PaperBLAST
PaperBLAST Hits for sp|Q59650|MURE_PSEAE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=murE PE=3 SV=2 (487 a.a., MPMSLNQLFP...)
Show query sequence
>sp|Q59650|MURE_PSEAE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=murE PE=3 SV=2
MPMSLNQLFPQAERDLLIRELTLDSRGVRPGDLFLAVPGGRQDGRAHIADALAKGAAAVA
YEAEGAGELPPSDAPLIAVKGLAAQLSAVAGRFYGEPSRGLDLIGVTGTNGKTSVSQLVA
QALDLLGERCGIVGTLGTGFYGALESGRHTTPDPLAVQATLATLKQAGARAVAMEVSSHG
LDQGRVAALGFDIAVFTNLSRDHLDYHGSMEAYAAAKAKLFAWPGLRCRVINLDDDFGRR
LAGEEQDSELITYSLTDSSAFLYCREARFGDAGIEAALVTPHGEGLLRSPLLGRFNLSNL
LAAVGALLGLGYPLGDILRTLPQLQGPVGRMQRLGGGDKPLVVVDYAHTPDALEKVLEAL
RPHAAARLLCLFGCGGDRDAGKRPLMAAIAERLADEVLVTDDNPRTEASAAIIADIRKGF
AAADKVTFLPSRGEAIAHLIASAAVDDVVLLAGKGHEDYQEIDGVRHPFSDIEQAERALA
AWEVPHA
Running BLASTp...
Found 251 similar proteins in the literature:
murE / GB|AAG07805.1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase; EC 6.3.2.13 from Pseudomonas aeruginosa (see 2 papers)
PA4417 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Pseudomonas aeruginosa PAO1
NP_253107 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
Salvà-Serra, Frontiers in microbiology 2022 - “...murC UDP-N-acetylmuramatealanine ligase 9 27 1.04 0.40 1.31 0.00 1.83 0.00 Up 1.19 0.04 WP_003094133.1 PA4417 murE UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase 16 47 1.09 0.05 1.01 0.70 1.50 0.00 Up 1.29 0.00 WP_003094332.1 PA4450 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase 15 74 1.03 0.49 1.08 0.03 2.64 0.00 Up 1.20...”
- The role of peptidoglycan hydrolases in the formation and toxicity of Pseudomonas aeruginosa membrane vesicles
Chen, microLife 2022 - “...(sltH) rlpA sltB1 pbpA murG PA4413 ftsW PA4414 murD PA4417 murE PA4418 PA4450 ftsI (PBP3) murA PA4700 PA4749 PA4947 PA5045 PA5485 mrcB (PBP1b) glmM amiB mrcA...”
- A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
Xu, PloS one 2013 - “...),PA4406( lpxC ),PA4410( ddlB ),PA4411( murC ), PA4412( murG ),PA4414( murD ),PA4415( mraY ),PA4416( murF )PA4417( murE ),PA4425( yraO ),PA4442( cysN ),PA4443( cysD ), PA4450( murA ),PA4457( KdsD ),PA4524( nadC ),PA4529( coaE ), PA4561( ribF ),PA4655( hemH ),PA4666( hemA ),PA4670( prs ), PA4729( panB ),PA4730( panC...”
- A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
Sigurdsson, PloS one 2012 - “...(PA4694), IlvD (PA0353) Cell 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...”
- Recombinant expression screening of P. aeruginosa bacterial inner membrane proteins
Madhavan, BMC biotechnology 2010 - “...markers with weights given in kDA, Lane 6 PA4083 (MW = 26 kDa), Lane 7 PA4417 (MW = 51 kDa), Lane 8 PA5199 (MW = 49 kDa). Proteins that were expressed tended to be expressed at more than one temperature or in more than one strain....”
- Beta-lactam antibiotics: from antibiosis to resistance and bacteriology
Kong, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2010 - “...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 N- acetylglucosamine transferase MurI murI PA4662 Glutamate racemase MraY mraY PA4415 Phospho-N-acetylmuramoyl-pentapeptide-transferase MraW mraW PA4420...”
- Pseudomonas aeruginosa MurE amide ligase: enzyme kinetics and peptide inhibitor.
Paradis-Bleau, The Biochemical journal 2009 (PubMed)- GeneRIF: Pseudomonas aeruginosa MurE amide ligase: enzyme kinetics and peptide inhibitor
PA14_57410 UDP-N-acetylmuramyl tripeptide synthase from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage
- Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...murF PA14_57390 UDP- N -acetylmuramoylalanyl- D -glutamyl-2.6-diaminopimelate D -alanyl- D -alanine ligase 11.12 X murE PA14_57410 UDP- N -acetylmuramoylalanyl- D -glutamate2. 6-diaminopimelate ligase 55.53 9.29 rmlC PA14_68210 dTDP-4-dehydrorhamnose 3.5-epimerase 12.92 3.34 Glycogen metabolism glgA PA14_36570 Glycogen synthase 3.09 5.06 PA14_36580 PA14_36580 Glycosyl hydrolase 19.03 11.25 PA14_36590...”
PP1332 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase from Pseudomonas putida KT2440
74% identity, 98% coverage
HI1133 UDP-N-acetylmuramyl-tripeptide synthetase (murE) from Haemophilus influenzae Rd KW20
46% identity, 97% coverage
APL_RS00065 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Actinobacillus pleuropneumoniae serovar 5b str. L20
48% identity, 92% coverage
- Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
Dai, Frontiers in cellular and infection microbiology 2018 - “...RecA ssb (HI0250) APL_RS04100 A4U84_RS00055 HAPS_RS01845 93 92 Cytoplasmic Single-strand DNA-binding protein UNKNOWN murE (HI1133) APL_RS00065 A4U84_RS01305 HAPS_RS00570 95 97 Cytoplasmic UDP-N-acetylmuramoylalanyl-D-glutamate2,6-diaminopimelate ligase ligA (HI1100) APL_RS06830 A4U84_RS01895 HAPS_RS00055 99 99 Cytoplasmic NAD-dependent DNA ligase LigA HI0660 APL_RS07145 Unknown Function unknown HI0659 APL_RS07140 A4U84_RS04905 d HAPS_RS01545 d...”
NGO1541 MurE from Neisseria gonorrhoeae FA 1090
49% identity, 94% coverage
VY92_RS06600 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Avibacterium paragallinarum
47% identity, 95% coverage
- The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation
Huo, Frontiers in microbiology 2021 - “...information on the primers is listed in Supplementary Table 1 . The qPCR programs for VY92_RS06600, VY92_RS09125, VY92_RS09790, VY92_RS03730, and VY92_RS03735 were as follows: 1 cycle of 95C for 3 min; 35 cycles of 95C for 30 s, 60C for 30 s, and 72C for 40...”
- “...under iron-restriction condition. Here, three upregulated genes (VY92_RS03730, VY92_RS03735, and VY92_RS00335) and four downregulated genes (VY92_RS06600, VY92_RS09125, VY92_RS09790, and VY92_RS01655) were selected as representative DEGs for qPCR. Among them, VY92_RS03730, VY92_RS03735, and VY92_RS00335 were annotated as the heme utilization protein HutZ, heme utilization cystosolic carrier protein...”
BPSL3030 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diami nopimelate ligase from Burkholderia pseudomallei K96243
51% identity, 90% coverage
BCAL3467 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-dia minopimelate ligase from Burkholderia cenocepacia J2315
51% identity, 88% coverage
P0E69_16650 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Chimaeribacter arupi
48% identity, 92% 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 - “...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 murI 4187076..4187939 glutamate racemase P0E69_09125 murJ 2034271..2035806 murein biosynthesis integral membrane protein MurJ P0E69_02530 mpl...”
Bphy_2678 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Burkholderia phymatum STM815
Bphy_2678 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Paraburkholderia phymatum STM815
48% identity, 88% coverage
STM0123 UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase from Salmonella typhimurium LT2
49% identity, 93% coverage
- Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets
Kocabaş, PloS one 2022 - “...nucleotide sugar metabolism Yes STM0129 murC UDP-N-acetylmuramateL-alanine ligase Peptidoglycan biosynthesis. D-Glutamine and D-glutamate metabolism Yes STM0123 murE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase Peptidoglycan biosynthesis.Lysine biosynthesis Yes STM0128 murG UDP-N-acetylglucosamineN-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase Peptidoglycan biosynthesis Yes STM0124 murF UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase Peptidoglycan biosynthesis.Lysine biosynthesis Yes STM3725 coaD Phosphopantetheine adenylyltransferase Pantothenate and...”
- Identifying essential genes in bacterial metabolic networks with machine learning methods
Plaimas, BMC systems biology 2010 - “...ORF Gene Symbol EC Enzyme Evidence a) Intersection of our predictions with the experimental screen STM0123 murE 6.3.2.13 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase ** STM0128 murG 2.4.1.227 N-acetylglucosaminyl transferase * STM0129 murC 6.3.2.8 UDP-N-acetylmuramate-L-alanine ligase ** STM0154 lpdA 1.8.1.4 Dihydrolipoamide dehydrogenase STM0218 pyrH 2.7.4.22 Uridylate kinase * STM0221 uppS...”
1e8cB / P22188 Structure of mure the udp-n-acetylmuramyl tripeptide synthetase from e. Coli (see paper)
50% identity, 91% coverage
- Ligands: uridine-5'-diphosphate-n-acetylmuramoyl-l-alanine-d-glutamate; 2,6-diaminopimelic acid (1e8cB)
MurE / b0085 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase (EC 6.3.2.13) from Escherichia coli K-12 substr. MG1655 (see 19 papers)
murE / P22188 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase (EC 6.3.2.13) from Escherichia coli (strain K12) (see 17 papers)
MURE_ECOLI / P22188 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase; Meso-A2pm-adding enzyme; Meso-diaminopimelate-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.13 from Escherichia coli (strain K12) (see 4 papers)
murE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase; EC 6.3.2.13 from Escherichia coli K12 (see 10 papers)
NP_414627 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Escherichia coli str. K-12 substr. MG1655
b0085 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Escherichia coli str. K-12 substr. MG1655
50% identity, 92% coverage
- function: Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6- diaminoheptanedioate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl- gamma-D-glutamyl-meso-2,6-diaminoheptanedioate + ADP + phosphate + H(+) (RHEA:23676)
cofactor: Mg(2+) - Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum
Matuszewski, Genetics 2015 - “...study was supported by the Austrian Science Fund (grant P 22581-B17 to M.K. and grant P22188 to Reinhard Brger), the Austrian Agency for International Cooperation in Education and Research (grant FR06/2014 to J.H.), Campus France (grant PHC AMADEUS 31642SJ to M.K.), and a Writing-Up Fellowship from...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...UDP-N-acetylglucosamine-1carboxyvinyltransferase 5.81/44,817.65 MurE P22188 5.43/53,212.40 MurG P17443 UDP-N-acetylmuramoylalanyl-Dglutamate-2,6diaminopimelate...”
- Divergence of function in sequence-related groups of Escherichia coli proteins
Nahum, Genome research 2001 - “...b0086 P17952 P14900 P22188 P11880 UDP-N-acetylmuramate-alanine ligase UDP-N-acetylmuramoylalanine-D-glutamate ligase UDP-N-acetylmuramoylalanyl-D-glutamate...”
- Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetylmuramyl-tripeptide synthetase of Escherichia coli.
Michaud, The Biochemical journal 1990 - GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data
Treffon, Journal of clinical microbiology 2023 (secret) - Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes
Strittmatter, Applied and environmental microbiology 2023 (secret) - CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
Zaharia, BMC bioinformatics 2019 - “...Figure 3 b shows the genes coding for enzymes involved in this trail: murE ( b0085 ), murF ( b0086 ), mraY ( b0087 ), murD ( b0088 ), murG ( b0090 ), and murC ( b0091 ). Note that the trail produced by CoMetGeNe was...”
- Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example
He, Frontiers in microbiology 2017 - “...of Escherichia coli strains. Gene ID Gene (protein) Position Mutation Affected codon Function Reference Co-culture b0085 murE 94633 C<->T CTG<->TTG Peptidoglycan biosynthetic process Herring et al., 2006 b0462 acrB 481615 C<->T GGC<->GAC peptidoglycan-based cell wall Minty et al., 2011 481849 G<->A CCT<->CTT 482766 C<->T CTG<->CTA b0635...”
- More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
Göhler, BMC systems biology 2011 - “...* -0.075 3.914 b1596 ynfM 0.927 0.007 b4052 dnaB -0.018 3.864 b2600 tyrA 0.915 2.065 b0085 murE $ 0.167 3.659 b2505 yfgH 0.820 0.425 b0822 ybiV 0.284 3.653 b0333 prpC 0.729 0.021 b2683 ygaH -0.077 3.628 b0331 prpB 0.713 0.024 b0436 tig -0.260 3.620 b3939 metB...”
- Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy
Li, PLoS neglected tropical diseases 2011 - “...wbm0238 455 UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase 27.9 ftsH b3178 644 wbm0490 609 protease, ATP-dependent zinc-metallo 46.5 murE b0085 495 wbm0492 496 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase 25.2 murD b0088 438 wbm0508 498 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase 22.8 murG b0090 355 wbm0557 343 N-acetylglucosaminyl transferase 22.4 ddl b0092 306 wbm0570 339 D-alanine:D-alanine ligase 29.4...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...E. coli _iAF1260 SS TLM CPGB VLIM CEB LBR genes b0003 b0004, b0025, b0029 b0071 b0085 b0096 b0004 b0052, b0103, b0109 b0072 b0086 b0179 b0031 b0131, b0133, b0134 b0073 b0087 b0181 b0166 b0142, b0154, b0159 b0074 b0088 b0182 b2472 b0173, b0174, b0369 b3770 b0090 b0524 b2478...”
- Divergence of function in sequence-related groups of Escherichia coli proteins
Nahum, Genome research 2001 - “...murD murE murF b0091 b0088 b0085 b0086 P17952 P14900 P22188 P11880 UDP-N-acetylmuramate-alanine ligase UDP-N-acetylmuramoylalanine-D-glutamate ligase...”
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SO4224 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase from Shewanella oneidensis MR-1
47% identity, 96% coverage
- Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
Chourey, Applied and environmental microbiology 2006 - “...SO4228, SO4227, ftsL (SO4226), ftsI (SO4225), murE (SO4224), murF (SO4223), mraY (SO4222), murD (SO4221), ftsW (SO4220), murG (SO4219), murC (SO4218), ftsQ...”
Q5A_003275 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Serratia inhibens PRI-2C
49% identity, 93% coverage
- Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C
Schmidt, Scientific reports 2017 - “...for the Pyrimidine-specific ribonucleoside hydrolase RihA), Q5A_018030 (coding for the putative HTH-type transcriptional regulator YahB), Q5A_003275 (coding for the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase) and Q5A_011375 (coding for a hypothetical protein). Most of the DEGs at t1 were assigned to functions involved in energy metabolism, transport and binding proteins,...”
- “...chaperone YfcS (Q5A_021485) is involved in pilus organization. At both t1 and t2, the gene Q5A_003275 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase) was up-regulated, which is involved in the biosynthesis of bacterial cell-wall peptidoglycan 66 . At t2 on the proteomics level, two proteins, UDP-N-acetylmuramateL-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase (Q5A_001880) and UDP-N-acetylglucosamine 1-carboxyvinyltransferase...”
BB4202 Possible murein precusor biosynthesis bifunctional protein from Bordetella bronchiseptica RB50
47% identity, 50% coverage
Q5ZX16 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
42% identity, 98% coverage
- Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach
Khan, Microbiology spectrum 2022 - “...tr| Q5ZXL1 Multidrug resistance protein Beta-lactam resistance; cationic antimicrobial peptide (CAMP) resistance 2 K01928 tr| Q5ZX16 UDP- N -acetylmuramoyl- l -alanyl- d -glutamate-2,6-diaminopimelate ligase Lysine biosynthesis; peptidoglycan biosynthesis 3 K03587 tr| Q5ZX17 Peptidoglycan d,d -transpeptidase FtsI Peptidoglycan biosynthesis; beta-lactam resistance 4 K05515 tr| Q5ZVR5 Peptidoglycan d,d...”
- “...and subcellular localization Serial no. Accession no. Protein factor Microbiome similarity Subcellular localization 1 tr| Q5ZX16 MurE <46 Cytoplasmic 2 sp| Q5ZUD8 Tig <45 Cytoplasmic 3 tr| Q5ZS84 MviN <47 Inner membrane 4 sp| Q5ZW98 Kup1 <47 Outer membrane 5 sp| Q5ZV69 TolB <44 Inner membrane...”
ACIAD3365 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase from Acinetobacter sp. ADP1
42% identity, 93% coverage
slr0528 UDP-MurNac-tripeptide synthetase from Synechocystis sp. PCC 6803
44% identity, 92% coverage
- Absence of KpsM (Slr0977) Impairs the Secretion of Extracellular Polymeric Substances (EPS) and Impacts Carbon Fluxes in Synechocystis sp. PCC 6803
Santos, mSphere 2021 - “...-Acetylmuramate-alanine ligase 2.2 Transcription sll1689 sigE ; rpoD Sigma factor E 1.8 Amino acid metabolism slr0528 murE UDP-MurNAc-tripeptide synthetase 1.7 Transporters sll0923 epsB ; wzc Exopolysaccharide export protein 2.0 sll1581 gumB Polysaccharide biosynthesis/export 1.8 Other signaling and cellular processes slr0328 wzb Low-mol-wt protein-tyrosine phosphatase 2.7 TABLE2...”
- Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803
Chen, Biotechnology for biofuels 2014 - “...factor induced protein Slr0015 -1.541 31.7 Lipid-A-disaccharide synthase, putative Slr0298 -1.75 13.8 FraH protein homolog Slr0528 -1.601 21.3 UDP-N-acetylmuramyl-tripeptide synthetase Slr0774 -1.79 21.2 -1.701 21.2 Protein-export membrane protein SecD Slr0984 -1.88 115.3 CDP-glucose 4,6-dehydratase (EC 4.2.1.45) NAD+dependent Slr1271 -1.94 11.8 -2.237 11.8 UDP-N-acetyl-D-mannosaminuronic acid transferase Slr1510...”
- Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803
Zhu, Biotechnology for biofuels 2013 - “...protein mtrc precursor, putative sll1395 1.91 2.61 1.54 dTDP-6--6-deoxy-L-mannose-dehydrogenase sll2010 1.60 1.78 2.89 UDP-N-acetylmuramoylalanine--D-glutamate ligase slr0528 2.52 1.91 2.45 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase slr0993 1.75 2.33 4.21 Putative peptidase slr1166 2.86 1.68 2.36 UDP-glucose:tetrahydrobiopterin glucosyltransferase slr1196 4.07 1.91 2.74 Periplasmic protein, function unknown slr1744 1.89 1.92 2.42...”
- “...in cell envelope function were up-regulated upon butanol exposure, such as sll2010 encoding UDP-N-acetylmuramoylalanine--D-glutamate ligase, slr0528 encoding UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase and sll088 encoding UDP-N-acetylglucosamine--peptide n-acetylglucosaminyltransferase (Table 3 ). Their up-regulation was supposed to strengthen cell wall structure against butanol stress. vi. Regulatory genes: Previous proteomic analysis...”
- Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light
Huang, Journal of bacteriology 2002 - “...0.22 0.53 0.2 0.91 0.17 0.63 0.11 nlpD murE rfbU slr0993 slr0528 slr1064 0.67 0.34 0.65 0.12 1.04 0.26 0.64 0.31 0.69 0.12 0.89 0.1 0.24 0.12 0.49 0.11 0.47...”
E5A72_RS05230 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Acinetobacter baumannii ATCC 17978
41% identity, 96% coverage
WP_000218550 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Acinetobacter baumannii
42% identity, 92% coverage
MXAN_5609 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase from Myxococcus xanthus DK 1622
41% identity, 91% coverage
- Peripheral rods: a specialized developmental cell type in Myxococcus xanthus
Whitfield, Genomics 2020 - “...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 transcripts during stationary phase. Table 5 Transcriptome Analysis of genes encoding developmental proteins of the cellular envelope. Protein...”
Pnuc_0162 UDP-N-acetylmuramyl-tripeptide synthetase from Polynucleobacter sp. QLW-P1DMWA-1
45% identity, 87% coverage
A1S_3203 UDP-N-acetylmuramoylalanyl-D-glutamate-2 6-diaminopimelate ligase from Acinetobacter baumannii ATCC 17978
45% identity, 79% coverage
CD2664 putative UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelat e ligase from Clostridium difficile 630
37% identity, 99% coverage
- "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores
Swarge, Proteomics. Clinical applications 2018 - “...as an important structural component of spore coat. 40 Its ortholog protein encoded by MurE (CD2664) in P. difficile was identified in our proteome set. The role of MurE in spore assembly remains unstudied. Protein CD3559 (FtsH2) is an ortholog of SpoVK, 41 a protein involved...”
- Investigation of the Cross-talk Mechanism in Caco-2 Cells during Clostridium difficile Infection through Genetic-and-Epigenetic Interspecies Networks: Big Data Mining and Genome-Wide Identification
Li, Frontiers in immunology 2017 - “...et al. predicted 76 essential C. difficile genes ( 19 ). Seven C. difficile proteins (CD2664, CD2335, CD3550, CD0198, CD1225, CD0130, and CD0123) in the HPN of the early stage of CDI (Figure S3 in Supplementary Material) and three C. difficile proteins (CD2588, CD1816, and CD0130)...”
- “...considered as essential genes for C. difficile growth ( 20 ). Thirteen C. difficile proteins (CD2664, CD2335, CD0067, CD3550, CD3540, CD0198, CD1255, CD2714, CD3256, CD1316, CD0095, CD2739, and CD0123) in the HPN of the early stage of CDI (Figure S3 in Supplementary Material) and 15 C....”
- Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores
Dembek, PloS one 2013 - “...CD2653 UDP-N-acetylmuramoylalanineD-glutamate ligase 0.0105 +1.5 CD2654 phospho-N-acetylmuramoyl-pentapeptide-transferase 0.0145 +1.7 CD2655 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alan ine ligase 0.00508 +2.4 CD2664 putative UDP-N-acetylmuramoylalanyl-D-glutamate2,6-diaminopimelate ligase 0.0344 +2.4 CD3563 putative spore cortex-lytic enzyme 0.0245 +2.2 CD1898 putative phage-related cell wall hydrolase (endolysin) 0.0174 6.1 10.1371/journal.pone.0064011.t005 Table 5 List of differentially regulated putative secondary...”
- Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile
Saujet, PLoS genetics 2013 - “...K envelopes CD0119 glmM Phosphoglucosamine mutase 0.49 CD0120 glmS Glucosamine-fructose-6-P aminotransferase 0.52 K / A CD2664 murE UDP-N-acetylmuramyl-tripeptide synthetase 0.45 0.42 K / A CD3007 Putative L,D-transpeptidases 0.37 0.48 + CD2184 Putative N-acetylmuramoyl-L-alanine amidase 0.21 0.13 K CD1898 Putative N-acetylmuramoyl-L-alanine amidase 0.12 K + CD1898-CD1897 CD1897...”
- “...protein 0.03 0.01 0.01 CD1613 cotA Spore outer coat layer protein CotA 0.13 0.10 0.05 CD2664 murE UDP-N-acetylmuramyl-tripeptide synthetase 0.51 0.45 0.42 CD3230 bclA2 Putative exosporium glycoprotein 0.16 0.12 0.04 CD3349 bclA3 Exosporium glycoprotein BclA3 0.12 0.01 0.02 CD3620 Conserved hypothetical protein 0.35 0.34 0.04 qRT-PCR...”
MURE_BACCR / Q819Q0 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase; Meso-A2pm-adding enzyme; Meso-diaminopimelate-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.13 from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) (see paper)
38% identity, 94% coverage
- function: Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6- diaminoheptanedioate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl- gamma-D-glutamyl-meso-2,6-diaminoheptanedioate + ADP + phosphate + H(+) (RHEA:23676)
cofactor: Mg(2+)
VspiD_010100019130 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase from Verrucomicrobium spinosum DSM 4136
41% identity, 93% 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 - “...d -glutamate ligase 6.3.2.9 VspiD_010100019115 MurE UDP- N -acetylmuramoyl- l -alanyl- d -glutamate:2,6-Diaminopimelate ligase 6.3.2.13 VspiD_010100019130 MurF UDP- N -acetylmuramoyl-tripeptide: d -alanyl- d -alanine ligase 6.3.2.10 VspiD_010100019125 AlaR Alanine racemase 5.1.1.1 VspiD_010100000100 Ddl d -alanine: d -alanine ligase 6.3.2.4 VspiD_010100018175 MraY Phospho- N -acetylmuramoyl-pentapeptide transferase 2.7.8.13...”
- 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 - “...(ORF) for protein expression and purification The open reading frame annotated by the locus tag (VspiD_010100019130) UDP- N -acetylmuramoyl- l -alanyl- d -glutamate: meso -2,6-diaminopimelate ligase was amplified by PCR. The following forward and reverse primers were used: murE Vs -forward 5-CACC ATG ACCATTTTGCGCGATCTTATCGAGGGT-3 and murE...”
- “...d -alanine ligase 6.3.2.4 VspiD_010100019115 MurD UDP- N -acetylmuramoyl- l -alanine: d -glutamate ligase 6.3.2.9 VspiD_010100019130 MurE UDP- N -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:...”
- Genomic and Biochemical Analysis of the Diaminopimelate and Lysine Biosynthesis Pathway in Verrucomicrobium spinosum: Identification and Partial Characterization of L,L-Diaminopimelate Aminotransferase and UDP-N-Acetylmuramoylalanyl-D-glutamyl-2,6-meso-Diaminopimelate Ligase
Nachar, Frontiers in microbiology 2012 - “...in the identification of the murE ortholog from V. spinosum annotated by the locus tag VspiD_010100019130, which is 37% identical to the C. trachomatis MurE. Crude soluble protein extract from V. spinosum contains DapL activity If V. spinosum utilizes the DapL pathway for diaminopimelate/lysine biosynthesis, as...”
- “...length ORFs annotated by the locus tags VspiD_010100012510 ( dapL , L,L -diaminopimelate aminotransferase) and VspiD_010100019130 ( murE , UDP- N -acetylmuramoylalanyl- d -glutamyl-2,6- meso -diaminopimelate ligase) were amplified by PCR. The ORFs were amplified using: 12pmol of forward and reverse primers, 1mM MgSO 4 ,...”
LMOf2365_2070 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Listeria monocytogenes str. 4b F2365
38% identity, 94% coverage
- Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
Chakravarty, Frontiers in microbiology 2021 - “...5.5 Metabolism adhE LMOf2365_1656 Acetaldehyde dehydrogenase/alcohol dehydrogenase 48.1 71.2 LMOf2365_0250 Serine O-acetyltransferase 5.8 4.4 murE LMOf2365_2070 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase 5.7 4.5 Translation LMOf2365_2879 tRNA-Glu 25.3 4.8 LMOf2365_2913 tRNA Leu 11.5 4.1 hly LMOf2365_0213 Listeriolysin O 70.0 3.7 Transcription factors LMOf2365_2205 Sigma-54 dependent transcriptional regulator 10.7 5.5 Changes...”
all1663 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Nostoc sp. PCC 7120
43% identity, 96% coverage
Q03523 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Bacillus subtilis (strain 168)
BSU15180 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Bacillus subtilis subsp. subtilis str. 168
38% identity, 94% coverage
LM6179_2810 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Listeria monocytogenes 6179
38% identity, 93% coverage
lmo2038 similar to UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase from Listeria monocytogenes EGD-e
38% identity, 93% coverage
FN1225 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--meso-lanthionine ligase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Q8R635 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)
37% identity, 94% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...Unchanged 11 11 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...”
- “...FN1614, FN1717, FN1827, FN1830. 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...”
- Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions
Kumar, BMC microbiology 2016 - “...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 5 Microbial metabolism...”
lp_0977 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diami nopimelate ligase from Lactobacillus plantarum WCFS1
38% identity, 87% coverage
F452_RS0104190 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Porphyromonas gulae DSM 15663
39% identity, 94% coverage
- Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
Lee, Journal of veterinary science 2019 - “...Peptidoglycan related function F452_RS0103705 N-acetylmuramic acid 6-phosphate etherase 5.06E-21 6.70 F452_RS0108880 Polysaccharide deacetylase 1.83E-28 7.34 F452_RS0104190 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 5.09E-83 10.03 F452_RS0104215 UDP-N-acetylmuramate--alanine ligase 2.58E-92 11.04 F452_RS0106650 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 5.77E-41 4.26 F452_RS0104195 Phospho-N-acetylmuramoyl-pentapeptide transferase 7.50E-80 9.51 F452_RS0100970 Penicillin-binding protein 1A 1.44E-86 6.85 F452_RS0106225 D-alanine--D-alanine ligase 1.85E-23...”
SMc01861 PROBABLE UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2, 6-DIAMINOPIMELATE LIGASE PROTEIN from Sinorhizobium meliloti 1021
40% identity, 94% coverage
Bresu_2781 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Brevundimonas subvibrioides ATCC 15264
42% identity, 95% coverage
Atu2099 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Agrobacterium tumefaciens str. C58 (Cereon)
39% identity, 97% 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 - “...Pgi atu0404 glucose-6-phosphate isomerase 6,64 Atu4046 atu4046 ABC transporter substrate-binding protein (glycine betaine) 6,22 MurE atu2099 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6- diaminopimelate ligase 5,87 Atu1879 atu1879 ABC transporter, substrate binding protein (amino acid) 4,50 Atu0157 atu0157 ABC transporter, substrate binding protein 3,87 Atu4678 atu4678 ABC transporter substrate-binding protein (amino acid)...”
- Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
Curtis, Molecular microbiology 2014 - “...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 E MurG CC_2551 E Bresu_2776 E Atu2096 E MraY CCNA_02640 c E Bresu_2779 E Atu2097 E Ddl CC_2543 E Bresu_2690 E Atu2089 E...”
SAMCFNEI73_Ch2467 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Sinorhizobium americanum
40% identity, 95% coverage
PG0576 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase from Porphyromonas gingivalis W83
38% identity, 94% coverage
- Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
Moon, BMC microbiology 2014 - “...cell division and synthesis of peptidoglycan [ 29 ]-[ 31 ]: PG0575 (penicillin-binding protein 2), PG0576 ( murE ), PG0577 ( mraY ), PG0578 ( murD ), PG0579 ( ftsW ), PG0580 ( murG ), PG0581 ( murC ), PG0582 ( ftsQ ), PG0583 ( ftsA...”
- “...: Biosynthesis and degradation of murein sacculus and peptidoglycan PG0575 Penicillin-binding protein 2 1.41 c PG0576 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase 1.42 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...”
- The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis
Priyadarshini, Microbiology (Reading, England) 2013 - “...encoding enzymes involved in peptidoglycan precursor synthesis (PG0576, PG0577, PG0578, PG0580 and PG0581) was also down, indicating that the P. gingivalis...”
RC0912 UDP-N-acetylmuramoylalanyl-D-glutamate-- 2,6-diaminopimelate ligase [EC:6.3.2.13] from Rickettsia conorii str. Malish 7
35% identity, 98% coverage
- Deciphering <i>Rickettsia conorii</i> metabolic pathways: A treasure map to therapeutic targets
Prajapat, Biotechnology notes (Amsterdam, Netherlands) 2025 - “...wall biosynthesis, and dipicolinic acid Metabolism Cytoplasm No RC0911 UDP-N-AcMur_synth Peptidoglycan synthesis Metabolism Cytoplasm Yes RC0912 UDP-N-AcMur-Glu-dNH2Pim_ligase Peptidoglycan synthesis Metabolism Cytoplasm Yes RC1086 Glyco_hydro_3_N Hydrolyse the glycosidic bond between two or more carbohydrates Metabolism Cytoplasm Yes RC0008 Lipid_A_LpxA Lipopolysaacharide synthesis Metabolism Cytoplasm Yes RC0010 LpxD Involved...”
X276_18755 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Clostridium beijerinckii NRRL B-598
33% identity, 92% coverage
KSE_21280 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Kitasatospora setae KM-6054
42% identity, 88% coverage
O05954 glutamate formimidoyltransferase (EC 2.1.2.5) from Homo sapiens (see paper)
35% identity, 100% coverage
CC_2559 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase from Caulobacter crescentus CB15
39% identity, 98% coverage
Hore_09040 UDP-N-acetylmuramyl-tripeptide synthetase from Halothermothrix orenii H 168
38% identity, 93% coverage
SE0718 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase from Staphylococcus epidermidis ATCC 12228
SERP0607 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Staphylococcus epidermidis RP62A
SERP_RS03100 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L- lysine ligase from Staphylococcus epidermidis RP62A
34% identity, 93% coverage
- Release of extracellular ATP by bacteria during growth
Mempin, BMC microbiology 2013 - “...Phage type 8 [ 12 ] SE0052 Clinical isolate, Phage type 13 [ 12 ] SE0718 Clinical isolate, Phage type 4 [ 12 ] SE0430 Clinical isolate, Phage type 4 [ 12 ] Salmonella enterica Serovar Typhimurium ST3665 Clinical isolate [ 12 ] ST3744 Clinical isolate...”
- 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 - “...SERP2293 SERP2295 SERP2296 SERP2294 SERP2292 SERP1731 SERP0405 SERP0993 SERP0607 SERP0746 Annotation 30 min cydA cydB qoxC qoxD nuoF sdhA sdhB sdhC atpC atpD...”
- Identification of Genes Controlled by the Essential YycFG Two-Component System Reveals a Role for Biofilm Modulation in Staphylococcus epidermidis
Xu, Frontiers in microbiology 2017 - “...transport system regulatory protein Phosphonate transport Gebhard and Cook, 2008 SERP_RS11250 SERP_RS11245 SERP_RS11240 161 TTAACACTACCTTAACA SERP_RS03100 murE UDP-N-acetylmuramoy-L-alanyl-D-glutamate-L-lysine ligase Cell wall synthesis Gardete et al., 2004 ; Zaher and Green, 2011 SERP_RS03105 SERP_RS03120 prfC peptide-chain-release factor 3 Protein production accuracy 226 ATTACAATAAGATTACA SERP_RS02025 ltaS Glycerol phosphate...”
AWH67_RS03970 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Bartonella bacilliformis
36% identity, 98% coverage
NP_219774 UDP-N-acetylmuramoylalanylglutamyl DAP Ligase from Chlamydia trachomatis D/UW-3/CX
38% identity, 95% coverage
Q49WE7 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase from Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)
35% identity, 92% 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 - “...17 unique metabolic pathways (UMPs). Protein Name (Protein ID) Common Pathway Unique Pathway UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase (Q49WE7) ssp00550-Peptidoglycan biosynthesis Penicillin-binding protein 1 (Q49WW3) ssp01100-Metabolic pathways ssp00550-Peptidoglycan biosynthesis ssp01501-beta-Lactam resistance Protein translocase subunit SecE (Q49V45) ssp03060-Protein export ssp03070-Bacterial secretion system Aspartokinase (Q49XJ5) ssp01210-2-Oxocarboxylic acid metabolism ssp01230-Biosynthesis of amino...”
SCO2089 putative UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase from Streptomyces coelicolor A3(2)
41% identity, 90% coverage
RC1_0618 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Rhodospirillum centenum SW
42% identity, 93% coverage
CTL0521 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Chlamydia trachomatis 434/Bu
37% identity, 95% coverage
8g6pA / G7CMG5 Crystal structure of mycobacterium thermoresistibile mure in complex with adp and 2,6-diaminopimelic acid (see paper)
41% identity, 92% coverage
- Ligands: adenosine-5'-diphosphate; 2,6-diaminopimelic acid; magnesium ion (8g6pA)
BMEI0574 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE from Brucella melitensis 16M
37% identity, 94% coverage
CCC13826_1740 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Campylobacter concisus 13826
40% identity, 77% coverage
Q72R81 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
36% identity, 78% coverage
Q8F4J4 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
36% identity, 78% coverage
murE / O86491 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--lysine ligase (EC 6.3.2.7) from Staphylococcus aureus (strain COL) (see 4 papers)
MURE_STAA8 / Q2FZP6 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase; L-lysine-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:L-Lys ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.7 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see 4 papers)
Q2FZP6 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase (EC 6.3.2.7) from Staphylococcus aureus (see paper)
4c12A / Q2FZP6 X-ray crystal structure of staphylococcus aureus mure with udp-murnac- ala-glu-lys and adp (see paper)
SAUSA300_0919 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAOUHSC_00954 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL1023 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Staphylococcus aureus subsp. aureus COL
33% identity, 92% coverage
- function: Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Cannot use diaminopimelate as substrate (PubMed:10498701, PubMed:14114846, PubMed:20659527). Can accept L-ornithine as substrate, but the efficiency is 400-fold lower than that with L-lysine (PubMed:20659527). Seems to have a role in beta-lactam antibiotic resistance (PubMed:14996801).
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + L-lysine + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L- lysine + ADP + phosphate + H(+) (RHEA:17969)
cofactor: Mg(2+) - Ligands: uridine 5'diphospho n-acetyl muramoyl-l-alanyl-d-glutamyl-l-lysine; adenosine-5'-diphosphate; magnesium ion (4c12A)
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...pyrimidines, nucleosides, and nucleotides SAUSA300_0368 RpsR 0.33 Protein synthesis SAUSA300_1357 AroC 0.33 Amino acid biosynthesis SAUSA300_0919 MurE 0.32 Cell envelope SAUSA300_1156 ProS 0.32 Protein synthesis SAUSA300_0753 0.30 Conserved hypothetical protein SAUSA300_0741 UvrB 0.29 DNA metabolism SAUSA300_0692 SaeQ 0.27 Conserved hypothetical protein SAUSA300_1523 0.27 Conserved hypothetical protein...”
- A Novel Workflow for In Silico Prediction of Bioactive Peptides: An Exploration of Solanum lycopersicum By-Products
Morena, Biomolecules 2024 - “...30.94 2.68 R31, H181, R187 *, E381 D1, T9, A13 Target: Staphylococcus aureus ; UniProt: Q2FZP6; PDB: 4C12. * Residues of the active domain G110S116, N151, T152T513, S179, and R187. DAGASKTYPQQAGTIRKGGHIVIKNRP Q9AXQ6 Eukaryotic translation initiation factor 5A-1 27 32.07 4.96 D5(A), E7(A), K8(A), R10(A), M1(B) D1,...”
- Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin
Sierra, Nucleic acids research 2020 - “...n/a murA2 SAOUHSC_02365 UDP- N -acetylglucosamine 1-carboxyvinyltransferase [470/CACAUA] Cell wall organization or biogenesis [GO:0071554] murE SAOUHSC_00954 UDP- N -acetylmuramoylalanyl- d -glutamate- l -lysine ligase [1330/GACAUA] Cell wall organization or biogenesis [GO:0071554] murI SAOUHSC_01106 Glutamate racemase [94/UACUUA] Cell wall organization or biogenesis [GO:0071554] oatA SAOUHSC_02885 O -Acetylation...”
- 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 - “...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 3 Biosynthesis and degradation of...”
SA0876 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Staphylococcus aureus subsp. aureus N315
33% identity, 92% coverage
SXYL_01914 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L- lysine ligase from Staphylococcus xylosus
32% identity, 95% coverage
- Adaptation of Staphylococcus xylosus to Nutrients and Osmotic Stress in a Salted Meat Model
Vermassen, Frontiers in microbiology 2016 - “...5.7 5.2 6.1 SXYL_01706-05 mraY, murD Phospho-N-acetylmuramoyl-pentapeptide-transferase, UDP-N-acetylmuramoylalanineD-glutamate ligase 8.3 * 5.0 * 3.1 * SXYL_01914 murE UDP-N-acetylmuramoyl-L-alanyl-D-glutamateL-lysine ligase 6.2 5.2 3.6 SXYL_02166 uppP Undecaprenyl-diphosphatase 2.5 2.3 2.2 SXYL_01624 uppS Isoprenyl transferase 6.1 3.0 2.5 SXYL_01707 pbp1 Penicillin-binding protein 1 4.3 2.7 2.0 SXYL_01304 pbp3 Penicillin-binding...”
RSP_2099 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase from Rhodobacter sphaeroides 2.4.1
40% identity, 94% coverage
- The NtrYX Two-Component System Regulates the Bacterial Cell Envelope
Lemmer, mBio 2020 - “...10 2 RSP_2098 ftsI Cell division protein FtsI (penicillin-binding protein 3) 0.45 3.0 10 3 RSP_2099 murE UDP- N -acetylmuramoylalanyl- d -glutamate 2,6-diaminopimelate ligase 0.27 3.5 10 -2 RSP_2100 murF UDP- N -acetylmuramoyl-tripeptide d -alanyl- d -alanine ligase 0.38 8.7 10 2 RSP_2101 mraY Phospho- N...”
Q89FU2 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)
38% identity, 96% coverage
- Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency.
Suyal, Scientific reports 2019 - “...while , FusA (Elongation factor G, Q0SFF3); CobB (Hydrogenobyrinate a,c-diamide synthase, Q98KP1); MurE1 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase, Q89FU2); HbdA (3-hydroxybutyryl-CoA dehydrogenase, Q45223); ureB (Urease subunit beta, Q98CY6); hemZ (Ferrochelatase, Q0S0F7) and rpoA (DNA-directed RNA polymerase subunit alpha, Q0S3E7) were found to have higher BC under NB . GO-based...”
Cj1641 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diami ligase from Campylobacter jejuni subsp. jejuni NCTC 11168
38% identity, 76% coverage
- MicroGlycoDB: A database of microbial glycans using Semantic Web technologies
Lee, BBA advances 2024 - “...information obtained through an extensive search across pertinent literature and databases. For example, for the cj1641 gene of C. jejuni , the relevant enzyme product information was retrieved from the UniProtKB, CAZy, PDB, and Enzyme Commission (EC) databases. The enzyme reaction components, such as the donor...”
- Campylobacter jejuni Virulence Factors Identified by Modulating Their Synthesis on Ribosomes With Altered rRNA Methylation
Sałamaszyńska-Guz, Frontiers in cellular and infection microbiology 2021 - “...tlyA inactivation, albeit to a lesser degree than mlaEFD ; however, expression of tkt and cj1641 immediately upstream and downstream of these genes remained unaffected ( Figure2 ). The abundances of MlaE, MlaF, MlaD and CJ1640 were partially restored to around two-thirds of the wild-type levels...”
- “...as CJ1640) was consistently reduced, *P < 0.05, (but outside our cut-off criteria), while its CJ1641 neighbor was unchanged. These three additional proteins are shown here for comparison. The error bars represent standard deviations from three biological replicates. Inactivation of cdtC and mlaEFD Decreases the Virulence...”
- Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans
Peters, Communications biology 2021 - “...Cj1631c NA 62.0% 470282_A_A-core g00386 Cj1631c NA 62.0% 469774_G_G-core g00386 Cj1631c NA 62.0% 597240_G_G-core g01291 Cj1641 murE 62.0% g01925_00012-c g01925 Cj1711c rsmA 62.0% # Among most associated GWAS hits. *Gene with high number of GWAS hits. Reflecting our empirical clinical evidence, we observed variation in risk...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj1398, cj1400c, cj1401c, cj1402c, cj1404, cj1407c, cj1424c, cj1428c, cj1476c, cj1498c, cj1515c, cj1529c, cj1530, cj1605c, cj1634c, cj1641, cj1645, cj1672c, cj1685c FBA & transposon mutagenesis of this study cj0027, cj0116, cj0117, cj0324, cj0387, cj0394c, cj0442, cj0514, cj0516, cj0581, cj0597, cj0639c, cj0641, cj0686, cj0840c, cj0894c, cj0927, cj1008c, cj1045c, cj1054c,...”
2wtzB / P9WJL3 Mure ligase of mycobacterium tuberculosis (see paper)
40% identity, 90% coverage
- Ligand: uridine-5'-diphosphate-n-acetylmuramoyl-l-alanine-d-glutamate (2wtzB)
murE / P9WJL3 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase (EC 6.3.2.13) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
P9WJL3 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (EC 6.3.2.13) from Mycobacterium tuberculosis (see paper)
NP_216674 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Mycobacterium tuberculosis H37Rv
MT2217 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Mycobacterium tuberculosis CDC1551
Rv2158c UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Mycobacterium tuberculosis H37Rv
40% identity, 85% coverage
- ATP-dependent MurE ligase in Mycobacterium tuberculosis: biochemical and structural characterisation.
Basavannacharya, Tuberculosis (Edinburgh, Scotland) 2010 (PubMed)- GeneRIF: It is evident that Mtb-MurE is highly specific in adding m-DAP to UDP-MurNAc-dipeptide and ATP-hydrolysis is an absolute requirement for its activity.
- Essential residues for the enzyme activity of ATP-dependent MurE ligase from Mycobacterium tuberculosis.
Basavannacharya, Protein & cell 2010 - GeneRIF: This study provides an insight into the residues essential for the catalytic activity and substrate binding of the ATP-dependent MurE ligase.
- Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development
Moraes, Tuberculosis (Edinburgh, Scotland) 2015 - “...0.26 MurD MT2214 88.1% (86.9%) 3.86 (4.44) 0.66 (0.62) 2JFG [ 101 ] 0.37 MurE MT2217 93.3% (93.1%) 5.91 (6.09) 0.85 (0.80) 2XJA [ 3 , 114 ] 0.27 MurE MT2217 93.4% (91.2%) 5.89 (5.18) 0.78 (0.76) 1E8C [ 112 ] 0.30 MurF MT2216 89% (88.7%)...”
- Role of a Putative Alkylhydroperoxidase Rv2159c in the Oxidative Stress Response and Virulence of Mycobacterium tuberculosis
Bhargavi, Pathogens (Basel, Switzerland) 2022 - “...carried out using upstream ~1000 bases flanking left arm of Rv2160c and downstream right arm Rv2158c sequence regions. The amplified regions were ligated and cloned onto an antibiotic-resistant cassette of p0004-SacB plasmid for homologous recombination. The recombinant clones were screened using the Van91I restriction site; this...”
- Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis
Kuang, Acta pharmaceutica Sinica. B 2022 - “...catalyzed byMurC (Rv2151c). Subsequently, MurD (Rv2155c) catalyzes d -isoglutamate binding of l -alanine residues; MurE (Rv2158c) catalyzes m -DAP attachment of d -isoglutamate residues; and MurF (Rv2157c) is responsible for addition of d -alanyl- d -alanine to the m -DAP residues, resulting in Park's nucleotide. MurX/MraY...”
- Uncovering Beta-Lactam Susceptibility Patterns in Clinical Isolates of Mycobacterium tuberculosis through Whole-Genome Sequencing
Olivença, Microbiology spectrum 2022 - “...(3) 4.1.2.1 (23) 2416167 G>T F76L 4 (2.33) 4.4.1.1 (4) >64 5.7 16.0 2.0 4.473 Rv2158c murE 2420535 C>A G25V 50 (29.07) 4.3.4.2 (50) 25.6 0.9 2.5 0.5 0.922 Rv2981c ddl 3336825 T>C T365A 151 (87.79) All except 4.7 (11) and 4.8 (10) 46.6 1.8 4.1...”
- α-Glucosidase Inhibitor Can Effectively Inhibit the Risk of Tuberculosis in Patients with Diabetes: A Nested Case-Control Study
Lin, BioMed research international 2020 - “...Therefore, acarbose is effective as a competitive inhibitor of M.tb treS [ 36 ]. murE (Rv2158c) is an essential gene of M.tb because it encodes a protein, UDP- N -acetylmuramoyl- l -alanyl- d -glutamate: meso -diaminopimelate ligase, that catalyses mycobacterial peptidoglycan organisms and synthesises the necessary...”
- Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism
Yimer, Frontiers in microbiology 2020 - “...murD Rv2155c 5, 7 3, 4 UDP- N -acetylmuramoyl- L -alanyl- D -glutamate2,6-diaminopimelate ligase murE Rv2158c 3, 5, 7 4 Isoniazid-induced protein IniC iniC Rv0343 5, 7 3, 4 Isoniazid-induced protein IniA iniA Rv0342 5, 7 3, 4 Proteins required for PDIM/phenolglycolipid (PGL) biosynthesis including PpsA,...”
- Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall
Batt, Cell surface (Amsterdam, Netherlands) 2020 - “...to the UDP-MurGlyc/NAc by the ATP-dependant Mur ligases: MurC, MurD and MurE (Rv2152c, Rv2155c and Rv2158c), which ligate L-Ala, D- iso Glu and m- DAP sequentially ( Kurosu et al., 2007 , Munshi et al., 2013 ). The peptide sidechain is completed by MurF (Rv2157c) adding...”
- Revisiting Anti-tuberculosis Therapeutic Strategies That Target the Peptidoglycan Structure and Synthesis
Catalão, Frontiers in microbiology 2019 - “...(Rv2151c). This is followed by d -isoglutamate addition by MurD (Rv2155c), m-DAP addition by MurE (Rv2158c), and finally d -alanyl- d -alanine addition by MurF (Rv2157c). This generates the muramyl-pentapeptide product UDP-Mur N Ac/Glyc- l -Ala- d -isoGlu- m -DAP- d -Ala- d -Ala, also known...”
- Detection of a Putative TetR-Like Gene Related to Mycobacterium bovis BCG Growth in Cholesterol Using a gfp-Transposon Mutagenesis System
Otal, Frontiers in microbiology 2017 - “...work Rv3540c-R: GTGCGGATACGAAAACGAAT yrb E4A (Rv3501c) Rv3501c-F: CTACGCGTTCTCGGTCTTTC 55C This work Rv3501c-R: AGTATCAATTCGCGCAGTCC mur E (Rv2158c) Rv2158c-F: CGCCTTCACCAATCTCTCC 55C This work Rv2158c-R: AGTCCGGATCGAACAATGAC Small RNAS MTS2823 MTS2823-F: GAGAAGGTTCGGTCTCCCGAC 58C This work MTS2823-R: TTACGCAGACCCGCAACACT MTS0997 MTS0997-F: AAGCAGGCCCGGTTAGTGA 58C This work MTS0997-R: CACCGGTACACATGGGCAGA rnp B rnpB-F: TTCACAGAGCAGGGTGATTG 62C...”
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E7FUC9 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (EC 6.3.2.13) from Erysipelothrix rhusiopathiae (see paper)
32% identity, 94% coverage
NBX27_04865 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Erysipelothrix rhusiopathiae
32% identity, 94% coverage
- Human Erysipelothrix rhusiopathiae infection via bath water - case report and genome announcement
Zautner, Frontiers in cellular and infection microbiology 2022 - “...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 -acetylglucosaminyltransferase NBX27_05455 murI glutamate racemase NBX27_05555 murJ/mviN murein biosynthesis integral membrane protein MurJ NBX27_00365 alr...”
murE / Q9WY79 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase (EC 6.3.2.7; EC 6.3.2.37) from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see 2 papers)
MURE_THEMA / Q9WY79 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase; D-lysine-adding enzyme; L-lysine-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:LD-Lys ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.37; EC 6.3.2.7 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
36% identity, 96% coverage
- function: Catalyzes the addition of both L- and D-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use meso-diaminopimelate as the amino acid substrate in vitro, although much less efficiently.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + L-lysine + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L- lysine + ADP + phosphate + H(+) (RHEA:17969)
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + D-lysine + ATP = N(6)-(UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D- glutamyl)-D-lysine + ADP + phosphate + H(+) (RHEA:25273)
DIP1603 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate from Corynebacterium diphtheriae NCTC 13129
36% identity, 90% coverage
- Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
Wittchen, BMC genomics 2018 - “...transport; Transcription; Amino Acid metabolism and transport; Post-translational modification, protein turnover, and chaperones; Function unknown DIP1603 - DIP1596 8 not detected murE, murF, mraY, murD , DIP1599, murG, murC , DIP1596. Cell wall, membrane, envelop biogenesis DIP1720 - DIP1713 8 not detected dnaJ2 , DIP1719, DIP1718,...”
4bubB / Q9WY79 Crystal structure of mure ligase from thermotoga maritima in complex with adp (see paper)
36% identity, 96% coverage
- Ligand: adenosine-5'-diphosphate (4bubB)
O69557 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (EC 6.3.2.13) from Mycobacterium leprae (see paper)
ML0909 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diami nopime ligase (meso-diaminopimelate-adding enzyme). from Mycobacterium leprae TN
40% identity, 88% coverage
- Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases
Ojo, Frontiers in cellular and infection microbiology 2021 - “...transcript levels than that of MFP5 ( Table1 ). These included the murC (ML0915), murE (ML0909) and murD (ML0912) genes, encoding proteins involved with peptidoglycan biosynthesis, and embA (ML0105c) and embC (ML0106c) genes encoding arabinosyltransferases ( Figure5 ). Three genes with the highest fold change in...”
- “...held in axenic medium, transcript levels of murD (ML0912 ), ftsZ (ML0913), murC (ML0915), murE (ML0909), and arabinosyltransferases encoded by embA (ML0105c) and embC (ML0106c) were significantly increased. This may indicate an increased effort by M. leprae to maintain its cell wall integrity in the axenic...”
cg2374 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Corynebacterium glutamicum ATCC 13032
37% identity, 89% coverage
BB0201 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) from Borrelia burgdorferi B31
31% identity, 94% coverage
MURE_ARATH / F4I3P9 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase MurE homolog, chloroplastic; AtMurE; Protein ALBINO OR PALE-GREEN 13; Protein PIGMENT DEFECTIVE EMBRYO 316 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G63680 MURE; ATP binding / acid-amino acid ligase/ ligase from Arabidopsis thaliana
NP_001321889 ALBINO OR PALE-GREEN 13 from Arabidopsis thaliana
32% identity, 60% coverage
- function: Involved in chloroplast biogenesis. Required for thylakoid membrane development. Seems to be required for plastid-encoded plastid RNA polymerase (PEP)-dependent gene expression.
subunit: Component of the plastid-encoded plastid RNA polymerase (PEP) complex.
disruption phenotype: Albino phenotype and seedling lethality under normal growth conditions. - Defining the heterogeneous composition of Arabidopsis thylakoid membrane
Trotta, The Plant journal : for cell and molecular biology 2025 (no snippet) - Plastid retrograde signaling: A developmental perspective
Loudya, The Plant cell 2024 - “...AT2G34640 THA1 Gramene: AT1G08630 THA1 Araport: AT1G08630 fc2 Gramene: AT2G30390 fc2 Araport: AT2G30390 murE Gramene: AT1G63680 murE Araport: AT1G63680 MORF2 Gramene: AT2G33430 MORF2 Araport: AT2G33430 GUN1 Gramene: AT2G31400 GUN1 Araport: AT2G31400 TIC100 Gramene: AT5G22640 TIC100 Araport: AT5G22640 References Agrawal S , Karcher D , Ruf S...”
- The Chloroplast Envelope of Angiosperms Contains a Peptidoglycan Layer
Tran, Cells 2023 - “...12 ]. In the Arabidopsis genome, only four homologs of PGN pathway genes ( MurE (At1g63680), MraY (At4g18270), MurG (at1g73740) and DDL (At1g08840), Figure 1 ) were found. It is noteworthy, that all sequenced plant genomes to date harbor at least these four homologs (from here...”
- Arabidopsis Response to Inhibitor of Cytokinin Degradation INCYDE: Modulations of Cytokinin Signaling and Plant Proteome
Berková, Plants (Basel, Switzerland) 2020 - “...0.70 5.9 10 4 AT4G37000 Chlorophyll biosynthesis Red chlorophyll catabolite reductase 0.65 1.9 10 3 AT1G63680 Chloroplast biogenesis UDP- N -acetylmuramoyl- l -alanyl- d -glutamate-2,6-diaminopimelate ligase 0.77 8.1 10 5 AT1G08520 Chloroplast biogenesis Magnesium-chelatase subunit 0.68 9.6 10 4 AT2G04030 Chloroplast biogenesis Heat shock protein 90-5...”
- Arabidopsis Seedling Lethal 1 Interacting With Plastid-Encoded RNA Polymerase Complex Proteins Is Essential for Chloroplast Development
Jiang, Frontiers in plant science 2020 - “...At4g20130; PAP6/FLN1, At3g54090; FLN2, At1g69200; PAP10/Trxz, At3g06730; PAP4/FSD2, At5g51100; PAP9/FSD3, At5g23310; PAP8/PTAC6, At1g21600; and PAP11/MurE-Like, At1g63680; Kindgren and Strand, 2015 ) as prey. These assays showed that SL1 interacted with three PEP-associated proteins, including PAP12/PTAC7, PAP5/PTAC12, and PAP7/PTAC14, but no other PEP complex proteins ( Figure...”
- Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)
Liu, BMC plant biology 2015 - “...normalized expression value. Red line: qRT-PCR data, Blue line: RNA-seq data. Triplet 722, homolog of AT1G63680 encoding an acid-amino acid ligase; Triplet 272, homolog of AT3G47690 encoding microtubule end binding protein EB1A; Triplet 1681, homolog of AT3G10370 encoding glycerol-3-phosphate dehydrogenase SDP6; Triplet 2282, homolog of AT1G05675...”
- Nuclear-encoded factors associated with the chloroplast transcription machinery of higher plants
Yu, Frontiers in plant science 2014 - “...reductase activity in vitro Pfalz et al., 2006 ; Arsova et al., 2010 PAP11/AtMurE a AT1G63680 Arabidopsis / Mustard Chloroplast b Low PEP activity Mur ligase family protein Unknown Pfalz et al., 2006 ; Garcia et al., 2008 pTAC7/PAP12 a AT5G24314 Arabidopsis / Mustard Chloroplast b...”
- A purification strategy for analysis of the DNA/RNA-associated sub-proteome from chloroplasts of mustard cotyledons
Schröter, Frontiers in plant science 2014 - “...AT3G06730 cTP 0.858 RC 3 Pfalz et al., 2006 UDP-N-acetylmuamoylalanyl-d-glutamate-2,6-diaminopimelate ligase (MurE) 3 28.3 240254313 AT1G63680 cTP 0.695 RC 3 Pfalz et al., 2006 TRANSLATION Alpha-nascent polypeptide associated complex like protein 1 (Alpha-NAC-like protein 1) 1 29.2.4 15230476 AT3G12390 This work Alpha-nascent polypeptide associated complex like...”
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- An Arabidopsis homolog of the bacterial peptidoglycan synthesis enzyme MurE has an essential role in chloroplast development.
Garcia, The Plant journal : for cell and molecular biology 2008 (PubMed)- GeneRIF: The isolation and characterization of three T-DNA-tagged and one Ds-tagged mutant alleles of AtMurE in A. thaliana are reported; divergence of the A. thaliana protein from the bacterial and moss MurE proteins is also reported.
Wbm0492 UDP-N-acetylmuramyl tripeptide synthase from Wolbachia endosymbiont strain TRS of Brugia malayi
Q5GSE4 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase from Wolbachia sp. subsp. Brugia malayi (strain TRS)
36% identity, 79% coverage
- Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq
Grote, PLoS neglected tropical diseases 2017 - “...29 ]. Genes involved in lipid II/ peptidoglycan biosynthesis ( wBm0493 , metC , and wBm0492 , murE ) and wBm0490 , a protein shown to interact with ftsH , a gene required for cell division, were also found to be significantly up-regulated in F120. Among...”
- Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy
Li, PLoS neglected tropical diseases 2011 - “...UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase 27.9 ftsH b3178 644 wbm0490 609 protease, ATP-dependent zinc-metallo 46.5 murE b0085 495 wbm0492 496 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase 25.2 murD b0088 438 wbm0508 498 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase 22.8 murG b0090 355 wbm0557 343 N-acetylglucosaminyl transferase 22.4 ddl b0092 306 wbm0570 339 D-alanine:D-alanine ligase 29.4 ftsQ b0093...”
- 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 - “...Q5GTG5 UDP-N-acetylmuramateL-alanine ligase 15. FDT084 Q5GTH4 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 46. FDT117 Q5GSE4 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2 16. FDT085 Q5GTJ4 Bifunctional protein GlmU 47. FDT118 Q5GS79 UDP-N-acetylglucosamineN-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 17. FDT086 Q5GSI1 Acetyl/propionyl-CoA carboxylase;alpha subunit 48. FDT119 Q5GS12 NADH-quinone oxidoreductase subunit K 18. FDT087 Q5GSM8...”
DR_0297 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase from Deinococcus radiodurans R1
35% identity, 96% coverage
C4WRH2 Putative UDP-N-acetylmuranoylanalyl-D-2-6-diaminoligase from Raphanus sativus
32% identity, 53% coverage
TTC1904 No description from Thermus thermophilus HB27
37% identity, 99% coverage
TTHA0100 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase from Thermus thermophilus HB8
37% identity, 99% coverage
TP0933 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) from Treponema pallidum subsp. pallidum str. Nichols
32% identity, 81% coverage
MSMEG_4232 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase from Mycobacterium smegmatis str. MC2 155
39% identity, 89% coverage
MURE_MAIZE / K7WCC7 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase MurE homolog, chloroplastic; ZmMURE from Zea mays (Maize) (see 2 papers)
31% identity, 62% coverage
- function: Required for the activity of the plastid-encoded RNA polymerase (PEP) and full expression of genes transcribed by PEP (PubMed:24246379). Required for the proper build-up and formation of the PEP-complex (PubMed:25599833).
subunit: Component of the plastid-encoded plastid RNA polymerase (PEP) complex.
disruption phenotype: Pale yellow-green leaf phenotype. Reduced levels of plastid ribosomes and defects in plastid mRNA metabolism.
2wtzC / P9WJL3 Mure ligase of mycobacterium tuberculosis (see paper)
36% identity, 91% coverage
- Ligand: uridine-5'-diphosphate-n-acetylmuramoyl-l-alanine-d-glutamate (2wtzC)
HMPREF0389_00596 Mur ligase family protein from Filifactor alocis ATCC 35896
27% identity, 87% coverage
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...HMPREF0389_00868 DAK 2 domain protein 58.8 11/0.06 2 C-7.50 EC-0.73 DhaL profile domain Nonsecretory 26. HMPREF0389_00596 UDP-N-muramyl tripeptide synthetase 57.06 145/0.13 16 C-7.50 EC-0.73 Cell wall tripeptide synthetase domain Nonsecretory 27. HMPREF0389_00480 Amido transferase family protein 54.7 345/0.54 34 C-7.5 EC-0.73 GATB domain Nonsecretory 28. HMPREF0389_01130...”
MURE_STRP1 / Q9A196 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase; L-lysine-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:L-Lys ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.7 from Streptococcus pyogenes serotype M1
30% identity, 92% coverage
- function: Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + L-lysine + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L- lysine + ADP + phosphate + H(+) (RHEA:17969)
MURE_STRPN / Q97PS1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase; L-lysine-adding enzyme; UDP-MurNAc-L-Ala-D-Glu:L-Lys ligase; UDP-MurNAc-tripeptide synthetase; UDP-N-acetylmuramyl-tripeptide synthetase; EC 6.3.2.7 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (see paper)
SP_1530 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Streptococcus pneumoniae TIGR4
29% identity, 93% coverage
- function: Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + L-lysine + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L- lysine + ADP + phosphate + H(+) (RHEA:17969) - Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae
Nishimoto, Cell reports 2022 - “...P80L (CCTCTT) SP_0350 Cps4E 1,280,284 F218L (TTTCTT) SP_1358 ABC transporter, ATP-binding/permease protein 1,442,712 A430S (GCGTCG) SP_1530 MurE 2,125,225 A586E (GCGGAG) SP_2205 DHH subfamily 1 protein T4EP2 308,636 Y586S (TATTCT) SP_0336 PBP2X 324,228 P80L (CCTCTT) SP_0350 Cps4E 1,280,284 F218L (TTTCTT) SP_1358 ABC transporter, ATP-binding/permease protein 1,442,712 A430S...”
- “...protein T4EP3 308,636 Y586S (TATTCT) SP_0336 PBP2X 324,228 P80L (CCTCTT) SP_0350 Cps4E 1,442,712 A430S (GCGTCG) SP_1530 MurE 2,125,225 A586E (GCGGAG) SP_2205 DHH subfamily 1 protein T4EP4 308,636 Y586S (TATTCT) SP_0336 PBP2X 324,228 P80L (CCTCTT) SP_0350 Cps4E 1,207,068 1 bp SP_1274 licD2 protein 1,280,284 F218L (TTTCTT) SP_1358...”
- A bacterial pan-genome makes gene essentiality strain-dependent and evolvable
Rosconi, Nature microbiology 2022 - “...presented two compensatory mutations associated with the cell wall: one mutation is located in murE (SP_1530 A430S), which is involved in peptidoglycan synthesis, and the second mutation is located in a non-characterized membrane protein coding gene (SP_0454 H581N), which forms a complex with BacA 71 (right...”
SGO_RS08025 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L- lysine ligase from Streptococcus gordonii str. Challis substr. CH1
28% identity, 95% coverage
SSU05_0651 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Streptococcus suis 05ZYH33
A4VU28 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase from Streptococcus suis (strain 05ZYH33)
29% identity, 95% coverage
- DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
Jiang, Microbiology spectrum 2023 - “...helicase 13.908 1.6915 + A4VT05 SSU05_0276 rpmG 50S ribosomal protein L33 5.9249 1.6104 + A4VU28 SSU05_0651 murE UDP- N -acetylmuramoyl- l -alanyl- d -glutamate- l -lysine ligase 53.209 1.6102 + A4VX26 SSU05_1699 Pseudouridine synthase 27.371 1.5572 + A4VSE1 SSU05_0058 Heme/copper-type cytochrome/quinol oxidase, subunit 1 58.375 1.5452...”
- 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 - “...involved in cell wall biosynthesis, including four that were down-regulated proteins, i.e., MurD (SSU05_0476), MurE (SSU05_0651), MurG (SSU05_0477), and Pbp1A (SSU05_0414). Table 3 Differentially expressed proteins associated with cell growth and division, virulence, and fatty acid metabolism. Protein name Locus Functions Ratio( mnmE /SC19) Unique peptides...”
- “...DNA mismatch repair protein 0.8078 17 22.10 Pbp1A SSU05_0414 Penicillin-binding protein 0.8134 24 36.88 MurE 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...”
- DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
Jiang, Microbiology spectrum 2023 - “...II helicase 13.908 1.6915 + A4VT05 SSU05_0276 rpmG 50S ribosomal protein L33 5.9249 1.6104 + A4VU28 SSU05_0651 murE UDP- N -acetylmuramoyl- l -alanyl- d -glutamate- l -lysine ligase 53.209 1.6102 + A4VX26 SSU05_1699 Pseudouridine synthase 27.371 1.5572 + A4VSE1 SSU05_0058 Heme/copper-type cytochrome/quinol oxidase, subunit 1 58.375...”
SMU_RS07620 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L- lysine ligase from Streptococcus mutans UA159
Q8DST2 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
26% identity, 97% coverage
- Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans
Qin, Microbiology spectrum 2024 - “...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, SepF SMU_RS03260 2.5 Autolysin SMU_RS04965 2.4...”
- S-glutathionylation proteome profiling reveals a crucial role of a thioredoxin-like protein in interspecies competition and cariogenecity of Streptococcus mutans
Li, PLoS pathogens 2020 - “...ptsG 498 Putative PTS system, glucose-specific IIABC component Q8DV96 Peptidoglycan biosynthesis murF 449 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase Q8DST2 murE 99 UDP-N-acetylmuramoyl-L-alanyl-D-glutamateL-lysine ligase Q8DVE3 murD 260 UDP-N-acetylmuramoylalanineD-glutamate ligase S-glutathionylation of proteins is differentially modified after the deletion of gshAB and gsT The gshAB gene encodes a bifunctional glutathione synthetase,...”
T303_02880 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L- lysine ligase from Streptococcus thermophilus ASCC 1275
28% identity, 94% coverage
spr1384 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine Ligase from Streptococcus pneumoniae R6
SPD_1359 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Streptococcus pneumoniae D39
29% identity, 93% coverage
LSA0280 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Lactobacillus sakei subsp. sakei 23K
28% identity, 88% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...-0.6 LSA1879 gidA Cell division protein GidA -0.6 Cell envelope biogenesis, outer membrane Cell wall LSA0280 murE UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase -0.6 -0.6 -0.7 LSA0621 pbp2A Bifunctional glycolsyltransferase/transpeptidase penicillin binding protein 2A 0.7 LSA0648 lsa0648 Putative penicillin-binding protein precursor (beta-lactamase class C) 1.0 LSA0862 lsa0862 N-acetylmuramoyl-L-alanine amidase precursor...”
LACR_1987 UDP-N-acetylmuramyl tripeptide synthase from Lactococcus lactis subsp. cremoris SK11
29% identity, 94% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...LACR_0803 hypothetical protein positive 1.3 LACR_2218 hypothetical protein positive 2.1 LACR_2270 hypothetical protein positive 18.7 LACR_1987 murE UDP-N-acetylmuramoylalanyl-D-glutamate2,6-diaminopimelate ligase positive 3.6 LACR_1104 hypothetical protein negative 5.0 LACR_0812 putative effector of murein hydrolase LrgA positive 4.1 LACR_1019 hypothetical protein negative 4.4 LACR_1523 DNA-binding response regulator positive 5.0...”
LSEI_0223 UDP-N-acetylmuramyl tripeptide synthase from Lactobacillus casei ATCC 334
27% identity, 89% coverage
LCABL_02120 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase from Lacticaseibacillus paracasei
LCABL_02120 UDP-N-acetylmuramyl-tripeptide synthetase (UDP-MurNAc-tripeptide synthetase) from Lactobacillus casei BL23
27% identity, 89% coverage
BDP_1521 mur UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-- lysine ligase from Bifidobacterium dentium Bd1
29% identity, 86% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...BDP_0546 BDP_1149 BDP_1548 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...”
X276_18750 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Clostridium beijerinckii NRRL B-598
21% identity, 92% coverage
lmo0856 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino pimelate-D-alanyl-D-alanyl ligase from Listeria monocytogenes EGD-e
24% identity, 72% coverage
- New Insights into the Lactic Acid Resistance Determinants of Listeria monocytogenes Based on Transposon Sequencing and Transcriptome Sequencing Analyses
Liu, Microbiology spectrum 2023 - “...corrected P value (BH)<0.05) ( Fig.2 and Table1 ). A single gene, murF (locus tag lmo0856), encoding a UDP- N -acetylmuramoylalanyl- d -glutamyl-2,6-diaminopimelate- d -alanyl- d -alanyl ligase, was identified by Tn-seq with the highest fold change (FC=13.5). Another significant gene, lmo2248 (FC,4.4), was a putative...”
- “...by Tn-seq analysis Synonym Gene name Annotation Fold change a P value BH value b lmo0856 murF UDP- N -acetylmuramoylalanyl- d -glutamyl-2,6-diamino pimelate- d -alanyl- d -alanyl ligase 13.5 3.6E-02 6.6E-03 lmo2248 hypothetical protein 4.4 1.3E-03 6.6E-03 lmo1222 pheT Phenylalanyl-tRNA synthetase subunit beta 4.1 3.3E-02 NS...”
LM6179_1168 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Listeria monocytogenes 6179
24% identity, 71% coverage
SE1680 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanyl ligase from Staphylococcus epidermidis ATCC 12228
24% identity, 90% coverage
CD2655 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alan ine ligase from Clostridium difficile 630
CD630_26550, CDIF630erm_02909 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Clostridioides difficile 630
22% identity, 73% coverage
- Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores
Dembek, PloS one 2013 - “...peptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 0.022 +1.4 CD2653 UDP-N-acetylmuramoylalanineD-glutamate ligase 0.0105 +1.5 CD2654 phospho-N-acetylmuramoyl-pentapeptide-transferase 0.0145 +1.7 CD2655 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alan ine ligase 0.00508 +2.4 CD2664 putative UDP-N-acetylmuramoylalanyl-D-glutamate2,6-diaminopimelate ligase 0.0344 +2.4 CD3563 putative spore cortex-lytic enzyme 0.0245 +2.2 CD1898 putative phage-related cell wall hydrolase (endolysin) 0.0174 6.1 10.1371/journal.pone.0064011.t005 Table 5...”
- Clostridium difficile transcriptome analysis using pig ligated loop model reveals modulation of pathways not modulated in vitro
Scaria, The Journal of infectious diseases 2011 - “...both studies, many putative virulent factors, such as murF (CD2655), cell wall hydrolase (CD2402), and capsular proteins (CD2769 and CD2770), were not DE in the...”
- Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection
Janvilisri, The Journal of infectious diseases 2010 - “...during infection. Examples include the up-regulation of genes encoding the cell wall proteins murF ( CD2655 ), a putative cell wall hydrolase ( CD2402 ), a cell surface protein ( CD2735 ), capsular proteins ( CD2769, CD2770 ), chemosensory proteins ( CD0537, CD0542 ), and a...”
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...D -glutamate ligase 0.77 0.11 1.45 0.42 CD630_26540 CDIF630erm_02908 mraY Phospho- N -acetylmuramoyl-pentapeptide-transferase 0.82 2.37 CD630_26550 CDIF630erm_02909 murF UDP- N -acetylmuramoyl-tripeptide D -alanyl- D -alanine ligase 2.59 -0.26 2.74 0.21 CD630_27780 CDIF630erm_03041 Glycosyl transferase family protein 0.98 -0.10 1.26 0.10 CD630_27790 CDIF630erm_03042 manC Mannose-1-phosphate guanylyltransferase 1.33...”
- “...-glutamate ligase 0.77 0.11 1.45 0.42 CD630_26540 CDIF630erm_02908 mraY Phospho- N -acetylmuramoyl-pentapeptide-transferase 0.82 2.37 CD630_26550 CDIF630erm_02909 murF UDP- N -acetylmuramoyl-tripeptide D -alanyl- D -alanine ligase 2.59 -0.26 2.74 0.21 CD630_27780 CDIF630erm_03041 Glycosyl transferase family protein 0.98 -0.10 1.26 0.10 CD630_27790 CDIF630erm_03042 manC Mannose-1-phosphate guanylyltransferase 1.33 0.81...”
CwatDRAFT_4119 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanyl ligase from Crocosphaera watsonii WH 8501
25% identity, 89% coverage
Hore_09050 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Halothermothrix orenii H 168
25% identity, 82% coverage
H375_1990 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Rickettsia prowazekii str. Breinl
28% identity, 50% coverage
CPZ21_02270 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Staphylococcus epidermidis
25% identity, 73% coverage
CPE2213 cyanophycin synthetase from Clostridium perfringens str. 13
21% identity, 44% coverage
Bresu_2778 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Brevundimonas subvibrioides ATCC 15264
34% identity, 31% coverage
SO4223 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Shewanella oneidensis MR-1
26% identity, 76% coverage
- Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
Chourey, Applied and environmental microbiology 2006 - “...ftsL (SO4226), ftsI (SO4225), murE (SO4224), murF (SO4223), mraY (SO4222), murD (SO4221), ftsW (SO4220), murG (SO4219), murC (SO4218), ftsQ (SO4217), ftsA...”
Tsac_0535 cyanophycin synthetase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
25% identity, 36% coverage
PEPE_RS07585 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Pediococcus pentosaceus ATCC 25745
24% identity, 81% coverage
Q8RDP8 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)
FN1461 Histidinol-phosphatase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
22% identity, 59% coverage
- Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions
Kumar, BMC microbiology 2016 - “...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 5 Microbial metabolism in diverse...”
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...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 11 11 10 10...”
- “...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 ; Hendrickson etal. 2012 )....”
WP_011591070 cyanophycin synthetase from Clostridium perfringens
21% identity, 44% coverage
lpg2618 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanyl ligase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
26% identity, 74% coverage
SGO_0671 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus gordonii str. Challis substr. CH1
A8AW14 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)
27% identity, 48% coverage
- Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1
Robertsson, BMC microbiology 2020 - “...A8AVB5 5.3/5.16 23,000/27598 583 10 52% Cell envelope biosynthesis murd a) UDP-N-acetylmuramoylalanine D-glutamate ligase murdD (SGO_0671) A8AW14 5.4/5.07 46,000/48257 253 4 12% pgam a) Phosphoglucosamine mutase glmM (SGO_0889) A8AWM5 4.6/4.71 52,000/48396 592 7 26% + rmla-1 Glucose-1-phosphatethymidylyltransferase rfbA-1(SGO_1009) A8AWY8 5.1/4.92 28,000/32213 42 1 g) 3% +...”
- Response of fatty acid synthesis genes to the binding of human salivary amylase by Streptococcus gordonii
Nikitkova, Applied and environmental microbiology 2012 - “...sequence SGO_0091 IMP-F SGO_0091 IMP-R SGO_1834-F SGO_1834-R SGO_0671 murD-F SGO_0671 murD-R SGO_1541 atpC-F SGO_1541 atpC-R SGO_1546 atpF-F SGO_1546 atpF-R...”
- “...(SGO_1890); murD, encoding UDP-N-acetylmuramoyl-L-alanylD-glutamate synthetase (SGO_0671); two genes involved in oxidation phosphorylation, atpF, encoding ATP...”
- Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1
Robertsson, BMC microbiology 2020 - “...5.3/5.16 23,000/27598 583 10 52% Cell envelope biosynthesis murd a) UDP-N-acetylmuramoylalanine D-glutamate ligase murdD (SGO_0671) A8AW14 5.4/5.07 46,000/48257 253 4 12% pgam a) Phosphoglucosamine mutase glmM (SGO_0889) A8AWM5 4.6/4.71 52,000/48396 592 7 26% + rmla-1 Glucose-1-phosphatethymidylyltransferase rfbA-1(SGO_1009) A8AWY8 5.1/4.92 28,000/32213 42 1 g) 3% + rmla-2...”
BL1356 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase from Bifidobacterium longum NCC2705
26% identity, 87% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...BLD_0446 BL1317 BL1323 BLD_0181 BLD_0175 BL1320 BLD_0178 BL1356 BLD_0221 BL0345 BL1319 BL1321 BLD_0179 BLD_1112 BLD_0177 BL1324 BL1561 BL1267 NCC2705 BLD_0182...”
Q0SQX0 cyanophycin synthase (L-aspartate-adding) (EC 6.3.2.29); cyanophycin synthase (L-arginine-adding) (EC 6.3.2.30) from Clostridium perfringens (see paper)
21% identity, 42% coverage
RC0911 UDP-N-acetylmuramoylalanyl-D-glutamyl- 2,6-diaminopimelate--D-alanyl-D-alanyl ligase [EC:6.3.2.15] from Rickettsia conorii str. Malish 7
28% identity, 50% coverage
- Deciphering <i>Rickettsia conorii</i> metabolic pathways: A treasure map to therapeutic targets
Prajapat, Biotechnology notes (Amsterdam, Netherlands) 2025 - “...Metabolism Cytoplasm Yes RC0579 DAP_epimerase_DapF Bacterial cell wall biosynthesis, and dipicolinic acid Metabolism Cytoplasm No RC0911 UDP-N-AcMur_synth Peptidoglycan synthesis Metabolism Cytoplasm Yes RC0912 UDP-N-AcMur-Glu-dNH2Pim_ligase Peptidoglycan synthesis Metabolism Cytoplasm Yes RC1086 Glyco_hydro_3_N Hydrolyse the glycosidic bond between two or more carbohydrates Metabolism Cytoplasm Yes RC0008 Lipid_A_LpxA Lipopolysaacharide...”
M9UYB0 cyanophycin synthase (L-aspartate-adding) (EC 6.3.2.29); cyanophycin synthase (L-arginine-adding) (EC 6.3.2.30) from uncultured bacterium (see paper)
26% identity, 41% coverage
RC0560 UDP-N-acetylmuramoylalanine--D-glutamate ligase [EC:6.3.2.9] from Rickettsia conorii str. Malish 7
31% identity, 32% coverage
RC0331 UDP-N-acetylmuramate--alanine ligase [EC:6.3.2.8] from Rickettsia conorii str. Malish 7
21% identity, 72% coverage
- Deciphering <i>Rickettsia conorii</i> metabolic pathways: A treasure map to therapeutic targets
Prajapat, Biotechnology notes (Amsterdam, Netherlands) 2025 - “...one compound to another Transport Cytoplasm No 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...”
Q8DV96 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
25% identity, 71% coverage
slr1351 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diamino-pimelate-D-alanyl-D-alanine ligase from Synechocystis sp. PCC 6803
29% identity, 71% coverage
- Integrative analysis of the salt stress response in cyanobacteria
Klähn, Biology direct 2021 - “...identified proteins of the functional category Murein sacculus and peptidoglycan . These proteins include MurF (Slr1351), DacB (Slr0804), MurA (Slr0017), MurG (slr1656) and MltA (Sll0016), which all are enzymes probably involved in cell wall or cell envelope biogenesis (Additional file 1 : Table S6). Their coordinated...”
- Sycrp2 Is Essential for Twitching Motility in the Cyanobacterium Synechocystis sp. Strain PCC 6803
Song, Journal of bacteriology 2018 - “...binds to proposed 259 CRP target sites upstream of slr1351 (murF), sll1874 (chlAII), sll1708 (narL), slr0442 and 260 sll1268 in vitro (46), and the genes...”
- Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803
Pei, Biotechnology for biofuels 2017 - “...factor RpoD 45 Nc122 (Ncr1650) 1.042 0.848 nc60 1,748,9231,749,070 <<> 44.8 sll1247 Hypothetical protein 30 slr1351 UDP- N -acetylmuramoylalanyl- d -glutamyl-2,6-diamino-pimelate- d -alanyl- d -alanine ligase 76 Nc60 (SyR7) 0.912 1.229 nc117 3,250,5493,250,647 >>> 10.1 slr0550 Dihydrodipicolinate synthase 262 slr0551 Hypothetical protein 353 Nc117 (Ncr1600) 1.519...”
- Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers
Holmquist, Nucleic acids research 2011 - “...nomenclature. ( B and C ) Titration curves for His-SyCrp1 binding to the endogenous wild-type slr1351 (closed circles; 1) and sll1268 (closed circles; 3) substrates are compared with their respective chimeric substrates slr1351/sll1268 (open circles; 2) and sll1268/slr1351 (open circles; 4) listed in panel A. The...”
- “...named according to the target gene. These dsDNA substrates are not italicized (e.g. the 40mer slr1351). PSSM #3 derivation PSSM #3 was a de novo hypothesis. Given how hypothesis generation is not amenable to method or result reporting, Introduction in Supplementary Data ( Supplementary Figures S13...”
- Illumination stimulates cAMP receptor protein-dependent transcriptional activation from regulatory regions containing class I and class II promoter elements in Synechocystis sp. PCC 6803
Hedger, Microbiology (Reading, England) 2009 - “...Crp binds proposed Crp target sites upstream of slr1351 (murF), sll1874 (chlAII), sll1708 (narL), slr0442 and sll1268 in vitro, and that slr0442 is...”
- “...Crp binding to three of the 11 target sequences (slr1351, sll1874 and sll1708) predicted by Ochoa de Alda & Houmard (2000). Most recently, an interspecies...”
- Evidence for a major role of antisense RNAs in cyanobacterial gene regulation
Georg, Molecular systems biology 2009 - “...and SyR4), sll0048sll0737 (SyR5), rps1 (slr1984) dnaG (sll1868) (SyR6), sll0208 rfbA (sll0207) (SyR9), sll1247 murF (slr1351) (SyR7), and llal.2 (sll0790) ksgA (SyR8). The length range of these ncRNAs is 80350 nt ( Figure 4 ), a typical size distribution for bacterial ncRNAs. New asRNAs An overview...”
Q8E6P1 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus agalactiae serotype III (strain NEM316)
28% identity, 54% coverage
- Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
Gaur, Current research in pharmacology and drug discovery 2022 - “...subtilis (Accession no. Q03522 ), Thermotoga maritima (Accession no. Q9WY76 ), Streptococcus agalactiae (Accession no. Q8E6P1 ), Borrelia burgdorferi (Accession no. O51532 ), Staph. aureus (Accession no. P0A091 ), Leptospira interrogans (Accession no. Q8F7V4 ) Streptococcus pneumonia e (Accession no. C1CD51), Haemophilus influenzae (Accession no. Q4QLG0...”
- “...no. Q03522 ), MurD Thermotoga maritima (Accession no. Q9WY76 ), MurD Streptococcus agalactiae (Accession no. Q8E6P1 ), MurD Borrelia burgdorferi (Accession no. O51532 ), MurD Staph. aureus (Accession no. P0A091 ), MurD Leptospira interrogans (Accession no. Q8F7V4 )M, urD Streptococcus pneumoniae (Accession no. C1CD51), MurD Haemophilus...”
all0036 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase from Nostoc sp. PCC 7120
30% identity, 64% coverage
7ti7A / B7H1N2 Crystal structure of udp-n-acetylmuramoylalanine-d-glutamate ligase from acinetobacter baumannii ab5075-uw in complex with adp
25% identity, 72% coverage
- Ligands: adenosine-5'-diphosphate; calcium ion (7ti7A)
BDP_1544 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase from Bifidobacterium dentium Bd1
34% identity, 33% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...BDP_1149 BDP_1548 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...”
4qf5A / A0A0J9X1Z8 Crystal structure i of murf from acinetobacter baumannii (see paper)
23% identity, 75% coverage
- Ligands: adenosine-5'-triphosphate; magnesium ion (4qf5A)
A0A0J9X1Z8 UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (EC 6.3.2.10) from Acinetobacter baumannii (see 2 papers)
23% identity, 75% coverage
BAB1_1449 Cytoplasmic peptidoglycan synthetase, N-terminal:Cytoplasmic peptidoglycan synthetase, C-terminal:UDP-N-acetylmuramate--ala... from Brucella melitensis biovar Abortus 2308
27% identity, 42% coverage
BSU15200 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase from Bacillus subtilis subsp. subtilis str. 168
Q03522 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Bacillus subtilis (strain 168)
26% identity, 48% coverage
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...murC BSU29790 Yes 6.3.2.8 1GQQ H. influenzae murD BSU15200 Yes 6.3.2.9 3LK7 Streptococcus agalactiae murE BSU15180 Yes 6.3.2.13 4C13 S. aureus murF BSU04570 Yes...”
- Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
Gaur, Current research in pharmacology and drug discovery 2022 - “...from E.coli (Accession no. A0A4C3NEP4), M.tuberculosi s (Accession no. A5U4I2), Bacil lus subtilis (Accession no. Q03522 ), Thermotoga maritima (Accession no. Q9WY76 ), Streptococcus agalactiae (Accession no. Q8E6P1 ), Borrelia burgdorferi (Accession no. O51532 ), Staph. aureus (Accession no. P0A091 ), Leptospira interrogans (Accession no. Q8F7V4...”
- “...coli (Accession no. A0A4C3NEP4), MurD M. tuberculosis (Accession no. A5U4I2) MurD Bacillus subtilis (Accession no. Q03522 ), MurD Thermotoga maritima (Accession no. Q9WY76 ), MurD Streptococcus agalactiae (Accession no. Q8E6P1 ), MurD Borrelia burgdorferi (Accession no. O51532 ), MurD Staph. aureus (Accession no. P0A091 ), MurD...”
- Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
Reddy, PloS one 2015 - “...synthesis P70965 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 MurAA 35.32 13 0.89 0.64 0.41 13 0.886 0.609 0.303 Q03522 UDP-N-acetylmuramoylalanineD-glutamate ligase MurD 31.04 13 0.98 0.67 0.47 4 1.145 0.979 0.824 P40778 UDP-N-acetylmuramateL-alanine ligase MurC 25.46 9 1.03 0.71 0.54 6 1.173 1.528 0.522 Q03523 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase MurE 37.04...”
- Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
Reddy, PloS one 2015 - “...synthesis P70965 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 MurAA 35.32 13 0.89 0.64 0.41 13 1.36 0.702 0.549 Q03522 UDP-N-acetylmuramoylalanineD-glutamate ligase MurD 31.04 13 0.98 0.67 0.47 4 1.115 1.039 0.812 P40778 UDP-N-acetylmuramateL-alanine ligase MurC 25.46 9 1.03 0.71 0.54 6 1.296 1.170 0.580 Q03523 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase MurE 37.04...”
TRQ7_RS03655 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Thermotoga sp. RQ7
29% identity, 46% coverage
- Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation
Gautam, BMC research notes 2022 - “...Ribonuclease HII Transition: GA Missense: A237T 26360 TRQ7_RS00155 Galactose-1-phosphate uridylyltransferase Transition: CT Missense: P274L 721511 TRQ7_RS03655 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D- alanine ligase Transition: GA Missense: D148N 731443 TRQ7_RS03700 NADH-quinone oxidoreductase subunit NuoE Transition: CT Missense: S15L 1021158 TRQ7_RS05125 Hypothetical protein Transition: GA Missense: G148D 1352603 TRQ7_RS06890 Hypothetical protein Transition:...”
Blon_0893 UDP-N-acetylmuramyl-tripeptide synthetase from Bifidobacterium longum subsp. infantis ATCC 15697
25% identity, 87% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...Blon_0079, Blon_0850 Blon_0856 Blon_0853 Blon_0320 Blon_0852 Blon_0893 Blon_0854 Blon_0857 Blon_2254 Blon_2321 B. longum subsp. infantis ATCC 15697 BAD_1508...”
HI1134 UDP-MurNAc-pentapeptide synthetase (murF) from Haemophilus influenzae Rd KW20
22% identity, 77% coverage
PFL_5065 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Pseudomonas fluorescens Pf-5
26% identity, 80% coverage
DQM59_RS07770 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Streptococcus mutans
26% identity, 48% coverage
- Adaptation to simulated microgravity in Streptococcus mutans
Fernander, NPJ microgravity 2022 - “...DQM59_RS10195 (sprV) 0.10 T104A vicK 0.74 0.15 C 20512131/4689 spaP 0.08 S721L spaP 0.35 K373N DQM59_RS07770 ( murD ) 63 0.28 0.46 Q31* DQM59_RS04330 ( ridA ) 0.71 F219L DQM59_RS06715 0.22 K373N DQM59_RS07770 ( murD ) 0.25 R34S DQM59_RS10195 (sprV) 0.08 H21Y DQM59_RS10195 (sprV) 0.54 K15N...”
SMU_RS02625 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Streptococcus mutans UA159
Q8DVE3 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
26% identity, 48% coverage
- Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans
Qin, Microbiology spectrum 2024 - “...Phosphoglycerate mutase, GpmA Cell envelope SMU_RS03380 4 2.3 Aminoacyltransferase, MurM SMU_RS01525 3.2 Glucose-6-phosphate isomerase, GPI SMU_RS02625 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...”
- S-glutathionylation proteome profiling reveals a crucial role of a thioredoxin-like protein in interspecies competition and cariogenecity of Streptococcus mutans
Li, PLoS pathogens 2020 - “...glucose-specific IIABC component Q8DV96 Peptidoglycan biosynthesis murF 449 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase Q8DST2 murE 99 UDP-N-acetylmuramoyl-L-alanyl-D-glutamateL-lysine ligase Q8DVE3 murD 260 UDP-N-acetylmuramoylalanineD-glutamate ligase S-glutathionylation of proteins is differentially modified after the deletion of gshAB and gsT The gshAB gene encodes a bifunctional glutathione synthetase, which is involved in synthesizing...”
BLJ_1297 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Bifidobacterium longum subsp. longum JDM301
32% identity, 30% coverage
- Adaptational changes in physiological and transcriptional responses of Bifidobacterium longum involved in acid stress resistance after successive batch cultures
Wei, Microbial cell factories 2019 - “...under pH challenge A total of 11 genes (BLJ_0153, BLJ_0225, BLJ_0390, BLJ_1055, BLJ_1847, BLJ_2036, BLJ_1295, BLJ_1297, BLJ_1298, BLJ_1299, BLJ_1301) including a gene cluster (BLJ_1295-BLJ_1301) involved in peptidoglycan biosynthesis were upregulated at low pH in JDM301AR compared with normal condition (Additional file 2 ). However, only two...”
BL1321 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Bifidobacterium longum NCC2705
34% identity, 30% coverage
Atu2093 UDP-N-acetylmuramate--L-alanine ligase from Agrobacterium tumefaciens str. C58 (Cereon)
Q8UDM9 UDP-N-acetylmuramate--L-alanine ligase from Agrobacterium fabrum (strain C58 / ATCC 33970)
28% identity, 42% coverage
RT0584 UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D- alanine ligase from Rickettsia typhi str. wilmington
28% identity, 41% coverage
FTN_1112 cyanophycin synthetase from Francisella tularensis subsp. novicida U112
25% identity, 38% coverage
GALLO_RS03570 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Streptococcus gallolyticus UCN34
39% identity, 22% coverage
- Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus
Qureshi, Frontiers in genetics 2021 - “...methyltransferase B GALLO_RS03395 DEG10180247 36.364 Glutamine ABC transporter permease GALLO_RS03550 DEG10450136 35.789 Penicillin-binding protein 2B GALLO_RS03570 DEG10460377 35.294 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase GALLO_RS03600 DEG10050249 35.135 1-acyl-sn-glycerol-3-phosphate acyltransferase Drug Target Prioritization To determine the potential therapeutic targets, various factors were considered, including molecular weight from ProtParam ( ExPASy, 2020...”
BFF93_RS07335 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Elizabethkingia meningoseptica
22% identity, 72% coverage
FTA_0880 UDP-N-acetylmuramyl tripeptide synthase with glutame ligase domain from Francisella tularensis subsp. holarctica FTA
25% identity, 38% coverage
3zl8A / Q9WY78 Crystal structure of murf ligase from thermotoga maritima in complex with adp (see paper)
28% identity, 46% coverage
- Ligand: adenosine-5'-diphosphate (3zl8A)
Blon_0854 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Bifidobacterium longum subsp. infantis ATCC 15697
33% identity, 30% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...Blon_0850 Blon_0856 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...”
Tfu_1108 UDP-N-acetylmuramoylalanine-D-glutamate ligase from Thermobifida fusca YX
35% identity, 31% coverage
SCO2086 UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase from Streptomyces coelicolor A3(2)
33% identity, 32% coverage
- Development of Series of Affinity Tags in Streptomyces
Mao, Scientific reports 2017 - “...protein 14 0.9107 1 SCO2295, hypothetical protein 15 0.9009 1 SCO5443, alpha-amylase 16 0.8982 1 SCO2086, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase, MurD 17 0.8935 1 SCO2935, transcriptional regulator 18 0.8911 1 SCO1849, cobalamin biosynthesis protein, or cobaltochelatase subunit CobN 19 0.8785 1 SCO3857, regulatory protein 20 0.8738 1 SCO5486,...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...0.86 0.01 0.49 0.32 SCO2085 fts W putative cell division protein 0.82 0.81 0.59 0.50 SCO2086 murD 0.58 0.23 0.35 0.45 SCO2087 murX 0.41 0.05 0.51 0.30 SCO2088 murF 1.18 0.73 0.67 0.01 SCO2089 murE 0.73 0.47 0.36 0.31 SCO2090 ftsl cell division protein 0.80 0.01...”
- “...SCO2084 murG 0.85602 0.00677 0.485989 0.319639 SCO2085 putative cell division protein 0.816624 0.80742 0.592214 0.502565 SCO2086 murD 0.580506 0.225348 0.347674 0.449973 SCO2087 murX 0.405731 0.049645 0.509959 0.3047 SCO2088 murF 1.175078 0.730925 0.667383 0.006107 SCO2089 murE 0.734068 0.470869 0.363458 0.308295 SCO2345 putative peptidodoglycan-binding membrane protein 0.0329 0.016338...”
A6T4M9 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
26% identity, 65% coverage
- Homology modeling, molecular docking and electrostatic potential analysis of MurF ligase from Klebsiella pneumonia
Sivaramakrishnan, Bioinformation 2012 - “...[ 7 10 ]. Sequence analysis and physiochemical characterization : KN-MurF Ligase protein sequence (ID: A6T4M9) was retrieved from Uniprot database in FASTA format. Its physiochemical characterization was computed using the Expasy Protparam program. Secondary structure prediction analysis was performed using SABLE program [ 11 ]....”
- “...18 ]. Hence, EC-MurF (PDB ID: 1GG4_A) was chosen as template to predict target KN-MurF (A6T4M9) structure due to global sequence similarity of 80% between two sequences, higher coverage >90% of aligned sequence, with least E-value (0) and higher score (721) than other PDB hits. Since,...”
Q6GHQ2 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus (strain MRSA252)
SAR1159 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus subsp. aureus MRSA252
KQ76_RS05595 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Staphylococcus aureus
27% identity, 48% coverage
murD / P0A091 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase (EC 6.3.2.9) from Staphylococcus aureus (see 2 papers)
MURD_STAA8 / Q2FZ92 UDP-N-acetylmuramoylalanine--D-glutamate ligase; D-glutamic acid-adding enzyme; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; EC 6.3.2.9 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see paper)
USA300HOU_RS05945 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Staphylococcus aureus subsp. aureus USA300_TCH1516
A7X1C4 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus (strain Mu3 / ATCC 700698)
P0A090 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus (strain N315)
P0A091 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus
SA1026 UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase from Staphylococcus aureus subsp. aureus N315
SAV1183 UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_01147 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL1196 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Staphylococcus aureus subsp. aureus COL
YP_499689 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase from Staphylococcus aureus subsp. aureus NCTC 8325
27% identity, 48% coverage
- function: Cell wall formation (PubMed:20659527). Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA) (PubMed:20659527).
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + ADP + phosphate + H(+) (RHEA:16429) - Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
Xu, Frontiers in microbiology 2016 - “...reductase USA300HOU_RS12610 hutI 1.50 2.99E-02 Imidazolonepropionase USA300HOU_RS02380 gltD 1.50 4.97E-02 Glutamate synthase (NADPH) small subunit USA300HOU_RS05945 murD 1.50 2.66E-02 UDP-N-acetylmuramoylalanineD-glutamate ligase USA300HOU_RS08555 1.49 2.77E-02 Biotin carboxylase USA300HOU_RS12615 hutU 1.49 3.30E-02 Urocanate hydratase USA300HOU_RS13410 1.47 3.09E-02 Possible decarboxylase USA300HOU_RS12085 rpmD 1.46 2.95E-02 Ribosomal protein L30 USA300HOU_RS11770 1.46...”
- Computational Target-Based Screening of Anti-MRSA Natural Products Reveals Potential Multitarget Mechanisms of Action through Peptidoglycan Synthesis Proteins
Oselusi, ACS omega 2022 - “...MurA Q2FWD4 48761.46 78.10 92.90 97.85 0.552 MurC Q2FXJ0 46051.24 66.20 88.90 75.06 0.393 MurD A7X1C4 51966.39 91.86 94.20 98.63 0.539 MurF A0A0H2WWP1 47688.48 65.77 86.90 88.50 0.433 MurG Q2FYL5 38118.98 68.96 88.40 81.74 0.379 3.2 Quality Assessment and Validation of the Modeled Structures The program...”
- Exploring the potential of bis(thiazol-5-yl)phenylmethane derivatives as novel candidates against genetically defined multidrug-resistant Staphylococcus aureus
Kavaliauskas, PloS one 2024 - “...MurA2, MurC, MurD, MurF, MurG, MurP, MurQ and MurZ (with accession number Q6G7L0, Q5HE76, Q2FXJ0, P0A090, Q2FWH4, Q5HG02, W8U768, Q7A1Y2 and A0A2S6DFC3, respectively). Docking of ligand-protein interaction We resorted to virtual screening using Autodock Vina, a target-specific scoring method useful for virtual screening [ 21 23...”
- “...Proteins with their respective ( AlphaFold ) entries: MurA1 (Q6G7L0), MurA2 (Q5HE76), MurC (Q2FXJ0), MurD (P0A090), MurF (Q2FWH4), MurG (Q5HG02), MurP (W8U768), MurQ (Q7A1Y2) and MurZ (A0A2S6DFC3). Proteins with their respective ( PDB ) entries: MurB (1HSK), MurE (4C12) and MurT (6GS2). After performing the initial...”
- Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
Gaur, Current research in pharmacology and drug discovery 2022 - “...agalactiae (Accession no. Q8E6P1 ), Borrelia burgdorferi (Accession no. O51532 ), Staph. aureus (Accession no. P0A091 ), Leptospira interrogans (Accession no. Q8F7V4 ) Streptococcus pneumonia e (Accession no. C1CD51), Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (MurD Accession no. from www.unipro.org ). Fig.3...”
- “...no. Q8E6P1 ), MurD Borrelia burgdorferi (Accession no. O51532 ), MurD Staph. aureus (Accession no. P0A091 ), MurD Leptospira interrogans (Accession no. Q8F7V4 )M, urD Streptococcus pneumoniae (Accession no. C1CD51), MurD Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (Accession no. from www.unipro.org )....”
- Manniosides G-J, New Ursane- and Lupane-Type Saponins from Schefflera mannii (Hook.f.) Harms
Tonga, Molecules (Basel, Switzerland) 2024 - “...extract, fractions, and some compounds isolated from S. mannii. Samples Minimum Inhibitory Concentrations (MIC, g/mL) SA1026 SE35984 EC10536 KP13882 MeOH extract 1024 nd 512 512 EtOAc fraction 512 128 128 256 n -BuOH fraction 1024 64 256 256 5 nd nd nd nd 9 nd nd...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...lytM SA0457 SA0523 gcaD SA0620 SA0905 stcA atl SA1023 SA1026 SA1027 SA1212 SA1267 SA1898 SA2097 SA2356 SA2442 SA2446 SA2455 SA2456 SA2457 ftsL murD div1b opp-2D...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...SA0871 hypoyhetical protein sa_c304s144_a_at 4.9 15 15 SA0985 putative surface protein sa_c470s302_at 2.9 2.5 5 SA1026 hypothetical protein sa_c485s314_at 281.2 ND 15 SA1033 hypothetical protein sa_c1195s976_at 3.2 2.5 2.5 SA1225 hypothetical protein sa_c1449s1223_a_at 2.3 15 15 SA1306 hypothetical protein sa_c1705s1441_a_at 27.1 2.5 2.5 SA1375 hypothetical protein...”
- “...SA0978 hypothetical protein sa_c429s262_a_at * 10.1 2.5 2.5 SA1017 hypothetical protein sa_c470s302_at 3.5 2.5 15 SA1026 hypothetical protein sa_c517s346_a_at * 6.8 15 stable SA1041 hypothetical protein sa_c525s350_at * 14.2 2.5 2.5 SA1044 hypothetical protein sa_c807s608_a_at * 4.3 2.5 2.5 SA1112 hypothetical protein sa_c863s665_at * 9.2 2.5...”
- Transcriptomic and functional analysis of an autolysis-deficient, teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus
Renzoni, Antimicrobial agents and chemotherapy 2006 - “...SA2062 SA1964 SA1028 SA1029 SA0249 SA1193 SA1902 SA0693 SA1562 SA1026 SA0876 SA1886 fmtA sarV fmtB ftsA ftsZ scdA fmtC/mprF murA murB murC murD murE murF SA1926...”
- Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
Chang, Frontiers in cellular and infection microbiology 2022 - “...dehydrogenase aroE 0.02 SAV0363 -2.12 GTP-binding protein 0.02 SACOL1793 -2.11 Conserved hypothetical protein ytpQ 0.01 SAV1183 -2.08 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthase murD 0.02 MW2067 -2.06 Hypothetical protein 0.04 SACOL1390 -2.05 DNA topoisomerase IV, A subunit parC 0.02 Table3 Induced functional categories. Category Term Count % P-Value Swiss-Prot PIR...”
- Modulation of cell wall synthesis and susceptibility to vancomycin by the two-component system AirSR in Staphylococcus aureus NCTC8325
Sun, BMC microbiology 2013 - “...group 1 4.24 SAOUHSC_01106 murI Glutamate racemase, MurI 2.12 SAOUHSC_01145 pbp1 Penicillin-binding protein 1 2.05 SAOUHSC_01147 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase, MurD 2.58 SAOUHSC_01148 ftsQ Cell division protein, putative 2.38 SAOUHSC_01346 Glycine betaine transporter, putative 4.62 SAOUHSC_01400 Alanine racemase, putative 2.81 SAOUHSC_02317 murF UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase 2.3 SAOUHSC_02318 ddl...”
- 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 - “...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 3 Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides 2.38 SACOL0543 glmU UDP-N-acetylglucosamine pyrophosphorylase 2.21 SACOL2103...”
- Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
Menzel, Antimicrobial agents and chemotherapy 2011 - “...SACOL0684 SACOL0991 SACOL0994 SACOL1193 SACOL1195 SACOL1196 SACOL1319 SACOL2450 SACOL2452 SACOL2453 SACOL2475 Nucleotide metabolism; upregulated ORFs SACOL0791...”
- Purification and biochemical characterization of Mur ligases from Staphylococcus aureus.
Patin, Biochimie 2010 (PubMed)- GeneRIF: Data show that MurD activity is inhibited by excess ATP concentration.
stu0731 UDP-N-acetylmuramoylalanine-D-glutamate ligase from Streptococcus thermophilus LMG 18311
27% identity, 72% coverage
RC1_0615 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase from Rhodospirillum centenum SW
36% identity, 27% coverage
Q8YM75 UDP-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) from Nostoc sp. PCC 7120 = FACHB-418 (see paper)
alr5065 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Nostoc sp. PCC 7120
25% identity, 71% 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 - “..., 40 , 41 ]; the mur operon murB ( alr5066 ) and murC ( alr5065 ) [ 42 ]; mreB ( all0087 ), mreC ( all0086 ), mreD ( all0085 ) [ 43 ], mdrA ( alr5045 ) and alr2270 [ 44 ]; cydiv (...”
- 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 - “...in diazotrophic growth. In addition, 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...”
- “...targets were several mRNAs encoding enzymes involved in peptidoglycan metabolism, such as alr2458 (alanine racemase), alr5065 ( murC ), all4316 ( mraY ), alr0093 ( hcwA , amiC2 ), or all3826 (a penicillin binding protein [PBP]). Several of the predicted targets corresponded to proteins known to...”
- Mutation of the murC and murB Genes Impairs Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
Videau, Journal of bacteriology 2016 - “...the identification of two peptidoglycan synthesis genes, murC (alr5065) and murB (alr5066), as required for heterocyst development. The murC and murB genes are...”
- “...synthesis by the murine ligase genes murC (alr5065) and murB (alr5066) for maintenance of patterned gene expression, filament integrity, and overall...”
F9UKZ5 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
23% identity, 91% coverage
Hore_09100 UDP-N-acetylmuramate--alanine ligase from Halothermothrix orenii H 168
23% identity, 72% coverage
PMM0610 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Prochlorococcus marinus sp. MED4
24% identity, 42% coverage
- Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium
Ting, Journal of bacteriology 2007 - “...follows: PMM0549 (MED4, CsoS1-1), PMM0022 (MED4, MurC), PMM0610 (MED4, MurF), PMM0197 (MED4, MurG), PMM0617 (MED4, MurI), PMM1709 (MED4, MraY), PMT1199...”
ZMO_RS03720 UDP-N-acetylmuramate--L-alanine ligase from Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
24% identity, 55% coverage
MURD_STRPY / P0C0D7 UDP-N-acetylmuramoylalanine--D-glutamate ligase; D-glutamic acid-adding enzyme; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; EC 6.3.2.9 from Streptococcus pyogenes (see paper)
SpyM3_1176 putative uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Streptococcus pyogenes MGAS315
31% identity, 48% coverage
- function: Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + ADP + phosphate + H(+) (RHEA:16429) - Novel regulatory small RNAs in Streptococcus pyogenes
Tesorero, PloS one 2013 - “...Z SSRC26 SPyM3_1166 isoleucyl-tRNA synthetase <<< SPyM3_1167 putative cell-division initiation protein <<< Q, Z SSRC27 SPyM3_1176 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase <<< SPyM3_1177 hypothetical protein <<< Q, P SSRC28 SPyM3_1190 asparagine synthetase AsnA <<< SPyM3_1191 carbamate kinase <<< Q, Z SSRC29 SPyM3_1276 hypothetical protein <<< SPyM3_1277 hypothetical protein <<<...”
CC_2556 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Caulobacter vibrioides CB15
28% identity, 51% coverage
FN1456 UDP-N-acetylmuramate--alanine ligase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Q8RDQ2 UDP-N-acetylmuramate--L-alanine ligase from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)
25% identity, 51% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...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 11...”
- “...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 ; Hendrickson...”
- Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions
Kumar, BMC microbiology 2016 - “...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 5...”
AC5_A0061 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Clostridium perfringens CPE str. F4969
21% identity, 73% coverage
Bresu_1060 UDP-N-acetylmuramate--L-alanine ligase from Brevundimonas subvibrioides ATCC 15264
25% identity, 55% coverage
- Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
Curtis, Molecular microbiology 2014 - “...subvibrioides where two potential homologs are present in the genome. However, Bresu_2692 was essential while Bresu_1060 was not, suggesting that if the latter participates in peptidoglycan precursor synthesis, it is not sufficient. A. tumefaciens has two Alr (alanine racemase) homologs while the other organisms only have...”
- “...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 E MurG CC_2551 E Bresu_2776 E...”
TP0903 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) from Treponema pallidum subsp. pallidum str. Nichols
31% identity, 31% coverage
Q88WZ5 UDP-N-acetylmuramate--L-alanine ligase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
26% identity, 64% coverage
B1745_01165 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Lactobacillus amylolyticus
23% identity, 80% coverage
CNX70_22615 cyanophycin synthetase from Janthinobacterium svalbardensis
24% identity, 41% coverage
PP1333 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Pseudomonas putida KT2440
24% identity, 91% coverage
Q6FCQ7 cyanophycin synthase (L-aspartate-adding) (EC 6.3.2.29) from Acinetobacter sp. (see paper)
ACIAD1279 putative UDP-N-acetylmuramyl tripeptide synthase from Acinetobacter sp. ADP1
26% identity, 38% coverage
murF / CAH57484.1 D-alanine:D-alanine-adding enzyme from Actinoplanes teichomyceticus (see paper)
28% identity, 62% coverage
VspiD_010100019125 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Verrucomicrobium spinosum DSM 4136
28% identity, 70% coverage
HZ99_12130 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Pseudomonas fluorescens
27% identity, 57% coverage
- Transcriptomic analysis of the response of Pseudomonas fluorescens to epigallocatechin gallate by RNA-seq
Liu, PloS one 2017 - “...and maintenance of cellular shape and integrity [ 62 63 ]. The expression of murF (HZ99_12130), which encodes for an enzyme that catalyzes the last cytoplasmic step in peptidoglycan biosynthesis, was upregulated in response to subinhibitory doses of EGCG in Staphylococcus aureus [ 28 ]. In...”
- “...peptidoglycan biosynthesis protein MviN HZ99_13545 3.56 1.05E-02 LD-carboxypeptidase HZ99_17745 2.42 7.97E-03 glucosamine fructose-6-phosphate aminotransferase GlmS HZ99_12130 1.98 4.14E-02 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase MurF HZ99_06200 -2.36 2.52E-02 D-alanyl-D-alanine endopeptidase PBP7 Cell wall related proteins and exopolysaccharides HZ99_06855 8.84 1.03E-05 porin OprD HZ99_18605 7.28 5.74E-03 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB HZ99_20290 7.11...”
PA4416 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Pseudomonas aeruginosa PAO1
30% identity, 68% coverage
- Novel drug targets in cell wall biosynthesis exploited by gene disruption in Pseudomonas aeruginosa
Elamin, PloS one 2017 - “...of six cell wall biosynthesis targets ( murA , PA4450; murD , PA4414; murF , PA4416; ppiB , PA1793; rmlA , PA5163; waaA , PA4988) in P . aeruginosa PAO1, and characterized these in order to find out whether these genes and their products contribute to...”
- “...with a number of k.o mutants in murA , PA4450; murD , PA4414; murF , PA4416; ppiB , PA1793; rmlA , PA5163; waaA , PA4988. By using this genetic approach, we could assess directly the role of selected targets in pathogenesis and virulence in mice. Material...”
- A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation
Xu, PloS one 2013 - “...PA4397( panE ),PA4406( lpxC ),PA4410( ddlB ),PA4411( murC ), PA4412( murG ),PA4414( murD ),PA4415( mraY ),PA4416( murF )PA4417( murE ),PA4425( yraO ),PA4442( cysN ),PA4443( cysD ), PA4450( murA ),PA4457( KdsD ),PA4524( nadC ),PA4529( coaE ), PA4561( ribF ),PA4655( hemH ),PA4666( hemA ),PA4670( prs ), PA4729( panB...”
- Contribution of cell elongation to the biofilm formation of Pseudomonas aeruginosa during anaerobic respiration
Yoon, PloS one 2011 - “...during anaerobic vs. aerobic respiration. We then examined transcript levels of murD (PA4414) and murF (PA4416) genes encoding UDP-N-acetylmuramoylalanine-D-glutamate ligase and UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanyl ligase, two important enzymes involved in peptidoglycan synthesis. Likewise, transcript levels of these two genes in PAO1 grown by anaerobic respiration were only 13%...”
- Beta-lactam antibiotics: from antibiosis to resistance and bacteriology
Kong, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2010 - “...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 N- acetylglucosamine transferase MurI murI PA4662 Glutamate racemase MraY mraY PA4415 Phospho-N-acetylmuramoyl-pentapeptide-transferase MraW mraW PA4420 Peptidoglycan biosynthetic process with methyl transferase...”
L141766 D-Ala-D-Ala adding enzyme (EC 6.3.2.15) from Lactococcus lactis subsp. lactis Il1403
24% identity, 71% coverage
Q9EY48 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Pseudomonas aeruginosa
30% identity, 68% coverage
BB4200 putative peptidoglycan synthesis protein from Bordetella bronchiseptica RB50
34% identity, 26% coverage
PA14_57390 UDP-N-acetylmuramyl pentapeptide synthase from Pseudomonas aeruginosa UCBPP-PA14
30% identity, 68% coverage
- Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...L -alanyl- D -glutamate synthetase 46.8 10.56 mraY PA14_57380 Phospho- N -acetylmuramoyl-pentapeptide-transferase 13.67 2.18 murF PA14_57390 UDP- N -acetylmuramoylalanyl- D -glutamyl-2.6-diaminopimelate D -alanyl- D -alanine ligase 11.12 X murE PA14_57410 UDP- N -acetylmuramoylalanyl- D -glutamate2. 6-diaminopimelate ligase 55.53 9.29 rmlC PA14_68210 dTDP-4-dehydrorhamnose 3.5-epimerase 12.92 3.34 Glycogen...”
PMM0022 Probable UDP-N-acetylmuramate-alanine ligase from Prochlorococcus marinus sp. MED4
21% identity, 53% coverage
- Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium
Ting, Journal of bacteriology 2007 - “...Table 1 are as follows: PMM0549 (MED4, CsoS1-1), PMM0022 (MED4, MurC), PMM0610 (MED4, MurF), PMM0197 (MED4, MurG), PMM0617 (MED4, MurI), PMM1709 (MED4, MraY),...”
ERH_0655 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Erysipelothrix rhusiopathiae str. Fujisawa
32% identity, 23% coverage
NBX27_03210 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Erysipelothrix rhusiopathiae
32% identity, 23% coverage
- Human Erysipelothrix rhusiopathiae infection via bath water - case report and genome announcement
Zautner, Frontiers in cellular and infection microbiology 2022 - “...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 -acetylglucosaminyltransferase NBX27_05455 murI glutamate racemase NBX27_05555 murJ/mviN murein biosynthesis integral membrane protein MurJ NBX27_00365 alr alanine racemase NBX27_00660 glmM...”
- “...does not seem to be the case, since the predicted function of the murF gene (NBX27_03210) was a UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase, and thus the pentapeptide stem ending would be D-Ala-D-Ala. Nevertheless, E. rhusiopathiae has some peculiarities concerning the cell wall peptidoglycan structure. There was a discrepancy in...”
B3QFN0 UDP-N-acetylmuramate--L-alanine ligase from Rhodopseudomonas palustris (strain TIE-1)
26% identity, 57% coverage
MSMEG_4231 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Mycobacterium smegmatis str. MC2 155
29% identity, 48% coverage
Atu2098 UDP-MurNAc-pentapeptide synthetase from Agrobacterium tumefaciens str. C58 (Cereon)
26% identity, 70% coverage
LSA1616 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Lactobacillus sakei subsp. sakei 23K
24% identity, 61% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...Putative undecaprenol kinase (bacitracine resistance protein A) 0.6 LSA1613 alr Alanine racemase -0.8 -0.9 -0.7 LSA1616 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase -0.5 Cell envelope and cellular processes LSA0162 lsa0162 Putative Bifunctional glycosyl transferase, family 8 -1.2 -1.5 LSA1246 lsa1246 Putative glycosyl transferase, family 2 -0.9 LSA1558 lsa1558 Putative...”
BDP_1546 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Bifidobacterium dentium Bd1
30% identity, 44% coverage
- Genomic insights into bifidobacteria
Lee, Microbiology and molecular biology reviews : MMBR 2010 - “...BDP_1163 BDP_0546 BDP_1149 BDP_1548 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...”
RC1_0617 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Rhodospirillum centenum SW
31% identity, 41% coverage
Wbm0238 UDP-N-acetylmuramyl pentapeptide synthase from Wolbachia endosymbiont strain TRS of Brugia malayi
Q5GT47 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Wolbachia sp. subsp. Brugia malayi (strain TRS)
21% identity, 73% coverage
BCAL3466 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diami nopimelate--D-alanyl-D-alanyl ligase from Burkholderia cenocepacia J2315
29% identity, 80% coverage
lpg2616 UDP-N-muramoylalanine-D-glutamate ligase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
27% identity, 31% coverage
cg2373 D-alanine:D-alanine-adding enzyme from Corynebacterium glutamicum ATCC 13032
NCgl2082 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Corynebacterium glutamicum ATCC 13032
28% identity, 45% coverage
RB6114 Mur ligase family protein from Rhodopirellula baltica SH 1
26% identity, 48% coverage
TC_RS00755 bifunctional UDP-N-acetylmuramate--L-alanine ligase/D-alanine--D-alanine ligase from Chlamydia muridarum str. Nigg
25% identity, 37% coverage
TC0143 UDP-N-acetylmuramate--alanine ligase/D-alanine--D-alanine ligase from Chlamydia muridarum Nigg
25% identity, 36% coverage
CDR20291_3355 UDP-N-acetylmuramate--L-alanine ligase from Clostridium difficile R20291
23% identity, 83% coverage
NELON_RS02740 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Neisseria elongata subsp. glycolytica ATCC 29315
27% identity, 73% coverage
B8ZMZ6 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-1)
29% identity, 30% coverage
SPD_0598 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus pneumoniae D39
spr0603 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Streptococcus pneumoniae R6
29% identity, 30% coverage
SP_0688 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase from Streptococcus pneumoniae TIGR4
29% identity, 30% coverage
Q9WY73 UDP-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) from Thermotoga maritima (see paper)
TM0231 UDP-N-acetylmuramate--alanine ligase from Thermotoga maritima MSB8
27% identity, 54% coverage
RB6114 probable UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase from Pirellula sp. 1
26% identity, 46% coverage
BMF81_03482 UDP-N-acetylmuramate--L-alanine ligase from Nodularia spumigena UHCC 0039
26% identity, 60% coverage
C1CD51 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Streptococcus pneumoniae (strain JJA)
30% identity, 30% coverage
- Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
Gaur, Current research in pharmacology and drug discovery 2022 - “...(Accession no. P0A091 ), Leptospira interrogans (Accession no. Q8F7V4 ) Streptococcus pneumonia e (Accession no. C1CD51), Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (MurD Accession no. from www.unipro.org ). Fig.3 MurD from E.coli is closely related to MurD from Haemophilus influenza and belongs...”
- “...no. P0A091 ), MurD Leptospira interrogans (Accession no. Q8F7V4 )M, urD Streptococcus pneumoniae (Accession no. C1CD51), MurD Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (Accession no. from www.unipro.org ). Fig.4 4.1 Physiochemical properties of MurD Specific activities of the MurD enzyme from gram-positive...”
4cvmA / Q9HVZ7 Pamurf in complex with amp-pnp and udp-murnac-tripeptide (mdap)
30% identity, 68% coverage
- Ligands: alanine; uridine-5'-diphosphate; phosphoaminophosphonic acid-adenylate ester; magnesium ion (4cvmA)
MAB_2007 UDP-N-acetylmuramate--L-alanine ligase MurC from Mycobacterium abscessus ATCC 19977
27% identity, 53% coverage
SSU_RS02355 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Streptococcus suis P1/7
25% identity, 48% coverage
gvip562 cyanophycin synthetase from Gloeobacter violaceus PCC 7421
27% identity, 44% coverage
TWT226 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Tropheryma whipplei str. Twist
30% identity, 27% coverage
SSU05_0476 UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase from Streptococcus suis 05ZYH33
25% identity, 48% coverage
- Proteomic and Metabolomic Analyses Provide Insights into the Mechanism on Arginine Metabolism Regulated by tRNA Modification Enzymes GidA and MnmE of Streptococcus suis
Gao, Frontiers in cellular and infection microbiology 2020 - “...RnhC SSU05_0226 Ribonuclease HIII 0.6607 3 6.76 PrpC SSU05_0472 Protein phosphatase 0.7162 11 59.59 MurD SSU05_0476 D-glutamic acid-adding enzyme 0.7614 19 55.68 MurG SSU05_0477 UDP-N-acetylglucosamine 0.7703 7 28.81 DnaE SSU05_0542 DNA-directed DNA polymerase 0.6931 20 20.66 TopA SSU05_0985 DNA topoisomerase I 0.7542 23 35.29 FtsK SSU05_1335...”
- 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 - “...(iii) five involved in cell wall biosynthesis, including four that were down-regulated proteins, i.e., MurD (SSU05_0476), MurE (SSU05_0651), MurG (SSU05_0477), and Pbp1A (SSU05_0414). Table 3 Differentially expressed proteins associated with cell growth and division, virulence, and fatty acid metabolism. Protein name Locus Functions Ratio( mnmE /SC19)...”
- “...TopA SSU05_0985 DNA topoisomerase I 0.7188 23 35.29 MurG SSU05_0477 UDP-N-acetylglucosamine 0.7245 7 28.81 MurD SSU05_0476 D-glutamic acid-adding enzyme 0.7625 19 55.68 FtsK SSU05_1335 DNA segregation ATPase 0.7736 23 27.50 MutS SSU05_2123 DNA mismatch repair protein 0.8078 17 22.10 Pbp1A SSU05_0414 Penicillin-binding protein 0.8134 24 36.88...”
- GidA, a tRNA Modification Enzyme, Contributes to the Growth, and Virulence of Streptococcus suis Serotype 2
Gao, Frontiers in cellular and infection microbiology 2016 - “...subunit A 0.8140 9 16.43 GyrB SSU05_1510 DNA gyrase subunit B 0.7152 2 45.38 MurD SSU05_0476 UDP- N -acetylmuramoyl-L-alanyl-D-glutamate synthetase 0.7718 14 39.87 PcrA SSU05_0731 Superfamily I DNA/RNA helicase 0.8044 15 20.42 PhpP SSU05_0427 Serine/threonine protein phosphatase 0.8067 11 59.59 RecN SSU05_1651 DNA repair ATPase 0.8321...”
CV_4345 UDP-N-acetylmuramoylalanine-D-glutamate ligase from Chromobacterium violaceum ATCC 12472
31% identity, 29% coverage
Q8F7V4 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
29% identity, 33% coverage
GSU3073, WP_010943698 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Geobacter sulfurreducens PCA
29% identity, 44% coverage
- CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
Zaharia, BMC bioinformatics 2019 - “...d) which should be catalyzed by MurF (Fig. 3 a). However, the KEGG GENES entry GSU3073 is annotated as murF [ 38 ] but the gene is not associated to reaction R04617 in the pathway map as of the writing of this paper (August 3, 2018...”
- “...performed by enzymes encoded by neighboring genes. We confirmed the functional annotation murF for gene GSU3073 by performing a protein BLAST [ 39 ] for the E. coli MurF query sequence against G. sulfurreducens (NCBI taxon 35554). The matching protein WP_010943698 (40% identity, 98% query cover,...”
- “...the E. coli MurF query sequence against G. sulfurreducens (NCBI taxon 35554). The matching protein WP_010943698 (40% identity, 98% query cover, E-value 1e 76) corresponds to gene GSU3073 via the identical protein YP_006589581. The missing reaction R04617 for G. sulfurreducens (gsu) is hence an instance of...”
- Proteogenomic analysis of bacteria and archaea: a 46 organism case study
Venter, PloS one 2011 - “...B, peptides fall within two different translation frames which are located within Geobacter sulfurreducens pseudogene GSU3073. This situation can arise when the underlying genome sequence is erroneous and contains artificial indels, or if the two regions are separately translated. C, peptides fall in a single open...”
NGO1535 MurD from Neisseria gonorrhoeae FA 1090
29% identity, 52% coverage
- Inactivation of Genes Encoding MutL and MutS Proteins Influences Adhesion and Biofilm Formation by Neisseria gonorrhoeae
Płaczkiewicz, Microorganisms 2019 - “...biofilm formation were differentially expressed. In N. gonorrhoeae mutL::km , these genes are ngo0206 , ngo1535 , and ngo1822 ( secY ), and in N. gonorrhoeae mutS::km , they are ngo0626 and ngo0834 ( Figure S1 and Table S2 ). The ngo0206 gene, which expression was...”
- “...gonorrhoeae is engaged in intraspecies communication that allows bacteria to communicate about cell density. The ngo1535 ( murD ) gene, whose expression was increased 2.45-fold ( p = 3.97 10 4 ) in the gonococcal mutL mutant compared to the parental strain ( Table S2 ),...”
LIMLP_03520 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase from Leptospira interrogans serovar Manilae
29% identity, 33% coverage
P96613 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase from Bacillus subtilis (strain 168)
BSU04570 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanine ligase from Bacillus subtilis subsp. subtilis str. 168
27% identity, 44% coverage
HI1136 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) from Haemophilus influenzae Rd KW20
25% identity, 47% coverage
Q52953 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Rhizobium meliloti (strain 1021)
31% identity, 29% coverage
TEL01S_RS09220 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Pseudothermotoga elfii DSM 9442 = NBRC 107921
32% identity, 21% coverage
murF / P9WJL1 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Rv2157c Probable UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate- D-alanyl-D-alanyl ligase MurF from Mycobacterium tuberculosis H37Rv
27% identity, 69% coverage
- Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis
Kuang, Acta pharmaceutica Sinica. B 2022 - “...l -alanine residues; MurE (Rv2158c) catalyzes m -DAP attachment of d -isoglutamate residues; and MurF (Rv2157c) is responsible for addition of d -alanyl- d -alanine to the m -DAP residues, resulting in Park's nucleotide. MurX/MraY (Rv2156c) is a phospho-MurNAc-pentapeptide translocase that catalyzes decaprenyl phosphate transfer to...”
- PanB over-representation as part of pyrazinamide action: a proteomic insight
Barros, Future microbiology 2021 (PubMed)- “...tuberculosis proteins identified, the specific acidification in the culture medium induced the over-representation of MurF (Rv2157c), and its under-representation was induced by 12 h of PZA exposure. PanB (Rv2225) was over-represented at 24 h of PZA exposure. Conclusion: The authors highlight the over-representation of PanB in...”
- Genomic signatures of pre-resistance in Mycobacterium tuberculosis
Torres, Nature communications 2021 - “...0.01 Metabolism and respiration Rv1751 Rv1751 4.43 0.42 1.6710 05 0.02 Metabolism and respiration murF Rv2157c 2.38 0.54 2.7810 05 0.03 Cell wall and cell processes Rv3712 Rv3712 0.93 0.58 310 05 0.05 Metabolism and respiration asnB Rv2201 3.62 0.48 3.1410 05 0.02 Metabolism and respiration...”
- Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study
Sinha, BMC bioinformatics 2020 - “...(UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase/ Peptidoglycan biosynthesis) 6.1.1.14 (GlycinetRNA ligase) Rv0041 6.1.1.7 AlaninetRNA ligase Rv2555c 6.3.2.10 (MurF synthetase) Rv2157c 6.3.1.2 (Glutamine synthetase) Rv2222c 1.14.13.83 (Precorrin-3B synthase/porphyrin and chlorophyll metabolism) 2.1.1.131 (Precorrin-3B C(17)-methyltransferase) Rv2066 2.1.1.130 (Precorrin-2C (20)-methyltransferase) Rv2066 1.3.3.3 (Coprogen oxidase/porphyrin and chlorophyll metabolism) 1.3.3.4 (Protoporphyrinogen oxidase) Rv2677c 4.1.1.37 (Uroporphyrinogen...”
- Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism
Yimer, Frontiers in microbiology 2020 - “...fadh Rv1175c 5, 7 3, 4 UDP- N -acetylmuramoyl-tripeptide D -alanyl- D -alanine ligase murF Rv2157c 3, 5, 7 4 UDP- N -acetylmuramoylalanine D -glutamate ligase murD Rv2155c 5, 7 3, 4 UDP- N -acetylmuramoyl- L -alanyl- D -glutamate2,6-diaminopimelate ligase murE Rv2158c 3, 5, 7 4...”
- Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall
Batt, Cell surface (Amsterdam, Netherlands) 2020 - “...al., 2007 , Munshi et al., 2013 ). The peptide sidechain is completed by MurF (Rv2157c) adding a D-Ala:D-Ala dipeptide subunit ( Munshi et al., 2013 ), which is synthesised by Ddl, a D-Ala-D-Ala ligase (Rv2981c) ( Bruning et al., 2011 ). This muramyl-pentapeptide unit, known...”
- Revisiting Anti-tuberculosis Therapeutic Strategies That Target the Peptidoglycan Structure and Synthesis
Catalão, Frontiers in microbiology 2019 - “...(Rv2155c), m-DAP addition by MurE (Rv2158c), and finally d -alanyl- d -alanine addition by MurF (Rv2157c). This generates the muramyl-pentapeptide product UDP-Mur N Ac/Glyc- l -Ala- d -isoGlu- m -DAP- d -Ala- d -Ala, also known as Parks nucleotide ( Figure 1 ; Pavelka etal., 2014...”
- Comparative Proteomic Analysis of Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains Reveals Differentially Abundant Proteins Linked to Slow Growth and Virulence
Yimer, Frontiers in microbiology 2017 - “.... Protein name Protein IDs Gene symbol Rv number Fold change UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase I6YCL0 murF Rv2157c 6.01 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase I6X3E1 murE Rv2158c 4.64 Isoniazid inducible protein IniC I6XV19 iniC Rv0343 7.74 Acyl-CoA ligase FadD31 I6Y7V6 fadD31 Rv1925 7.97 Fatty-acid-CoA ligase FadD9 Q50631 fadD9 Rv2590 7.15 Polyketide...”
- More
DR_0627 UDP-N-acetylmuramate--alanine ligase from Deinococcus radiodurans R1
25% identity, 72% coverage
WP_011614691 cyanophycin synthetase from Cupriavidus necator
H16_A0775 cyanophycin synthetase from Ralstonia eutropha H16
29% identity, 31% coverage
Q88V80 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
27% identity, 47% coverage
Atu2096 UDP-N-acetylmuramoyl-L-alanyl-D-glutamatesynthetase from Agrobacterium tumefaciens str. C58 (Cereon)
29% identity, 29% coverage
HMPREF0536_11260 bifunctional folylpolyglutamate synthase/dihydrofolate synthase from Limosilactobacillus reuteri MM4-1A
23% identity, 68% coverage
WP_011614690 cyanophycin synthetase from Cupriavidus necator
H16_A0774 cyanophycin synthetase from Ralstonia eutropha H16
26% identity, 42% coverage
HMPREF9957_1097 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Streptococcus mitis SK1080
35% identity, 22% coverage
- Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, Three S. oralis Subspecies, and S. infantis
Kilian, mBio 2019 - “...mitis strains B6, SK1080, and SK637 have, in the same locus, genes (smi_1064 in B6, HMPREF9957_1097 in SK1080, and Sm_SK637_00942) encoding another LPXTG cell wall anchor domain protein of 1,702, 1,256, and 2,522 amino acids (aa), respectively, with homology to proteins annotated as collagen adhesin/mucus binding...”
MTH734 UDP-MurNac-tripeptide synthetase from Methanothermobacter thermautotrophicus str. Delta H
25% identity, 77% coverage
pc0631 putative alanine racemase from Parachlamydia sp. UWE25
31% identity, 16% coverage
SP_1670 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Streptococcus pneumoniae TIGR4
32% identity, 26% coverage
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...2/2 Upregulated 38805 SP_1648, SP_1649, SP_1650 3/3 Upregulated 38808 SP_1662, SP_1665 2/8 Upregulated 38809 SP_1669, SP_1670 2/3 Upregulated 38833 SP_1774, SP_1775 2/3 Upregulated 38839 SP_1802, SP_1803, SP_1804 3/4 Upregulated 38854 SP_1860, SP_1861, SP_1862, SP_1863 4/4 Upregulated 38857 SP_1869, SP_1870, SP_1871 3/3 Upregulated 38862 SP_1906, SP_1907 2/2...”
SPD_1483 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Streptococcus pneumoniae D39
32% identity, 26% coverage
2am1A / Q8DNV6 Sp protein ligand 1 (see paper)
32% identity, 26% coverage
- Ligand: 2,4-dichloro-n-(3-cyano-4,5,6,7-tetrahydro-benzothiophen-2yl)-5-(morpholine-4-sulfonyl)-benzamide (2am1A)
MT2216 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Mycobacterium tuberculosis CDC1551
27% identity, 69% coverage
lpg2614 UDP-N-acetylmuramate:L-alanine ligase MurC from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
27% identity, 35% coverage
P0E69_16645 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Chimaeribacter arupi
25% identity, 89% 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 - “...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 murI 4187076..4187939 glutamate racemase P0E69_09125 murJ 2034271..2035806 murein biosynthesis integral membrane protein MurJ P0E69_02530 mpl 533726..535093 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase P0E69_10225 mrdA,...”
Q4QLG0 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Haemophilus influenzae (strain 86-028NP)
24% identity, 47% coverage
- Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
Gaur, Current research in pharmacology and drug discovery 2022 - “...interrogans (Accession no. Q8F7V4 ) Streptococcus pneumonia e (Accession no. C1CD51), Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (MurD Accession no. from www.unipro.org ). Fig.3 MurD from E.coli is closely related to MurD from Haemophilus influenza and belongs to a single clade. Both...”
- “...(Accession no. Q8F7V4 )M, urD Streptococcus pneumoniae (Accession no. C1CD51), MurD Haemophilus influenzae (Accession no. Q4QLG0 ). (output of Clustal Omega) (Accession no. from www.unipro.org ). Fig.4 4.1 Physiochemical properties of MurD Specific activities of the MurD enzyme from gram-positive bacteria E. faecalis and Staph aureus...”
MXAN_5608 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Myxococcus xanthus DK 1622
27% identity, 70% coverage
- Peripheral rods: a specialized developmental cell type in Myxococcus xanthus
Whitfield, Genomics 2020 - “...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 transcripts during stationary phase. Table 5 Transcriptome Analysis of genes encoding developmental proteins of the...”
BCAL3464 UDP-N-acetylmuramoylalanine--D-glutamate ligase from Burkholderia cenocepacia J2315
44% identity, 13% coverage
BPSL3029 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diamino pimelate--D-alanyl-D-alanyl ligase from Burkholderia pseudomallei K96243
27% identity, 40% coverage
CT756 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminoligase from Chlamydia trachomatis D/UW-3/CX
36% identity, 21% coverage
STM0124 D-alanine:D-alanine-adding enzyme from Salmonella typhimurium LT2
SL1344_0124 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
25% identity, 73% coverage
- Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets
Kocabaş, PloS one 2022 - “...UDP-N-acetylmuramoyl-L-alanyl-D-glutamate2,6-diaminopimelate ligase Peptidoglycan biosynthesis.Lysine biosynthesis Yes STM0128 murG UDP-N-acetylglucosamineN-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase Peptidoglycan biosynthesis Yes STM0124 murF UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase Peptidoglycan biosynthesis.Lysine biosynthesis Yes STM3725 coaD Phosphopantetheine adenylyltransferase Pantothenate and CoA biosynthesis Yes Analysis of the prioritized drug targets The prioritized drug targets ( Table 3 )...”
- Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
Harvey, Infection and immunity 2011 - “...hook protein 2.64 0.03 Cell wall/membrane biogenesis STM0124 murF D-Alanine-D-alanine 2.09 0.044 Energy production and conversion STM4439 cybC Cytochrome b562...”
- 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 - “...1.63E10 2-Oxoglutarate dehydrogenase E1 component SL1344_3433 cap 1,123 54,257 5.474 8.81E09 Septum formation protein Maf SL1344_0124 murF 10 4,709 5.450 9.98E16 UDP- N -acetylmuramoylalanyl-d-glutamyl-2,6-diaminopimelated-alanalanyl ligase SL1344_0628 mrdA 39 5,599 5.358 1.24E12 Penicillin-binding protein 2 SL1344_1820 zwf 219 12,961 5.356 2.86E08 Glucose 6-phosphate dehydrogenase SL1344_4496 deoB 216...”
Franean1_7139 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Frankia sp. EAN1pec
30% identity, 41% coverage
tcp1 / CAE53342.1 murF-like protein from Actinoplanes teichomyceticus (see paper)
30% identity, 44% coverage
DR_0768 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Deinococcus radiodurans R1
27% identity, 73% coverage
FOLCP_HALSA / Q9HS44 Probable bifunctional folylpolyglutamate synthase/dihydropteroate synthase; EC 6.3.2.17; EC 2.5.1.15 from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium) (see paper)
34% identity, 20% coverage
- function: Can complement an H.volcanii mutant strain that is thymidine auxotroph because it lacks the two dihydrofolate reductase genes encoded by hdrA and hdrB.
catalytic activity: (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + L-glutamate + ATP = (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n+1) + ADP + phosphate + H(+) (RHEA:10580)
catalytic activity: (7,8-dihydropterin-6-yl)methyl diphosphate + 4-aminobenzoate = 7,8-dihydropteroate + diphosphate (RHEA:19949)
cofactor: Mg(2+)
CTL0125 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Chlamydia trachomatis 434/Bu
L225667R_RS04090 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Chlamydia trachomatis L2/25667R
21% identity, 72% coverage
- Tryptophan Availability during Persistence of Chlamydia trachomatis Directly Impacts Expression of Chlamydial Cell Division Proteins
Riffaud, Infection and immunity 2023 (secret) - Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor
Huang, Frontiers in microbiology 2021 - “...370 1.51 1.760.30 2.61E-02 ftsK CTL0108 DNA translocase FtsK aAAAGAAT-N12-ATCGAAGA 398 1.52 2.470.36 5.89E-03 murF CTL0125 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase TtAAGAAg-N12-ATCGAAcC 348 2.08 2.670.50 9.46E-03 miaA CTL0135 tRNA dimethylallyltransferase aAAAGAAT-N11-ATaGAAAA 430 1.69 nd na ctl0252 CTL0252 Hypothetical protein TAAAGATT-N11-ATaGAgGT 91 2.32 1.680.24 5.19E-02 pmpI CTL0254 Outer membrane protein...”
- Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene Transfer
LaBrie, mBio 2019 - “...ctl0105 ( ct736 ) Hypothetical phosphatidyl ethanolamine-binding proteins 129068 191/453 WIHWI T GWMISPRSDAQWNENSRX [V65T; 83/150] ctl0125 murF UDP-N-acetylmuramoyl-tripeptide- d -alanyl- d -alanine ligase 169474 1,328/1,353 ELETL T GWMISPRSDAQWNENSRX [L404T; 462/450] ctl0175 ( ct806 ) h ptr Periplasmic Zn-dependent peptidase 223999 1,236/2,871 INSLE Y NRLDDKSPVX [S422X; 422/957]...”
- An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis
O'Neill, Wellcome open research 2021 - “...Intergenic 761,933 (1) N/A L225667R_RS03810 817,240 (2) Phosphoenolpyruvate carboxykinase (GTP) L225667R_RS03925 843,195 (1) Hypothetical protein L225667R_RS04090 886,327 (1) UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase L225667R_RS04185 906,134 (1) 1-acyl-sn-glycerol-3-phosphate acyltransferase L225667R_RS04255 919,907 (1) Hypothetical protein L225667R_RS04455 966,486 (1) Insulinase family protein L225667R_RS04525 982,510 (1) Hypothetical protein L225667R_RS04710 1,023,666 (1) Autotransporter domain-containing...”
PFREUD_15540 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
32% identity, 44% coverage
Mra / b0086 D-alanyl-D-alanine-adding enzyme (EC 6.3.2.10) from Escherichia coli K-12 substr. MG1655 (see 20 papers)
murF / P11880 D-alanyl-D-alanine-adding enzyme (EC 6.3.2.10) from Escherichia coli (strain K12) (see 19 papers)
MURF_ECOLI / P11880 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; D-alanyl-D-alanine-adding enzyme; UDP-MurNAc-pentapeptide synthetase; EC 6.3.2.10 from Escherichia coli (strain K12) (see paper)
P11880 UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (EC 6.3.2.10); UDP-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) from Escherichia coli (see 3 papers)
NP_414628 D-alanyl-D-alanine-adding enzyme from Escherichia coli str. K-12 substr. MG1655
b0086 UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D- alanine ligase from Escherichia coli str. K-12 substr. MG1655
25% identity, 65% coverage
- function: Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.
catalytic activity: UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso- 2,6-diaminoheptanedioate + D-alanyl-D-alanine + ATP = UDP-N-acetyl- alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl- D-alanyl-D-alanine + ADP + phosphate + H(+) (RHEA:28374)
subunit: Monomer. - Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (-)-epicatechin.
Rambaher, Journal of computer-aided molecular design 2023 - “...from E. coli was obtained from the UniProtKB database [ 15 ] with the code P11880 and an automated search was conducted to identify the most similar templates. The resulting templates were subsequently prioritized according to the quality of the resultant models. Among these, the crystal...”
- Quantitative proteomic analysis reveals the influence of plantaricin BM-1 on metabolic pathways and peptidoglycan synthesis in Escherichia coli K12
Wang, PloS one 2020 - “...MurC Enzyme; murein sacculus, peptidoglycan P22634 Glutamate racemase 1.28 0.001415 MurI Enzyme; murein sacculus, peptidoglycan P11880 UDP-N-acetylmuramoyl-tripeptide: D-alanyl-D-alanine ligase 1.26 0.001793 MurF Enzyme; murein sacculus, peptidoglycan P0AD65 Transpeptidase involved in peptidoglycan synthesis 1.23 0.02935 MrdA Enzyme; cell division KEGG pathway analysis showed significant ( p <...”
- Divergence of function in sequence-related groups of Escherichia coli proteins
Nahum, Genome research 2001 - “...P17952 P14900 P22188 P11880 UDP-N-acetylmuramate-alanine ligase UDP-N-acetylmuramoylalanine-D-glutamate ligase UDP-N-acetylmuramoylalanyl-D-glutamate...”
- Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli.
Duncan, Biochemistry 1990 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
Zaharia, BMC bioinformatics 2019 - “...the genes coding for enzymes involved in this trail: murE ( b0085 ), murF ( b0086 ), mraY ( b0087 ), murD ( b0088 ), murG ( b0090 ), and murC ( b0091 ). Note that the trail produced by CoMetGeNe was obtained by skipping gene...”
- Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
Ge, Journal of biosciences 2011 - “...4450142 3.14 ytfR b4230 13 48080 48753 1.77 kefC b0047 13 94377 94642 3.08 murE b0086 14 500178 500563 1.77 gsk b0477 14 2443970 2444451 3.08 mepA b2328 15 2052323 2052876 1.77 amn b1982 15 2750846 2751039 3.08 smpA b2617 16 2347485 2347798 1.77 yfaH b2238...”
- Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy
Li, PLoS neglected tropical diseases 2011 - “...mreB b3251 347 wbm0154 358 cell wall structural complex MreBCD, actin-like component MreB 53.0 murF b0086 452 wbm0238 455 UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase 27.9 ftsH b3178 644 wbm0490 609 protease, ATP-dependent zinc-metallo 46.5 murE b0085 495 wbm0492 496 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase 25.2 murD b0088 438 wbm0508 498 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...CEB LBR genes b0003 b0004, b0025, b0029 b0071 b0085 b0096 b0004 b0052, b0103, b0109 b0072 b0086 b0179 b0031 b0131, b0133, b0134 b0073 b0087 b0181 b0166 b0142, b0154, b0159 b0074 b0088 b0182 b2472 b0173, b0174, b0369 b3770 b0090 b0524 b2478 b0414, b0415, b0417 b3771 b0091 b0914 b2838...”
- Divergence of function in sequence-related groups of Escherichia coli proteins
Nahum, Genome research 2001 - “...murE murF b0091 b0088 b0085 b0086 P17952 P14900 P22188 P11880 UDP-N-acetylmuramate-alanine ligase UDP-N-acetylmuramoylalanine-D-glutamate ligase...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b2552 b0440 b2237 b4036 b0096 b4034 b4035 b0168 b1531 b0086 b0578 b2281 b2279 b0113 b4025 b1101 b1658 b3317 b3319 b3305 b3985 b3318 b3312 b3314 b3321 b3316...”
UTI89_C0095 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase from Escherichia coli UTI89
26% identity, 65% coverage
- Glycosuria Alters Uropathogenic Escherichia coli Global Gene Expression and Virulence
Islam, mSphere 2022 - “...FC) for a : GenBank definition LB vs fU LB vs fUG fU vs fUG UTI89_C0095 murF 0.7417 0.3595 1.1134* UDP- N -acetylmuramoyl-tripeptide d -alanyl- d -alanine ligase UTI89_C0096 mraY 0.9774 0.1922 1.1833* Phospho- N -acetylmuramoyl-pentapeptide-transferase UTI89_C0099 murG 1.2970* 0.0013 1.3099* Undecaprenyldiphospho-muramoylpentapeptide beta- N -acetylglucosaminyltransferase UTI89_C0275...”
- “...cationic antimicrobial peptide (CAMP) resistance. Compared to UTI89-fU, UTI89-fUG showed significantly increased expression of murF (UTI89_C0095), mraY (UTI89_C0096), murG (UTI89_C0099), and murC (UTI89_C0101) and CAMP resistance gene pagP (UTI89_C0626). Mur enzymes (MurABCDEF) catalyze synthesis of UDP N -acetyl muramyl pentapeptide from UDP N- acetylglucosamine, a major...”
Cbei_0107 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase from Clostridium beijerincki NCIMB 8052
28% identity, 26% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory