PaperBLAST

PaperBLAST Hits for sp|Q9HZM7|MURB_PSEAE UDP-N-acetylenolpyruvoylglucosamine reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=murB PE=1 SV=1 (339 a.a., MSLELQEHCS...)

Show query sequence

>sp|Q9HZM7|MURB_PSEAE UDP-N-acetylenolpyruvoylglucosamine reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=murB PE=1 SV=1
MSLELQEHCSLKPYNTFGIDVRARLLAHARDEADVREALALARERGLPLLVIGGGSNLLL
TRDVEALVLRMASQGRRIVSDAADSVLVEAEAGEAWDPFVQWSLERGLAGLENLSLIPGT
VGAAPMQNIGAYGVELKDVFDSLTALDRQDGTLREFDRQACRFGYRDSLFKQEPDRWLIL
RVRLRLTRRERLHLDYGPVRQRLEEEGIASPTARDVSRVICAIRREKLPDPAVLGNAGSF
FKNPLVDATQAERLRQAFPDLVGYPQADGRLKLAAGWLIDKGGWKGFRDGPVGVHAQQAL
VLVNHGGATGAQVRALAERIQEDVRRRFGVELEPEPNLY

Running BLASTp...

Found 83 similar proteins in the literature:

Q9HZM7 UDP-N-acetylmuramate dehydrogenase (EC 1.3.1.98) from Pseudomonas aeruginosa (see paper)
PA2977 UDP-N-acetylenolpyruvoylglucosamine reductase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa
  Dettman, Genome biology and evolution 2014
  • “...lipoprotein PA3141 wbpM , nucleotide sugar epimerase/dehydratase, LPS biosynthesis PA3127 Putative bleomycin resistance protein, glyoxalase/dioxygenase PA2977 murB , UDP-N-acetylenolpyruvylglucosamine reductase, peptidoglycan biosynthesis PA2403 Peptidase, iron-regulated membrane protein PA4528 pilD , type IV prepilin peptidase, fimbrial biogenesis protein, adherance to host or biofilm PA4999 waaL , O-antigen...”
• Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates
  Chen, PloS one 2013
  • “...aeruginosa drug targets [19] , we produced and crystallized P. aeruginosa MurB (PaMurB; gene locus PA2977). Here, we present the crystal structure of NADP + -bound PaMurB, which establishes the co-localization of the NADPH and UNAGEP binding sites and supports a ping pong reaction mechanism with...”
  • “...of flavin. Materials and Methods Production and purification of PaMurB The coding sequence for PaMurB (PA2977 gene) was amplified by PCR using the P. aeruginosa PAO1 genomic DNA template (ATCC 47085) and cloned into the pNIC28-Bsa4 vector (GenBank Accession No. EF198106) using the ligation-independent cloning method....”
• A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
  Xu, PloS one 2013
  • “...bacA ),PA2165( glgA ), PA2584( pgsA ),PA2629( purB ),PA2962( tmk ),PA2964( pabC ), PA2967( fabG ),PA2977( murB ),PA2979( kdsB ),PA2981( lpxK ), PA3088( yfjB ),PA3108( purF ),PA3111( folC ),PA3112( accD ), PA3163( cmk ),PA3337( rfaD ),PA3636( kdsA ),PA3637( pyrG ), PA3643( lpxB ),PA3644( lpxA ),PA3651( cdsA...”
• A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
  Sigurdsson, PloS one 2012
  • “...envelope biosynthesis GlmU (PA5552), GlmS (PA5549), MurI (PA4662), MraY (PA4415), MurE (PA4417), MurC (PA4411), MurB (PA2977) DdlB (PA4410), DdlA (PA4201), MurA (PA4450),MurD (PA4414) Cell envelope biosynthesis- O-antigen RmlA (PA5163) RmlC (PA5164) RmlB (PA5161) Citrate acid cycle SdhC (PA1581), SdhD (PA1582) Coenzyme A biosynthesis CoaE (PA4529), Dfp...”
• Beta-lactam antibiotics: from antibiosis to resistance and bacteriology
  Kong, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2010
  • “...Class D beta-lactamase Mur & Mra proteins MurA murA PA4450 UDP-N-acetylglucosamine enolpyruvyl transferase MurB murB PA2977 UDP-N-acetylpyruvoylglucosamine reductase MurC murC PA4411 UDP-N-acetylmuramate--alanine ligase MurD murD PA4414 UDP-N-acetylmuramoylalanine--D-glutamate ligase MurE murE PA4417 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase MurF murF PA4416 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase MurG murG PA4412 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol...”
• Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA
  Brencic, Molecular microbiology 2009
  • “...genes that were detected more than once include PA4611, which was detected four times, and PA2977, PA4489 and PA4744, each of which was detected twice ( Table S2 ). These genes were not identified as members of the P. aeruginosa PAK RsmA regulon and their RBSs...”
  • “...by RsmA directly. In addition to the PA0081 and PA4492 genes, four other genes (PA4611, PA2977, PA4498, and PA4744) were detected in the RNA-RsmA co-purification experiment more than once ( Table S2 ). The RBS sequences of these genes do not contain the minimal ANGGA motif,...”

4jayA / Q9HZM7 Crystal structure of p. Aeruginosa murb in complex with NADP+ (see paper)
100% identity, 100% coverage

• Ligands: flavin-adenine dinucleotide; nadp nicotinamide-adenine-dinucleotide phosphate; potassium ion (4jayA)

Smlt2127 putative UDP-N-acetylenolpyruvoylglucosamine reductase from Stenotrophomonas maltophilia K279a
47% identity, 95% coverage

• Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia
  Roscetto, Journal of bacteriology 2012
  • “...selected 10 genes, five downregulated (Smlt0706, Smlt0708, Smlt2127, Smlt2314, and Smlt3559) and five upregulated (Smlt1742, Smlt3003, Smlt3461, Smlt4085, and...”
  • “...Smlt1134 Smlt1163 Smlt1306 Smlt1408 Smlt1736 Smlt2083 Smlt2127 Smlt2270 Smlt2282 Smlt2310 Smlt2314 Smlt2362 Smlt2558 Smlt2954 Smlt3161 Smlt3301 Smlt3314...”

B0V744 UDP-N-acetylenolpyruvoylglucosamine reductase from Acinetobacter baumannii (strain AYE)
43% identity, 96% coverage

• Prioritization of Mur family drug targets against A. baumannii and identification of their homologous proteins through molecular phylogeny, primary sequence, and structural analysis
  Amera, Journal, genetic engineering & biotechnology 2020
  • “...proteins were used in this study namely MurA (Accession No: B0V7N7 ), MurB (Accession No: B0V744 ), MurC (Accession No: B0V9F6 ), MurD (Accession No: B0VDD5 ), MurE (Accession No: A0A0R4J6I7), MurF (Accession No: A0A0R4J6Z4), MraY (Accession No: B0V8P2), and MurG (Accession No: B0V9F5). Physiochemical properties...”
  • “...39.4 to 54.9 kDa and the theoretical pI of six Mur proteins (Accession IDs: B0V7N7, B0V744, B0V9F6, B0VDD5, A0A0R4J6I7, and A0A0R4J6Z4) is less than 6.18 but the remaining two Mur proteins (B0V8P2 and B0V9F5) are higher than 9.02. Based on the results of II values, the...”

NGO0394 putative UDP-N-acetylenolpyruvoylglucosamine reductase from Neisseria gonorrhoeae FA 1090
48% identity, 95% coverage

• cis- and trans-Acting Factors Influence Expression of the norM-Encoded Efflux Pump of Neisseria gonorrhoeae and Levels of Gonococcal Susceptibility to Substrate Antimicrobials
  Rouquette-Loughlin, Antimicrobial agents and chemotherapy 2018
  • “...contains three downstream genes annotated as murB (NGO0394), which encodes a putative UDPN-acetylenolpyruvoylglucosamine reductase involved in the initial steps...”

Q9JV28 UDP-N-acetylenolpyruvoylglucosamine reductase from Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491)
49% identity, 95% coverage

• Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates.
  Seo, Biodegradation 2013
  • “...Tryptophan 2-monooxygenase 24/3 P0A3V2 Primary metabolism UDP-N-acetylmuramate--L-alanine ligase 32/4 Q8UDM9 Primary metabolism UDP-N-acetylenolpyruvoylglucosamine reductase 43/6 Q9JV28 Primary metabolism Thiamine-phosphate pyrophosphorylase 36/3 Q9S2V2 Primary metabolism ATP synthase epsilon chain 45/7 Q9JW69 Primary metabolism Long-chain-fatty-acid--CoA ligase 25/4 P63521 Primary metabolism Phosphoenolpyruvate carboxykinase [ATP] 46/5 Q8UJ94 Primary metabolism L-Serine...”

NMAA_0640 UDP-N-acetylmuramate dehydrogenase from Neisseria meningitidis WUE 2594
49% identity, 95% coverage

• Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages
  Watkins, Scientific reports 2017
  • “...751743 NMAA_0638 863 Exact match 11 (796), 162 (45) USA, 1964 NADH(P)-binding Unknown E 753236 NMAA_0640 1385 Exact match 11 (812), 41/44 (407), 60 (54), 4 (14), 865 (11), 254 (9), 213 (9) USA, 1937 UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) Metabolism E 754454 NMAA_0641 842 Exact match...”

ABO_1059 UDP-N-acetylenolpyruvoylglucosamine reductase from Alcanivorax borkumensis SK2
48% identity, 95% coverage

• Hydrocarbonoclastic Alcanivorax Isolates Exhibit Different Physiological and Expression Responses to n-dodecane
  Barbato, Frontiers in microbiology 2016
  • “...genes followed a peculiar activation pattern: mur B gene involved in biosynthesis of murein monomers (ABO_1059, log 2 FC = 4.03) was upregulated in SK2 and the genes ddl , responsible for the synthesis of D-ala/D-ala dymer (B5T_03486, log 2 FC = 2.16), and murD ,...”

P0E69_18550 UDP-N-acetylmuramate dehydrogenase from Chimaeribacter arupi
44% identity, 94% coverage

• Chimaeribacter arupi a new member of the Yersineacea family has the characteristics of a human pathogen
  Riediger, Frontiers in cellular and infection microbiology 2023
  • “...biogenesis and peptidoglycan biosynthesis. Locus tag Gene Position Predicted function P0E69_17720 murA 3852794..3854059 UDP-N-acetylglucosamine 1-carboxyvinyltransferase P0E69_18550 murB 4046461..4047498 UDP-N-acetylmuramate dehydrogenase P0E69_16620 murC 3610420..3611895 UDP-N-acetylmuramateL-alanine ligase P0E69_16635 murD 3614246..3615562 UDP-N-acetylmuramoyl-L-alanineD-glutamate ligase P0E69_16650 murE 3617999..3619486 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase P0E69_16645 murF 3616641..3618002 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase P0E69_16625 murG 3611917..3613023 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase P0E69_19215...”

ACIAD1945 UDP-N-acetylenolpyruvoylglucosamine reductase, FAD-binding from Acinetobacter sp. ADP1
39% identity, 98% coverage

• iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
  Jiang, Frontiers in microbiology 2019
  • “...0.33 0.46 Triphosphoribosyl-dephospho-CoA synthase mdcB ACIAD1754 0.25 0.17 0.16 0.19 UDP- N -acetylenolpyruvoylglucosamine reductase murB ACIAD1945 0.25 0.82 0.61 0.52 Phosphoglucosamine mutase glmM ACIAD3502 0.64 0.61 0.77 0.58 Phosphoserine phosphatase serB ACIAD3567 0.59 0.44 0.65 0.59 Lyase Fatty acid oxidation complex subunit alpha fadB ACIAD0335 0.76...”

PG1342 UDP-N-acetylenolpyruvoylglucosamine reductase from Porphyromonas gingivalis W83
42% identity, 98% coverage

• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...c PG0577 Phospho-N-acetylmuramoyl-pentapeptide-transferase 1.56 PG0578 UDP-N-acetylmuramoylalanine--D-glutamateligase 1.58 PG0580 N-acetylglucosaminyl transferase 1.78 PG0581 UDP-N-acetylmuramate--L-alanine ligase 1.81 PG1342 UDP-N-acetylenolpyruvoylglucosamine reductase 2.17 PG0729 D-alanylalanine synthetase 1.80 PG1097 Mur ligase domain protein/alanine racemase 1.58 Cellular process: Cell division PG0579 Cell division protein FtsW 1.74 PG0582 Cell division protein FtsQ 1.80...”

murB / AAA24185.1 UDP-N-acetylpyruvoylglucosamine reductase from Escherichia coli (see paper)
46% identity, 95% coverage

YijB / b3972 UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) from Escherichia coli K-12 substr. MG1655 (see 17 papers)
murB / P08373 UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) from Escherichia coli (strain K12) (see 30 papers)
P08373 UDP-N-acetylenolpyruvoylglucosamine reductase from Escherichia coli (strain K12)
b3972 UDP-N-acetylenolpyruvoylglucosamine reductase from Escherichia coli str. K-12 substr. MG1655
45% identity, 95% coverage

• Mode action prediction of catechin from Uncaria gambir Roxb. against UDP-N-acetylenolpyruvyl-glucosamine reductase (MurB enzyme) of Streptococcus mutans: In silico study.
  Dharsono, Journal of advanced pharmaceutical technology & research 2022
  • “...for in silico analysis UDP- N -acetylenolpyruvylglucosamine reductase (MurB enzyme) as the protein with code P08373 was obtained from UniProt ( https://www.uniprot.org/ ). The ligands of U. gambir content were catechin and chlorhexidine, determined as control ligands, obtained from PubChem ( https://www.pubchem.ncbi.nlm.nih.gov/ ). In silico of...”
• High-throughput comparison of gene fitness among related bacteria
  Canals, BMC genomics 2012
  • “...14 15 20 27 15 15 STM14_4971.J murB UDP- N - acetylenolpyruvoylglucosamine reductase STM4136 t3489 b3972 42 48 26 22 8 24 13 21 * Details for all genes can be found in Additional file 5 : Table S2. Genes were ranked by the number of...”
• Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy
  Li, PLoS neglected tropical diseases 2011
  • “...ftsK b0890 1329 wbm0644 707 DNA translocase at septal ring sorting daughter chromsomes 33.7 murB b3972 342 wbm0778 295 UDP-N-acetylenolpyruvoylglucosamine reductase, FAD-binding 19.3 *Only major E. coli cell-division proteins are shown. Sequence analysis of w Bm- ftsZ w Bm- ftsZ exists as a single gene on...”
• Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
  Xu, BMC bioinformatics 2009
  • “...b2574, b2615, b2746 b3729 b2747, b2763, b2764 b3730 b2927, b3041, b3058 b3967 b3177, b3187, b3360 b3972 b3368, b3634, b3639 b3804, b3805, b3850 b3974, b3990, b3991 b3992, b3993, b3994 b3997, b4039, b4040 b4407, s0001 SS MM APM GM MLM PPB genes b0159 b0159 b0175 b0185 b0522, b0523...”

STY3742 UDP-N-acetylenolpyruvoylglucosamine reductase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t3489 UDP-N-acetylenolpyruvoylglucosamine reductase from Salmonella enterica subsp. enterica serovar Typhi Ty2
46% identity, 95% coverage

• Differences in gene content among Salmonella enterica serovar typhi isolates
  Boyd, Journal of clinical microbiology 2003
  • “...there is an amplification of 31 genes (STY3709 to STY3742) (region A in Fig. 1A). The amplified region encodes gene clusters required for thiamine biosynthesis...”
• High-throughput comparison of gene fitness among related bacteria
  Canals, BMC genomics 2012
  • “...38 14 15 20 27 15 15 STM14_4971.J murB UDP- N - acetylenolpyruvoylglucosamine reductase STM4136 t3489 b3972 42 48 26 22 8 24 13 21 * Details for all genes can be found in Additional file 5 : Table S2. Genes were ranked by the number...”

2q85A / P08373 Crystal structure of e. Coli mur b bound to a naphthyl tetronic acid inihibitor
45% identity, 96% coverage

• Ligands: (5z)-3-(4-chlorophenyl)-4-hydroxy-5-(1-naphthylmethylene)furan-2(5h)-one; flavin-adenine dinucleotide (2q85A)

SL1344_4081 UDP-N-acetylmuramate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
STM4137 UDP-N-acetylenolpyruvoylglucosamine reductase from Salmonella typhimurium LT2
45% identity, 95% coverage

• Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium
  Ondari, Infection and immunity 2017
  • “...nagA 113 3,794 4.192 7.88E07 N -acetylglucosamine6-phosphate deacetylase SL1344_0629 ybeA 111 2,881 3.820 1.45E06 (Pseudouridine1915-N3)-methyltransferase SL1344_4081 murB 99 2,347 3.620 1.55E06 UDP N -acetylenolpyruvoylglucosamine reductase SL1344_3894 cyaA 5,791 67,552 3.522 4.62E04 Adenylate cyclase SL1344_3376 sapG 270 3,361 3.226 6.53E04 trk system potassium uptake protein SL1344_1474 125...”
• Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray
  Reen, Applied and environmental microbiology 2005
  • “...all strains. The region encompassing genes STM3993 to STM4137 was amplified in serovar Typhimurium strain C5391 (Fig. 3). The amplification spanned the area...”

HI0268 UDP-N-acetylenolpyruvoylglucosamine reductase (murB) from Haemophilus influenzae Rd KW20
42% identity, 96% coverage

• Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor
  López-López, mSystems 2022
  • “...3.5.1.18 HI0102 ( dapE ) Succinyl-diaminopimelate desuccinylase 4.3.3.7 HI0255 ( dapA ) 4-Hydroxy-tetrahydrodipicolinate synthase 1.3.1.98 HI0268 ( murB ) UDP-N-acetylenolpyruvoylglucosamine reductase 2.4.1.129, 3.4.16.4 HI0440 ( ponA ) Penicillin-binding protein 1A 2.7.7.23, 2.3.1.157 HI0642 ( glmU ) Bifunctional protein GlmU 1.2.1.11 HI0646 ( asd ) Aspartate-semialdehyde dehydrogenase...”
• Elucidation of essential and nonessential genes in the Haemophilus influenzae Rd cell wall biosynthetic pathway by targeted gene disruption
  Trepod, Antimicrobial agents and chemotherapy 2005
  • “...HI0624 HI0865 HI1579 HI0197 HI1135 HI1337 HI1463 HI0831 HI0268 HI1139 HI1136 HI1133 HI1134 HI1138 HI1739 HI1081 HI0140 HI0032 HI0364 HI0440 HI1725 HI0829 a b...”

SF5M90T_3956 UDP-N-acetylmuramate dehydrogenase from Shigella flexneri 5a str. M90T
45% identity, 95% coverage

• RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
  Vergara-Irigaray, BMC genomics 2014
  • “...SF5M90T_3951 murI glutamate racemase 0.93 -0.48 SF5M90T_3821 rfaD ADP-L-glycero-D-mannoheptose-6-epimerase 0.82 SF5M90T_1241 tonB transport protein -1.72 SF5M90T_3956 murB UDP-N-acetylenolpyruvoylglucosamine reductase -2.23 -0.60 Cell motility SF5M90T_1938 fliQ flagellar biosynthetic protein 3.55 Intracellular trafficking, secretion and vesicular transport SF5M90T_3964 secE preprotein translocase 0.87 -1.06 -0.76 SF5M90T_3580 tatC Sec-independent protein...”

3i99A / Q9KV40 The crystal structure of the udp-n-acetylenolpyruvoylglucosamine reductase from the vibrio cholerae o1 biovar tor
42% identity, 98% coverage

• Ligand: flavin-adenine dinucleotide (3i99A)

Entcl_4187 UDP-N-acetylmuramate dehydrogenase from [Enterobacter] lignolyticus SCF1
45% identity, 95% coverage

• Complete genome sequence of "Enterobacter lignolyticus" SCF1
  Deangelis, Standards in genomic sciences 2011
  • “...pectinesterase (EC 3.1.1.11) Entcl_2112 LDA2 vanillyl-alcohol oxidase (EC 1.1.3.38) Entcl_1569 LDA2 D-lactate dehydrogenase (EC 1.1.1.28) Entcl_4187 LDA2 UDP-N-acetylmuramate dehydrogenase (EC 1.1.1.158) Entcl_3603 LO1 putative laccase (EC 1.10.3.2) Entcl_0735 LO1 putative laccase (EC 1.10.3.2) Entcl_4301 LO2 catalase/peroxidase (EC 1.11.1.6, 1.11.1.7) Enzyme families are as per the CAZy...”

A1S_2050 UDP-N-acetylenolpyruvoylglucosamine reductase FAD-binding from Acinetobacter baumannii ATCC 17978
44% identity, 83% 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
  • “...KZA74_01910 A1S_3115 NSD NSD ddrR and umuDAb KZA74_07370 A1S_2051 upreg NSD ddrR and umuDAb murB A1S_2050 NSD NSD ddrR and umuDAb recA A1S_1962 NSD NSD ddrR and umuDAb KZA74_09100 A1S_3727 NSD NSD ddrR and umuDAb KZA74_10320 A1S_1587 downreg NSD ddrR and umuDAb KZA74_10405 A1S_1584 downreg NSD...”

W5S_RS01035 UDP-N-acetylmuramate dehydrogenase from Pectobacterium parmentieri
42% identity, 94% coverage

• Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria
  Zoledowska, Microorganisms 2019
  • “...database (TTD). Locus Gene Candidate Drug Targets Function EC No. W5S_RS00975 WP_012822018.1 5,10-methylenetetrahydrofolate reductase 1.5.1.20 W5S_RS01035 WP_012822025.1 UDP-N-acetylenolpyruvoylglucosamine reductase 1.1.1.158 W5S_RS01045 WP_012822027.1 pantothenate kinase 2.7.1.33 W5S_RS09185 WP_014699609.1 GTP cyclohydrolase I 3.5.4.16 W5S_RS10395 WP_014699824.1 NAD synthetase 6.3.1.5 W5S_RS13505 WP_014700413.1 Thymidylate kinase 2.7.4.9 W5S_RS06665 WP_014699128.1 bifunctional folylpolyglutamate synthase/...”

SCO4643 UDP-N-acetylenolpyruvoylglucosamine reductase from Streptomyces coelicolor A3(2)
36% identity, 85% coverage

• Functional analysis of the N-acetylglucosamine metabolic genes of Streptomyces coelicolor and role in control of development and antibiotic production
  Świątek, Journal of bacteriology 2012
  • “...SCO4860 SCO4284 SCO5236 SCO2907 SCO2905 SCO4285 SCO2949 SCO5998 SCO4643 SCO4307 SCO5841 SCO1391 nagA nagB nagE2 nagF nagK murA murA2 murB murQ ptsH ptsI...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...transglycosylase 0.237226 0.17562 0.03522 0.2261 SCO4439 putative D-alanyl- D -alanine carboxypeptidase 0.74865 0.93049 0.177585 1.21329 SCO4643 murB 0.01505 0.20659 0.197283 0.35551 SCO5039 putative penicillin-binding protein 0.590106 0.70926 0.891819 0.313533 SCO5301 putative penicillin-binding protein 0.19347 0.13131 0.547233 0.22028 SCO5365 putative transferase 1.11236 0.27334 0.569152 1.16844 SCO5467 muramoyl-pentapeptide...”

MUL_4552 UDP-N-acetylenolpyruvoylglucosamine reductase MurB from Mycobacterium ulcerans Agy99
37% identity, 91% coverage

• Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer
  Stinear, Genome research 2007
  • “...in this 71-kb region include (1) murB (MUL_4552), encoding a reductase required for peptidoglycan biosynthesis; (2) icl (MUL_4536), encoding isocitrate lyase,...”

Blon_2254 UDP-N-acetylmuramate dehydrogenase from Bifidobacterium longum subsp. infantis ATCC 15697
34% identity, 74% coverage

• Genomic insights into bifidobacteria
  Lee, Microbiology and molecular biology reviews : MMBR 2010
  • “...Blon_0853 Blon_0320 Blon_0852 Blon_0893 Blon_0854 Blon_0857 Blon_2254 Blon_2321 B. longum subsp. infantis ATCC 15697 BAD_1508 BAD_1507 BAD_1509 BAD_0816...”

5jzxA / P9WJL9 Crystal structure of udp-n-acetylenolpyruvoylglucosamine reductase (murb) from mycobacterium tuberculosis (see paper)
36% identity, 92% coverage

• Ligand: flavin-adenine dinucleotide (5jzxA)

P9WJL9 UDP-N-acetylmuramate dehydrogenase (EC 1.3.1.98) from Mycobacterium tuberculosis (see paper)
MT0500 UDP-N-acetylenolpyruvoylglucosamine reductase from Mycobacterium tuberculosis CDC1551
NP_214996 UDP-N-acetylenolpyruvoylglucosamine reductase from Mycobacterium tuberculosis H37Rv
Rv0482 UDP-N-acetylenolpyruvoylglucosamine reductase from Mycobacterium tuberculosis H37Rv
35% identity, 91% coverage

• Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development
  Moraes, Tuberculosis (Edinburgh, Scotland) 2015
  • “...0.63 MurA MT1355 94.1% (93.2%) 5.09 (6.24) 0.79 (0.75) 3SWE [ 49 ] 0.25 MurB MT0500 87.0% (89.0%) 5.74 (5.01) 0.73 (0.62) 1MBT [ 68 ] 0.48 MurC MT2211 93.4% (92.4%) 4.55 (5.29) 0.79 (0.74) 3P31 [ 77 ] 0.26 MurD MT2214 88.1% (86.9%) 3.86 (4.44)...”
• Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis.
  Eniyan, Biochimica et biophysica acta. Proteins and proteomics 2018 (PubMed)
  • GeneRIF: findings indicate a detail mechanism about the closed to open state by binding of NADPH and UDP-N-acetylglucosamine-enolpyruvate (UDP-GlcNAc-EP) induces the conformational changes of MurB structure that may trigger the MurB catalytic reaction.
• Identification of hotspot regions of MurB oxidoreductase enzyme using homology modeling, molecular dynamics and molecular docking techniques.
  Kumar, Journal of molecular modeling 2011 (PubMed)
  • GeneRIF: Estimation of binding free energy by docking analysis indicated the importance of Tyr155, Arg156, Ser237, Asn241 and His304 residues within the Mycobacterium tuberculosis-MurB binding pocket.
• Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
  Rifat, mBio 2021
  • “...NE MAB_4775c NE Hypothetical protein ldt Mt4 (Rv0192) NE MAB_4537c NE Hypothetical protein ldt Mt5 (Rv0482) NE MAB_4061c NE Hypothetical protein Amidases ami1 (Rv3717) NE MAB_0318c GA Hypothetical protein ami2 (Rv3915) ES MAB_4942 ES N -Acetylmuramoyl- l -alanine amidase CwlM ami3 (Rv3811) NE MAB_0168c GA Putative...”
• Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall
  Batt, Cell surface (Amsterdam, Netherlands) 2020
  • “...or converted into UDP-MurNAc, a process that is carried out by MurA (Rv1315) and MurB (Rv0482). MurA, a UDP-GlcNAc enolpyruvyl transferase, first transfers enolpyruvate, from phosphoenolpyruvate, to the UDP-GlcNAc, forming UDP-N-acetylenolpyruvylglucosamine ( De Smet et al., 1999 ). MurB (Rv0482) is a UDP-N-acetylenolpyruvylglucosamine reductase that next...”
• Revisiting Anti-tuberculosis Therapeutic Strategies That Target the Peptidoglycan Structure and Synthesis
  Catalão, Frontiers in microbiology 2019
  • “...N -acetylmuramic acid (UDP-Mur N Ac)-pentapeptide. MurA (Rv1315), a UDP- N -acetylglucosamine 1-carboxyvinyltransferase, and MurB (Rv0482), a UDP- N -acetylenolpyruvoylglucosamine reductase, are implicated in the formation of UDP-Mur N Ac. NamH (Rv3808), a UDP- N -acetylmuramic acid hydroxylase, hydroxylates UDP-Mur N Ac to UDP- N -glycolylmuramic...”
• Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics
  Gupta, High-throughput 2018
  • “...tuberculosis H37Rv) Figure Number Ins/Del Location Mutational Results # putative UDP- N -acetylenolpyruvoyl-glucosamine reductase (MurB) Rv0482 Figure 3 A, Figure S1 4aa Ins 249298 Essential putative 3-phosphoadenosine 5-phosphosulfate reductase (CysH) (PAPS reductase, thioredoxin dep) Rv2392 Figure 3 B, Figure S2 7aa Ins 1771 Essential (growth defect)...”
• Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress
  Williams, Molecular microbiology 2015
  • “...Rv1162, Rv1163, Rv1164, Rv1737, Rv2329, Rv2391 u2 <0.001 11 5 Citrate/oxaloacetate metabolism Rv0211, Rv0337, Rv0467, Rv0482, Rv0889, Rv0896, Rv1023, Rv1130, Rv1131, Rv1315, Rv1475, Rv1595, Rv1915, Rv3565 u3 0.01 1 1 Phthiocerol precursor ligase Rv2930 Down d1 <0.001 9 5 Rv1408, Rv1436, Rv1437, Rv1438, Rv1449, Rv1611, Rv1612,...”
• Mycobacterium tuberculosis H37Rv: In Silico Drug Targets Identification by Metabolic Pathways Analysis
  Amir, International journal of evolutionary biology 2014
  • “...Rv0113 Phosphoheptose isomerase (EC: 5. ..) Yes 42. Rv1315 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC: 2.5.1.7) Yes 43. Rv0482 UDP-N-acetylenolpyruvoylglucosamine reductase (EC: 1.1.1.158) Yes 44. Rv2152c UDP-N-acetylmuramate-L-alanine ligase (EC: 6.3.2.8) Yes 45. Rv2155c UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase (EC: 6.3.2.9) Yes 46. Rv2157c UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanyl ligase MurF Yes 47. Rv2156c Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC: 2.7.8.13)...”
  • “...cell wall organization, growth, peptidoglycan biosynthetic process, regulation of cell shape UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity 41. Rv0482 Cytoplasm Cell cycle, cell division, cellular cell wall organization, oxidation-reduction process, peptidoglycan biosynthetic process, regulation of cell shape UDP-N-acetylmuramate dehydrogenase activity, flavin adenine dinucleotide binding 42. Rv2152c Cytoplasm Cell cycle,...”
• Genomic mapping of cAMP receptor protein (CRP Mt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor
  Kahramanoglou, Nucleic acids research 2014
  • “...1 Rv3616c espA 983.5 between divergent genes Rv3617 ephA 55.5 11.6 571602 571601.5 0.5 1 Rv0482 murB >500 Internal to gene 571517.5 84.5 3 Rv0483 lprQ 150.5 Upstream of gene Rv0482 murB >500 Internal to gene Rv0483 lprQ 234.5 Upstream of gene 11.0 2752669 2752680.5 11.5...”
• The cell envelope glycoconjugates of Mycobacterium tuberculosis
  Angala, Critical reviews in biochemistry and molecular biology 2014
  • “...formation of UDP-MurNAc from UDP-GlcNAc in a two-step reaction catalyzed by MurA (Rv1315) and MurB (Rv0482) is the first committed step in the biosynthesis of Parks nucleotide (UDP- N -acetylmuramyl-L-alanyl-D-glutamyl- meso -diaminopimelyl-D-alanyl-D-alanine). UDP-GlcNAc is the product of the phosphoglucosamine mutase GlmM (Rv3441c) and the UDP- N...”
• More

BAD_RS01580 FAD-binding protein from Bifidobacterium adolescentis ATCC 15703
32% identity, 76% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...BAD_RS06090 1.14 cscA Beta(12)fructofuranosidase 47.64 21.63 ko01100/ko00500/ko00052 BAD_RS05480 1.11 BAD_1030 Mannan endo1,4betamannosidase 29.85 13.79 ko00051 BAD_RS01580 1.08 murB UDPNacetylenolpyruvoylglucosamine reductase 198.47 93.71 ko01100/ko00520/ko00550 BAD_RS08480 1.06 bglB Betaglucosidase 137.7 66.25 ko01100/ko01110/ko00500/ko00460 BAD_RS07395 1.05 bgaB Betagalactosidase I 175.7 84.64 ko00052 BAD_RS05595 1.05 acn Aconitate hydratase 137.1 283.08 ko01100/ko01110/ko01130/ko01230/ko01120/ko01200/ko01210/ko00630/ko00020...”

BDP_0408 murB UDP-N-acetylenolpyruvoylglucosamine reductase from Bifidobacterium dentium Bd1
31% identity, 82% coverage

• Genomic insights into bifidobacteria
  Lee, Microbiology and molecular biology reviews : MMBR 2010
  • “...BDP_1542 BDP_1545 BDP_0283 BDP_1546 BDP_1521 BDP_1544 BDP_1541 BDP_0408 BDP_0275 B. dentium Bd1 Locus tag Balac_1377 Balac_1378 Balac_1376 Balac_0808 Balac_0496...”

BL1561 UDP-N-acetylenolpyruvoylglucosamine reductase from Bifidobacterium longum NCC2705
32% identity, 79% coverage

• Genomic insights into bifidobacteria
  Lee, Microbiology and molecular biology reviews : MMBR 2010
  • “...BL1319 BL1321 BLD_0179 BLD_1112 BLD_0177 BL1324 BL1561 BL1267 NCC2705 BLD_0182 BLD_1681 BLD_1600 DJO10A Blon_2390 Blon_1169 Blon_0546 Blon_1151 Blon_0079,...”

OJAG_01210 UDP-N-acetylmuramate dehydrogenase from Oerskovia enterophila
35% identity, 83% coverage

• Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium
  Jag, Standards in genomic sciences 2017
  • “...N-acetylglucosamine enopyruvate can subsequently be converted to N-acetylmuramic acid via an UDP-N-acetylmuramate dehydrogenase (encoded by OJAG_01210). N-acetylmuramic acid would be metabolized through the peptidoglycan biosynthesis pathway or the D-glutamin and D-glutamate metabolism (OJAG_14230; _ OJAG 14240). Additionally, genes encoding enzymes for xylose degradation were found in...”

5jzxB / P9WJL9 Crystal structure of udp-n-acetylenolpyruvoylglucosamine reductase (murb) from mycobacterium tuberculosis (see paper)
34% identity, 99% coverage

• Ligand: flavin-adenine dinucleotide (5jzxB)

Q3Y1W9 UDP-N-acetylenolpyruvoylglucosamine reductase from Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
28% identity, 92% coverage

• Proteomic characterization of persisters in Enterococcus faecium
  Pont, BMC microbiology 2024
  • “...protein -1.78 11,804 Q3Y303 MarR family transcriptional regulator -1.72 pgsA Q3Y0P3 CDP-diacylglycerolglycerol-3-phosphate 3-phosphatidyltransferase -1.69 murB Q3Y1W9 UDP-N-acetylenolpyruvoylglucosamine reductase -1.67 mobC I3U5U5 Mobilization protein C -1.57 -3.45 12,063 I3U3U9 M20/M25/M40 family peptidase 1.51 polA I3U2E8 DNA polymerase I 1.51 erpQ Q3XZG3 ErpQ protein 1.54 cspA I3U0N2 Cold...”

D6YVJ9 UDP-N-acetylenolpyruvoylglucosamine reductase from Waddlia chondrophila (strain ATCC VR-1470 / WSU 86-1044)
27% identity, 99% coverage

• Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein
  Chowdhury, Heliyon 2021
  • “...Chorismate synthase (D6YWA2), Glycerol-3-phosphate dehydrogenase [NAD(P)+] (D6YST7), Putative D-alanyl-D-alanine carboxypeptidase (D6YS23), UDP-N-acetylenol pyruvoyl glucosamine reductase (D6YVJ9), DNA topoisomerase (D6YVX0), Putative multidrug resistance protein MdtC (D6YSV9). Among the eight proteins, DNA topoisomerase and Putative multidrug resistance protein MdtC were metabolic pathways independent and the rest were metabolic...”
  • “...Ceftolozane, Carindacillin, Cefmetazole, Ertapenem, Cefpiramide, Cefoperazone, Cefoxitin, Ceftizoxime 1.24E-29 116 6 UDP-N-acetylenol pyruvoyl glucosamine reductase D6YVJ9 P61432 DB03147 Flavin adenine dinucleotide 3.22E-48 160 Metabolic Pathway Independent 7 DNA topoisomerase D6YVX0 Q06AK7 DB00487, DB01051 Pefloxacin, Novobiocin 3.63E-36 142 8 Putative multidrug resistance protein MdtC D6YSV9 P31224 DB03619,...”

B1745_04590 UDP-N-acetylmuramate dehydrogenase from Lactobacillus amylolyticus
26% identity, 98% coverage

• Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
  Fei, Food science & nutrition 2022
  • “...DalanylDalanine carboxypeptidase 1.44 B1745_02005 bcrC phospholipid phosphatase 1.44 B1745_03140 fumC class II fumarate hydratase 1.43 B1745_04590 murB UDP N acetylenolpyruvoylglucosamine reductase 1.38 B1745_04460 glgC YebC/PmpR family DNAbinding transcriptional regulator 1.36 B1745_04525 spp HAD family hydrolase 1.33 B1745_03145 frdA flavocytochrome c 1.32 B1745_02465 galE UDPglucose4epimerase 1.30 B1745_07245...”

CDR20291_3224 UDP-N-acetylenolpyruvoylglucosamine reductase from Clostridium difficile R20291
26% identity, 96% coverage

• Proteomic Signatures of Clostridium difficile Stressed with Metronidazole, Vancomycin, or Fidaxomicin
  Maaß, Cells 2018
  • “...RimM x x x CDIF630erm_03522 DapB1 CDR20291_3086 4-hydroxy-tetrahydrodipicolinate reductase x x x x CDIF630erm_03707 MurB CDR20291_3224 UDP- N -acetylenolpyruvoyl-glucosamine reductase x x CDIF630erm_02841 RpoZ CDR20291_2474 DNA-directed RNA polymerase subunit omega x x CDIF630erm_01509 CDIF630erm_01509 CDR20291_1195 putative pyridoxine kinase x CDIF630erm_02877 CDIF630erm_02877 CDR20291_2507 putative pyridoxal 5-phosphate-dependent enzyme...”

Q8YM74 UDP-N-acetylmuramate dehydrogenase (EC 1.3.1.98) from Anabaena sp. (see paper)
alr5066 UDP-N-acetylenolpyruvylglucosamine reductase from Nostoc sp. PCC 7120
26% identity, 99% coverage

• Final Destination? Pinpointing Hyella disjuncta sp. nov. PCC 6712 (Cyanobacteria) Based on Taxonomic Aspects, Multicellularity, Nitrogen Fixation and Biosynthetic Gene Clusters
  Jung, Life (Basel, Switzerland) 2021
  • “...( alr0094 ) [ 39 , 40 , 41 ]; the mur operon murB ( alr5066 ) and murC ( alr5065 ) [ 42 ]; mreB ( all0087 ), mreC ( all0086 ), mreD ( all0085 ) [ 43 ], mdrA ( alr5045 ) and alr2270...”
• The Integrity of the Cell Wall and Its Remodeling during Heterocyst Differentiation Are Regulated by Phylogenetically Conserved Small RNA Yfr1 in Nostoc sp. Strain PCC 7120
  Brenes-Álvarez, mBio 2020
  • “...strains with mutations in the peptidoglycan synthesis enzymes MurC ( alr5065 ) and MurB ( alr5066 ) ( 13 ) and in some penicillin binding proteins (PBPs) (those encoded by all2981 , alr4579 , and alr5051 ) ( 14 , 15 ) show alterations in heterocyst...”
• Mutation of the murC and murB Genes Impairs Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
  Videau, Journal of bacteriology 2016
  • “...two peptidoglycan synthesis genes, murC (alr5065) and murB (alr5066), as required for heterocyst development. The murC and murB genes are predicted to encode a...”
  • “...the murine ligase genes murC (alr5065) and murB (alr5066) for maintenance of patterned gene expression, filament integrity, and overall development. This work...”

BMF81_03481 UDP-N-acetylmuramate dehydrogenase from Nodularia spumigena UHCC 0039
26% identity, 97% coverage

• Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
  Teikari, Frontiers in microbiology 2018
  • “...N-acetylmuramoyl-L-alanine amidase 2.6 GO:0071840 BMF81_03893 N-acetylmuramoyl-L-alanine amidase 1.67 GO:0071704 BMF81_02030 lytC Peptidoglycan-N-acetylglucosamine deacetylase 1.27 GO:0071704 BMF81_03481 murB UDP-N-acetylenolpyruvoylglucosamine reductase 1.45 GO:0071704 BMF81_03482 murC UDP-N-acetylmuramate L-alanine ligase 1.28 TRANSCRITPION AND TRANSLATION GO:0016987 BMF81_01360 sigB RNA polymerase sigma factor 2.08 GO:0016987 BMF81_00786 sigG RNA polymerase sigma factor 1.25...”

Q8Y776 UDP-N-acetylenolpyruvoylglucosamine reductase from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo1420 weakly similar to UDP-N-acetylglucosaminyl-3-enolpyruvate reductase from Listeria monocytogenes EGD-e
26% identity, 99% coverage

• Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
  Pinilla, Data in brief 2022
  • “...free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins Q8Y776 lmo1420 murB Nis / LNis UDP- N -acetylenolpyruvoylglucosamine reductase; cell wall formation Q92EH3 lmo0484 isdG Nis / LNis Heme-degrading monooxygenase IsdG; allows bacterial pathogens to use the host heme as...”
• Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
  Pinilla, Data in brief 2022
  • “...subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins Q8Y776 lmo1420 murB Nis / LNis UDP- N -acetylenolpyruvoylglucosamine reductase; cell wall formation Q92EH3 lmo0484 isdG Nis / LNis Heme-degrading monooxygenase IsdG; allows bacterial pathogens to use the host heme as an...”
• Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
  Orsi, BMC evolutionary biology 2008
  • “..., lmo0860 , lmo0877 , lmo1087 , proA , lmo0992 , smbA , lmo1401 , lmo1420 , opuCC , trpD , lmo1693 , purK , lmo1825 , panB , lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487 , lmo0878 , lmo1004 , lmo1011 , and...”
  • “..., lmo1087 , proA ( lmo1259 ), lmo0992 , smbA ( lmo1313 ), lmo1401 , lmo1420 , opuCC ( lmo1426 ), trpD ( lmo1631 ), lmo1693 , purK ( lmo1774 ), lmo1825 , panB ( lmo1902 ), lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487...”

OG1RF_RS10725 UDP-N-acetylmuramate dehydrogenase from Enterococcus faecalis OG1RF
Q830P3 UDP-N-acetylenolpyruvoylglucosamine reductase from Enterococcus faecalis (strain ATCC 700802 / V583)
EF2733 UDP-N-acetylenolpyruvoylglucosamine reductase from Enterococcus faecalis V583
27% identity, 92% coverage

• Bacillus subtilis natto Derivatives Inhibit Enterococcal Biofilm Formation via Restructuring of the Cell Envelope
  Lin, Frontiers in microbiology 2021
  • “...OG1RF_RS06740 Forward 5-CGTGTCGTTGTCGTTGGTGG-3 Reverse 5-ATGCGGTCTAACCCGTCAACT-3 This study OG1RF_RS10140 murA Forward 5-GCTTCCACTGCTGCTCCTTG-3 Reverse 5-GCGTCGAATGAACGCTGACT-3 This study OG1RF_RS10725 murB Forward 5-AGCGGTTGCTTCAGTTCACG-3 Reverse 5- TGCAGAAGTGCTGTTGGCAG 3 This study OG1RF_RS03015 murF Forward 5- GCAGCGAATGGTGCCGAAAT-3 Reverse 5- TGCTGCGCCATTGCTTGATG 3 This study OG1RF_RS03765 murG Forward 5- TTGACCGGCGCTCGTTTAGT-3 Reverse 5- CGCCGTTGCCATCTGTTGTC -3 This...”
  • “...pathway and WalK/WalR regulatory system, the relative expression of UDP-GlcNAc enolpyruvyl transferase (murA; OG1RF_RS10140), murB (OG1RF_RS10725), murF (OG1RF_RS03015), and murG (OG1RF_RS03765) in the peptidoglycan biosynthesis pathway and the response regulator-encoding gene walR (OG1RF_RS05030) in the WalK/WalR two-component system were assessed further using RT-qPCR. As shown in...”
• Identification and comparison of protein composition of biofilms in response to EGCG from <i>Enterococcus faecalis</i> and <i>Staphylococcus lugdunensis</i>, which showed opposite patterns in biofilm-forming abilities
  Cho, Biofilm 2024
  • “...A0A133Q8C0 EF_1312 EQ (812)_03780 S1 RNA binding domain protein Q830N8 A0A292DE51 trmR tRNA 5-hydroxyuridine methyltransferase Q830P3 A0A133Q1I3 murB UDP-N-acetylenolpyruvoylglucosamine reductase Q839G8 A0A133PZU5 tuf Elongation factor Tu Q832Q8 A0A133Q3P9 hflX GTPase HflX Q836G9 A0A133Q747 EF_2413 HMPREF3225_01109 HD domain protein Q839Q9 A0A133Q657 sdhA-1 sdaAA l -serine dehydratase Q833Y4...”
• Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (Ocimum basilicum L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study
  Evangelina, Advances and applications in bioinformatics and chemistry : AABC 2021
  • “...for this assay was chlorhexidine. MurA enzyme (protein data bank ID: 1UAE), MurB enzyme (UniProtKB: Q830P3), PBP (protein data bank ID: 6MKG), and SrtA (protein data bank ID: 2KW8) were used for screening antibacterial activity in this research. The 3D structure was retrieved from RSCB Protein...”
• Effectiveness of Bioactive Compound as Antibacterial and Anti-Quorum Sensing Agent from Myrmecodia pendans: An In Silico Study
  Satari, Molecules (Basel, Switzerland) 2021
  • “...from Protein Data Bank, while others were retrieved from UniProt. They were MurB (UniProt ID: Q830P3), RNA polymerase subunit beta (UniProt ID: Q82Z41), ribosomal subunit 30S (UniProt ID: Q82ZI6), ribosomal subunit 50S (UniProt ID: Q839E6), FsrB (UniProt ID: G8ADN9), and GBAP (UniProt ID: G8ADP0). Meanwhile, the...”
  • “...from Protein Data Bank. Meanwhile, others were retrieved from UniProt. They are MurB (UniProt ID: Q830P3), RNA polymerase subunit beta (UniProt ID: Q82Z41), ribosomal subunit 30S (UniProt ID: Q82ZI6), ribosomal subunit 50S (UniProt ID: Q839E6), FsrB (UniProt ID: G8ADN9), and GBAP (UniProt ID: G8ADP0), which were...”
• The two-component system CroRS acts as a master regulator of cell envelope homeostasis to confer antimicrobial tolerance in the bacterial pathogen Enterococcus faecalis
  Todd, Molecular microbiology 2023
  • “...pbp1B/pbpZ 2.2 Penicillinbinding protein 1B EF2585 murT 3.3 mur ligase EF2586 gatD 3.0 Glutamine amidotransferase EF2733 murB 2.7 UDP N acetylenolpyruvoylglucosamine reductase EF2857 pbp2B/pbpA 4.8 Penicillinbinding protein 2B EF2860 pbp 2.5 Putative peptidoglycan transpeptidase Epa polysaccharide biosynthesis EF2170 c epaX 2.1 Glycosyl transferase group 2 family...”
• The two-component system CroRS regulates isoprenoid flux to mediate antimicrobial tolerance in the bacterial pathogenEnterococcus faecalis
  Todd, 2022
• Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
  Gilmore, mBio 2020
  • “...C Fe UE l -Serine dehydratase, 2C iron-sulfur-dependent, 2C alpha subunit 0.052 100 E SAW_02536 EF2733 Important ABC Redox UDP- N -acetylenolpyruvoylglucosamine reductase 0.011 100 M SAW_02674 EF2881 Critical ABC Redox 3-Oxoacyl-[acyl-carrier-protein] reductase 0.000 100 I SAW_02691 EF2899 Critical AC Fe Ferredoxin-NADP reductase 0.000 100 O...”

LMOf2365_1439 UDP-N-acetylenolpyruvoylglucosamine reductase from Listeria monocytogenes str. 4b F2365
25% identity, 99% coverage

• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in <i>Listeria monocytogenes</i>
  Ogunleye, Frontiers in microbiology 2024
  • “...Peptidoglycan biosynthesis LMOf2365_2499 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1: EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ( murA -)1 1.5 1.1E-02 LMOf2365_1439 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain ( murB ) 1.9 9.0E-04 LMOf2365_1483 Undecaprenol kinas: Prokaryotic diacylglycerol kinase ( dgkA ) 1.5 4.6E-03 LMOf2365_2069 Phospho-N-acetylmuramoyl-pentapeptide-transferase: Glycosyl transferase family 4 ( mraY ) 1.6...”

SSA_1047 UDP-N-acetylenolpyruvoylglucosamine reductase, putative from Streptococcus sanguinis SK36
26% identity, 96% coverage

• Involvement of signal peptidase I in Streptococcus sanguinis biofilm formation
  Aynapudi, Microbiology (Reading, England) 2017
  • “...a nonfunctional Ldh. Moreover, the KEGG database shows that many enzymes are (NAD+)-dependent, such as SSA_1047 (MurB involved in peptidoglycan biosynthesis), SSA_2168 (GpsA involved in glycerophospholipid biosynthesis) and SSA_1938 (FabK involved in fatty acid biosynthesis). We suggest that a nonfunctional lactate dehydrogenase may be impacting on...”

3tx1A / Q8Y776 X-ray crystal structure of listeria monocytogenes egd-e udp-n- acetylenolpyruvylglucosamine reductase (murb)
25% identity, 99% coverage

• Ligand: flavin-adenine dinucleotide (3tx1A)

BA5315 UDP-N-acetylenolpyruvoylglucosamine reductase from Bacillus anthracis str. Ames
BAS4937 UDP-N-acetylenolpyruvoylglucosamine reductase from Bacillus anthracis str. Sterne
25% identity, 96% coverage

• Evaluation of the metS and murB loci for antibiotic discovery using targeted antisense RNA expression analysis in Bacillus anthracis
  Kedar, Antimicrobial agents and chemotherapy 2007
  • “...metS1 (BA0036), metS2 (BA5278), murB1 (BA4048), and murB2 (BA5315) genes was derived from the GenBank entry for the complete genome sequence of B. anthracis...”
  • “...AATAATGTCGACTCATCAAATGAACCATTCTTG CCGGCTCTTGCTTTAATAAG TTCATTTAAGAATATCGCAGTAAAC murB2 BA5315 MB2-1 MB2-2 MB2-3 MB2-4 MB2-5 MB2-6...”
• Ser/Thr protein kinase PrkC-mediated regulation of GroEL is critical for biofilm formation in Bacillus anthracis
  Arora, NPJ biofilms and microbiomes 2017
  • “...1 Bas0107, fusA Elongation factor-G 2 Bas3470 Transketolase 3 Bas0253, groEL GroEL, 60kDa chaperone 4 Bas4937, murB UDP-N-acetylenolpyruvoylglucosamine reductase 5 Bas4985, eno Phosphopyruvate hydratase 6 Bas5155 ATP synthase F0F1 subunit beta 7 Bas3882 Pyruvate dehydrogenase E1 component subunit beta 8 Bas4070 Leucine dehydrogenase 9 Bas3677, tsf...”

COLAER_01957 UDP-N-acetylmuramate dehydrogenase from Collinsella aerofaciens ATCC 25986
27% identity, 96% coverage

• Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome
  Culligan, The ISME journal 2012
  • “...(closest relative being Collinsella aerofaciens) (COLAER_01955, COLAER_01957 and COLAER_01981), a high G C, Gram-positive member of the Actinobacteria...”
  • “...The genes; galE(3) (COLAER_01955), murB(3) (COLAER_01957) and mazG(3) (COLAER_01981), encode hypothetical proteins similar to UDP-glucose 4-epimerase...”

4pytA / Q65JX9 Crystal structure of a murb family ep-udp-n-acetylglucosamine reductase (see paper)
26% identity, 97% coverage

• Ligand: flavin-adenine dinucleotide (4pytA)

ZY05719_03880 UDP-N-acetylmuramate dehydrogenase from Streptococcus suis
SSU05_0804 UDP-N-acetylenolpyruvoylglucosamine reductase from Streptococcus suis 05ZYH33
26% identity, 96% coverage

• Establishment of Streptococcus suis Biofilm Infection Model In Vivo and Comparative Analysis of Gene Expression Profiles between In Vivo and In Vitro Biofilms
  Yi, Microbiology spectrum 2023
  • “...protein ZY05719_06545 AKG40647.1 Cell surface protein ZY05719_06925 AKG40717.1 Flotillin Cell wall ZY05719_09420 AKG41193.1 Penicillin-binding protein ZY05719_03880; murB AKG40137.1 UDP- N -acetylenolpyruvoylglucosamine reductase Transmembrane transport ZY05719_03890 AKG40139.1 Spermidine/putrescine ABC transporter permease I ZY05719_03235 AKG40022.1 MFS transporter ZY05719_09375 AKG41185.1 Bacterocin transport accessory protein, Bta Transcriptional regulation ZY05719_08635 AKG41044.1...”
  • “...genes in the in vitro biofilm transcriptomic data, with the exceptions being ZY05719_02660, ZY05719_02335, ZY05719_06545, ZY05719_03880, ZY05719_09920, and ZY05719_03235, which to a certain extent verifies the reliability of SCOTS technology in the screening of gene expression differences under specific conditions (Table S2). In addition, about 8.7%...”
• MnmE, a Central tRNA-Modifying GTPase, Is Essential for the Growth, Pathogenicity, and Arginine Metabolism of Streptococcus suis Serotype 2
  Gao, Frontiers in cellular and infection microbiology 2019
  • “...SSU05_0651 UDP-MurNAc-tripeptide synthetase 0.8158 11 27.70 ParB SSU05_2193 Chromosome partitioning protein 1.2174 6 22.44 MurB SSU05_0804 UDP-N-acetylmuramate dehydrogenase 1.2363 10 37.09 FtsE SSU05_1411 Cell division ATP-binding protein 1.2679 12 51.74 VIRULENCE-ASSOCIATED PROTEINS SadP SSU05_0272 Translation initiation factor 2 GTPase 0.5742 16 47.28 STK SSU05_0428 Serine/threonine protein...”

BA4048 UDP-N-acetylenolpyruvoylglucosamine reductase from Bacillus anthracis str. Ames
27% identity, 96% coverage

• Evaluation of the metS and murB loci for antibiotic discovery using targeted antisense RNA expression analysis in Bacillus anthracis
  Kedar, Antimicrobial agents and chemotherapy 2007
  • “...of B. anthracis metS1 (BA0036), metS2 (BA5278), murB1 (BA4048), and murB2 (BA5315) genes was derived from the GenBank entry for the complete genome sequence...”
  • “...Primer name Primer sequence murB1 BA4048 MB1-1 MB1-2 MB1-3 MB1-4 MB1-5 MB1-6 AATAATGGATCCTACAATCGTTCCAAAAGCAG AATAATGGCGCGCCAAACAATCTCCCCCATACTC...”

BB0598 UDP-N-acetylmuramate dehydrogenase (murB) from Borrelia burgdorferi B31
23% identity, 96% coverage

• Plasticity in early immune evasion strategies of a bacterial pathogen
  Bernard, Proceedings of the National Academy of Sciences of the United States of America 2018
  • “...Appendix, Fig. S2C), expression of bb0405, bb0090, and bb0598 was found specifically induced in bba57 mutants in vivo (Fig. 2D). Overall, these results indicate...”
  • “...0.1 0.1 * 1000 1000 1010 0.01 0.01 bb0405 bb0090 bb0598 PNAS PLUS Re-infection Relative level of B. burgdorferi (copies of flaB/106 -actin) *** *** *** *** Skin...”
• Acetyl-Phosphate Is Not a Global Regulatory Bridge between Virulence and Central Metabolism in Borrelia burgdorferi
  Richards, PloS one 2015
  • “...-P, a peptidoglycan precursor ( Fig 1 ). The genes bb0622 ( ackA ) and bb0598 ( pta ) encode enzymes that catalyze the first two steps of this pathway ( Fig 1 , shaded area). Acetate kinase (AckA) enzymatically catalyzes the conversion of acetate to...”
• EbfC (YbaB) is a new type of bacterial nucleoid-associated protein and a global regulator of gene expression in the Lyme disease spirochete
  Jutras, Journal of bacteriology 2012
  • “...proS (BB0402) nucA (BB0411) ligA (BB0552) murB (BB0598) ptsG (BB0645) xylR-1 (BB0693) pbp3 (BB0732) ABC transporter ATP-binding protein (BB0742) xylR-2...”
• Rrp1, a cyclic-di-GMP-producing response regulator, is an important regulator of Borrelia burgdorferi core cellular functions
  Rogers, Molecular microbiology 2009
  • “...ksgA ) NM 198 0.0166 BB0596 methyl-accepting chemotaxis protein ( mcp-2 ) CH 240 0.0114 BB0598 UDP- N -acetylmuramate dehydrogenase ( murB ) CE 104 0.0475 BB0600 hypothetical protein U 13.6 0.0181 Narasimhan et al . (2002) BB0604 L-lactate permease ( lctP ) TP 4.63 0.0297...”

SMU_RS04475 UDP-N-acetylmuramate dehydrogenase from Streptococcus mutans UA159
25% identity, 96% coverage

• Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans
  Qin, Microbiology spectrum 2024
  • “...2.6 4 UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase, MurD SMU_RS08200 2.4 Isoprenyl transferase, UppS SMU_RS07130 2.3 UDP-N-acetylglucosamine 1-carboxyvinyltransferase, MurA2 SMU_RS04475 2 2 UDP-N-acetylmuramate dehydrogenase, MurB SMU_RS07620 2 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, MurE Cell division SMU_RS02635 7 FtsQ-type POTRA domain-containing protein, FtsQ SMU_RS02645 6.5 Cell division protein, FtsZ SMU_RS02655 3.5 Cell division protein,...”

Bresu_2691 UDP-N-acetylmuramate dehydrogenase from Brevundimonas subvibrioides ATCC 15264
29% identity, 96% coverage

• Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
  Curtis, Molecular microbiology 2014
  • “...precursor synthesis Gene Gene Gene MurA CC_2350 E Bresu_2247 E Atu0539 E MurB CC_2545 E Bresu_2691 E Atu2092 E MurC CC_2546 E Bresu_2692 Bresu_1060 E N Atu2093 E MurD CC_2556 E Bresu_2778 E Atu2096 E MurE CC_2559 E Bresu_2781 E Atu2099 E MurF CC_2558 E Bresu_2780...”

B8ZKN7 UDP-N-acetylenolpyruvoylglucosamine reductase from Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-1)
spr1247 UDP-N-acetylenolpyruvoylglucosamine reductase from Streptococcus pneumoniae R6
24% identity, 96% coverage

• <i>In Silico</i> Identification and Characterization of Drug Targets in <i>Streptococcus pneumoniae</i> ATCC 700669 (Serotype 23F) by Subtractive Genomics
  Duguma, BioMed research international 2024
  • “...of the reaction: phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxy vinyl)-D-glucosamine 6 murB UDP-N-acetylmuramate dehydrogenase B8ZKN7 Cytoplasmic Peptidoglycan biosynthetic process (uridine diphospho-N-acetyl glucose amine enolpyruvate reductase activity) 7 MurC UDP-N-acetylmuramate--alanine ligase B8ZLC2 Cytoplasmic Cell wall formation; UDP-N-acetylmuramate-L-alanine ligase activity, peptidoglycan biosynthesis 8 MurD UDP-N-acetylmuramoyl alanine-D-glutamate ligase...”
• COMPOSITION FOR SCREENING ANTIBIOTICS COMPRISING GENE SPR1247 FROM STREPTOCOCCUS PNEUMONIAE OR PROTEIN ENCODED THEREBY ESSENTIAL TO SURVIVAL OF STREPTOCOCCUS PNEUMONIAE, AND METHOD FOR SCREENING ANTIBIOTICS USING THE SAME
  SONG, 2004

J8Y18_19300 UDP-N-acetylmuramate dehydrogenase from Bacillus cereus
27% identity, 96% coverage

• Investigating the Role of OrbF in Biofilm Biosynthesis and Regulation of Biofilm-Associated Genes in Bacillus cereus BC1
  Sun, Foods (Basel, Switzerland) 2024
  • “...J8Y18_18390 ), putative proteins ( J8Y18_18430 , J8Y18_22905 , J8Y18_08480 , J8Y18_03975 ), UDP-N-acetylglucosamine dehydrogenase (J8Y18_19300 ), coproporphyrinogen III oxidase (J8Y18_04490 ), acetyl lactate synthase small subunit ( J8Y18_07090 ), DNA topoisomerase IV subunit A ( J8Y18_17815 ), phosphoribosylamine-glycine ligase ThiC (J8Y18_25845 ), glycosyltransferase family I...”
  • “...reason for its biofilm defect. The genes encoding nitrate/nitrite reductase ( J8Y18_07220 ), UDP-N-acetylmuramate dehydrogenase (J8Y18_19300 ), and UDP-N-acetylgalactosamine lipid carrier transferase ( J8Y18_08880 ) participate in sugar metabolism and redox reactions. Nitrate/nitrite reductases are predominantly intracellular enzymes capable of efficiently degrading nitrate, suggesting their involvement...”

GSU3067 UDP-N-acetylenolpyruvoylglucosamine reductase from Geobacter sulfurreducens PCA
30% identity, 91% coverage

• Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production
  Butler, BMC genomics 2012
  • “...subunit GSU3058 15.6 32 KN400_3000 squalene cyclase domain protein GSU3061 12.3 107 KN400_3006 UDP-N-acetylenolpyruvylglucosamine reductase GSU3067 21.1 58 KN400_3214 cytochrome c GSU3274 28.8 32 KN400_3301 sensor histidine kinase GSU3357 22.2 146 KN400_3348 OmpJ-related porin GSU3403 29.9 97 KN400_3368 dihydrolipoamide dehydrogenase-related protein GSU3424 16.4 86 Some genes...”
  • “...KN400_2637 36.6 1.35 GSU2773 conserved domain protein none 1.62 GSU2779 transcriptional regulator KN400_2716 18.0 3.77 GSU3067 UDP-N-acetylenolpyruvylglucosamine reductase KN400_3006 21.1 1.32 GSU3403* OmpJ porin KN400_3348 29.9 2.76 In addition to these copper proteins, a transcriptional regulator (GSU2779) with homology to CueR, a copper-responsive transcriptional activator [...”

Oter_2637 UDP-N-acetylenolpyruvoylglucosamine reductase from Opitutus terrae PB90-1
WP_012375453 UDP-N-acetylmuramate dehydrogenase from Opitutus terrae PB90-1
28% identity, 41% coverage

• CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
  Zaharia, BMC bioinformatics 2019
  • “...possess peptidoglycan cell walls. We propose the candidate murC gene in O. terrae to be Oter_2637 , following a protein BLAST [ 39 ] for the E. coli MurC query sequence (WP_012375453 with 29% identity, 94% query cover, E-value 5e 41). Uncovering unexpected gene ordering patterns...”
• CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
  Zaharia, BMC bioinformatics 2019
  • “..., following a protein BLAST [ 39 ] for the E. coli MurC query sequence (WP_012375453 with 29% identity, 94% query cover, E-value 5e 41). Uncovering unexpected gene ordering patterns Figure 4 a shows a CoMetGeNe trail for E. coli in the glycine, serine, and threonine...”

RC0332 UDP-N-acetylenolpyruvoylglucosamine reductase [EC:1.1.1.158] from Rickettsia conorii str. Malish 7
24% identity, 88% coverage

• Deciphering <i>Rickettsia conorii</i> metabolic pathways: A treasure map to therapeutic targets
  Prajapat, Biotechnology notes (Amsterdam, Netherlands) 2025
  • “...RC0249 PBP_1c Peptidoglycan synthesis Metabolism Inner membrane Yes RC0331 UDP-N-AcMur_Ala_ligase_MurC Peptidoglycan synthesis Metabolism Cytoplasm Yes RC0332 MurB Bacterial cell wall biosynthesis Metabolism Cytoplasm Yes RC0536 Peptidase_S11 Protein degration Proteolysis Periplasm Yes RC0560 MurD Peptidoglycan synthesis Metabolism Cytoplasm Yes RC0562 GlcNAc_MurG Peptidoglycan synthesis Metabolism Cytoplasm Yes RC0852...”

gbs1179 Unknown from Streptococcus agalactiae NEM316
25% identity, 96% coverage

• A naturally occurring gene amplification leading to sulfonamide and trimethoprim resistance in Streptococcus agalactiae
  Brochet, Journal of bacteriology 2008
  • “...gbs1172 gbs1173 gbs1174 gbs1175 gbs1176 gbs1177 gbs1178 gbs1179 gbs1180 gbs1181 gbs1182 gbs1183 gbs1184 gbs1185 Description of product VOL. 190, 2008 TANDEM...”

Wbm0778 UDP-N-acetylmuramate dehydrogenase from Wolbachia endosymbiont strain TRS of Brugia malayi
Q5GRK8 UDP-N-acetylenolpyruvoylglucosamine reductase from Wolbachia sp. subsp. Brugia malayi (strain TRS)
24% identity, 89% coverage

• Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy
  Li, PLoS neglected tropical diseases 2011
  • “...1329 wbm0644 707 DNA translocase at septal ring sorting daughter chromsomes 33.7 murB b3972 342 wbm0778 295 UDP-N-acetylenolpyruvoylglucosamine reductase, FAD-binding 19.3 *Only major E. coli cell-division proteins are shown. Sequence analysis of w Bm- ftsZ w Bm- ftsZ exists as a single gene on the chromosome...”
• 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
  • “...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 UDP-N-acetylmuramoylalanineD-glutamate ligase 36. FDT106 Q5GTN6 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 6. FDT075 Q5GS66 D-alanineD-alanine ligase 37. FDT107 Q5GSU3 30S ribosomal protein S10...”

SpyM3_0763 putative UDP-N-acetylenolpyruvoylglucosamine reductase from Streptococcus pyogenes MGAS315
25% identity, 98% coverage

• Novel regulatory small RNAs in Streptococcus pyogenes
  Tesorero, PloS one 2013
  • “...component E3 >>> SPyM3_0665 extracellular hyaluronate lyase <<< Q, Z SSRC20 SPyM3_0762 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase >>> SPyM3_0763 UDP-N-acetylenolpyruvoylglucosamine reductase >>> Q, P SSRC21 SPyM3_0851 putative anaerobic ribonucleotide reductase <<< SPyM3_0852 putative cardiolipin synthetase <<< Q, P [20] , [42] SSRC22 SPyM3_0918 hypothetical protein <<< SPyM3_0919 hypothetical protein...”

CC_2545 UDP-N-acetylmuramate dehydrogenase from Caulobacter vibrioides CB15
25% identity, 96% coverage

• Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
  Curtis, Molecular microbiology 2014
  • “...tumefaciens Peptidoglycan precursor synthesis Gene Gene Gene MurA CC_2350 E Bresu_2247 E Atu0539 E MurB CC_2545 E Bresu_2691 E Atu2092 E MurC CC_2546 E Bresu_2692 Bresu_1060 E N Atu2093 E MurD CC_2556 E Bresu_2778 E Atu2096 E MurE CC_2559 E Bresu_2781 E Atu2099 E MurF CC_2558...”

KN400_3006 UDP-N-acetylmuramate dehydrogenase from Geobacter sulfurreducens KN400
30% identity, 91% coverage

• Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production
  Butler, BMC genomics 2012
  • “...oxidoreductase (FNOR) beta subunit GSU3058 15.6 32 KN400_3000 squalene cyclase domain protein GSU3061 12.3 107 KN400_3006 UDP-N-acetylenolpyruvylglucosamine reductase GSU3067 21.1 58 KN400_3214 cytochrome c GSU3274 28.8 32 KN400_3301 sensor histidine kinase GSU3357 22.2 146 KN400_3348 OmpJ-related porin GSU3403 29.9 97 KN400_3368 dihydrolipoamide dehydrogenase-related protein GSU3424 16.4...”
  • “...GSU2773 conserved domain protein none 1.62 GSU2779 transcriptional regulator KN400_2716 18.0 3.77 GSU3067 UDP-N-acetylenolpyruvylglucosamine reductase KN400_3006 21.1 1.32 GSU3403* OmpJ porin KN400_3348 29.9 2.76 In addition to these copper proteins, a transcriptional regulator (GSU2779) with homology to CueR, a copper-responsive transcriptional activator [ 30 ], has...”

SACOL0801 UDP-N-acetylenolpyruvoylglucosamine reductase from Staphylococcus aureus subsp. aureus COL
25% identity, 89% coverage

• Antimicrobial effect and mode of action of terpeneless cold-pressed Valencia orange essential oil on methicillin-resistant Staphylococcus aureus
  Muthaiyan, Journal of applied microbiology 2012
  • “...degradation of murein sacculus and peptidoglycan 3.71 SACOL0697 tagX teichoic acid biosynthesis protein X 3.51 SACOL0801 murB UDP-N-acetylenolpyruvoylglucosamine reductase 2.97 SACOL1023 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase 2.89 SACOL1194 pbp1 penicillin-binding protein 1 2.5 SACOL1196 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase 2.45 SACOL2074 NA D-alanine--D-alanine ligase 2.39 SACOL1687 NA N-acetylmuramoyl-L-alanine amidase, family...”

SERP0405 UDP-N-acetylenolpyruvoylglucosamine reductase from Staphylococcus epidermidis RP62A
26% identity, 89% coverage

• Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline
  Sung, Cells 2022
  • “...Beta sliding clamp 1000.00 10.91 1.07 SERP0262 argS fig|176279.9.peg.250 J Arginine--tRNA ligase 1000.00 4.25 55.70 SERP0405 murB fig|176279.9.peg.385 M UDP-N-acetylenolpyruvoylglucosamine reductase 0.00 0.00 1000.00 SERP0044 rpsF fig|176279.9.peg.43 J 30S ribosomal protein S6 1.81 1.09 1.09 SERP0046 rpsR fig|176279.9.peg.45 J 30S ribosomal protein S18 0.00 0.00 1000.00...”
• Silver coordination polymers for prevention of implant infection: thiol interaction, impact on respiratory chain enzymes, and hydroxyl radical induction
  Gordon, Antimicrobial agents and chemotherapy 2010
  • “...SERP0520 SERP0521 SERP2293 SERP2295 SERP2296 SERP2294 SERP2292 SERP1731 SERP0405 SERP0993 SERP0607 SERP0746 Annotation 30 min cydA cydB qoxC qoxD nuoF sdhA sdhB...”

CA_C0510 UDP-N-acetylmuramate dehydrogenase from Clostridium acetobutylicum ATCC 824
CAC0510 UDP-N-acetylenolpyruvoylglucosamine reductase (murB) from Clostridium acetobutylicum ATCC 824
24% identity, 98% coverage

• Oxidoreduction potential controlling for increasing the fermentability of enzymatically hydrolyzed steam-exploded corn stover for butanol production
  Xia, Microbial cell factories 2022
  • “...of NADPH were respiratory chain (EMP19, 94.9995.68%) and TCA cycle (PYR3, 2.653.00%). Amino acid metabolism (CA_C0510) and carbohydrate metabolism (SULFUR5, CA_C2390) at 60h tended to decrease. The reaction of fatty acids (CA_C1589, CA_C0764) and COA synthesis (CA_C3254) was significantly enhanced. Table 3 Simulation of metabolic flux...”
• Small RNAs in the genus Clostridium
  Chen, mBio 2011
  • “...investigated whether clindamycin treatment affected the expression of sCAC610 and the putative clindamycin resistance gene (CAC0510) in C.acetobutylicum . The MIC of C.acetobutylicum to clindamycin is 10g/ml for solid media, but it is >200g/ml for liquid cultures ( 40 ). Therefore, we employed a range of...”

B0B960 UDP-N-acetylenolpyruvoylglucosamine reductase from Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu)
CTL0203 UDP-N-acetylenolpyruvoylglucosamine reductase from Chlamydia trachomatis 434/Bu
26% identity, 98% coverage

• Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
  Brinkworth, mSystems 2018
  • “...CTL0167 2.95 1.24E4 Glycogen synthase Energy metabolism B0B925 murB CTL0203 2.52 6.41E3 UDP-N-acetylenolpyruvoylglucosamine reductase Other B0B960 CTL0525 CTL0525 2.38 4.53E5 TPR-containing domain Hypothetical A0A0H3MKX6 recA CTL0018 2.21 1.98E3 Recombinase A DNA replication and repair B0B8M5 CTL0339 CTL0339 2.2 2.29E3 Phosphatidylcholine-hydrolyzing phospholipase D Other A0A0H3MCY1 aroL CTL0621...”
• Tryptophan Availability during Persistence of Chlamydia trachomatis Directly Impacts Expression of Chlamydial Cell Division Proteins
  Riffaud, Infection and immunity 2023 (secret)
• Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
  Brinkworth, mSystems 2018
  • “...B Amino acid biosynthesis A0A0H3MD30 glgA CTL0167 2.95 1.24E4 Glycogen synthase Energy metabolism B0B925 murB CTL0203 2.52 6.41E3 UDP-N-acetylenolpyruvoylglucosamine reductase Other B0B960 CTL0525 CTL0525 2.38 4.53E5 TPR-containing domain Hypothetical A0A0H3MKX6 recA CTL0018 2.21 1.98E3 Recombinase A DNA replication and repair B0B8M5 CTL0339 CTL0339 2.2 2.29E3 Phosphatidylcholine-hydrolyzing...”

SA0693 hypothetical protein from Staphylococcus aureus subsp. aureus N315
24% identity, 89% coverage

• Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria
  Cui, Proceedings of the National Academy of Sciences of the United States of America 2012
  • “...nagA Probable N-acetylglucosamine-6-phosphate deacetylase SA0693 -- Similar to UDP-N-acetylenolpyruvoylglucosamine reductase SA1902 murA...”
• Transcriptomic and functional analysis of an autolysis-deficient, teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus
  Renzoni, Antimicrobial agents and chemotherapy 2006
  • “...0.001 SA0909 SA2062 SA1964 SA1028 SA1029 SA0249 SA1193 SA1902 SA0693 SA1562 SA1026 SA0876 SA1886 fmtA sarV fmtB ftsA ftsZ scdA fmtC/mprF murA murB murC murD...”

1hskA / P61431 Crystal structure of s. Aureus murb (see paper)
24% identity, 89% coverage

• Ligand: flavin-adenine dinucleotide (1hskA)

WP_011013593 UDP-N-acetylmuramate dehydrogenase from Corynebacterium glutamicum
25% identity, 97% coverage

• Double deletion of murA and murB induced temperature sensitivity in Corynebacterium glutamicum.
  Shi, Bioengineered 2019
  • GeneRIF: Deletion of murA and murB decreased the peptidoglycan synthesis and induced temperature sensitivity.

murB / P61431 UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) from Staphylococcus aureus (see paper)
Q54A20 UDP-N-acetylmuramate dehydrogenase (EC 1.3.1.98) from Staphylococcus aureus (see paper)
murB / BAC56587.1 UDP-N-acetylenolpyruvylglucosamine reductase from Staphylococcus aureus (see paper)
B4602_RS03795 UDP-N-acetylmuramate dehydrogenase from Staphylococcus aureus
A8Z012 UDP-N-acetylenolpyruvoylglucosamine reductase from Staphylococcus aureus (strain USA300 / TCH1516)
P61432 UDP-N-acetylenolpyruvoylglucosamine reductase from Staphylococcus aureus (strain MW2)
24% identity, 89% coverage

• Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus
  Wang, Frontiers in pharmacology 2023
  • “...exposed to TA. Accession Gene name Protein ID Description Log2 FC Gene Protein Cell envelope B4602_RS03795 murB WP_000608440.1 UDP-N-acetylenolpyruvylglucosamine reductase 0.21 0.36 B4602_RS07210 murG WP_000160904.1 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase 0.34 0.38 B4602_RS00765 murQ WP_042727603.1 N-acetylmuramic acid 6-phosphate etherase 0.42 0.72 B4602_RS11895 fmhX WP_000413866.1 Peptidoglycan interpeptide bridge formation enzyme...”
• Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach
  Rahman, International journal of peptide research and therapeutics 2021
  • “...acid biosynthesis (Q93QD4, A8Z088, Q6GI75), folate biosynthesis (Q2FY51, Q2G0Q7, Q2FXR9), peptidoglycan biosynthesis (Q2FZ94, Q2FYI0, A8Z4Y6, A8Z012), and ribosome (Q2FEP5, A8YZP4, A8Z2N6, A8YZN7), etc. Table 2 Predicted drug targets against S . aureus USA300_TCH1516 strain Sl No. UniProt Protein name Sl No. UniProt Protein name 1 A8Z2L6...”
  • “...Thioredoxin-disulfide reductase 15 Q2FYG6 Heptaprenyl diphosphate syntase component II 42 P0A017 Dihydrofolate reductase (folA) 16 A8Z012 UDP-N-acetylenolpyruvoylglucosamine reductase (murB) 43 Q2FIB3 Glucose-6-phosphate isomerase (pgi) 17 A8Z4D3 Nicotinate-nucleotide adenylyltransferase (nadD) 44 A8YZP4 30S ribosomal protein S7 (rpsG) 18 A8Z2S7 Ammonia-dependent NAD (+) synthetase (nadE) 45 A8Z1J1 D-alanineD-alanyl...”
• Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein.
  Chowdhury, Heliyon 2021
  • “...Carindacillin, Cefmetazole, Ertapenem, Cefpiramide, Cefoperazone, Cefoxitin, Ceftizoxime 1.24E-29 116 6 UDP-N-acetylenol pyruvoyl glucosamine reductase D6YVJ9 P61432 DB03147 Flavin adenine dinucleotide 3.22E-48 160 Metabolic Pathway Independent 7 DNA topoisomerase D6YVX0 Q06AK7 DB00487, DB01051 Pefloxacin, Novobiocin 3.63E-36 142 8 Putative multidrug resistance protein MdtC D6YSV9 P31224 DB03619, DB04209...”

FSDG_RS09645 UDP-N-acetylmuramate dehydrogenase from Fusobacterium animalis 7_1
23% identity, 96% coverage

• A survey of Fusobacterium nucleatum genes modulated by host cell infection
  Cochrane, Microbial genomics 2020
  • “...bit score of >100and E value >0.01 [FSDG_RS02815 (Lipopolysaccharide (LPS) biosynthesis protein); FSDG_RS08715 (haemolysin III); FSDG_RS09645 (UDP- N -acetylenolpyruvoylglucosamine reductase); FSDG_RS10170 (ATP binding protein); FSDG_RS10175 (ABC transporter ATP binding protein)] (File S1). Infection with CRC-associated strain F. nucleatum 7-3 results in similar activation of fusobacterial genes...”

Q49VT7 UDP-N-acetylenolpyruvoylglucosamine reductase from Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)
24% identity, 96% coverage

• In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus
  Shahid, International journal of environmental research and public health 2020
  • “...secondary metabolites ssp01130-Biosynthesis of antibiotics Chromosomal replication initiator protein DnaA (Q4A180) ssp02020-Two-component system UDP-N-acetylenolpyruvoylglucosamine reductase (Q49VT7) ssp00550-Peptidoglycan biosynthesis D-alanine-D-alanine ligase (Q49Z31) ssp01502-Vancomycin resistance ssp00473-D-Alanine metabolism ssp00550-Peptidoglycan biosynthesis UDP-N-acetylmuramoylalanine-D-glutamate ligase (Q49WW5) ssp00550-Peptidoglycan biosynthesis Alanine racemase (Q49Z24) ssp01502-Vancomycin resistance ijerph-17-03644-t002_Table 2 Table 2 Subcellular localization prediction of proteins...”

MURB_BACSU / P18579 UDP-N-acetylenolpyruvoylglucosamine reductase; UDP-N-acetylmuramate dehydrogenase; EC 1.3.1.98 from Bacillus subtilis (strain 168) (see paper)
BSU15230 UDP-N-acetylenolpyruvoylglucosamine reductase from Bacillus subtilis subsp. subtilis str. 168
NP_389406 UDP-N-acetylenolpyruvoylglucosamine reductase from Bacillus subtilis subsp. subtilis str. 168
23% identity, 96% coverage

• function: Cell wall formation.
  catalytic activity: UDP-N-acetyl-alpha-D-muramate + NADP(+) = UDP-N-acetyl-3-O-(1- carboxyvinyl)-alpha-D-glucosamine + NADPH + H(+) (RHEA:12248)
  cofactor: FAD
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...murAA BSU36760 Yes 2.5.1.7 3SG1 B. anthracis murB BSU15230 Yes 1.1.1.158 4PYT Unidentified murC BSU29790 Yes 6.3.2.8 1GQQ H. influenzae murD BSU15200 Yes...”
• Localization of the Bacillus subtilis murB gene within the dcw cluster is important for growth and sporulation.
  Real, Journal of bacteriology 2006
  • GeneRIF: In these species it(murB gene) contributes to the optimal expression of cell division and PG biosynthetic functions during both vegetative growth and spore development.

Q8RDQ3 UDP-N-acetylenolpyruvoylglucosamine reductase from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)
FN1455 UDP-N-acetylenolpyruvoylglucosamine reductase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
23% identity, 85% coverage

• Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions
  Kumar, BMC microbiology 2016
  • “...accession number S. No. Uniprot ID No. of Proteins KEGG pathway KEGG ID 1 Q8RIQ1, Q8RDQ3, Q8RDQ2, Q8RDQ1, Q8R635, Q8R5N5, Q8RDP8, Q8RDQ4, Q8RG00, Q8RFV2, Q8REF2, Q8REA2 12 Peptidoglycan biosynthesis fnu00550 2 Q8RFU2, Q8R691, Q8R6A2, Q8RE91, Q8RFA8 5 Lipopolysaccharide biosynthesis fnu00540 3 Q8RFB7, Q8RED6, Q8R612, Q8R609, Q8RHW6...”
• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...7 14 16 12 Covers FN0060, FN0406, FN0525, FN0580, FN1155, FN1161, FN1211, FN1225, FN1326, FN1454, FN1455, FN1456, FN1457, FN1458, FN1461, FN1520, FN1991. Table 7 Fatty acid biosynthesis. FnPg versus Fn FnSg versus Fn FnPgSg versus Fn FnPgSg versus FnPg PgSg versus FnPg FnPgSg versus FnSg Total...”
  • “...2 Covers FN0022, FN0175, FN0176, FN0177, FN0265, FN0562, FN1010, FN1155, FN1211, FN1225, FN1326, FN1451, FN1452, FN1455, FN1456, FN1457, FN1458, FN1461, FN1520, FN1978, FN2013, FN2017. Stress Studies with the other two organisms, Pg and Sg, found evidence of physiological support between the species (Kuboniwa etal. 2009 ;...”

NBX27_02770 UDP-N-acetylmuramate dehydrogenase from Erysipelothrix rhusiopathiae
24% identity, 98% coverage

• Human Erysipelothrix rhusiopathiae infection via bath water - case report and genome announcement
  Zautner, Frontiers in cellular and infection microbiology 2022
  • “...mg/L. Table5 Enzymes involved in peptidoglycan biosynthesis. Locus tag Gene Predicted function NBX27_08175 murA UDP-N-acetylglucosamine-1-carboxyvinyltransferase NBX27_02770 murB UDP-N-acetylmuramate dehydrogenase NBX27_02935 murC UDP-N-acetylmuramateL-alanine ligase or UDP-N-acetylmuramateL-serine ligase? NBX27_02805 murD UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase NBX27_04865 murE UDP-N-acetylmuramoylalanyl-D-glutamateL-alanine ligase NBX27_03210 murF UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase NBX27_02800 mraY Phospho-N-acetylmuramoyl-pentapeptide-transferase NBX27_04480 murG Undecaprenyldiphospho-muramoylpentapeptide beta- N...”

EF2489 MurB family protein from Enterococcus faecalis V583
28% identity, 22% coverage

• The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
  Vebø, PloS one 2009
  • “...) Cell envelope 2.4 [10] EF2488 lipoprotein, putative ( cpsH ) Cell envelope 2.5 [10] EF2489 MurB family protein ( cpsG ) Cell envelope 2.9 [10] EF2490 conserved hypothetical protein ( cpsF ) Hypothetical proteins 3.2 [10] EF2491 glycosyl transferase, group 2 family protein ( cpsE...”

ZMO0833 UDP-N-acetylenolpyruvoylglucosamine reductase from Zymomonas mobilis subsp. mobilis ZM4
23% identity, 98% coverage

• Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
  Yan, Applied and environmental microbiology 2019
  • “...quinone oxidoreductase; three reductase genes (ZMO0833, encoding a 169 UDP-N-acetylenolpyruvoylglucosamine reductase, ZMO1303, encoding a 170...”
  • “...in the presence of BQ, 185 including ZMO1772, ZMO0833, ZMO1303, ZMO1984, ZMO1949, ZMO1696, ZMO1576 and 186 ZMO1399. These genes were respectively inserted into...”
• Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
  Yi, Biotechnology for biofuels 2015
  • “...metabolism ZMO0759 Hydroxyacylglutathione hydrolase 2.66 2.66 Carbohydrate metabolism ZMO0788 Gluconate 2-dehydrogenase 2.73 2.69 Carbohydrate metabolism ZMO0833 UDP- N -acetylenolpyruvoylglucosamine reductase 2.06 2.14 Energy metabolism ZMO0003 Adenylylsulfate kinase 2.40 2.01 Energy metabolism ZMO0004 Sulfate adenylyltransferase subunit 1 3.39 2.31 Energy metabolism ZMO0005 Sulfate adenylyltransferase subunit 2 3.09...”
  • “...genes, ZMO0157 encoded d -isomer specific 2-hydroxyacid dehydrogenase NAD binding, ZMO0788 encoded a gluconate 2-dehydrogenase, ZMO0833 encoded UDP- N -acetylenolpyruvoylglucosamine reductase, ZMO1222 encoded 3-oxoacyl-(acyl-carrier-protein) reductase, ZMO1254 encoded redoxin domain protein, ZMO1303 encoded a pyrroline-5-carboxylate reductase, ZMO1399 encoded fatty acid hydroxylase, ZMO1576 encoded short-chain dehydrogenase/reductase SDR, ZMO1696...”

MXAN_5602 UDP-N-acetylenolpyruvoylglucosamine reductase from Myxococcus xanthus DK 1622
26% identity, 98% coverage

• Peripheral rods: a specialized developmental cell type in Myxococcus xanthus
  Whitfield, Genomics 2020
  • “...MxDK1622 tag Stationary/ Peripheral MreC MXAN_2645 4.53 Penicillin-binding protein MXAN_2647 3.28 MreB MXAN_2648 4.29 MurB MXAN_5602 2.29 MurC MXAN_5603 2.92 MurG MXAN_5604 3.10 MurD MXAN_5606 3.76 MraY MXAN_5607 2.04 MurF MXAN_5608 0.00 MurE MXAN_5609 0.00 Final column represent log2-Fold change where negative values demonstrate downregulation of...”

HP1418 UDP-N-acetylenolpyruvoylglucosamine reductase (murB) from Helicobacter pylori 26695
26% identity, 84% coverage

• Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
  Thiele, Journal of bacteriology 2005
  • “...HP1108 to HP1111 HP1118 HP1180 HP1257 HP1385 HP1399 HP1418 HP1491 HP1495 HP1505 pyrE fbp rocF murB tal ribD L-Asparagine, L-aspartate, L-threonine D-Glucose...”
• Genome-scale metabolic model of Helicobacter pylori 26695
  Schilling, Journal of bacteriology 2002
  • “...HP1038 HP0372 HP1099 HP1100 HP1385 HP0509 HP0735 HP0086 HP1418 HP0740 HP0589, HP0590, HP0591, HP0588 HP1110, HP1111, HP1108, HP1109 HP1257 HP0832 HP1495 HP0824,...”
• Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis
  Chalker, Journal of bacteriology 2001
  • “...HP0588, HP0589, HP0590, HP0808, HP0975, HP1108, HP1109, HP1418, HP1563, HP1553, HP0740, and HP1159), a small number of chloramphenicol-resistant colonies was...”

Atu2092 UDP-N-acetylenolpyruvoylglucosamine reductase from Agrobacterium tumefaciens str. C58 (Cereon)
24% identity, 92% coverage

• Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region
  Overlöper, RNA biology 2014
  • “...RplI atu1088 50S ribosomal protein L9 0,18 AtpH atu2625 ATP Synthase delta chain 0,16 MurB atu2092 UDP-N-acetylenolpyruvoylglucosamine reductase 0,08 RplY atu2227 50S ribosomal protein L25 0,05 List of proteins with altered abundance in three replicates of the AbcR1 strain in comparison to the WT (fold changes...”
• Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
  Curtis, Molecular microbiology 2014
  • “...Gene Gene Gene MurA CC_2350 E Bresu_2247 E Atu0539 E MurB CC_2545 E Bresu_2691 E Atu2092 E MurC CC_2546 E Bresu_2692 Bresu_1060 E N Atu2093 E MurD CC_2556 E Bresu_2778 E Atu2096 E MurE CC_2559 E Bresu_2781 E Atu2099 E MurF CC_2558 E Bresu_2780 E Atu2098...”

9dtkA / A5VRH5 Crystal structure of udp-n-acetylenolpyruvoylglucosamine reductase (murb) from brucella ovis (see paper)
BOV_RS06850 UDP-N-acetylmuramate dehydrogenase from Brucella ovis ATCC 25840
29% identity, 92% coverage

• Ligands: flavin-adenine dinucleotide; uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid (9dtkA)
• Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
  Minjárez-Sáenz, Microbiology spectrum 2022
  • “...21-320 BOV_RS04255 (dusA) ABQ61966.1 FMN NAD(P)H 3B0P (46) 9 1.3.1.98 UDP-N-acetylmuramate dehydrogenase FAD_binding_4 (PF01565) 42-172 BOV_RS06850 (MurB) ABQ61769.1 FAD NADPH 3TX1 (35) murB_C (PF02873) 206-304 10 1.3.5.1 Succinate dehydrogenase flavoprotein subunit FAD_binding_2 (PF00890) 24-419 BOV_RS08985 (sdhA) ABQ61077.1 FAD 2H88 _A (63) Succ_DH_flav_C (PF02910) 474-613 11 1.3.5.2...”

Q5SJC8 UDP-N-acetylmuramate dehydrogenase (EC 1.3.1.98) from Thermus caldophilus (see paper)
28% identity, 93% coverage

2gqtA / Q5SJC8 Crystal structure of udp-n-acetylenolpyruvylglucosamine reductase (murb) from thermus caldophilus (see paper)
28% identity, 93% coverage

• Ligand: flavin-adenine dinucleotide (2gqtA)

VspiD_010100018130 UDP-N-acetylmuramate--alanine ligase from Verrucomicrobium spinosum DSM 4136
27% identity, 38% coverage

• Identification and Partial Characterization of a Novel UDP-N-Acetylenolpyruvoylglucosamine Reductase/UDP-N-Acetylmuramate:l-Alanine Ligase Fusion Enzyme from Verrucomicrobium spinosum DSM 4136(T)
  Naqvi, Frontiers in microbiology 2016
  • “...Verrucomicrobium spinosum possesses a novel fusion open reading frame (ORF) annotated by the locus tag (VspiD_010100018130). The ORF, which is predicted to encode the enzymes UDP- N -acetylenolpyruvoylglucosamine reductase (MurB) and UDP- N -acetylmuramate: l -alanine ligase (MurC) that are involved in the cytoplasmic steps of...”
  • “...the V. spinosum murB/C open reading frame (ORF) The ORF annotated by the locus tag (VspiD_010100018130) UDP- N -acetylenolpyruvoylglucosamine reductase /UDP- N -acetylmuramate: l -alanine ligase was amplified by PCR using the primers murB/C Vs -forward (5-C ACC ATG AATCACGCCGTCGTCAGTTTGTTGAA G-3) and murB/C Vs -reverse (5-...”
• Biochemical characterization of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136(T.)
  McGroty, PloS one 2013
  • “...-acetylmuramoyl- l -alanyl- d -glutamate: meso -2,6-diaminopimelate ligase 6.3.2.13 VspiD_010100026230 UppP Undecaprenyl pyrophosphate phosphatase 3.6.1.27 VspiD_010100018130 MurB UDP- N -acetylenolpyruvoylglucosamine reductase 1.1.1.158 VspiD_010100018130 MurC UDP- N -acetylmuramate: l -alanine ligase 6.3.2.8 VspiD_010100000100 AlaR Alanine racemase 5.1.1.1 VspiD_010100008415 MurI Glutamate racemase 5.1.1.3 The annotated gene product names...”

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.