRIF: characterize the FLU-GluTR interaction by solving the crystal structures of the uncomplexed TPR domain of FLU (FLU(TPR)) at 1.45-A resolution and the complex of the dimeric domain of GluTR bound to FLU(TPR) at 2.4-A resolution
- Expression of yeast Hem1 controlled by Arabidopsis HemA1 promoter enhances leaf photosynthesis in transgenic tobacco.
Zhang, Molecular biology reports 2011 (PubMed)- GeneRIF: A gene encoding aminolevulinate synthase (ALA-S) in yeast (Saccharomyces cerevisiae YHem1) was introduced into the genome of tobacco (Nicoliana tabacum) under the control of Arabidopsis thaliana HemA1 gene promoter (AtHemA1 P).
- Overexpression of HEMA1 encoding glutamyl-tRNA reductase.
Schmied, Journal of plant physiology 2011 (PubMed)- GeneRIF: HEMA1 overexpression in etiolated and dark-grown Arabidopsis and tobacco seedlings leads to additional accumulation of protochlorophyllide.
- Mg-protoporphyrin IX and heme control HEMA, the gene encoding the first specific step of tetrapyrrole biosynthesis, in Chlamydomonas reinhardtii
Vasileuskaya, Eukaryotic cell 2005 - “...with those of Arabidopsis thaliana (A.t. HEMA1; NP_176125), Hordeum vulgare (H.v. HEMA1; BAA25167), Nostoc sp. strain PCC7120 (N.sp; NP_485085), Escherichia...”
- More
LOC107763283 glutamyl-tRNA reductase 1, chloroplastic from Nicotiana tabacum
33% identity, 76% coverage
- Preharvest Application of Exogenous 2,4-Epibrassinolide and Melatonin Enhances the Maturity and Flue-Cured Quality of Tobacco Leaves
Wei, Plants (Basel, Switzerland) 2024 - “...and carotenoid biosynthetic pathways. The results indicated that genes associated with chlorophyll biosynthesis, including hemA (LOC107763283), MgPEC (LOC107786828), and ChlD (LOC107820629), were significantly down-regulated after EBR treatment. In contrast, chlorophyll degradation genes CHL2 (LOC107767570), SGR (LOC107817134), PAOa (LOC107805002), and PAOb (LOC107817296) were significantly up-regulated. Under MT...”
MTH1012 glutamyl-tRNA reductase from Methanothermobacter thermautotrophicus str. Delta H
35% identity, 96% coverage
5yjlB / P42804 Crystal structure of arabidopsis glutamyl-tRNA reductase in complex with NADPH and gbp (see paper)
33% identity, 95% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (5yjlB)
gtr1 / AAD16897.1 glutamyl-tRNA reductase precursor from Glycine max (see paper)
33% identity, 76% coverage
MA0577 glutamyl-tRNA reductase from Methanosarcina acetivorans C2A
34% identity, 82% coverage
HEM1_METKA / Q9UXR8 Glutamyl-tRNA reductase; GluTR; EC 1.2.1.70 from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (see 2 papers)
Q9UXR8 glutamyl-tRNA reductase (EC 1.2.1.70) from Methanopyrus kandleri (see paper)
MK0200 Glutamyl-tRNA reductase from Methanopyrus kandleri AV19
35% identity, 91% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). In the absence of NADPH, exhibits substrate esterase activity, leading to the release of glutamate from tRNA.
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Homotetramer. - A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence
Storbeck, Archaea (Vancouver, B.C.) 2010 - “..._0308 _0307 _1740 _1738 _1739 _1737 _0309 + + + 44 45 Methanopyrus kandleri AV19 MK0200 MKT08 0198 0746 1550 1548 1495 0896 0980 + + + 45 46 Pyrococcus abyssi GE5 46 47 Pyrococcus furiosus DSM 3638 47 48 Pyrococcus horikoshii OT3 48 49 Thermococcus...”
Msp_1408 HemA from Methanosphaera stadtmanae DSM 3091
32% identity, 97% coverage
MJ0143 glutamyl-tRNA reductase (hemA) from Methanocaldococcus jannaschii DSM 2661
33% identity, 91% coverage
HEM11_HORVU / Q42843 Glutamyl-tRNA reductase 1, chloroplastic; GluTR; EC 1.2.1.70 from Hordeum vulgare (Barley) (see paper)
32% identity, 78% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA).
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
subunit: Homodimer. - Comparative proteomics analysis of proteins expressed in the I-1 and I-2 internodes of strawberry stolons
Fang, Proteome science 2011 - “...coproporphyrinogen oxidase activity Glycine max 43.6/6.7 42.2/5.2 84 31 10/32 104 Glutamyl-tRNA reductase 1, chloroplastic Q42843 NADP or NADPH binding Hordeum vulgare 58.1/8.7 42.1/4.9 70 24 11/48 Transcription 18 Homeobox-leucine zipper protein GLABRA 2 OS P46607 sequence-specific DNA binding Arabidopsis thaliana 83.7/6.1 15.0/6.4 63 31 20/90...”
Rv0509 glutamyl-tRNA reductase from Mycobacterium tuberculosis H37Rv
34% identity, 90% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...Phosphoadenylyl-sulfate reductase Rv2392 MAB_1661c MCNS_35620 AWC07_21315 gltX Glutamyl-tRNA synthetase Rv2992c MAB_3298c AWC07_23235 hemA Glutamyl-tRNA reductase Rv0509 MAB_3993c MCNS_03960 AWC07_11800 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase Rv0512 MAB_3990c MCNS_03990 XA26_52000 H0P51_RS04270 EET03_RS02885 hemC Porphobilinogen deaminase Rv0510 MAB_3992c MCNS_03970 XA26_52020 AWC07_11795 H0P51_RS04260 EET03_RS02875 hemD Uroporphyrinogen III methyltransferase/synthase Rv0511...”
- “...0 0 gltX Glutamyl-tRNA synthetase Rv2992c 170.96 11.21727537 89.43333333 42.90810128 107.7533333 76.94248949 hemA Glutamyl-tRNA reductase Rv0509 612.7766667 65.26401271 698.94 222.6659401 362.77 513.034254 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase Rv0512 279.2466667 19.95736511 165.0033333 36.41366075 160.32 114.4782576 hemC Porphobilinogen deaminase Rv0510 627.0233333 64.43651415 435.5433333 115.7868324 161.2566667 114.1554689 hemD...”
- TB or not to be: what specificities and impact do antibodies have during tuberculosis?
Hermann, Oxford open immunology 2021 - “...serine protease PepD x Rv0052 Conserved protein x Rv2922c Probable chromosome partition protein Smc x Rv0509 Probable glutamyl-tRNA reductase HemA x Rv1566c Possible Inv protein x Subsequent to these initial studies, a second microarray platform was developed in which all Mtb proteins were expressed as GST-fusion...”
- Comprehensive analysis of iron utilization by Mycobacterium tuberculosis
Zhang, PLoS pathogens 2020 - “...NE NE ES ES ES GD rv0455c Hypothetical protein NE ES ES NE NE ES rv0509 hemA Glutamyl-tRNA reductase ES ES GD NE NE NE rv0510 hemC Porphobilinogen deaminase GD ES GD NE NE NE rv0512 hemB Delta-aminolevulinic acid dehydratase ES ES GD NE NE NE...”
- Identification of Novel Antigens Recognized by Serum Antibodies in Bovine Tuberculosis
Lyashchenko, Clinical and vaccine immunology : CVI 2017 - “...(which were excluded from the data analyses): Rv0483, Rv0509, Rv1193, Rv2280, Rv3029c, and Rv3340, which were produced at APHA as described previously (30), and...”
- Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster
Bespyatykh, Scientific reports 2016 - “...identified on the gene regulatory network. Synonym Gene Reg TF Product Functional_category log2 fold p-value Rv0509 over Rv1353c glutamyl-tRNA reductase Intermediary metabolism and respiration Rv1464 over Rv1460 cysteine desulfurase Intermediary metabolism and respiration 1.56 0.0489072 Rv3094c fadE2 over Rv0494; Rv3095 hypothetical protein Intermediary metabolism and respiration...”
- Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
Anand, Scientific reports 2014 - “...HIV-1 strains resistant to more than one protease inhibitor. Adenosine (DB00640;ADN) 0.59 Rv0032; Rv0291; Rv0479c; Rv0509; Rv0545c; Rv1201c; Rv1650; Rv1836c; Rv1843c; Rv2296; Rv2482c; Rv2869c; Rv3037c; Rv3255c; Rv3579c; Rv3737; Rv3740c; Rv3825c; Rv3909; Used as an initial treatment for the termination of paroxysmal supraventricular tachycardia (PVST), including that...”
- Characterization of a novel heat shock protein (Hsp22.5) involved in the pathogenesis of Mycobacterium tuberculosis
Abomoelak, Journal of bacteriology 2011 - “...and H37Rv Rv0001 Rv0009 Rv0129c Rv0350 Rv0351 Rv0509 Rv0951 Rv1185c Rv2196 Rv2245 Rv2524c Rv2941 Rv3763 Rv3825c Rv3921c dnaA (replication initiation) cfp22...”
- Mycobacterium tuberculosis modulates its cell surface via an oligopeptide permease (Opp) transport system
Flores-Valdez, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009 - “...0.9 1.1 0.6 0.6 0.9 1.0 1.1 1.0 0.9 Rv0509 Rv0583c Rv0593c Rv0595c Rv0651 Rv0693 Rv0700 Rv0702 Rv0704 Rv0706 Rv0708 Rv0710 Rv0714 Rv0716 Rv0722 Rv0859 Rv0860...”
Cj0542 glutamyl-tRNA reductase from Campylobacter jejuni subsp. jejuni NCTC 11168
32% identity, 94% coverage
- Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism
Méric, Genome biology and evolution 2018 - “...when C. jejuni infects chicken (48) cj0389 serS 149 Seryl-tRNA synthetase J Translation 5 1 cj0542 hemA 213 Glutamyl-tRNA reductase H Coenzyme transport and metabolism genes 3 3 cj0767c coaD 286 Phosphopantetheine adenylyltransferase H Coenzyme transport and metabolism genes 3 1 cj1620c mutY 593 A/G-specific adenine...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj0321, cj0326, cj0332c, cj0360, cj0384c, cj0405, cj0432c, cj0433c, cj0434, cj0435, cj0437, cj0443, cj0453, cj0490, cj0541, cj0542, cj0559, cj0576, cj0580c, cj0585, cj0589, cj0638c, cj0647, cj0699c, cj0716, cj0764c, cj0766c, cj0767c, cj0795c, cj0798c, cj0806, cj0813, cj0821, cj0822, cj0847, cj0853c, cj0858c, cj0862c, cj0891c, cj0905c, cj0918c, cj0932c, cj0947c, cj0949c, cj0955c, cj0992c,...”
MCNS_03960 glutamyl-tRNA reductase from Mycobacterium conspicuum
33% identity, 93% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...Rv2392 MAB_1661c MCNS_35620 AWC07_21315 gltX Glutamyl-tRNA synthetase Rv2992c MAB_3298c AWC07_23235 hemA Glutamyl-tRNA reductase Rv0509 MAB_3993c MCNS_03960 AWC07_11800 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase Rv0512 MAB_3990c MCNS_03990 XA26_52000 H0P51_RS04270 EET03_RS02885 hemC Porphobilinogen deaminase Rv0510 MAB_3992c MCNS_03970 XA26_52020 AWC07_11795 H0P51_RS04260 EET03_RS02875 hemD Uroporphyrinogen III methyltransferase/synthase Rv0511 MCNS_03980 AWC07_14690...”
HP0239 glutamyl-tRNA reductase (hemA) from Helicobacter pylori 26695
30% identity, 94% coverage
Cp1002B_0289 glutamyl-tRNA reductase from Corynebacterium pseudotuberculosis
35% identity, 91% coverage
- Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis
Viana, PloS one 2018 - “...anchored) Adhesion - - Cp31_1977/ Cp1002B_0655 X Membrane anchored protein 2 Unknown - - Cp31_0279/ Cp1002B_0289 X Glutamyl-tRNA reductase ( hemA ) Metabolism - [ 74 ] Cp31_1028/ Cp1002B_1640 X Cobaltochelatase subunit CobN ( cobN ) Metabolism - - Cp31_1117/ Cp1002B_1551 X Sporulation regulator WhiA-like (...”
- “...Cp1002B_0655 298 - - - 6 (2.01) - - - Membrane anchored protein 2 Cp31_0279/ Cp1002B_0289 432 - - - - 1 (0.23) - - Glutamyl-tRNA reductase ( hemA ) Cp31_1028/ Cp1002B_1640 1201 - - - - 2 (0.17) - - Cobaltochelatase subunit CobN ( cobN...”
HEMA2 / P49294 glutamyl-tRNA reductase (EC 1.2.1.70) from Arabidopsis thaliana (see 2 papers)
HEM12_ARATH / P49294 Glutamyl-tRNA reductase 2, chloroplastic; GluTR; EC 1.2.1.70 from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
NP_172465 Glutamyl-tRNA reductase family protein from Arabidopsis thaliana
AT1G09940 HEMA2; glutamyl-tRNA reductase from Arabidopsis thaliana
32% identity, 78% coverage
- function: Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). Probably involved in wound-induced supply of heme to defensive hemoproteins outside plastids.
catalytic activity: (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L- glutamyl-tRNA(Glu) + NADPH + H(+) (RHEA:12344)
disruption phenotype: No visible phenotype, but decreased heme content in roots. - Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis.
Nagai, Plant physiology 2007 - GeneRIF: induced in photosynthetic tissues under oxidative conditions to supply heme for defensive hemoproteins outside plastids
- Mg-protoporphyrin IX and heme control HEMA, the gene encoding the first specific step of tetrapyrrole biosynthesis, in Chlamydomonas reinhardtii
Vasileuskaya, Eukaryotic cell 2005 - “...the following additional proteins: Arabidopsis thaliana HEMA2 (NP_172465), Hordeum vulgare HEMA2 (CAA60055) and HEMA3 (BAA25168), and Anabaena sp. (A.sp.;...”
- A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress
Karami, PloS one 2023 - “...was also up-regulated in C3 plants and down-regulated in C4 plants. Three down-regulated genes HEMA2 (AT1G09940), ferrochelatase 2 ( FC2 ; AT2G30390) and urophorphyrin methylase 1 ( UPM1; AT5G40850) were also detected only in C3 plants. The up-regulated gene protochlorophyllide oxidoreductase A ( PORA ; AT5G54190)...”
- Chloroplast-localized PITP7 is essential for plant growth and photosynthetic function in Arabidopsis
Kim, Physiologia plantarum 2022 - “...VTE2 (At2g18950), VTE3 (At3g63410), VTE4 (At1g64970), ZDS (At3g04870), DVR (At5g18660), HCAR (At1g04620), HEMA1 (At1g58290), HEMA2 (At1g09940), NOL (At5g04900), NYC1 (At4g13250), PorA (At5g54190), and PorB (At4g27440). Supporting information Figure S1. Molecular phylogenetic analysis of Sec14like proteins in Arabidopsis and other plant species using the maximumlikelihood method. Figure...”
- Genomic Regions Associated With Seed Meal Quality Traits in Brassica napus Germplasm
Bhinder, Frontiers in plant science 2022 - “...biosynthesis MTO1 SNC_027767.2_23748159 23748159 8113 AT3G01120 C01 4.47 Methionine accumulation Tryptophan HEMA2 SNC_027765.2_44309263 44309263 39699 AT1G09940 A09 3.19 Tryptophan biosynthesis GLU1 SNC_027766.2_21272659 21272659 34503 AT5G04140 A10 3.07 Tryptophan biosynthesis PGM SNC_027766.2_21272659 21272659 31690 AT5G04120 A10 3.07 Tryptophan biosynthesis -carotene HDR SNC_027771.2_29995244 29995244 32802 AT4G34350 C05 3.33...”
- Review: the effect of light on the key pigment compounds of photosensitive etiolated tea plant
Yue, Botanical studies 2021 - “...in plant Code Enzyme Abbreviation Gene Gene annotation 1 Glutamyl-tRNA reductase GluTR HEMA1 At1g58290 HEMA2 At1g09940 HEMA3 At2g31250 2 Glutamate-1-semialdehyde-2,1-aminomutase GSA-AM GSA1 At5g63570 GSA2 At3g48730 3 -Aminolevulinic acid dehydratase ALAD HEMB1 At1g69740 HEMB2 At1g44318 4 Porphobilinogen deaminase PBGD HEMC At5g08280 5 Uroporphyrinogen III synthase UROS HEMD...”
- chlB requirement for chlorophyll biosynthesis under short photoperiod in Marchantia polymorpha L
Ueda, Genome biology and evolution 2014 - “...Homologs in M . polymorpha CHL27 At3g56940 AB889743 FLU At3g14110 AB889744 HEMA At1g58290 (HEMA1) AB889745 At1g09940 (HEMA2) LPOR At5g54190 (PORA) AB889746 At4g27440 (PORB) At1g03630(PORC) DELLA At2g01570 (RGA) AB889747 At1g14920 (GAI) At1g66350 (RGL1) At3g03450 (RGL2) At5g17490 (RGL3) N ote .Gene IDs of LPOR and DELLA in A....”
- Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses
Kim, PloS one 2011 - “...ILL6 (IAA-leucine resistant (ILR)-like gene 6); metallopeptidase 35.55 AT4G24380 hydrolase, acting on ester bonds 36.05 AT1G09940 HEMA2; glutamyl-tRNA reductase 36.53 AT2G01180 ATPAP1 (PHOSPHATIDIC ACID PHOSPHATASE 1) 37.57 AT3G10930 similar to unknown protein [Arabidopsis thaliana] (TAIR:AT5G05300.1) 37.98 AT3G25780 AOC3 (ALLENE OXIDE CYCLASE 3) 38.15 AT1G16370 ATOCT6; carbohydrate...”
- Tetrapyrrole Metabolism in Arabidopsis thaliana
Tanaka, The arabidopsis book 2011 - “...GluTR isoforms and are named: HEMA1 (At1g58290), HEMA2 (At1g09940), and HEMA3 (At2g31250). The expression of HEMA1 is light-regulated and is predominant in...”
- RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis
Ren, Proceedings of the National Academy of Sciences of the United States of America 2010 - “...(phosphoglycerate/bisphosphoglycerate mutase family protein), At1g09940 (glutamyl-tRNA reductase), and At1g09950 (transcription factor-related). We sequenced...”
- More
MKAN_RS17640 glutamyl-tRNA reductase from Mycobacterium kansasii ATCC 12478
33% identity, 90% coverage
MUL_4598 glutamyl-tRNA reductase HemA from Mycobacterium ulcerans Agy99
33% identity, 89% coverage
HPF30_1056 glutamyl-tRNA reductase from Helicobacter pylori F30
30% identity, 94% coverage
- Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection
Furuta, PloS one 2015 - “...MU hefA Outer membrane protein HefA HPF30_0721 P Catalase-related peroxidase HPF30_0836 H hemA Glutamyl-tRNA reductase HPF30_1056 F purB Adenylosuccinate lyase HPF30_0276 K25 Outer membrane protein babB Outer membrane protein HPF30_0154 Outer membrane protein hopL Outer membrane protein HopL HPF30_0233 Outer membrane protein alpB Outer membrane protein...”
- “...M Putative outer membrane protein HPF30_0673 C ppa Pyrophosphate phospho-hydrolase HPF30_0706 H hemA Glutamyl-tRNA reductase HPF30_1056 M rfaJ-1 Putative lipopolysaccharide biosynthesis protein HPF30_1136 R engB Probable GTP-binding protein EngB HPF30_1459 hpaA Flagellar sheath adhesin HpaA HPF30_0534 K-2 K36 Outer membrane protein hopQ Outer membrane protein HPF30_0214...”
Cp31_0279 glutamyl-tRNA reductase from Corynebacterium pseudotuberculosis 31
35% identity, 91% coverage
A5BZY3 Glutamyl-tRNA reductase from Vitis vinifera
33% identity, 75% coverage
AWC07_11800 glutamyl-tRNA reductase from Mycobacterium gastri
33% identity, 90% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...MAB_1661c MCNS_35620 AWC07_21315 gltX Glutamyl-tRNA synthetase Rv2992c MAB_3298c AWC07_23235 hemA Glutamyl-tRNA reductase Rv0509 MAB_3993c MCNS_03960 AWC07_11800 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase Rv0512 MAB_3990c MCNS_03990 XA26_52000 H0P51_RS04270 EET03_RS02885 hemC Porphobilinogen deaminase Rv0510 MAB_3992c MCNS_03970 XA26_52020 AWC07_11795 H0P51_RS04260 EET03_RS02875 hemD Uroporphyrinogen III methyltransferase/synthase Rv0511 MCNS_03980 AWC07_14690 hemL...”
1gpjA / Q9UXR8 Glutamyl-tRNA reductase from methanopyrus kandleri (see paper)
36% identity, 76% coverage
- Ligands: glutamic acid; (2r,3r,4s,5s)-4-amino-2-[6-(dimethylamino)-9h-purin-9-yl]-5-(hydroxymethyl)tetrahydro-3-furanol (1gpjA)
MMP0088 Glutamyl-tRNA reductase from Methanococcus maripaludis S2
33% identity, 82% coverage
A5717_22190 glutamyl-tRNA reductase from Mycolicibacterium porcinum
32% identity, 92% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...cysH Phosphoadenylyl-sulfate reductase A5717_28590 SAMEA4434518_01414 MXEN_11291 gltX Glutamyl-tRNA synthetase A5717_14355 MXEN_16257 MSMEG_2383 hemA Glutamyl-tRNA reductase A5717_22190 SAMEA4434518_00496 MXEN_04673 MSMEG_0919 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase MKAN_RS17655 CDN37_RS17885 MPHLCCUG_RS22000 SAMEA4434518_00499 AWC27_RS21685 MSMEG_0956 hemC Porphobilinogen deaminase MKAN_RS17645 CDN37_RS17875 MPHLCCUG_RS22010 A5717_22195 SAMEA4434518_00497 MXEN_04668 AWC27_RS07580 MSMEG_0953 hemD Uroporphyrinogen III methyltransferase/synthase...”
Mbur_1229 Shikimate/quinate 5-dehydrogenase from Methanococcoides burtonii DSM 6242
33% identity, 86% coverage
MXEN_04673 glutamyl-tRNA reductase from Mycobacterium xenopi RIVM700367
33% identity, 92% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...reductase A5717_28590 SAMEA4434518_01414 MXEN_11291 gltX Glutamyl-tRNA synthetase A5717_14355 MXEN_16257 MSMEG_2383 hemA Glutamyl-tRNA reductase A5717_22190 SAMEA4434518_00496 MXEN_04673 MSMEG_0919 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase MKAN_RS17655 CDN37_RS17885 MPHLCCUG_RS22000 SAMEA4434518_00499 AWC27_RS21685 MSMEG_0956 hemC Porphobilinogen deaminase MKAN_RS17645 CDN37_RS17875 MPHLCCUG_RS22010 A5717_22195 SAMEA4434518_00497 MXEN_04668 AWC27_RS07580 MSMEG_0953 hemD Uroporphyrinogen III methyltransferase/synthase - A5717_10195...”
cg0497 glutamyl-tRNA reductase from Corynebacterium glutamicum ATCC 13032
C629_RS02480 glutamyl-tRNA reductase from Corynebacterium glutamicum SCgG2
33% identity, 90% coverage
Memar_0980 Shikimate/quinate 5-dehydrogenase from Methanoculleus marisnigri JR1
33% identity, 94% coverage
AT2G31250 HEMA3; NADP or NADPH binding / binding / catalytic/ glutamyl-tRNA reductase/ shikimate 5-dehydrogenase from Arabidopsis thaliana
31% identity, 76% coverage
Rru_A0749 Glutamyl-tRNA reductase from Rhodospirillum rubrum ATCC 11170
36% identity, 90% coverage
rrnAC1708 glutamyl-tRNA reductase from Haloarcula marismortui ATCC 43049
34% identity, 94% coverage
- A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence
Storbeck, Archaea (Vancouver, B.C.) 2010 - “...1592 1593M 1594M 2413 1125 + + + 18 1594M 19 Haloarcula marismortui ATCC 43049 RRNAC1708 2628 2610 3086 3088 3087 1709 1711 1711 3489 1363 + + + 19 20 Halobacterium sp. NRC-1 VNG1774G 2326G 2322G 2330G 2332G 2331G 1775C 1776G 1776G 1185G 1184GM +...”
- Genome information management and integrated data analysis with HaloLex
Pfeiffer, Archives of microbiology 2008 - “...OE1371R, HQ1286A rrnAC1690 1,545 1,509 Extended NP0624A, HQ1292A rrnAC1702 1,719 1,218 Extended NP1742A, OE3490R, HQ3347A rrnAC1708 1,347 1,089 Extended NP4502A, HQ3336A, OE3496R rrnAC1718 1,359 1,065 Extended NP4542A, OE3506F, HQ3330A rrnAC1726 1,527 1,485 Extended HQ3326A, OE3511F, NP4534A rrnAC1743 549 486 Extended HQ1673A, NP5358A, rrnAC3526 rrnAC1764 924 978...”
Hlac_2132 glutamyl-tRNA reductase from Halorubrum lacusprofundi ATCC 49239
34% identity, 83% coverage
MAB_3993c Glutamyl-tRNA reductase (HemA) from Mycobacterium abscessus ATCC 19977
32% identity, 94% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...reductase Rv2392 MAB_1661c MCNS_35620 AWC07_21315 gltX Glutamyl-tRNA synthetase Rv2992c MAB_3298c AWC07_23235 hemA Glutamyl-tRNA reductase Rv0509 MAB_3993c MCNS_03960 AWC07_11800 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase Rv0512 MAB_3990c MCNS_03990 XA26_52000 H0P51_RS04270 EET03_RS02885 hemC Porphobilinogen deaminase Rv0510 MAB_3992c MCNS_03970 XA26_52020 AWC07_11795 H0P51_RS04260 EET03_RS02875 hemD Uroporphyrinogen III methyltransferase/synthase Rv0511 MCNS_03980...”
- “...MAB_1661c 174.4733333 18.36925783 gltX Glutamyl-tRNA synthetase MAB_3298c 287.6433333 11.14623853 MSMEG_2383 156.9933333 19.13254383 hemA Glutamyl-tRNA reductase MAB_3993c 268.16 8.943438936 MSMEG_0919 174.06 98.84548143 hemB Probable delta-aminolevulinic acid dehydratase/porphobilinogen synthase MAB_3990c 349.51 54.2694122 MSMEG_0956 201.9733333 27.76189895 hemC Porphobilinogen deaminase MAB_3992c 638.4233333 82.95156076 MSMEG_0953 374.95 313.6007022 hemD Uroporphyrinogen III methyltransferase/synthase...”
H629_RS0106530 glutamyl-tRNA reductase from Leucobacter chironomi DSM 19883
29% identity, 92% coverage
Cthe_2525 glutamyl-tRNA reductase from Clostridium thermocellum ATCC 27405
Cthe_2525 glutamyl-tRNA reductase from Acetivibrio thermocellus ATCC 27405
30% identity, 72% coverage
- Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Ha-Tran, Microorganisms 2021 - “...Cthe_3016, Cthe_3018, Cthe_3019, Cthe_3020, Cthe_3022, Cthe_3023, and Cthe_3024), ammonia assimilation-related genes (Cthe_01970199) and porphyrin biosynthesis (Cthe_2525), but several gene involved in sulfate metabolism (Cthe_25312534, Cthe_25362538) were downregulated ( Table S5 ). On the other hand, GAs1 had highly expressed genes in both [NiFe] and [FeFe] hydrogenases...”
- “...(i.e., Cthe_3013, Cthe_3014, Cthe_3018, Cthe_3020, Cthe_0428, Cthe_0429, Cthe_0430), ammonia assimilation genes (Cthe_01970199), porphyrin biosynthesis gene (Cthe_2525, Cthe_2527, Cthe_2528, Cthe_2529), and sulfate transport (Cthe_2533). The results suggest that FAs1 and GAs1 did not suffer much from redox imbalance as hydrogen production was favorably maintained for cell redox...”
PTO0918 glutamyl-tRNA reductase from Picrophilus torridus DSM 9790
25% identity, 88% coverage
M1425_1955 glutamyl-tRNA reductase from Sulfolobus islandicus M.14.25
24% identity, 98% coverage
SSO0180 Glutamyl-tRNA reductase from Sulfolobus solfataricus P2
24% identity, 96% coverage
Ta0536 glutamyl-tRNA reductase related protein from Thermoplasma acidophilum DSM 1728
27% identity, 84% coverage
Saci_0777 glutamyl-tRNA reductase from Sulfolobus acidocaldarius DSM 639
28% identity, 82% coverage
TVN0590 Glutamyl-tRNA reductase from Thermoplasma volcanium GSS1
27% identity, 85% coverage
RM25_RS08900 glutamyl-tRNA reductase from Propionibacterium freudenreichii subsp. freudenreichii
29% identity, 86% coverage
ST0212 412aa long hypothetical glutamyl-tRNA reductase from Sulfolobus tokodaii str. 7
25% identity, 82% coverage
Pcal_2034 glutamyl-tRNA reductase from Pyrobaculum calidifontis JCM 11548
31% identity, 72% coverage
PAE0601 glutamyl tRNA reductase (hemA) from Pyrobaculum aerophilum str. IM2
28% identity, 87% coverage
APE_2296 glutamyl-tRNA reductase from Aeropyrum pernix K1
33% identity, 67% coverage
Tneu_1917 glutamyl-tRNA reductase from Thermoproteus neutrophilus V24Sta
29% identity, 66% coverage
CT662 Glutamyl tRNA Reductase from Chlamydia trachomatis D/UW-3/CX
29% identity, 49% coverage
- Culture-independent sequence analysis of Chlamydia trachomatis in urogenital specimens identifies regions of recombination and in-patient sequence mutations
Putman, Microbiology (Reading, England) 2013 - “...is less related to J/6276, including ORFs CT660 through CT662 (Fig. S3). This approximately 12-kb region is most similar to the sequences within the D/13-like...”
- Proof of concept: A bioinformatic and serological screening method for identifying new peptide antigens for Chlamydia trachomatis related sequelae in women
Stansfield, Results in immunology 2013 - “...frequently identified MOMP, HtrA, OmcB, TART, GroEL, LCR-E, and CT662 [10 ]. In another study using a western blot strategy on 2-D gels of the Chlamydia...”
CPn_0714 glutamyl-tRNA reductase from Chlamydia pneumoniae CWL029
25% identity, 75% coverage
- Genomic factors related to tissue tropism in Chlamydia pneumoniae infection
Weinmaier, BMC genomics 2015 - “...stimulate growth of Cpn but not C. trachomatis [ 20 ]. The glutamyl tRNA reductase (CPn_0714) mediates the metabolism of phenylalanine that is involved in the extracellular protein synthesis of the transcription termination factor Rho and the Nudix phosphohydrolase in C. trachomatis , thereby mitigating cellular...”
- “...C C C C C C G G G G G C C C 800,395 CPn_0714 Glutamyl tRNA Reductase G G G G G G G G G G G G G G T T G T T T T G 896,637 CPn_0793 sigma regulatory family...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory