PaperBLAST
PaperBLAST Hits for BRENDA::P0A6L2 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (Escherichia coli) (292 a.a., MFTGSIVAIV...)
Show query sequence
>BRENDA::P0A6L2 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (Escherichia coli)
MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVV
MMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFK
AIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSDD
FVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLH
NKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL
Running BLASTp...
Found 250 similar proteins in the literature:
DapA / b2478 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Escherichia coli K-12 substr. MG1655 (see 24 papers)
dapA / P0A6L2 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Escherichia coli (strain K12) (see 23 papers)
DAPA_ECOLI / P0A6L2 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Escherichia coli (strain K12) (see 11 papers)
P0A6L2 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Escherichia coli (see 15 papers)
NP_416973 4-hydroxy-tetrahydrodipicolinate synthase from Escherichia coli str. K-12 substr. MG1655
P0A6L3 4-hydroxy-tetrahydrodipicolinate synthase from Shigella flexneri
b2478 dihydrodipicolinate synthase from Escherichia coli str. K-12 substr. MG1655
100% identity, 100% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer; dimer of dimers. - Electrostatic fingerprints of catalytically active amino acids in enzymes.
Iyengar, Protein science : a publication of the Protein Society 2022 (no snippet) - Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...A0A438E022), Zea mays DHDPS1 (Zm1; UNIPROT ID: P26259), and Escherichia coli (Ec) DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1 with dots (.) representing interspacing residues. Sequences were aligned in BioEdit (v 7.2.5) ( Hall, 1999 ) using the ClustalW algorithm ( Thompson et...”
- “...DHDPS1 (UNIPROT ID: P26259) and DHDPS2 (UNIPORT ID: B4FLW2), and Escherichia coli DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1; identical residues are shown as dots (.), gaps are shown as dashes (-), and similar residues are highlighted in grey. Sequences were aligned in...”
- Mutations in DHDPSL are responsible for primary hyperoxaluria type III.
Belostotsky, American journal of human genetics 2010 - The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...acid dehydrogenase small subunit 6.17/47,607.29 DapA P0A6L2 Dihydrodipicolinate synthase 5.98/31,269.97 6.10/32,361 5.94/32,916 (DIGE 4.5-6.5) (4-5) (4-5) (4-5)...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus
North, Acta crystallographica. Section F, Structural biology and crystallization communications 2013 - “...(YP_006195476) and E. coli strain K12 (NP_416973) (extracted from http://www.ncbi.nlm.hih.gov, protein accession numbers in parentheses). This alignment was...”
- “...subspecies aureus 71193 and E. coli strain K12 (NP_416973). This was performed to investigate the 310 North et al. N-Acetylneuraminate lyase homology of...”
- The C-terminal domain of Escherichia coli dihydrodipicolinate synthase (DHDPS) is essential for maintenance of quaternary structure and efficient catalysis.
Guo, Biochemical and biophysical research communications 2009 (PubMed)- GeneRIF: This study investigated the C-terminal domain of E. coli DHDPS by characterising a C-terminal truncated DHDPS (DHDPS-H225*).
- Evolution of quaternary structure in a homotetrameric enzyme.
Griffin, Journal of molecular biology 2008 (PubMed)- GeneRIF: Results suggest that the homotetrameric structure of dihydrodipicolinate synthase reduces dynamic fluctuations present in the dimeric forms and increases specificity for the first substrate, pyruvate.
- Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase.
Dobson, Protein science : a publication of the Protein Society 2008 - GeneRIF: to probe the mechanism of dihydrodipicolinate synthase (DHDPS), inhibition of DHDPS by the substrate analog, beta-hydroxypyruvate was studied; crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved
- The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
Dobson, Acta crystallographica. Section D, Biological crystallography 2005 (PubMed)- GeneRIF: crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from E. coli are presented to 1.9 and 2.0 A, respectively
- Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase.
Dobson, Biochemistry 2005 (PubMed)- GeneRIF: evidence that Arg138 of dihydrodipicolinate synthase is responsible for binding the carboxyl of (S)-ASA and is not involved in the mechanism of (S)-lysine inhibition
- Expression from the Escherichia coli dapA promoter is regulated by intracellular levels of diaminopimelic acid.
Acord, FEMS microbiology letters 2004 (PubMed)- GeneRIF: The dapA promoter is activated by diaminopimelic acid.
- Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach
Oany, In silico pharmacology 2018 - “...Subcellular location PDB ID 1. 2. 3. 4. 5. Q83MD3 P0A6L3 P0A9R1 Q83IN8 P0A9M9 dxr dapA asd lysC pta 398 292 367 449 714 43346.9 31269.9 40017.8 48517.7 77172.0...”
- “...orange and purple color denote the protein, P0A6L3, P0A9M9, Q83MD3, Q83IN8 Q83MH9 and P0A9R1, respectively enzyme inhibitory activities were assessed for...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0181 b0166 b0142, b0154, b0159 b0074 b0088 b0182 b2472 b0173, b0174, b0369 b3770 b0090 b0524 b2478 b0414, b0415, b0417 b3771 b0091 b0914 b2838 b0420, b0421, b0423 b3774 b0954 b0915 b3359 b0475, b0750, b0907 b1093 b0918 b3433 b1096, b1208, b1210 b1094 b1094 b3809 b1277, b1662, b1740 b1288...”
5t25A / B7M7I1 Kinetic, spectral and structural characterization of the slow binding inhibitor acetopyruvate with dihydrodipicolinate synthase from escherichia coli.
100% identity, 100% coverage
NP_311367 dihydrodipicolinate synthase from Escherichia coli O157:H7 str. Sakai
Q3YZ74 4-hydroxy-tetrahydrodipicolinate synthase from Shigella sonnei (strain Ss046)
100% identity, 100% coverage
WP_061350668 4-hydroxy-tetrahydrodipicolinate synthase from Escherichia coli
100% identity, 100% coverage
WP_023259918 4-hydroxy-tetrahydrodipicolinate synthase from Salmonella enterica subsp. enterica serovar Manhattan str.
91% identity, 100% coverage
dhdps / CAC50571.1 dihydrodipicolinate synthetase from Yersinia enterocolitica (see paper)
81% identity, 100% coverage
WP_004941701 4-hydroxy-tetrahydrodipicolinate synthase from Serratia marcescens
79% identity, 100% coverage
YP_071290 dihydrodipicolinate synthase from Yersinia pseudotuberculosis IP 32953
78% identity, 98% coverage
APL_0899 dihydrodipicolinate synthase from Actinobacillus pleuropneumoniae L20
63% identity, 99% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...phosphate synthase subunit hisF 2.833 APL_0702 serC Phosphoserine aminotransferase 2.788 APL_0432 leuB 3-isopropylmalate dehydrogenase 2.643 APL_0899 dapA Dihydrodipicolinate synthase 2.401 APL_0211 glyA Glycine/serine hydroxymethyltransferase 2.398 APL_0133 cysB HTH-type transcriptional regulator CysB 2.340 APL_1853 ilvC Ketol-acid reductoisomerase 2.313 APL_0072 ilvE Branched-chain-amino-acid aminotransferase 2.001 APL_0859 trpCF Tryptophan biosynthesis...”
HI0255 dihydrodipicolinate synthetase (dapA) from Haemophilus influenzae Rd KW20
59% identity, 98% coverage
- Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor
López-López, mSystems 2022 - “...HI0089 ( thrA ) Bifunctional aspartokinase/homoserine dehydrogenase 3.5.1.18 HI0102 ( dapE ) Succinyl-diaminopimelate desuccinylase 4.3.3.7 HI0255 ( dapA ) 4-Hydroxy-tetrahydrodipicolinate synthase 1.3.1.98 HI0268 ( murB ) UDP-N-acetylenolpyruvoylglucosamine reductase 2.4.1.129, 3.4.16.4 HI0440 ( ponA ) Penicillin-binding protein 1A 2.7.7.23, 2.3.1.157 HI0642 ( glmU ) Bifunctional protein GlmU...”
- Evolution of competence and DNA uptake specificity in the Pasteurellaceae
Redfield, BMC evolutionary biology 2006 - “...and in E. coli: gapdH (HI0001), lepA (HI0016), ffh (HI0106), serS (HI0110), secD (HI0240), dapA (HI0255), ruvB (HI0312), xerC (HI0676), ispB (HI0881), secA (HI0909), crp (HI0957), and dnaJ (HI1238). Homologues were identified using the BLASTP program (E-val < 10 -50 ) in the BLAST package [...”
AHML_04540 4-hydroxy-tetrahydrodipicolinate synthase from Aeromonas hydrophila ML09-119
62% identity, 99% coverage
A5F699 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Vibrio cholerae (see paper)
58% identity, 99% coverage
PP1237 dihydrodipicolinate synthase from Pseudomonas putida KT2440
57% identity, 99% coverage
DAPA_PSEAE / Q9I4W3 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
Q9I4W3 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Pseudomonas aeruginosa (see 2 papers)
PA1010 dihydrodipicolinate synthase from Pseudomonas aeruginosa PAO1
57% identity, 100% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homodimer. - A Selective Culture Medium for Screening Cefiderocol Resistance in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii
Ibrahim, Journal of clinical microbiology 2023 (secret) - The Cysteine Desulfurase IscS Is a Significant Target of 2-Aminoacrylate Damage in Pseudomonas aeruginosa
Fulton, mBio 2022 - “...while the third contained an in-frame deletion. Mutations were identified in PA3814 ( iscS ), PA1010 ( dapA ) and PA1559 , respectively. In each case, Sanger sequencing confirmed the lesion identified by whole-genome analysis was present in the relevant strain. The three strains were phenotypically...”
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...HVO_2487 asd yes 51% MJ0205 Q57658 [ 138 ] 16225889 2a/9e HVO_1101 dapA yes 45% PA1010 Q9I4W3 [ 139 ] 21396954 2a HVO_1100 dapB yes 33% b0031 P04036 [ 140 ] 7893644 2a HVO_1099 dapD yes 32% b0166 P0A9D8 [ 141 ] 6365916 2a HVO_1096 dapE...”
- “...HVO_1967 pgi yes 36% MJ1605 Q59000 [ 311 ] 14655001 9e OE_1665R kdgA no 31% PA1010 Q9I4W3 [ 139 ] 21396954 GSP for dapA (see under 2a) 9e OE_1665R (cont.) probably 30% TTX_1156.1 TTX_1156a G4RJQ2 [ 315 ] 15869466 9e OE_1665R (cont.) probably 25% SSO3197 Q97U28...”
- Bis-(3'-5')-cyclic dimeric GMP regulates antimicrobial peptide resistance in Pseudomonas aeruginosa
Chua, Antimicrobial agents and chemotherapy 2013 - “...PA5131 PA3213 PA1833 PA0548 PA5497 PA1342 PA0067 PA1588 PA1010 PA3790 PA3194 PA1583 aprX pelA pvdO pilY1 Hypothetical protein O1Q_25902 PelA protein Protein...”
- Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion
Schnell, PloS one 2012 - “...DapD indicated by blue and red arrows, respectively. Right: Reactions catalyzed by dihydrodipicolinate synthase (DapA, PA1010) and tetrahydrodipicolinate N-succinyltransferase (DapD, PA3666). The structure of the substrate analogue 2-aminopimelate used as DapD substrate in this study is shown for comparison. Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyses the transfer of...”
- “...involve several regions of the polypeptide chain [25] , [28] , [29] . As dapA (PA1010) and dapD (PA3666) were suggested to be essential genes in P. aeruginosa [2] we set out to characterize these enzymes of the DAP pathway in this organism in more detail....”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...* PA0999 pqsD Oxoacylacyl carrier synthase I U 36.4 51 5.34 5.03 0.542 0.072 33 PA1010 dapA Dihydrodipicolinate synthase EM C 31.4 32 6.00 5.99 0.705 0.043 34 PA1013 purC Phosphoribosylaminoimidazole succinocarboxamide synthase F U 26.8 27 5.31 5.19 0.729 0.306 35 * PA1074 braC Branched...”
- V-antigen genotype and phenotype analyses of clinical isolates of Pseudomonas aeruginosa
Allmond, Journal of clinical microbiology 2004 - “...genotype PA103 PA1027 PA1111 PA1085 PA2009 PA2015 PA1007 PA1010 PA1001 PA1100 PA1019 PA1024 PA1034 PA1052 PA1060 PA1063 PA1064 PA1065 PA1067 PA1069 PA1070...”
- “...- PA103 PA1027 PA1111 PA1085 PA2009 PA2015 PA1007 PA1010 - negative control - size marker - 1.651.00.65- isolate from acute infection (non-cystic fibrosis)...”
- Acetylomics reveals an extensive acetylation diversity within <i>Pseudomonas aeruginosa</i>
Broeckaert, microLife 2024 (no snippet) - Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...asd yes 51% MJ0205 Q57658 [ 138 ] 16225889 2a/9e HVO_1101 dapA yes 45% PA1010 Q9I4W3 [ 139 ] 21396954 2a HVO_1100 dapB yes 33% b0031 P04036 [ 140 ] 7893644 2a HVO_1099 dapD yes 32% b0166 P0A9D8 [ 141 ] 6365916 2a HVO_1096 dapE yes...”
- “...pgi yes 36% MJ1605 Q59000 [ 311 ] 14655001 9e OE_1665R kdgA no 31% PA1010 Q9I4W3 [ 139 ] 21396954 GSP for dapA (see under 2a) 9e OE_1665R (cont.) probably 30% TTX_1156.1 TTX_1156a G4RJQ2 [ 315 ] 15869466 9e OE_1665R (cont.) probably 25% SSO3197 Q97U28 [...”
BN5_2718 4-hydroxy-tetrahydrodipicolinate synthase from Pseudomonas oleovorans CECT 5344
56% identity, 100% coverage
- Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344
Olaya-Abril, Frontiers in microbiology 2020 - “...a homologous DapA3 protein that shares 53% identity with DapA1. However, neither the dapA3 gene (BN5_2718) nor its encoded product (W6R4K8) were found induced or overproduced by the cyanide-containing jewelry residue in the transcriptomic and proteomic studies previously carried out in P. pseudoalcaligenes CECT5344 ( Luque-Almagro...”
- “...nitrate reductase nasA3 gene (BN5_2125), TonB-dependent siderophore receptor fhuA gene (BN5_2417), dihydrodipicolinate synthase dapA3 gene (BN5_2718), catalase-peroxidase katG gene (BN5_3669), and glutamine synthetase glnA9 gene (BN5_4197). Conclusion This study has highlighted that the dihydrodipicolinate synthase DapA1 of P. pseudoalcaligenes CECT5344 is relevant for the tolerance to...”
- Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS)
Ibáñez, PloS one 2017 - “...putative cytochrome c -related protein (BN5_2243), hypothetical protein (BN5_2245); D. Dihydrodipicolinate synthase ( dapA3 , BN5_2718), glycine cleavage system transcriptional repressor ( psfF , BN5_2719), putative permease PerM (BN5_2721), permease PerM, C-terminal (BN5_2722); E. Hypothetical protein (BN5_0755), ferrichrome transport system permease protein FhuB (BN5_0757), hypothetical protein...”
3puoA / Q9I4W3 Crystal structure of dihydrodipicolinate synthase from pseudomonas aeruginosa(psdhdps)complexed with l-lysine at 2.65a resolution (see paper)
57% identity, 100% coverage
4dxvA / D0CFC3 Crystal structure of dihydrodipicolinate synthase from acinetobacter baumannii complexed with mg and cl ions at 1.80 a resolution
51% identity, 100% coverage
- Ligand: magnesium ion (4dxvA)
4pfmA / A9DKW4 Shewanella benthica dhdps with lysine and pyruvate
51% identity, 98% coverage
CBU_1222 dihydrodipicolinate synthase from Coxiella burnetii RSA 493
48% identity, 98% coverage
RS_RS05700 4-hydroxy-tetrahydrodipicolinate synthase from Ralstonia pseudosolanacearum GMI1000
51% identity, 99% coverage
DAPA_NEIMB / Q9JZR4 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) (see paper)
Q9JZR4 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Neisseria meningitidis (see paper)
49% identity, 100% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer.
NGO0947 putative dihydrodipicolinate synthase from Neisseria gonorrhoeae FA 1090
49% identity, 100% coverage
YP_003106592 dihydrodipicolinate synthase from Brucella microti CCM 4915
45% identity, 100% coverage
WP_006165259 4-hydroxy-tetrahydrodipicolinate synthase from Brucella sp. 63/311
45% identity, 100% coverage
WP_021587874 4-hydroxy-tetrahydrodipicolinate synthase from Brucella intermedia
45% identity, 100% coverage
NP_697660 dihydrodipicolinate synthase from Brucella suis 1330
44% identity, 100% coverage
YP_003432886 dihydrodipicolinate synthase from Hydrogenobacter thermophilus TK-6
48% identity, 99% coverage
- Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species
Oshima, International journal of evolutionary biology 2012 - “...YP_003432414 thiol peroxidase YP_003432533 orotidine 5 -phosphate decarboxylase YP_003432615 S-adenosyl-methyltransferase YP_003432911 carbamoyl-phosphate synthase small subunit YP_003432886 dihydrodipicolinate synthase YP_003432967 membrane protein YP_003432968 GMP synthase YP_003433028 hypothetical protein HTH_1376 YP_003433124 homoserine kinase YP_003433221 UDP-glucose-4-epimerase YP_003433380 pantothenate metabolism flavoprotein YP_003433549 cell cycle protein...”
BMEI1301 DIHYDRODIPICOLINATE SYNTHASE from Brucella melitensis 16M
44% identity, 95% coverage
- Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M
Brambila-Tapia, PloS one 2014 - “...[8] BMEII0136 pheB Homoprotocatechuate 2,3-dioxygenase E 81 [7] BMEII0626 BMEII0626 Membrane dipeptidase E 269 [7] BMEI1301 dapA Dihydrodipicolinate synthase E/M 728 [7] BMEII0285 dppB Peptide ABC transporter permease E/P 105 [8] BMEI1606 prlS Sensory transduction histidine kinase E/R 185 [17] , [18] BMEI0233 purH Bifunctional phosphoribosylaminoimidazolecarboxamide...”
- “...radiotolerans JCM1831) ( Table 1 ). The genes with the highest number of orthologs were BMEI1301 ( dapA ), BMEI0296 ( purE ), BMEI1519 ( purD ), BMEI1127 ( purL ) and BMEI0781 ( rpoA ), with around 700 orthologs ( Table 1 ). Additionally, orthologs...”
- Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation
Jiang, PloS one 2013 - “...sugar transport systems, such as pyruvate carboxylase (BMEI0266), ribokinase (BMEII0089), 6-phosphogluconate dehydrogenase (BMEII1124), inosamine methylase (BMEI1301), glycosyl transferase (BMEII1101), ribose transport (BMEII0300), and glucose/galactose transport (BMEII1053) limit carbon or energy supply and affect gene regulation. In addition, the production of cyclic -1,2 glucan (BMEI1837) is necessary...”
- Attenuated signature-tagged mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice
Lestrate, Infection and immunity 2003 - “...BMEI1069 BMEII0591 BMEII0624 BMEI0433 BMEI0624 BMEI0705 BMEI1301 BMEII0485 BMEII0823 BMEI0357 BMEI1336 BMEII1066 BMEI0781 BMEII0527 BMEI1396 BMEII0151 BMEII0136...”
BAB1_0666 Dihydrodipicolinate synthetase:Dihydrodipicolinate synthase subfamily from Brucella melitensis biovar Abortus 2308
44% identity, 100% coverage
- Transcriptome analysis of the Brucella abortus BvrR/BvrS two-component regulatory system
Viadas, PloS one 2010 - “...aspB , aminotransferase 2.0 BAB1_0476 cfa , methyltransferase 1.9 BAB1_1366 fhuD , ABC transporter 1.8 BAB1_0666 dapA , dihydrodipicolinate synthase 1.8 BAB2_0712 lpdA , dihydrolipoamide dehydrogenase 1.7 BAB1_0260 flgJ , flagellar protein 1.6 BAB2_0863 glutaminase 1.5 BAB1_2043 fabG , 3-ketoacyl-(acyl-carrier-protein) reductase 1.4 BAB2_0928 nosZ , nitrous-oxide...”
- “...vjbR , but also motB (BAB2_1103), malK (BAB1_0241), norC (BAB2_0955), oppA (BAB1_1601), aspB (BAB1_1397), mosA (BAB1_0666) and three genes encoding hypothetical proteins (BAB1_1717, BAB1_0597 y BAB2_1127). B. melitensis malK mutant and B. suis aspB mutant were attenuated in cellular model of infection, and B. melitensis mutants...”
- Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
Lamontagne, BMC genomics 2010 - “...metallopeptidase, BAB1_1233 RpsM; S13 BAB1_1970 FadB BAB2_0642 Acyl-CoA zinc-binding region BAB1_1234 Adk BAB1_1971 EtfA dehydrogenase BAB1_0666 DapA BAB1_1241 RpsH; S8 BAB1_1988 HisC BAB2_0644 Metal-dependent BAB1_0671 RpoZ BAB1_1242 RpsN; S14 BAB1_1993 Ppa hydrolase BAB1_0688 PyrC-1 BAB1_1244 RplX; L24 BAB1_2006 RegA BAB2_0645 GatC BAB1_0697 CysS BAB1_1245 RplN; L14...”
W6R260 4-hydroxy-tetrahydrodipicolinate synthase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
43% identity, 90% coverage
SAR11_1062 dihydrodipicolinate synthase from Candidatus Pelagibacter ubique HTCC1062
46% identity, 100% coverage
dapA / Q04796 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Bacillus subtilis (strain 168) (see paper)
BSU16770 dihydrodipicolinate synthase from Bacillus subtilis subsp. subtilis str. 168
46% identity, 96% coverage
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...S. pneumoniae S. aureus D-Alanine-D-alanine BSU16760 BSU16750 BSU16770 BSU22490 BSU14180 No Yes Yes Yes Yes 2.7.2.4 1.2.1.11 4.2.1.52 1.3.1.26 2.3.1.89 1SFT...”
O67216 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Aquifex aeolicus (see paper)
46% identity, 99% coverage
DAPA_THEMA / Q9X1K9 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see 2 papers)
TM1521 dihydrodipicolinate synthase from Thermotoga maritima MSB8
43% identity, 99% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer; dimer of dimers. - Dihydrodipicolinate synthase from Thermotoga maritima
Pearce, The Biochemical journal 2006 - “...pairs encoding the predicted 5 - and 3 -ends of the TM1521 open reading frame [45] were used to amplify the dapA gene T. maritima strain MSB8 genomic DNA. The...”
DAPA_RHIML / Q07607 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 from Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti) (see 2 papers)
Q07607 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Sinorhizobium meliloti (see 2 papers)
45% identity, 100% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer.
1o5kA / Q9X1K9 Crystal structure of dihydrodipicolinate synthase (tm1521) from thermotoga maritima at 1.80 a resolution
43% identity, 99% coverage
- Ligand: calcium ion (1o5kA)
MM1201 Dihydrodipicolinate synthase from Methanosarcina mazei Goe1
45% identity, 100% coverage
CLJU_c04300 4-hydroxy-tetrahydrodipicolinate synthase from Clostridium ljungdahlii DSM 13528
44% identity, 100% coverage
- Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis
Philips, PloS one 2017 - “...as a gene encoding for nucleoside-5'-diphosphate-sugar dehydratase (CLJU_c37840) and a dihydrodipicolinate synthase ( dapA1 , CLJU_c04300) (Table R in S2 File ), remains unknown. Moreover, it should be noted that 86 of the upregulated genes and 107 of the downregulated genes are annotated as hypothetical proteins...”
- “...by autolysin [ 48 , 72 ], but the autolysin gene of C . ljungdahlii (CLJU_c04300) was not differentially expressed in the biofilm versus the planktonic condition (results not shown). The extracellular proteins involved in the C . ljungdahlii biofilm matrix could be the observed pilus-like...”
CSUI_001859 dihydrodipicolinate synthase from Cystoisospora suis
48% identity, 92% coverage
dapA / Q65JG7 dihydrodipicolinate synthase subunit (EC 4.3.3.7) from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46) (see paper)
44% identity, 95% coverage
X276_18055 4-hydroxy-tetrahydrodipicolinate synthase from Clostridium beijerinckii NRRL B-598
44% identity, 98% coverage
- Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Patakova, Scientific reports 2019 - “...(X276_18050), followed by condensation of semialdehyde aspartate with pyruvate catalysed by 4-hydroxy-tetrahydropicolinate synthase, dapA genes (X276_18055, X276_01925), resulting in the formation of 4-hydroxy-tetradipicolinate (HTPA). This may be spontaneously or enzymatically (by 4-hydroxy-tetrahydrodipicolinate reductase, dapB , gene X276_18060) dehydrated to dihydrodipicolinate (DHDPA). We identified two dapA genes,...”
Clocel_3115 4-hydroxy-tetrahydrodipicolinate synthase from Clostridium cellulovorans 743B
44% identity, 99% coverage
- Clostridium cellulovorans Proteomic Responses to Butanol Stress
Costa, Frontiers in microbiology 2021 - “...of a number of amino acids including proline and arginine (Clocel_2734, Clocel_3150, Clocel_1668), lysine (Clocel_1978, Clocel_3115), methionine (Clocel_1764, Clocel_2896, Clocel_3040), and branched chain amino acids (BCAA) (Clocel_1324, Clocel_1325, Clocel_0493) ( Table 1 and Supplementary Table 2 ). In addition, up-regulated proteins include four aminotransferases (Clocel_1948, Clocel_2059,...”
DAPA_AGRFC / Q8UGL3 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58)) (see paper)
Q8UGL3 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Agrobacterium tumefaciens (see 2 papers)
Atu1024 dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58 (Cereon)
45% identity, 99% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer; dimer of dimers. - Characterization of the mmsAB-araD1 (gguABC) genes of Agrobacterium tumefaciens
Zhao, Journal of bacteriology 2011 - “...araD (L-2-keto-3-deoxyarabonate dehydratase; 309) Atu5457 Atu1024 302 294 7e-20 4e-11 31/286 27/137 Dihydrodipicolinate synthase Dihydrodipicolinate synthase...”
4i7wA Agrobacterium tumefaciens dhdps with lysine and pyruvate
44% identity, 99% coverage
RHE_RS07055 4-hydroxy-tetrahydrodipicolinate synthase from Rhizobium etli CFN 42
45% identity, 99% coverage
X276_01925 4-hydroxy-tetrahydrodipicolinate synthase from Clostridium beijerinckii NRRL B-598
43% identity, 100% coverage
DAPA_METJA / Q57695 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
WP_010869742 4-hydroxy-tetrahydrodipicolinate synthase from Methanocaldococcus jannaschii DSM 2661
45% identity, 100% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer; dimer of dimers. - Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii.
Padmanabhan, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: The structure revealed that MjDHDPS forms a functional homotetramer, as observed in E. coli DHDPS, Thermotoga maritima DHDPS and Bacillus anthracis DHDPS. The binding-site region of MjDHDPS is similar to those found in other known DHDPS structures.
LIC10842 dihydrodipicolinate synthase protein from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
43% identity, 94% coverage
LIMLP_13480 4-hydroxy-tetrahydrodipicolinate synthase from Leptospira interrogans serovar Manilae
43% identity, 99% coverage
- Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence
Davignon, NPJ biofilms and microbiomes 2024 - “...Lysine metabolism, on the other hand, was predominantly upregulated, with dapB (LIMLP_13475, FC 1.5), dapA (LIMLP_13480, FC 1.5), and dapF (LIMLP_00400, FC 2.1) all showing increased expression. In contrast, the L -lysine 2,3-aminomutase encoding gene ablA (LIMLP_19035), involved in lysine degradation, was downregulated (FC 1.6), suggesting...”
N007_06870 4-hydroxy-tetrahydrodipicolinate synthase from Alicyclobacillus acidoterrestris ATCC 49025
42% identity, 99% coverage
Q8RBI5 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Caldanaerobacter subterraneus subsp. tengcongensis (see paper)
42% identity, 98% coverage
dapA2 dihydrodipicolinate synthase; EC 4.2.1.52 from Bacillus anthracis (see paper)
BA3935 dihydrodipicolinate synthase from Bacillus anthracis str. Ames
42% identity, 96% coverage
CD3223 dihydrodipicolinate synthase from Clostridium difficile 630
41% identity, 99% coverage
- Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation
Ternan, PloS one 2014 - “...(14 of 24 proteins) changed under heat stress. The increased abundance of dihydrodipicolinate synthase 2 (CD3223), involved in both lysine biosynthesis and in production of dipicolinate in spores recognised as one of the organism's main virulence factors suggests that cells under heat stress are more reliant...”
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...by CcpA. lysC (CD2054), aspartokinase; asd (CD3224), aspartate-semialdehyde dehydrogenase; dapA1 (CD3000), dihydrodipicolinate synthase 1; dapA2 (CD3223), dihydrodipicolinate synthase 2; dapA3 (CD3225), dihydrodipicolinate synthase 3; dapB1 (CD3226), dihydrodipicolinate reductase; dapH (CD3227), 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate; lysA (CD2053), diaminopimelate decarboxylase; thrC (CD2118), threonine synthase, thrB (CD2119), homoserine kinase; tdcB (CD2514), threonine...”
CPF_2161 dihydrodipicolinate synthase from Clostridium perfringens ATCC 13124
40% identity, 100% coverage
CPE1905 dihydrodipicolinate synthase from Clostridium perfringens str. 13
40% identity, 100% coverage
MMP0576 Dihydrodipicolinate synthase from Methanococcus maripaludis S2
44% identity, 99% coverage
Q6G468 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Bartonella henselae (see paper)
41% identity, 99% coverage
Q3M723 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) from Trichormus variabilis (see paper)
41% identity, 99% coverage
CD3225 dihydrodipicolinate synthase from Clostridium difficile 630
41% identity, 99% coverage
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...asd (CD3224), aspartate-semialdehyde dehydrogenase; dapA1 (CD3000), dihydrodipicolinate synthase 1; dapA2 (CD3223), dihydrodipicolinate synthase 2; dapA3 (CD3225), dihydrodipicolinate synthase 3; dapB1 (CD3226), dihydrodipicolinate reductase; dapH (CD3227), 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate; lysA (CD2053), diaminopimelate decarboxylase; thrC (CD2118), threonine synthase, thrB (CD2119), homoserine kinase; tdcB (CD2514), threonine dehydratase II; serA (CD0995), putative...”
5ktlA / Q3M723 Dihydrodipicolinate synthase from the industrial and evolutionarily important cyanobacteria anabaena variabilis. (see paper)
41% identity, 99% coverage
- Ligand: manganese (ii) ion (5ktlA)
7lvlA / A0A0F4VK59 Dihydrodipicolinate synthase bound with allosteric inhibitor (s)- lysine from candidatus liberibacter solanacearum
42% identity, 98% coverage
EfmE1162_2260 4-hydroxy-tetrahydrodipicolinate synthase from Enterococcus faecium E1162
41% identity, 98% coverage
- Genome-wide identification of ampicillin resistance determinants in Enterococcus faecium
Zhang, PLoS genetics 2012 - “...group 2 family protein 10.6 4.810 5 EfmE1162_0256 ZP_06676101 metallo-beta-lactamase superfamily protein 10.0 4.810 4 EfmE1162_2260 ZP_06678020 dihydrodipicolinate synthase 7.3 3.010 4 EfmE1162_2058 ZP_06677818 hydrolase, alpha/beta hydrolase fold family 7.1 1.710 4 EfmE1162_0669 ZP_06676514 nitroreductase family protein 6.8 2.810 4 EfmE1162_1943 ZP_06677703 chromosomal replication initiator protein...”
Q836D1 4-hydroxy-tetrahydrodipicolinate synthase from Enterococcus faecalis (strain ATCC 700802 / V583)
EF1184 dihydrodipicolinate synthase from Enterococcus faecalis V583
41% identity, 97% coverage
VspiD_010100011370 dihydrodipicolinate synthase from Verrucomicrobium spinosum DSM 4136
44% identity, 99% coverage
- 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 - “...2.7.2.4 ATP+aspartateADP+4-phospho-aspartate VspiD_010100030480 asd Aspartate semialdehyde dehydrogenase 1.2.1.11 aspartate 4-semialdehyde+orthophosphate+NADP + 4-phospho- L -aspartate+NADPH+H + VspiD_010100011370 dapA Dihydrodipicolinate synthase 4.2.1.52 Aspartate 4-semialdehyde+pyruvate L -2,3-dihydrodipicolinate+2H 2 O VspiD_010100011365 dapB Dihydrodipicolinate reductase 1.3.1.26 2,3,4,5-Tetrahydrodipicolinate+NADP+ L -2,3-dihydrodipicolinate+NADPH+H + - dapD 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate Nacyl-transferase 2.3.1.117 Acyl-CoA+2,3,4,5-tetrahydrodipicolinate+H 2 OCoA+ N -acyl-2- L...”
PHYSODRAFT_349787 hypothetical protein from Phytophthora sojae
39% identity, 100% coverage
- Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
Pang, Scientific reports 2016 - “...262095673 hypothetical protein PITG_19772 Nucleobase-containing compound metabolism 348684155 hypothetical protein PHYSODRAFT_478148 Others 348684075 hypothetical protein PHYSODRAFT_349787 Others 348683892 hypothetical protein PHYSODRAFT_353864 Others 348683825 putative dehydratase Others 348681277 hypothetical protein PHYSODRAFT_557322 Others 348673004 hypothetical protein PHYSODRAFT_354913 Others 348673003 hypothetical protein PHYSODRAFT_354912 Others 262105863 aldo/keto reductase family Others...”
Cj0806 dihydrodipicolinate synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
38% identity, 96% coverage
- The acid adaptive tolerance response in Campylobacter jejuni induces a global response, as suggested by proteomics and microarrays
Varsaki, Microbial biotechnology 2015 - “...pyridine nucleotide-disulfide oxidoreductase cj0559 null Pyrimidine metabolism Only detected after ATR Not-expressed 8 Dihydrodipicolinate synthase cj0806 dapA Amino acid biosynthesis Only detected after ATR Not-expressed 9 Putative methyltransferase cj1419c null Miscellaneous Only detected after ATR Not-expressed 10 Alkylhydroperoxide reductase cj0334 ahpC Oxidative stress resistance Upregulated Upregulated...”
- “...Pyrimidine metabolism Only detected after ATR R=1.75, P =0.01 (Upregulated) R=1.980.23, P =0.01 (Upregulated) 8 cj0806 dapA Amino acid biosynthesis Only detected after ATR R=2.01, P =0.02 (Upregulated) R=1.920.18, P =0.01 (Upregulated) 10 cj0334 ahpC Oxidative stress resistance Upregulated R=1.59, P =0.004 (Upregulated) R=2.150.47, P =0.05...”
- Progressive genome-wide introgression in agricultural Campylobacter coli
Sheppard, Molecular ecology 2013 - “...to form DHP. Cj0480 may catalyse a related lyase reaction, as there is another gene Cj0806 that could be the real dapA ; it may be involved as a lyase in a step of fucose catabolism? Cj0482/0483 ( uxaA ) Putative altronate or D-galactarate (sugar) hydrolase...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj0542, cj0559, cj0576, cj0580c, cj0585, cj0589, cj0638c, cj0647, cj0699c, cj0716, cj0764c, cj0766c, cj0767c, cj0795c, cj0798c, cj0806, cj0813, cj0821, cj0822, cj0847, cj0853c, cj0858c, cj0862c, cj0891c, cj0905c, cj0918c, cj0932c, cj0947c, cj0949c, cj0955c, cj0992c, cj0995c, cj1039, cj1044c, cj1046c, cj1048c, cj1067, cj1080c, cj1081c, cj1088c, cj1096c, cj1104, cj1114c, cj1133, cj1149c, cj1150c,...”
HVO_1101 dihydrodipicolinate synthase from Haloferax volcanii DS2
43% identity, 94% coverage
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...137 ] 15033471 2a HVO_2487 asd yes 51% MJ0205 Q57658 [ 138 ] 16225889 2a/9e HVO_1101 dapA yes 45% PA1010 Q9I4W3 [ 139 ] 21396954 2a HVO_1100 dapB yes 33% b0031 P04036 [ 140 ] 7893644 2a HVO_1099 dapD yes 32% b0166 P0A9D8 [ 141 ]...”
- “...Hbt. salinarum kdgA (OE_1665R). It is rather closely related (36% protein sequence) to Hfx. volcanii HVO_1101 (encoded by dapA ), which is involved in lysine biosynthesis, a biosynthetic pathway that is absent from Hbt. salinarum . The function assignment is based on distant homologs from Saccharolobus...”
DSY2498 hypothetical protein from Desulfitobacterium hafniense Y51
39% identity, 91% coverage
7kkdB / Q9PPB4 Dihydrodipicolinate synthase (dhdps) from c.Jejuni, n84a mutant with pyruvate bound in the active site and r,r-bislysine bound at the allosteric site
38% identity, 94% coverage
- Ligand: (2r,5r)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid (7kkdB)
slr0550 dihydrodipicolinate synthase from Synechocystis sp. PCC 6803
41% identity, 97% coverage
- Proteomic analysis of the regulatory networks of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803
Zhang, Frontiers in plant science 2022 - “...were significantly upregulated. The selected proteins in metabolic pathways were downregulated, except for dihydrodipicolinate synthase (slr0550). The remaining proteins, including ABC transporter-binding protein and cation efflux system protein involved in nickel and cobalt tolerance, were upregulated in the clpX strain, whereas the other proteins in ABC...”
- RNA helicase-regulated processing of the Synechocystis rimO-crhR operon results in differential cistron expression and accumulation of two sRNAs
Rosana, The Journal of biological chemistry 2020 (secret) - Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803
Bi, Frontiers in microbiology 2018 - “...Thus, the length of Nc117 was determined to be 102 nucleotides, which was located between slr0550 and a polycistron including slr0551, slr0552 , and slr0553 encoding three hypothetical proteins, as depicted in Figure 1B . Interestingly, the TATA box motif was also found right before the...”
- 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 - “...overexpression strain of Nc117 sRNA The WT/pJA2- nc117 + strain overexpressing nc117 , located between slr0550 and slr0551 , grew faster than the WT under 1.52.0% ( v/v ) ethanol and 0.200.25% ( v/v ) butanol conditions. No difference was observed when they both grew in...”
- “...-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 1.67 nc33 1,004,8851,005,121 <<< 40.2 sll1454 Nitrate reductase 108 sll1453 Nitrate transport protein NrtD 60 Nc33 1.607 0.815 nc85 2,383,7502,383,875...”
- Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803
Zhu, Biotechnology for biofuels 2013 - “...found increased abundances of aspartic acid and serine, which was consistent with the induction of slr0550 encoding dihydrodipicolinate synthase involved in aspartate pathway, and sll0455 encoding homoserine dehydrogenase involved in serine pathway, respectively (Table 5 ). In addition, increased abundance of glutamic acid inside the cells...”
O25657 4-hydroxy-tetrahydrodipicolinate synthase from Helicobacter pylori (strain ATCC 700392 / 26695)
HP1013 dihydrodipicolinate synthetase (dapA) from Helicobacter pylori 26695
40% identity, 88% coverage
4fhaA Structure of dihydrodipicolinate synthase from streptococcus pneumoniae,bound to pyruvate and lysine
39% identity, 92% coverage
SP_1014 dihydrodipicolinate synthase from Streptococcus pneumoniae TIGR4
40% identity, 86% coverage
- The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome
Nakamya, Pathogens (Basel, Switzerland) 2021 - “...SP_0323 SP_0323 2.6 <0.0001 PTS N-acetylgalactosamine PTS system EIIB SP_1277 pyrB 2.4 <0.0001 Aspartate carbamoyltransferase SP_1014 dapA 4.3 <0.0001 4-hydroxy-tetrahydrodipicolinate synthase SP_1013 asd 5.5 <0.0001 Aspartate-semialdehyde dehydrogenase FDR (False discovery rate). pathogens-10-01322-t004_Table 4 Table 4 Significant changes in metabolites in response to potABCD operon deletion. Locus...”
- Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae
Ayoola, Frontiers in microbiology 2019 - “...glnQ SP_0610 Amino acid ABC transporter, ATP-binding protein 1.7 Asd SP_1013 Aspartate-semialdehyde dehydrogenase 5.4 dapA SP_1014 4-hydroxy-tetrahydrodipicolinate synthase 4.8 lys9 SP_0919 Saccharopine dehydrogenase 26.4 SP_1994 SP_1994 Aminotransferase, class I 1.4 murI SP_1881 Glutamate racemase 1.7 Choline binding protein synthesis pspA SP_0117 Pneumococcal surface protein A 2.3...”
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...38655 SP_0918, SP_0919, SP_0920, SP_0921, SP_0922 5/5 Downregulated 38665 SP_0963, SP_0964 2/2 Downregulated 38674 SP_1013, SP_1014 2/2 Downregulated 38682 SP_1069, SP_1070, SP_1071 3/6 Downregulated 38684 SP_1079, SP_1080 2/2 Downregulated 38726 SP_1276, SP_1277, SP_1278 3/3 Downregulated 38731 SP_1294, SP_1295 2/3 Downregulated 38751 SP_1402, SP_1404, SP_1405 3/4 Downregulated...”
- Biofilm and planktonic pneumococci demonstrate disparate immunoreactivity to human convalescent sera
Sanchez, BMC microbiology 2011 - “...carbamoyltransferase, catabolic arcB (SP_2150) 4 2 Dihydrodipicolinate reductase dapB (SP_1555) 0 4 Dihydrodipicolinate synthase dapA (SP_1014) 0 3 Glucosamine-6-phosphate deaminase nagB (SP_1415) 0 2 Carbamoyl-phosphate synthase large chain carB (SP_1275) 5 5 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase dapH (SP_2097) 0 8 Aspartate--ammonia ligase asnA (SP_1970) 3 0 Dihydroxy-acid dehydratase...”
- Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
Hendriksen, Infection and immunity 2008 - “...spr0786 SP_0882 SP_0884 spr0788 SP_0885 SP_0955 SP_1013 SP_1014 SP_1119 SP_1126 spr1179 SP_1306 SP_1356 SP_1357 SP_1358 spr1302 SP_1651 SP_1659 SP_1688 spr1598...”
CG479_RS05485 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase from Bacillus cytotoxicus
37% identity, 93% coverage
- Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution
Stevens, Scientific reports 2019 - “...genomes of the B. cereus group. Locus in CH_13 a Gene in CH_13 Function b CG479_RS05485 CG479_RS05485 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase CG479_RS05500 hpaD 3,4-dihydroxyphenylacetate 2,3-dioxygenase CG479_RS05515 CG479_RS05515 cytidyltransferase CG479_RS05535 CG479_RS05535 4-hydroxyphenylacetate isomerase CG479_RS05530 CG479_RS05530 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase CG479_RS05525 CG479_RS05525 5-carboxymethyl-2-hydroxymuconate isomerase CG479_RS15270 CG479_RS15270 glycerophosphodiester phosphodiesterase G479_RS06185 G479_RS06185 LTA...”
spr0919 Dihydrodipicolinate synthase from Streptococcus pneumoniae R6
SPD_0901 dihydrodipicolinate synthase from Streptococcus pneumoniae D39
40% identity, 86% coverage
5ud6C / M1V4H9 Crystal structure of dhdps from cyanidioschyzon merolae with lysine bound
41% identity, 98% coverage
- Ligands: calcium ion; lysine (5ud6C)
Ssal_00884 4-hydroxy-tetrahydrodipicolinate synthase from Streptococcus salivarius 57.I
38% identity, 91% coverage
GPNADHDJ_01975 4-hydroxy-tetrahydrodipicolinate synthase from Stenotrophomonas maltophilia
42% identity, 92% coverage
CD16_RS00745 4-hydroxy-tetrahydrodipicolinate synthase from Candidatus Liberibacter asiaticus
39% identity, 93% coverage
- Integrated bacterial transcriptome and host metabolome analysis reveals insights into "Candidatus Liberibacter asiaticus" population dynamics in the fruit pith of three citrus cultivars with different tolerance
Li, Microbiology spectrum 2024 - “...and inorganic ion were also enriched in fruit pith of three cultivars, including 4-hydroxy-tetrahydrodipicolinate synthase (CD16_RS00745), phosphoserine transaminase (CD16_RS00135), UMP kinase (CD16_RS02145), guanylate kinase (CD16_RS05415), thymidylate synthase (CD16_RS04255), adenylosuccinate synthase (CD16_RS02965), type II toxin-antitoxin system RatA family toxin (CD16_RS02655), ferritin (CD16_RS02445), and superoxide dismutase (CD16_RS03555) (...”
Gasu_29240 dihydrodipicolinate synthase from Galdieria sulphuraria
38% identity, 81% coverage
- Bioinformatic Prediction and Characterization of Proteins in Porphyra dentata by Shotgun Proteomics
Yang, Frontiers in nutrition 2022 - “...5-methyltetrahydropteroyltriglutamatehomocysteine methyltransferase = Chondrus crispus CHC_T00009326001 2 4 79.4 6 Dihydrodipicolinate synthase = Galdieria sulphuraria Gasu_29240 12 46 34.2 7 4-hydroxyphenylpyruvate dioxygenase, 4HPPD = Chondrus crispus CHC_T00009321001 7 24 43.7 8 Alanine transaminase = Dumontia simplex CHC_T00009321001 21 74 54.8 9 Putative S-adenosylmethionine synthetase = Pyropia...”
TSC_c10420 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase from Thermus scotoductus SA-01
35% identity, 99% coverage
lp_2685 dihydrodipicolinate synthase from Lactobacillus plantarum WCFS1
F9URH0 4-hydroxy-tetrahydrodipicolinate synthase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
39% identity, 97% coverage
Marky_1261 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase from Marinithermus hydrothermalis DSM 14884
36% identity, 97% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...Meiothermus silvanus Mesil_1711 Mesil_2173 Mesil_2308 Mesil_0318 Oceanithermus profundus Ocepr_1316 Ocepr_1018 Ocepr_2076 Marinithermus hydrothermalis Marky_1492 Marky_1381 Marky_1261 Deinococcus radiodurans DR_1365 DR_2008 DR_1758 Deinococcus geothermalis Dgeo_1127 Dgeo_1782 Dgeo_0790 Deinococcus deserti Deide_11430 Deide_15740 Deide_1p00310, Deide_3p00120, Deide_3p01100 Deide_12830, Deide_21880 Deinococcus maricopensis Deima_1822 Deima_2680 Deima_2660 Deinococcus proteolyticus Deipr_0941 Deipr_0985 Deipr_1377* Deipr_1378*...”
Mrub_1335 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase from Meiothermus ruber DSM 1279
35% identity, 93% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...thermophilus HB8 TTHA0534 TTHA0545 TTHA0957 Thermus scotoductus TSC_c07050 TSC_c08140 TSC_c10420 TSC_c10870 Meiothermus ruber Mrub_0976 Mrub_1641 Mrub_1335 Mrub_0798 Meiothermus silvanus Mesil_1711 Mesil_2173 Mesil_2308 Mesil_0318 Oceanithermus profundus Ocepr_1316 Ocepr_1018 Ocepr_2076 Marinithermus hydrothermalis Marky_1492 Marky_1381 Marky_1261 Deinococcus radiodurans DR_1365 DR_2008 DR_1758 Deinococcus geothermalis Dgeo_1127 Dgeo_1782 Dgeo_0790 Deinococcus deserti Deide_11430...”
Riean_0023 4-hydroxy-tetrahydrodipicolinate synthase from Riemerella anatipestifer ATCC 11845 = DSM 15868
37% identity, 96% coverage
- Identification of the genes involved in Riemerella anatipestifer biofilm formation by random transposon mutagenesis
Hu, PloS one 2012 - “...of gene Biofilm reductionrate (%) Gene products Subcellular location a Function group (COGs) b BF19 Riean_0023 dihydrodipicolinate synthase/N-acetylneuraminate lyase 982 Cytoplasmic COG0329EM BF12 Riean_0186 aminopeptidase N 964 Outer Membrane c BF24 Riean_1039 cell division protein FtsQ 954 Cytoplasmic COG1589M BF34 Riean_0339 helix-turn-helix domain protein 945 Cytoplasmic...”
- “...was due to an inactivated gene, a biofilm-deficient mutant strain, BF19, in which dhdps gene (Riean_0023) was inactivated by the insertion of Tn4351, was used for the complementation experiment. A recombinant pCP29 plasmid that contained an expression cassette consisting of the R. anatipestifer ompA promoter and...”
Trad_1893 4-hydroxy-tetrahydrodipicolinate synthase from Truepera radiovictrix DSM 17093
36% identity, 96% coverage
A8GNF1 4-hydroxy-tetrahydrodipicolinate synthase from Rickettsia akari (strain Hartford)
34% identity, 96% coverage
TTHA0957 dihydrodipicolinate synthase from Thermus thermophilus HB8
34% identity, 98% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...-diaminopimelate aminotransferase Diaminopimelate decarboxylase Thermus thermophilus HB27 TTC0166 TTC0177 TTC0591 Thermus thermophilus HB8 TTHA0534 TTHA0545 TTHA0957 Thermus scotoductus TSC_c07050 TSC_c08140 TSC_c10420 TSC_c10870 Meiothermus ruber Mrub_0976 Mrub_1641 Mrub_1335 Mrub_0798 Meiothermus silvanus Mesil_1711 Mesil_2173 Mesil_2308 Mesil_0318 Oceanithermus profundus Ocepr_1316 Ocepr_1018 Ocepr_2076 Marinithermus hydrothermalis Marky_1492 Marky_1381 Marky_1261 Deinococcus radiodurans...”
TTC0591 No description from Thermus thermophilus HB27
34% identity, 98% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...dehydrogenase Dihydrodipicolinate synthase Dihydrodipicolinate reductase ll -diaminopimelate aminotransferase Diaminopimelate decarboxylase Thermus thermophilus HB27 TTC0166 TTC0177 TTC0591 Thermus thermophilus HB8 TTHA0534 TTHA0545 TTHA0957 Thermus scotoductus TSC_c07050 TSC_c08140 TSC_c10420 TSC_c10870 Meiothermus ruber Mrub_0976 Mrub_1641 Mrub_1335 Mrub_0798 Meiothermus silvanus Mesil_1711 Mesil_2173 Mesil_2308 Mesil_0318 Oceanithermus profundus Ocepr_1316 Ocepr_1018 Ocepr_2076 Marinithermus...”
MW1283 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus MW2
36% identity, 97% coverage
- New Antimicrobial Resistance Strategies: An Adaptive Resistance Network Conferring Reduced Glycopeptide Susceptibility in VISA
Aguglia, Antibiotics (Basel, Switzerland) 2023 - “...Peptidoglycan AA MW2286 Intermediate metabolic compound of lysine biosynthesis Malate:quinone oxidoreductase 1 Mqo1 MI-nsSNPs Val280Glu MW1283 L-lysine biosynthesis via the DAP pathway Dihydrodipicolinate synthase DapA MI-nsSNPs Ala101Thr Biosynthesis of lipotheicoic acid MW1125 LTA glycosylation YfhO membrane protein HI-nsSNPs Gly75 * Charge of the Cell Envelope MW1247...”
- Balancing the Virulence and Antimicrobial Resistance in VISA DAP-R CA-MRSA Superbug
Salemi, Antibiotics (Basel, Switzerland) 2022 - “...H Tyr130Hys MW0134 Capsular polysaccharide synthesis enzyme K Val120Glu MW2070 Cobalt-zinc-cadmium resistance protein czcD Asp52Glu MW1283 Dihydrodipicolinate synthase DapA Ala101Thr MW1247 Phosphatidylglycerol lysyl-transferase MprF Thr345Ala Leu538Phe MW2304 Proton/sodium-glutamate symport protein Val232Glu MW1324 Extracellular matrix-binding protein Ebh Val1768Asp MW2287 L-lactate permease LctP Ile178Phe MW1307 UDP-NAG--NAM-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine...”
- The SaeR/S gene regulatory system is essential for innate immune evasion by Staphylococcus aureus
Voyich, The Journal of infectious diseases 2009 - “...peroxidase 1.64 & 2.43 ME & ES MW1248 msrA methionine sulfoxide reductase A 2.25 ES MW1283 dapA dihydrodipicolinate synthase 2.37 ES MW1284 dapB dihydrodipicolinate reductase 2.28 ES MW1285 dapD tetrahydrodipicolinate acetyltransferase 2.15 ES MW1286 - hippurate hydrolase 2.24 ES MW1517 glyS glycyl-tRNA synthetase 2.08 ES MW1721...”
Q92I25 4-hydroxy-tetrahydrodipicolinate synthase from Rickettsia conorii (strain ATCC VR-613 / Malish 7)
33% identity, 96% coverage
DAPA_STAAR / Q6GH13 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Staphylococcus aureus (strain MRSA252) (see paper)
Q6GH13 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Staphylococcus aureus (see 2 papers)
SAR1407 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus MRSA252
36% identity, 97% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homodimer. In fact, exists in a monomer-dimer equilibrium in solution, shifted in favor of the dimer in presence of the substrate pyruvate; the monomer has significantly reduced activity compared with the dimer. - Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
Bernal, The Journal of biological chemistry 2010 - “...Dihydropicolinate synthase 2.66 Amino acid biosynthesis SAR1339 SA1165 thrC Threonine synthase 3.06 Amino acid biosynthesis SAR1407 SA1227 dapA Homoserine dehydrogenase 3.76 Amino acid biosynthesis SAR1024 SA0903 Conserved hypothetical protein 2.33 3.6 Up Carbohydrate transport and metabolism SAR2522 SA2220 Glycerate kinase 2.88 Up 14.8 Carbohydrate transport and...”
DAPA_STAAC / Q5HG25 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Staphylococcus aureus (strain COL) (see paper)
Q5HG25 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Staphylococcus aureus (see paper)
USA300HOU_RS07105 4-hydroxy-tetrahydrodipicolinate synthase from Staphylococcus aureus subsp. aureus USA300_TCH1516
SAOUHSC_01396 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1288 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1306 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus str. Newman
SACOL1430 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus COL
36% identity, 96% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homodimer. - Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
Xu, Frontiers in microbiology 2016 - “...ABC protein USA300HOU_RS01935 rpsF 1.56 2.29E-02 Ribosomal protein S6 USA300HOU_RS04620 dltA 1.55 2.45E-02 Long-chain-fatty-acidCoA ligase USA300HOU_RS07105 dapA 1.52 4.99E-02 dihydrodipicolinate synthase USA300HOU_RS04635 dltD 1.51 3.00E-02 D-alanine transfer protein DltD USA300HOU_RS07190 1.51 4.86E-02 Nitric-oxide reductase USA300HOU_RS12610 hutI 1.50 2.99E-02 Imidazolonepropionase USA300HOU_RS02380 gltD 1.50 4.97E-02 Glutamate synthase (NADPH)...”
- The roles of cell wall inhibition responsive protein CwrA in the pathogenicity of <i>Staphylococcus aureus</i>
Han, Virulence 2024 - “...carbamoyl-transferase; ArcB2 2.0 SAOUHSC_02561 ureC Urease subunit alpha; UreC 1.3 Lysine biosynthesisand 2-Oxocarboxylic acid metabolism SAOUHSC_01396 SAOUHSC_01396 4-hydroxy-tetrahydrodipicolinate synthase 2.8 SAOUHSC_02468 SAOUHSC_02468 Acetolactate synthase 2.5 SAOUHSC_01394 SAOUHSC_01394 Aspartate kinase 1.6 SAOUHSC_01319 SAOUHSC_01319 Aspartate kinase 1.4 Notably, the RNA-Seq profiles showed that the saeRS regulatory system was...”
- Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus
Fernández, Scientific reports 2017 - “...SAOUHSC_01276 glpK Glycerol kinase 2.56 SAOUHSC_01320 hom Homoserine dehydrogenase 3.25 SAOUHSC_01395 asd Aspartate-semialdehyde dehydrogenase 4.35 SAOUHSC_01396 dapA 4-hydroxy-tetrahydrodipicolinate synthase 4.40 SAOUHSC_01397 dapB 4-hydroxy-tetrahydrodipicolinate reductase 2.81 SAOUHSC_01466 recU Holliday junction resolvase RecU 3.02 SAOUHSC_01504 Ferredoxin, putative 3.37 SAOUHSC_01585 srrB Sensor protein SrrB 3.29 SAOUHSC_01586 srrA Transcriptional regulatory...”
- Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
Xiao, Antibiotics (Basel, Switzerland) 2022 - “...SAUSA300_0630 hypothetical ABC transporter ATP-binding protein 15.07 10.45 SAUSA300_1577 hypothetical TPR domain-containing protein 14.93 1.75 SAUSA300_1288 dapA dihydrodipicolinate synthase 14.75 7.53 SAUSA300_1937 hypothetical phi77 ORF045-like protein 14.69 8.83 SAUSA300_1419 hypothetical phiSLT ORF80-like protein 14.65 9.06 SAUSA300_2345 nirD nitrite reductase (NAD(P)H), small subunit 14.54 4.64 SAUSA300_1365 rpsA...”
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...carriers SAUSA300_0067 0.41 Unknown function SAUSA300_1634 CoaE 0.40 Biosynthesis of cofactors, prosthetic groups, and carriers SAUSA300_1288 DapA 0.40 Amino acid biosynthesis SAUSA300_1478 0.37 Cell envelope SAUSA300_1285 0.35 Transport and binding proteins SAUSA300_0971 PurL 0.35 Purines, pyrimidines, nucleosides, and nucleotides SAUSA300_0368 RpsR 0.33 Protein synthesis SAUSA300_1357 AroC...”
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...NWMN_1282 NWMN_1283 NWMN_1284 NWMN_1304 NWMN_1305 NWMN_1306 NWMN_1307 NWMN_1308 NWMN_1311 NWMN_1348 NWMN_1616 NWMN_1617 NWMN_1749 NWMN_1750 NWMN_1960 NWMN_1961...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...6.1 (1.4) SACOL1428 lysC Aspartate kinase 10.9 (1.7) SACOL1429 asd Aspartate semialdehyde dehydrogenase 14.2 (1.4) SACOL1430 dapA Dihydrodipicolinate synthase 13.5 (1.2) SACOL1431 dapB Dihydrodipicolinate reductase 14.4 (1.2) SACOL1432 dapD 2,3,4,5-tetrahydropyridine-2,6-dicarboxylateN-succinyltransferase 13.0 (1.1) ig_SACOL1432-3 Intergenic region between dapD andSACOL1433 26.4 (1.8) SACOL1433 M20/M25/M40 family peptidase 9.2 (1.3)...”
3di1B / Q5HG25 Crystal structure of the staphylococcus aureus dihydrodipicolinate synthase-pyruvate complex (see paper)
36% identity, 97% coverage
- Ligand: pyruvic acid (3di1B)
SA1227 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus N315
SAV1395 dihydrodipicolinate synthase from Staphylococcus aureus subsp. aureus Mu50
35% identity, 97% coverage
- Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
Bernal, The Journal of biological chemistry 2010 - “...synthase 2.66 Amino acid biosynthesis SAR1339 SA1165 thrC Threonine synthase 3.06 Amino acid biosynthesis SAR1407 SA1227 dapA Homoserine dehydrogenase 3.76 Amino acid biosynthesis SAR1024 SA0903 Conserved hypothetical protein 2.33 3.6 Up Carbohydrate transport and metabolism SAR2522 SA2220 Glycerate kinase 2.88 Up 14.8 Carbohydrate transport and metabolism...”
- 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 - “...sa_c9153s8021_a_at 3.5 2.5 30 cbf1 SA1898 3-5 exoribonuclease YhaM, sa_c1203s985_a_at * 4.7 2.5 2.5 def2 SA1227 polypeptide deformylase sa_c1207s989_a_at * 4.7 2.5 2.5 fmt SA1228 methionyl-tRNA formyltransferase sa_c1362s1136_a_at * 4.7 2.5 30 frr SA1278 ribosome recycling factor sa_c8835s7770_a_at * 2.5 15 stable fusA SA0593 elongation factor...”
- “...protein sa_c10576s9058_a_at 3.0 2.5 2.5 def SA1100 peptide deformylase sa_c1203s985_a_at * 6.0 2.5 2.5 def2 SA1227 polypeptide deformylase sa_c1207s989_a_at * 5.7 2.5 2.5 fmt SA1228 methionyl-tRNA formyltransferase sa_c1362s1136_a_at * 2.8 2.5 5 frr SA1278 ribosome recycling factor sa_c8835s7770_a_at * 2.9 15 15 fusA SA0593 elongation factor...”
- Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus
O'Neill, Antimicrobial agents and chemotherapy 2009 - “...SA0958 SA1019 SA1163 SA1164 SA1165 SA1166 SA1170 SA1226 SA1227 SA1228 SA1229 SA1230 SA1231 SA1235 SA1236 SA1238 SA1254 SA1255 SA1256 SA1257 SA1532 SA1545 SA1546...”
- Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance
Pietiäinen, BMC genomics 2009 - “...Catalase SA1216 3.8 2.4 Similar to oligoendopeptidase SA1219 5.4 4.2 Similar to phosphate ABC transporter SA1227 dapA 8.3 9.6 VCM Dihydrodipicolinate synthase SA1254 3.1 3.5 VraSR, VCM Hypothetical protein SA1476 4.2 5.3 3.3 VraSR, VCM Hypothetical protein SA1517 citC 4.9 5.8 3.1 VCM Isocitrate dehydrogenase SA1545...”
- Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
Jang, BMC genomics 2008 - “...in the class of "amino acid transport and metabolism", SA1225 ( lys C)-SA1226 ( asd )-SA1227 ( dap A)-SA1228 ( dap B)-SA1229 ( dap D), and SA1814 ( dap E) fall within a predicted operon and are all involved in diaminopimelate (DAP) biosynthesis (table 1 )....”
- “...pathway will probably not result in mammalian toxicity. Decisively SA1225 ( lys C)-SA1226 ( asd )-SA1227 ( dap A)-SA1228 ( dap B) and SA1229 ( dap D) show fold highest decreases as -54.6, -21.5, -27.3, -31.4, and -23.5 folds at 20 min and -7.7, -4.3, -5.2,...”
- Characterization of the oxygen-responsive NreABC regulon of Staphylococcus aureus
Schlag, Journal of bacteriology 2008 - “...of California, Berkeley Downregulated genes SA0691 SA1225 SA1226 SA1227 SA1228 SA1229 SA1759 SA2176 SA2183 SA2184 SA2185 SA2186 SA2187 SA2188 SA2189 SA2384 Gene...”
- Further insights into the mode of action of the lipoglycopeptide telavancin through global gene expression studies
Song, Antimicrobial agents and chemotherapy 2012 - “...Berkeley Locus ID Amino acid biosynthesis SAV1328 SAV1395 SAV1396 SAV1397 SAV1394 SACOL1364 SAV1329 Song et al. 3162 aac.asm.org bacitracin (48), and...”
BLJ_0490 4-hydroxy-tetrahydrodipicolinate synthase from Bifidobacterium longum subsp. longum JDM301
35% identity, 95% coverage
CPZ21_05260 4-hydroxy-tetrahydrodipicolinate synthase from Staphylococcus epidermidis
35% identity, 98% coverage
- Antibacterial Activity and Membrane-Targeting Mechanism of Aloe-Emodin Against Staphylococcus epidermidis
Li, Frontiers in microbiology 2021 - “...EC: 1. 1. 1. 3), 4-hydroxy-tetrahydrodipicolinate synthase (CPZ21_05255, EC: 4. 3. 3. 7), 4-hydroxy-tetrahydrodipicolinate reductase (CPZ21_05260, EC: 1. 17. 1. 8), tetrahydrodipicolinate N -acetyltransferase (dapD, EC: 2. 3. 1. 89), succinyl-diaminopimelate desuccinylase (CPZ21_10715, EC: 3. 5. 1. 18), and UDP- N -acetylmuramoyl-tripeptide D -alanyl- D -alanine...”
SERP_RS04835 4-hydroxy-tetrahydrodipicolinate synthase from Staphylococcus epidermidis RP62A
35% identity, 98% coverage
BL1193 dihydrodipicolinate synthase from Bifidobacterium longum NCC2705
BBMN68_956, PIB40_02760 4-hydroxy-tetrahydrodipicolinate synthase from Bifidobacterium longum subsp. longum BBMN68
35% identity, 95% coverage
- Bacillus licheniformis: A Producer of Antimicrobial Substances, including Antimycobacterials, Which Are Feasible for Medical Applications
Shleeva, Pharmaceutics 2023 - “...surfactin-like nature [ 122 , 166 ]. B. licheniformis F2.2 produced a non-lipopeptide type biosurfactant BL1193 together with lipopeptides, plipastatin, and surfactin in an amino acid-depleting medium. Plipastatin inhibited the growth of Gram-positive bacteria ( B. subtilis ), Gram-negative bacteria ( Pseudomonas aeruginosa and Escherichia coli...”
- “...sp.). Plipastatin and surfactin were abundantly produced in nutrient-rich medium. In addition, a non-lipopeptide-type biosurfactant BL1193 was produced upon the growth of the producer in a synthetic medium but not in a rich medium [ 103 ]. Lichenysins A surface-active substance known as lichenysin is produced...”
- Bifidobacterium longum LBUX23 Isolated from Feces of a Newborn; Potential Probiotic Properties and Genomic Characterization
Reyes-Castillo, Microorganisms 2023 - “...longum LBUX23 showed the presence of argC (NCBI Locus tag: PIB40_02085), argH (PIB40_02045), and dapA (PIB40_02760) genes, which have been reported as responsible for the ability to tolerate acid environments in other species of B. longum [ 26 ]. 3.3.7. Antioxidant Activity B. longum LBUX23 showed...”
- “...surviving < 10%, probably due to the presence of argC (PIB40_02085), argH (PIB40_02045), and dapA (PIB40_02760) genes. These genes have been previously reported by Sundararaman et al. 2021 [ 26 ] as those that confer to B. longum NCIM 5672 a survival advantage in an acid...”
- Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
Jin, PloS one 2012 - “...BBMN68_725 77.61 174.46 2.25 * M COG1207 glmU K04042, bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase [EC:2.7.7.23 2.3.1.157] BBMN68_956 127.77 346.11 2.71 * EM COG0329 dapA K01714, dihydrodipicolinate synthase [EC:4.2.1.52] BBMN68_615 17.64 35.36 2.00 * E COG0624 pePV K01439, succinyl-diaminopimelate desuccinylase [EC:3.5.1.18] BBMN68_1087 94.27 330.69 3.51 * I COG1211...”
- “...2 and Figure 5 , first, the genes ( BBMN68_1432 , BBMN68_949 , BBMN68_725 , BBMN68_956 and BBMN68_615 ) involved in the synthesis of the two main precursors of peptidoglycan, UDP-acetyl-glucosamine and meso-2, 6-diaminopimelate, were upregulated by more than 2 fold. Second, poly-undecaprenyl-PP (UND-PP), which is...”
Q42948 4-hydroxy-tetrahydrodipicolinate synthase, chloroplastic from Nicotiana tabacum
35% identity, 79% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (Al1; UNIPROT ID: D7LRV3), Nicotiana tabacum DHDPS (Nt; UNIPROT ID: Q42948), Oryza sativa DHDPS1 (Os1; UNIPROT ID: A0A0K0K9A6), Solanum lycopersicum DHDPS1 (Sl1; UNIPROT ID: A0A3Q7IMG0), Triticum aestivum DHDPS1 (Ta1; UNIPROT ID: P24846), Vitis vinifera DHDPS1 (Vv1; UNIPROT ID: A0A438E022), Zea mays...”
- “...lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2 (UNIPROT ID: Q9LWB9), Solanum lycopersicum DHDPS1 (UNIPROT ID: A0A3Q7IMG0) and DHDPS2 (UNIPROT ID: A0A3Q7FJL9), Triticum aestivum DHDPS1 (UNIPROT ID: P24846) and DHDPS2...”
B8DWI2 4-hydroxy-tetrahydrodipicolinate synthase from Bifidobacterium animalis subsp. lactis (strain AD011)
33% identity, 96% coverage
- A RESTful API for accessing microbial community data for MG-RAST
Wilke, PLoS computational biology 2015 - “...line call: mg-retrieve-uniprot.py md5 ffc62262a18b38671c3e337150ef535f source SwissProt Example output: ID DAPA_BIFA0 Reviewed; 303 AA. AC B8DWI2; DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot. DT 03-MAR-2009, sequence version 1. DT 16-OCT-2013, entry version 34. DE RecName: Full=4-hydroxy-tetrahydrodipicolinate synthase; DE Short=HTPA synthase; DE EC=4.3.3.7; GN Name=dapA; OrderedLocusNames=BLA_0534; OS Bifidobacterium animalis...”
D7LRV3 4-hydroxy-tetrahydrodipicolinate synthase from Arabidopsis lyrata subsp. lyrata
37% identity, 76% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...(At1; UNIPROT ID: Q9LZX6), AtDHDPS2 (At2; UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (Al1; UNIPROT ID: D7LRV3), Nicotiana tabacum DHDPS (Nt; UNIPROT ID: Q42948), Oryza sativa DHDPS1 (Os1; UNIPROT ID: A0A0K0K9A6), Solanum lycopersicum DHDPS1 (Sl1; UNIPROT ID: A0A3Q7IMG0), Triticum aestivum DHDPS1 (Ta1; UNIPROT ID: P24846), Vitis vinifera...”
- “...thaliana DHDPS1 (UNIPROT ID: Q9LZX6) and DHDPS2 (UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2 (UNIPROT ID: Q9LWB9), Solanum lycopersicum DHDPS1 (UNIPROT ID: A0A3Q7IMG0) and DHDPS2...”
IHV18_10020 4-hydroxy-tetrahydrodipicolinate synthase from Bifidobacterium breve
34% identity, 95% coverage
- Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants
Di, Microorganisms 2023 - “...UvrD-helicase domain-containing protein IHV18_10010 57,502 58,822 1 MFS transporter IHV18_10015 58,909 59,665 1 4-hydroxy-tetrahydrodipicolinate reductase IHV18_10020 dapA 59,770 60,676 1 4-hydroxy-tetrahydrodipicolinate synthase IHV18_10025 60,755 62,612 1 ribonuclease J IHV18_10030 pepN 62,653 >63,564 1 aminopeptidase N microorganisms-11-01649-t005_Table 5 Table 5 IS-FINDER results for the genetic region located...”
Q9LZX6 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic from Arabidopsis thaliana
NP_850730 dihydrodipicolinate synthase 1 from Arabidopsis thaliana
36% identity, 78% coverage
- Engineering a feedback inhibition-insensitive plant dihydrodipicolinate synthase to increase lysine content in Camelina sativa seeds
Huang, Transgenic research 2022 - “...plant and microbial DHDPS enzymes. Amino acid sequence alignment of DHDPSs from A. thaliana (AtDHDPS2, Q9LZX6, 365 aa), C. sativa CsDHDPS B4 (Csa16g004020, 364 aa) and CsDHDPS B6 (Csa05g092770, 365 aa), N. tabacum (NtDHDPS, NP_001313049, 359 aa), Z. mays (ZmDHDPS, NP_001105425.1, 380 aa), Vitis vinifera (VvDHDPS,...”
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...sequence alignment of residues involved in allosteric lysine binding. Sequences are AtDHDPS1 (At1; UNIPROT ID: Q9LZX6), AtDHDPS2 (At2; UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (Al1; UNIPROT ID: D7LRV3), Nicotiana tabacum DHDPS (Nt; UNIPROT ID: Q42948), Oryza sativa DHDPS1 (Os1; UNIPROT ID: A0A0K0K9A6), Solanum lycopersicum DHDPS1 (Sl1;...”
- “...Figure 2figure supplement 1. Sequence alignment of plant DHDPS enzymes. Arabidopsis thaliana DHDPS1 (UNIPROT ID: Q9LZX6) and DHDPS2 (UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2...”
- Function and Regulation of Chloroplast Peroxiredoxin IIE
Dreyer, Antioxidants (Basel, Switzerland) 2021 - “...Protein Name AT4G09000 P42643 14-3-3 AT5G10450 P48349 14-3-3 AT3G02520 Q96300 14-3-3 AT5G16050 P42645 14-3-3 AT3G60880 Q9LZX6 4-Hydroxy-tetrahydrodipicolinate synthase 1 AT1G02560 Q9S834 ATP-dependent Clp protease proteolytic subunit 5 AT5G03690 F4KGQ0 Fructose-bisphosphate aldolase 4 AT4G26530 O65581 Fructose-bisphosphate aldolase 5 AT5G49910 Q9LTX9 Heat shock 70 kDa protein 7 AT2G24200...”
- Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.
Hall, The FEBS journal 2021 (PubMed)- GeneRIF: Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.
AT3G60880 dihydrodipicolinate synthase 1 (DHDPS1) (DHDPS) (DHPS1) from Arabidopsis thaliana
36% identity, 78% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...al., 2000 ; Vauterin and Jacobs, 1994 ). In Arabidopsis thaliana , these genes are At3G60880 ( DHDPS1 ) and At2G45440 ( DHDPS2 ), which encode chloroplast-targeted AtDHDPS1 and AtDHDPS2, respectively ( Jones-Held et al., 2012 ). RNA sequencing data have elucidated that both DHDPS -...”
- “...resource Designation Source or reference Identifiers Additional information Gene ( Arabidopsis thaliana ) DHDPS1 TAIR At3G60880 Gene ( Arabidopsis thaliana ) DHDPS2 TAIR At2G45440 Cell line ( Homo sapiens ) HepG2 ATCC ATCC: HB-8065 RRID: CVCL_0027 Cell line ( Homo sapiens ) HEK293 ATCC ATCC:ACS-4500 RRID:...”
- Function and Regulation of Chloroplast Peroxiredoxin IIE
Dreyer, Antioxidants (Basel, Switzerland) 2021 - “...Accession Protein Name AT4G09000 P42643 14-3-3 AT5G10450 P48349 14-3-3 AT3G02520 Q96300 14-3-3 AT5G16050 P42645 14-3-3 AT3G60880 Q9LZX6 4-Hydroxy-tetrahydrodipicolinate synthase 1 AT1G02560 Q9S834 ATP-dependent Clp protease proteolytic subunit 5 AT5G03690 F4KGQ0 Fructose-bisphosphate aldolase 4 AT4G26530 O65581 Fructose-bisphosphate aldolase 5 AT5G49910 Q9LTX9 Heat shock 70 kDa protein 7...”
- Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
Liebthal, Antioxidants (Basel, Switzerland) 2020 - “...ribosomal protein S6 alpha (AT1G64510) MECDP synthase (AT1G63970) Acyl-ACP thioesterase ATL3 (AT1G68260) HTPA synthase 1 (AT3G60880) DAHP synthase 2 (AT4G33510) Elongation factor 1 alpha (AT4G20360) TRAF-like family protein (AT3G28220) HTPA reductase 1 (AT2G44040) Adenylosuccinate synthetase (AT3G57610) CDPME kinase (AT2G26930) Ferredoxin--NADP reductase (AT1G20020) 50S ribosomal protein L27...”
- Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana
Griffin, PloS one 2012 - “...stated, enzymes were manipulated at 4C or on ice. Cloning, Expression & Purification Plasmids encoding AT3G60880 ( At -DHDPS2) and AT3G59890 ( At -DHDPR2) were obtained from the Arabidopsis Information Resource (TAIR), Carnegie Institution of Washington, Stanford CA. Primer pairs encoding the predicted 5-3 ends of...”
- Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana
Jander, The arabidopsis book 2009 - “...NADPH NADP+ 2 H 2O dihydrodipicolinate synthase At3g60880 = DHDPS1 At2g45440 = DHDPS2 L-lysine L-2,3-dihydrodipicolinate H+, NAD(P)H NAD(P)+ dihydrodipicolinate...”
- “...of extensive research. Two A. thaliana genes, At3g60880 (DHDPS1) and At2g45440 (DHDPS2), encode dihydrodipicolinate synthases (Vauterin and Jacobs, 1994;...”
- Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters
Curien, Molecular systems biology 2009 - “...numbers AK1: At5g13280; AK2: At5g14060; AK3: At3g02020; AKIHSDH I:At1g31230; AKIIHSDH II: At4g19710; ASADH: At1g14810; DHDPS1: At3g60880; DHDPS2: At2g45440; HSK: At2g17265; CGS: At3g01120; TS1: At4g29840; TS2: At1g72810; TD: At3g10050. Supplementary Material Supplementary Materials Supplementary data, Supplementary figures S1-14, Supplementary tables S1-2 We thank Norbert Rolland for kindly...”
- Coordinations between gene modules control the operation of plant amino acid metabolic networks
Less, BMC systems biology 2009 - “...AT5G14060 258977_s_at AK1 AT5G13280 250291_at aspartate-semialdehyde dehydrogenase 2 ASD AT1G14810 262841_at dihydrodipicolinate synthase 3 DHDPS1 AT3G60880 251392_at DHDPS2 AT2G45440 245145_at dihydrodipicolinate reductase 4 DHDPR AT2G44040 267237_s_at DHDPR AT3G59890 267237_s_at DHDPR AT5G52100 248402_at L, L-diaminopimelate aminotransferase 5 AGD2 AT4G33680 253308_at diaminopimelate epimerase 6 DAPE AT3G53580 251948_at diaminopimelate...”
- GCN2-dependent phosphorylation of eukaryotic translation initiation factor-2alpha in Arabidopsis
Zhang, Journal of experimental botany 2008 - “...ACAATTTCTACTGCAAACGCCTTC AAAGCCAGAACCAGGGACAAC DHS2 At4g33510 GGTCACGCACCATCACTTACAA CTTGGGTCACAGTGAGTGTGGTAG HDH At5g63890 CAAAGACGCTGAGAAATGGGAG CTCGCATAATCCCCAACACTCT ALS At3g48560 ATGTTGGTGGTGGTTGTTTGAAT TCAACGTACTCGCAACAGGGA DHDPS1 At3g60880 TGTCGTTTGGAGTGGAAATGATG CATCAAACCCGGAACTAAATTGC PSP At1g18640 TCAAGAAGTGGAGGCAAAGCC ACGTGCTTCGAGATCAGTAGCAC AK/HSDH At1g31230 TCTGATTGTTCGTGGACCTGG GCAAGGCGAAGAATGTCACTG PAT1 At5g17990 CAATGCGGATGTGCTAAGACG CGGTTGCTAACCAGAAGAGCTG AtGCN2 At3g59410 CGCAAAGCACTCGATGAGTTG GATGTCCCAGAGCTATTTTCTTTGG NIA1 At1g37130 TGGTCAACCCACGTGAGAAA AACGTCGTGCGAGATCGAA NIA2 At1g77760 CGGTTAGGAACCTCGCTTTG TGGAAGTCTTTTCGACGAGTTG PP2A At1g13320 TAACGTGGCCAAAATGATGC GTTCTCCACAACCGCTTGGT...”
6vvhBBB / Q9LZX6 thaliana dihydrodipicolinate synthase isoform 1 (dhdps1) in complex with lysine (see paper)
36% identity, 91% coverage
dapA / CAA92211.1 dihydrodipicolinate synthase from Prochlorococcus marinus (see paper)
36% identity, 91% coverage
AWC34_RS13170 4-hydroxy-tetrahydrodipicolinate synthase from Staphylococcus equorum
32% identity, 96% coverage
Q9FVC8 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Arabidopsis thaliana (see paper)
NP_182068 dihydrodipicolinate synthase from Arabidopsis thaliana
AT2G45440 DHDPS2 (DIHYDRODIPICOLINATE SYNTHASE); catalytic/ dihydrodipicolinate synthase/ lyase from Arabidopsis thaliana
35% identity, 78% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...in allosteric lysine binding. Sequences are AtDHDPS1 (At1; UNIPROT ID: Q9LZX6), AtDHDPS2 (At2; UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (Al1; UNIPROT ID: D7LRV3), Nicotiana tabacum DHDPS (Nt; UNIPROT ID: Q42948), Oryza sativa DHDPS1 (Os1; UNIPROT ID: A0A0K0K9A6), Solanum lycopersicum DHDPS1 (Sl1; UNIPROT ID: A0A3Q7IMG0), Triticum aestivum...”
- “...alignment of plant DHDPS enzymes. Arabidopsis thaliana DHDPS1 (UNIPROT ID: Q9LZX6) and DHDPS2 (UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2 (UNIPROT ID: Q9LWB9), Solanum lycopersicum...”
- Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana.
Griffin, PloS one 2012 - GeneRIF: Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site.
- Crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase 2 from Arabidopsis thaliana.
Griffin, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - GeneRIF: the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS2 from Arabidopsis thaliana are reported.Diffraction-quality protein crystals belonged to space group P2(1)2(1)2
- Proteome Analysis of the ROF-FKBP Mutants Reveals Functional Relations among Heat Stress Responses, Plant Development, and Protein Quality Control during Heat Acclimation in Arabidopsis thaliana
Lefa, ACS omega 2024 - “...AT5G19100 HSP17.6B AT2G29500 AT3G20820 SDR1 AT3G61220 CRD AT1G03890 FDH1 AT5G14780 HSP17.6C AT1G53540 MAP1B AT1G13270 DHDPS1 AT2G45440 RGGB AT4G17520 KAS2 AT1G74960 HSP23.6 AT4G25200 CHLI1 AT4G18480 FLA9 AT1G03870 PORB AT4G27440 HSP26.5 AT1G52560 CHLD AT1G08520 psbH ATCG00710 5-METHYLT HIORIBOSE AT2G05830 HSP70-3 AT3G09440 XTH24 AT4G30270 HSP81-2 AT5G56030 PAT1 AT5G17990 HSP90-1...”
- Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions
Nose, PloS one 2023 - “...temp-90d -0.58 CUST_9575_PI429951308 reCj24221:MSWR:isotig24073 AT3G17390 0.0 MTO3 S-adenosylmethionine synthetase family prot temp-0h 0.56 CUST_8892_PI429951308 reCj23528:MSWR:isotig23380 AT2G45440 0.0 DHDPS2 dihydrodipicolinate synthase temp-0h 0.71 CUST_10056_PI429951308 reCj24708:----:isotig24560 AT3G12780 2.1E-50 PGK1 phosphoglycerate kinase 1 temp-60d 0.73 CUST_1587_PI429951308 reCj13430:----:isotig13285 AT4G24830 0.0 - arginosuccinate synthase family temp-0h 0.75 CUST_1081_PI429951308 reCj11634:MSWR:isotig11489 AT3G03780 0.0...”
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...Jacobs, 1994 ). In Arabidopsis thaliana , these genes are At3G60880 ( DHDPS1 ) and At2G45440 ( DHDPS2 ), which encode chloroplast-targeted AtDHDPS1 and AtDHDPS2, respectively ( Jones-Held et al., 2012 ). RNA sequencing data have elucidated that both DHDPS - encoding genes are expressed at...”
- “...Gene ( Arabidopsis thaliana ) DHDPS1 TAIR At3G60880 Gene ( Arabidopsis thaliana ) DHDPS2 TAIR At2G45440 Cell line ( Homo sapiens ) HepG2 ATCC ATCC: HB-8065 RRID: CVCL_0027 Cell line ( Homo sapiens ) HEK293 ATCC ATCC:ACS-4500 RRID: CVCL_0063 High-throughput chemical screen and analogue synthesis A...”
- Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis
Zhu, Frontiers in genetics 2020 - “...class-I AT1G36370 1.6290 Hyper Exon SHM7| Pyridoxal phosphate-dependent transferase AT1G74030 1.6688 Hyper Exon/intron/utr3 ENO1| Enolase AT2G45440 1.6816 Hyper Intron DHDPS2| Dihydrodipicolinate synthase, DapA AT4G01850 1.7869 Hyper Exon SAM2| S-adenosylmethionine synthetase AT4G23590 1.9377 Hyper Exon Pyridoxal phosphate-dependent transferase AT5G03290 1.9497 Hyper Exon IDH5| Isocitrate dehydrogenase NAD-dependent AT3G12780...”
- Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
Liebthal, Antioxidants (Basel, Switzerland) 2020 - “...Reduced Oxidized Reduced Oxidized 1 M NaCl 30S ribosomal protein S17 (AT1G79850) HTPA synthase 2 (AT2G45440) 30S ribosomal protein S6 alpha (AT1G64510) MECDP synthase (AT1G63970) Acyl-ACP thioesterase ATL3 (AT1G68260) HTPA synthase 1 (AT3G60880) DAHP synthase 2 (AT4G33510) Elongation factor 1 alpha (AT4G20360) TRAF-like family protein (AT3G28220)...”
- An L,L-diaminopimelate aminotransferase mutation leads to metabolic shifts and growth inhibition in Arabidopsis
Cavalcanti, Journal of experimental botany 2018 - “...plants were harvested for subsequent analysis. We additionally used the following mutant lines: (i) dhdps-2 (At2g45440), a T-DNA insertional line in the gene encoding dihydrodipicolinate synthase in the Wassilewskija (WS) background, which displays relatively lower Lys synthesis but consequently a strongly enhanced threonine synthesis ( Craciun...”
- “...(DHDPS). DHPDS is the first enzyme of the Lys biosynthesis pathway, and the DHDPS2 gene (At2g45440) encodes one of two DHDPS isozymes that contributes to the majority of the total DHDPS activity in Arabidopsis. TDNA insertion lines of DHDPS2 display relatively lower Lys biosynthesis, and, as...”
- Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting
Coker, Frontiers in plant science 2015 - “...AT5G20630 ATGER3, AT2G26680 AT5G46390 AT1G79280 NUA, AtTPR AT5G39790 AT2G40760 AT5G51350 AT2G26330 ER, QRP1 AT5G48600 ATCAP-C AT2G45440 DHDPS2 AT5G64240 MC3 AT2G30540 AT5G50740 AT3G02900 AT2G32880 AT5G57130 At 5 and 7 d.p.i., transcripts were classified as either upregulated or downregulated, then split into groups according to the ratio of...”
- The membrane-tethered transcription factor ANAC089 serves as redox-dependent suppressor of stromal ascorbate peroxidase gene expression
Klein, Frontiers in plant science 2012 - “...chloroplast (CM1) AT3G55120 0.594613 3.6e 32 Chalconeflavanone isomerase AT3G24170 0.592559 6.6e 32 Glutathione reductase, putative AT2G45440 0.585632 4.9e 31 Dihydrodipicolinate synthase 2 (DHDPS2) AT1G63290 0.569233 4.8e 29 Ribulose-phosphate 3-epimerase, cytosolic, putative AT4G16265 0.560068 5.5e 28 DNA-directed RNA polymerase II, putative AT1G18320 0.559598 6.3e 28 Mitochondrial import...”
- More
C9Z234 4-hydroxy-tetrahydrodipicolinate synthase from Streptomyces scabiei (strain 87.22)
35% identity, 92% coverage
D7LCJ3 4-hydroxy-tetrahydrodipicolinate synthase from Arabidopsis lyrata subsp. lyrata
35% identity, 78% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...and DHDPS2 (UNIPROT ID: Q9FVC8), Arabidopsis lyrata DHDPS1 (UNIPROT ID: D7LRV3) and DHDPS2 (UNIPROT ID: D7LCJ3), Nicotiana tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2 (UNIPROT ID: Q9LWB9), Solanum lycopersicum DHDPS1 (UNIPROT ID: A0A3Q7IMG0) and DHDPS2 (UNIPROT ID: A0A3Q7FJL9), Triticum aestivum...”
4hnnF / D7U7T8 Dihydrodipicolinate synthase from the common grapevine with pyruvate and lysine (see paper)
34% identity, 89% coverage
PsgB076_08550 4-hydroxy-tetrahydrodipicolinate synthase from Pseudomonas savastanoi pv. glycinea str. B076
32% identity, 97% coverage
A0A438E022 4-hydroxy-tetrahydrodipicolinate synthase from Vitis vinifera
34% identity, 77% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...ID: A0A3Q7IMG0), Triticum aestivum DHDPS1 (Ta1; UNIPROT ID: P24846), Vitis vinifera DHDPS1 (Vv1; UNIPROT ID: A0A438E022), Zea mays DHDPS1 (Zm1; UNIPROT ID: P26259), and Escherichia coli (Ec) DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1 with dots (.) representing interspacing residues. Sequences were aligned...”
- “...aestivum DHDPS1 (UNIPROT ID: P24846) and DHDPS2 (UNIPROT ID: P24847), Vitis vinifera DHDPS1 (UNIPROT ID: A0A438E022) and DHDPS2 (UNIPROT ID: D7U7T8), Zea mays DHDPS1 (UNIPROT ID: P26259) and DHDPS2 (UNIPORT ID: B4FLW2), and Escherichia coli DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1; identical...”
MAP2864c DapA_2 from Mycobacterium avium subsp. paratuberculosis str. k10
Q73VZ7 4-hydroxy-tetrahydrodipicolinate synthase from Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)
34% identity, 96% coverage
- Virulence and immunogenicity of genetically defined human and porcine isolates of M. avium subsp. hominissuis in an experimental mouse infection
Bruffaerts, PloS one 2017 - “...MAA104 MAP2800 enoyl-CoA hydratase [Mycobacterium avium subsp. hominissuis TH135] 2,00E-24 30% BAN30137.1 MAH TH135 31 MAP2864c dihydrodipicolinate synthase [Mycobacterium avium 104] 0 99% ABK66322.1 MAA104 32 MAP3413 aldehyde dehydrogenase (NAD) family protein [Mycobacterium avium 104] 0 99% ABK69290.1 MAA104 MAP3413 P-cumic aldehyde dehydrogenase [Mycobacterium avium subsp....”
- Antigenicity of recombinant maltose binding protein-Mycobacterium avium subsp. paratuberculosis fusion proteins with and without factor Xa cleaving
Gurung, Clinical and vaccine immunology : CVI 2013 - “...MAP1834c, MAP2280c, MAP2281c MAP1293, MAP1297, MAP1846c, MAP2864c MAP1588c, MAP1589c, MAP1653, MAP4340 MAP0593c, MAP0184c, MAP1586, MAP3555, MAP3864 MAP0508,...”
- “...not antigenic in this study. Similarly, proteins MAP0068, MAP2007, MAP2864c, and MAP3864 were found to be antigenic in this study but not by Kawaji et al. (13)....”
- Proteome Profile Changes Induced by Heterologous Overexpression of Mycobacterium tuberculosis-Derived Antigens PstS-1 (Rv0934) and Ag85B (Rv1886c) in Mycobacterium microti.
García-Ruiz, Biomolecules 2022 - “...Q73RX0 Fructose-bisphosphate aldolase activity. 33.645 891 + + + Yes 11 4-hydroxy-tetradihydrodipicolinate synthase (DapA) 1 Q73VZ7 Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). 30.973 350 - + + ND 12 p40 protein 4 Q9AIQ0 ND 36.232 1109 + - + Yes 13...”
D7U7T8 4-hydroxy-tetrahydrodipicolinate synthase from Vitis vinifera
34% identity, 78% coverage
DAPA_MYCTU / P9WP25 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 3 papers)
Rv2753c dihydrodipicolinate synthase from Mycobacterium tuberculosis H37Rv
NP_217269 4-hydroxy-tetrahydrodipicolinate synthase from Mycobacterium tuberculosis H37Rv
37% identity, 79% coverage
- function: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
catalytic activity: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy- 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O (RHEA:34171)
subunit: Homotetramer. - The glyceraldehyde-3-phosphate dehydrogenase GapDH of Corynebacterium diphtheriae is redox-controlled by protein S-mycothiolation under oxidative stress
Hillion, Scientific reports 2017 - “...DIP0511 4-hydroxy-tetrahydrodipicolinate synthase Cys141 (R)AVAAATSLPVIAYDIPVC 141 VHTK(L) DapA DIP1464 4-hydroxy-tetrahydrodipicolinate synthase Cys161 (R)SVVPIAPDTLC 161 R(L) Rv2753c DIP0974 DIP0974 Putative aminotransferase Cys138 (R)C 138 DAPHELPNDDIDLVFINSPSNPTGR(V) Rv1178 GlnA1 DIP1644 Glutamine synthetase Cys220 (R)QHPEC 220 GTGSQQEINYR(F) LeuB DIP1105 3-isopropylmalate dehydrogenase Cys130 (R)EGTEGLYC 130 GNGGTLR(E) Rv2995c Biosynthesis of nucleotides DIP1631...”
- Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing
Rienksma, BMC genomics 2015 - “...towards threonine, methionine and lysine showed an unexpected pattern (Figure 3 B): both dapA (BCG2769c; Rv2753c) and thrB (BCG1356; Rv1296), involved in initiation of threonine and lysine biosynthesis respectively were repressed, while metX (BCG3411; Rv3341), encoding an enzyme that initiates methionine biosynthesis, was induced. We conclude...”
- The cell envelope glycoconjugates of Mycobacterium tuberculosis
Angala, Critical reviews in biochemistry and molecular biology 2014 - “...L-aspartate in a series of eight reactions involving the enzymes Ask (Rv3709c), Asd (Rv3708c), DapA (Rv2753c), DapB (Rv2773c), DapC (Rv0858c), DapD (Rv1201c), DapE (Rv1202) and DapF (Rv2726c). As in other bacteria, the fully assembled sugar-peptide moiety of the Parks nucleotide is then transferred to a lipid...”
- Mycobacterium tuberculosis thymidylate synthase gene thyX is essential and potentially bifunctional, while thyA deletion confers resistance to p-aminosalicylic acid
Fivian-Hughes, Microbiology (Reading, England) 2012 - “...M. tuberculosis , as RT-PCR indicated that it is co-transcribed with its downstream genes dapA (Rv2753c) and Rv2752c ( Fig. 2a ; data not shown). After electroporation of pJH- thyX into M. tuberculosis H37Rv, potential single cross-over recombinants were analysed by PCR (results not shown), to...”
- Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis
Kefala, The Biochemical journal 2008 (PubMed)- “...of the enzyme dihydrodipicolinate synthase (KEGG entry Rv2753c, EC 4.2.1.52) from Mycobacterium tuberculosis (Mtb-DHDPS) was determined and refined at 2.28 A...”
- “...The enzyme DHDPS (dihydrodipicolinate synthase) (KEGG entry Rv2753c; EC 4.2.1.52) catalyses the first unique reaction of (S)-lysine biosynthesis [7]: an aldol...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis. Corrigendum
Kefala, Acta crystallographica. Section F, Structural biology and crystallization communications 2007 - “...S1744309107065566 Addenda and Errata Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis . Corrigendum DapA Kefala Georgia a Weiss Manfred S. a * a EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany Correspondence e-mail: msweiss@embl-hamburg.de Present address:...”
- “...Kefala & Weiss [(2006), Acta Cryst. F 62 , 11161119] . dihydrodipicolinate synthase Mycobacterium tuberculosis Rv2753c The first sentence of the Experimental methods section of the article by Kefala & Weiss (2006 ) should read as follows: Each gram of cell pellet was dissolved in 10ml...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis
Kefala, Acta crystallographica. Section F, Structural biology and crystallization communications 2006 - “...and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis. Corrigendum The first sentence of the Experimental methods section...”
- “...and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis ISSN 1744-3091 Georgia Kefala and Manfred S. Weiss* EMBL Hamburg...”
- A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis.
Evans, Archives of biochemistry and biophysics 2011 (PubMed)- GeneRIF: DHDPS-A204R, with disrupted quaternary structure, revealed a dimeric protein with an identical fold and active-site structure to the tetrameric wild-type enzyme
5j5dA / P9WP25 Crystal structure of dihydrodipicolinate synthase from mycobacterium tuberculosis in complex with alpha-ketopimelic acid (see paper)
37% identity, 80% coverage
- Ligand: 2-oxoheptanedioic acid (5j5dA)
DIP1464 dihydrodipicolinate synthase from Corynebacterium diphtheriae NCTC 13129
35% identity, 77% coverage
- Ribonuclease J-Mediated mRNA Turnover Modulates Cell Shape, Metabolism and Virulence in Corynebacterium diphtheriae
Luong, Microorganisms 2021 - “...genome, DIP1463, is part of a transcriptional unit [ 37 ], comprised of DIP1463 and DIP1464 (coding for a 4-hydroxy-tetrahydrodipicolinate synthase and involved in L-lysine biosynthesis) ( Figure 1 A). Similar to the Bacillus RNase J enzymes, the corynebacterial RnJ is predicted to harbor an N-terminal...”
- “...equipped with its own promoter but it is also part of a transcription unit with DIP1464. ( B ) RnJ harbors three domains-lactamase, -CASP, and C-terminal. The -lactamase region contains catalytic histidine residues in the motif II, which is highly conserved with other ribonuclease J proteins,...”
- The glyceraldehyde-3-phosphate dehydrogenase GapDH of Corynebacterium diphtheriae is redox-controlled by protein S-mycothiolation under oxidative stress
Hillion, Scientific reports 2017 - “...dehydrogenase Cys243 (R)VTYADVYC 243 EGISK(I) Rv1294 DIP0511 DIP0511 4-hydroxy-tetrahydrodipicolinate synthase Cys141 (R)AVAAATSLPVIAYDIPVC 141 VHTK(L) DapA DIP1464 4-hydroxy-tetrahydrodipicolinate synthase Cys161 (R)SVVPIAPDTLC 161 R(L) Rv2753c DIP0974 DIP0974 Putative aminotransferase Cys138 (R)C 138 DAPHELPNDDIDLVFINSPSNPTGR(V) Rv1178 GlnA1 DIP1644 Glutamine synthetase Cys220 (R)QHPEC 220 GTGSQQEINYR(F) LeuB DIP1105 3-isopropylmalate dehydrogenase Cys130 (R)EGTEGLYC...”
MMAR_1962 dihydrodipicolinate synthase DapA from Mycobacterium marinum M
38% identity, 79% coverage
dapA / P19808 dihydropicolinate synthase subunit (EC 4.3.3.7) from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (see paper)
P19808 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Corynebacterium glutamicum (see paper)
dapA / CAA79714.1 dihydrodipicolinate synthase from Corynebacterium glutamicum (see paper)
NCgl1896 4-hydroxy-tetrahydrodipicolinate synthase from Corynebacterium glutamicum ATCC 13032
35% identity, 95% coverage
B4FLW2 4-hydroxy-tetrahydrodipicolinate synthase from Zea mays
35% identity, 80% coverage
Q43038 4-hydroxy-tetrahydrodipicolinate synthase (Fragment) from Populus trichocarpa x Populus deltoides
34% identity, 72% coverage
P24846 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Triticum aestivum (see paper)
35% identity, 72% coverage
- Drought Stress Induces Morpho-Physiological and Proteome Changes of Pandanus amaryllifolius.
Amnan, Plants (Basel, Switzerland) 2022 - “...regulation Histidine kinase binding 3 Q9SI75 Elongation factor G, chloroplastic Protein biosynthesis Elongation factor 3 P24846 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic Amino acid biosynthesis Allosteric enzyme 3 Q41932 Oxygen-evolving enhancer protein 3-2, chloroplastic Photosynthesis (ET) Calcium ion binding 4 P25795 Aldehyde dehydrogenase family 7 member A1 Stress...”
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...ID: A0A0K0K9A6), Solanum lycopersicum DHDPS1 (Sl1; UNIPROT ID: A0A3Q7IMG0), Triticum aestivum DHDPS1 (Ta1; UNIPROT ID: P24846), Vitis vinifera DHDPS1 (Vv1; UNIPROT ID: A0A438E022), Zea mays DHDPS1 (Zm1; UNIPROT ID: P26259), and Escherichia coli (Ec) DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1 with dots...”
- “...lycopersicum DHDPS1 (UNIPROT ID: A0A3Q7IMG0) and DHDPS2 (UNIPROT ID: A0A3Q7FJL9), Triticum aestivum DHDPS1 (UNIPROT ID: P24846) and DHDPS2 (UNIPROT ID: P24847), Vitis vinifera DHDPS1 (UNIPROT ID: A0A438E022) and DHDPS2 (UNIPROT ID: D7U7T8), Zea mays DHDPS1 (UNIPROT ID: P26259) and DHDPS2 (UNIPORT ID: B4FLW2), and Escherichia coli...”
B8ARJ0 4-hydroxy-tetrahydrodipicolinate synthase from Oryza sativa subsp. indica
34% identity, 79% coverage
- Comparative Proteomic Analysis Provides New Insights into Improved Grain-filling in Ratoon Season Rice
Zeng, Rice (New York, N.Y.) 2024 - “...rice AJNT-4x and its diploid counterpart AJNT-2x. The study revealed an upregulation of proteins B8AM24, B8ARJ0, B8AQM6, and A2ZCE6 in AJNT-4x grains of superior quality, known to play roles in lysine biosynthesis, cell growth, and endosperm development. Luo et al. ( 2021 ) improved the grain-filling...”
- iTRAQ-based quantitative glutelin proteomic analysis reveals differentially expressed proteins in the physiological metabolism process during endosperm development and their impacts on yield and quality in autotetraploid rice
Xian, Plant science : an international journal of experimental plant biology 2021 (PubMed)- “...upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and P37833. Among them, B8AM24 and B8ARJ0 were related to the lysine...”
P26259 4-hydroxy-tetrahydrodipicolinate synthase, chloroplastic from Zea mays
34% identity, 73% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...ID: P24846), Vitis vinifera DHDPS1 (Vv1; UNIPROT ID: A0A438E022), Zea mays DHDPS1 (Zm1; UNIPROT ID: P26259), and Escherichia coli (Ec) DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1 with dots (.) representing interspacing residues. Sequences were aligned in BioEdit (v 7.2.5) ( Hall, 1999...”
- “...vinifera DHDPS1 (UNIPROT ID: A0A438E022) and DHDPS2 (UNIPROT ID: D7U7T8), Zea mays DHDPS1 (UNIPROT ID: P26259) and DHDPS2 (UNIPORT ID: B4FLW2), and Escherichia coli DHDPS (UNIPROT ID: P0A6L2). Residues are numbered according to AtDHDPS1; identical residues are shown as dots (.), gaps are shown as dashes...”
BPSL0346 dihydrodipicolinate synthetase family protein from Burkholderia pseudomallei K96243
33% identity, 92% coverage
- Identification of Burkholderia pseudomallei Genes Induced During Infection of Macrophages by Differential Fluorescence Induction
Jitprasutwit, Frontiers in microbiology 2020 - “...2,274 5.4% 60 2 bpsl0125 * + 1/4 31 229 222 1,410 15.5% 7 3 bpsl0346 * 1/1 76 96 42 903 4.7% 54 4 bpsl1534 * + 1/2 27 293 276 1,806 15.3% 17 5 bpsl2987 * + 6/6 121 342 257 504 50.9% 85...”
- “...secretory pathway 5.84 5.66 2.90 4.30 bpsl0125 tRNA and rRNA cytosine-C5-methylases 8.01 9.96 5.07 8.60 bpsl0346 Dihydrodipicolinate synthetase 8.56 6.98 5.62 5.62 bpsl1534 Poly-beta-hydroxybutyrate polymerase 1.06 0.64 4.00 0.72 bpsl2987 Thiol peroxidase 1.50 0.14 4.44 1.22 bpss0479 Ribonucleotide reductase 2.61 5.98 0.33 4.62 bpss0769 Esterase/lipase 9.86...”
P24847 4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic from Triticum aestivum
34% identity, 74% coverage
YjhH / b4298 KpLE2 phage-like element; putative 2-dehydro-3-deoxy-D-pentonate aldolase (EC 4.1.2.28) from Escherichia coli K-12 substr. MG1655 (see 8 papers)
yjhH / P39359 KpLE2 phage-like element; putative 2-dehydro-3-deoxy-D-pentonate aldolase (EC 4.1.2.28) from Escherichia coli (strain K12) (see 7 papers)
YJHH_ECOLI / P39359 Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 from Escherichia coli (strain K12) (see paper)
30% identity, 97% coverage
- function: Functions as a 2-dehydro-3-deoxy-D-pentonate aldolase.
catalytic activity: 2-dehydro-3-deoxy-D-arabinonate = glycolaldehyde + pyruvate (RHEA:20609)
disruption phenotype: Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhH-yagE double mutant cannot use D- xylonate as the sole source of carbon.
5ui3C Crystal structure of dhdps from chlamydomonas reinhardtii
33% identity, 90% coverage
- Ligand: 2-oxoglutaric acid (5ui3C)
Q9LWB9 4-hydroxy-tetrahydrodipicolinate synthase from Oryza sativa
34% identity, 80% coverage
- Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants
Soares, eLife 2021 - “...tabacum DHDPS (UNIPROT ID: Q42948), Oryza sativa DHDPS1 (UNIPROT ID: A0A0K0K9A6) and DHDPS2 (UNIPROT ID: Q9LWB9), Solanum lycopersicum DHDPS1 (UNIPROT ID: A0A3Q7IMG0) and DHDPS2 (UNIPROT ID: A0A3Q7FJL9), Triticum aestivum DHDPS1 (UNIPROT ID: P24846) and DHDPS2 (UNIPROT ID: P24847), Vitis vinifera DHDPS1 (UNIPROT ID: A0A438E022) and DHDPS2...”
Q81CD9 4-hydroxy-tetrahydrodipicolinate synthase from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
30% identity, 79% coverage
- Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks
Zhao, eLife 2014 - “...Q73CR9, Q73CS0, Q7CFV0, Q7CTP1, Q7CTP2, Q7CTP3, Q7CTP4, Q7CTQ2, Q7CTQ3, Q7CTQ5, Q7CVK1, Q7NU77, Q81CD6, Q81CD7, Q81CD8, Q81CD9, Q81CE0, Q81HB0, Q81HB1, Q8FYS0, Q8P833, Q8YFD6, Q92WR9, Q92WS1, Q9I476, Q9I489, and Q9I492. Funding Information This paper was supported by the following grants: National Institute of General Medical Sciences FundRef identification...”
PPA0642 dihydrodipicolinate synthase from Propionibacterium acnes KPA171202
32% identity, 99% coverage
- Comparative genomics and transcriptomics of Propionibacterium acnes
Brzuszkiewicz, PloS one 2011 - “...glutamate (PPA2166/PPA2167), to process threonine to glycine (PPA0402/403) and to interconvert aspartate, homoserine and lysine (PPA0642, PPA1258, PPA1470, PPA1998) were all upregulated in strain 266. In addition, transcription of genes encoding enzymes that provide the electron acceptor for anaerobic respiration, fumarate, was affected: argininosuccinate lyase (PPA1346)...”
HD73_3145 4-hydroxy-tetrahydrodipicolinate synthase from Bacillus thuringiensis serovar kurstaki str. HD73
30% identity, 79% coverage
- Sox transcription in sarcosine utilization is controlled by Sigma(54) and SoxR in Bacillus thuringiensis HD73
Peng, Scientific reports 2016 - “...( soxI , HD73_3147), aldehyde dehydrogenase ( soxH , HD73_3146), dihydrodipicolinate synthase ( soxG , HD73_3145), proline racemase ( soxE , HD73_3143), sarcosine oxidase, subunit ( soxB , HD73_3142), Sigma 54 -dependent transcriptional activator ( soxR , HD73_3141), hypothetical protein ( soxC/D/F , HD73_3140/HD73_3139/HD73_3144), and sarcosine...”
- Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis
Peng, Frontiers in microbiology 2015 - “...18.422 HD73_3142 Sarcosine oxidase, beta subunit 35.033 HD73_3143 Proline racemase 35.278 HD73_3144 Hypothetical protein 31.999 HD73_3145 Dihydrodipicolinate synthase 34.853 HD73_3146 Aldehyde dehydrogenase 28.844 HD73_3147 Amino acid carrier protein 37.362 HD73_3213 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha 25.424 HD73_3214 TPP-dependent acetoin dehydrogenase E1 alpha-subunit 19.979 HD73_3215 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit...”
VP1335 probable dihydrodipicolinate synthetase from Vibrio parahaemolyticus RIMD 2210633
28% identity, 95% coverage
- Pathogenic Characteristics of and Variation in Vibrio parahaemolyticus Isolated from Acute Diarrhoeal Patients in Southeastern China from 2013 to 2017
Chen, Infection and drug resistance 2020 - “...VP1694 ( vscF ), the T3SS2 genes VP1362 ( vopB2 ), VP1339 ( vscC2 ), VP1335 ( vscS2 ) and VP1327 ( vopT ), and the T3SS2 genes ( vscC2, vopB2, vopC and vscS2 ) were detected by four-multiplex PCR. 22 The pathogenic group was defined...”
- Virulence, Antimicrobial Susceptibility, Molecular and Epidemiological Characteristics of a New Serotype of Vibrio parahaemolyticus From Diarrhea Patients
Zhu, Frontiers in microbiology 2020 - “...VP1694 ( vscF ), the T3SS2 genes VP1362 ( vopB2 ), VP1339 ( vscC2 ), VP1335 ( vscS2 ), and VP1327 ( vopT ), and the T3SS2 genes ( vscC2 , vopB2 , vopC , and vscS2 ) were detected on 2% agarose gel electrophoresis after...”
- A Comprehensive Epidemiological Research for Clinical Vibrio parahaemolyticus in Shanghai
Li, Frontiers in microbiology 2017 - “...and VP1694 [ vscF ]), T3SS2 genes (VP1362 [ vopB2 ], VP1339 [ vscC2 ], VP1335 [ vscS2 ] and VP1327 [ vopT ]) and the T3SS2 genes ( vscC2 , vopB2 , vopC , vscS2 ) were tested by conventional PCR ( Jones et al.,...”
- “...( vopB2 ) 34 2 3 1 VP1339 ( vscC2 ) 34 1 3 1 VP1335 ( vscS2 ) 34 1 2 1 VP1327 ( vopT ) 34 1 2 1 All 4 genes present 34 1 2 1 T3SS2 vscC2 0 3 4 0 vopB2...”
- Biochemical, serological, and virulence characterization of clinical and oyster Vibrio parahaemolyticus isolates
Jones, Journal of clinical microbiology 2012 - “...presence of T3SS2 genes (VP1362 [vopB2], VP1339 [vscC2], VP1335 [vscS2], and VP1327 [vopT]) was tested using a conventional multiplex PCR. The 30-l reaction...”
MAB_3084c Dihydrodipicolinate synthase DapA from Mycobacterium abscessus ATCC 19977
31% identity, 98% coverage
ACS91_24330 dihydrodipicolinate synthase family protein from Vibrio parahaemolyticus
28% identity, 95% coverage
XAC2547 dihydrodipicolinate synthetase from Xanthomonas axonopodis pv. citri str. 306
28% identity, 96% coverage
EAM_RS12125 dihydrodipicolinate synthase family protein from Erwinia amylovora ATCC 49946
29% identity, 94% coverage
YagE / b0268 CP4-6 prophage; putative 2-dehydro-3-deoxygluconate aldolase (EC 4.1.2.28; EC 4.1.2.51) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yagE / P75682 CP4-6 prophage; putative 2-dehydro-3-deoxygluconate aldolase (EC 4.1.2.28; EC 4.1.2.51) from Escherichia coli (strain K12) (see 8 papers)
YAGE_ECOLI / P75682 Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 from Escherichia coli (strain K12) (see 4 papers)
P75682 2-dehydro-3-deoxyglucarate aldolase (EC 4.1.2.20) from Escherichia coli (see paper)
31% identity, 78% coverage
- function: Catalyzes the formation of 2-keto-3-deoxy-gluconate (KDG) from pyruvate and glyceraldehyde (PubMed:21294156). May also function as a 2-dehydro-3-deoxy-D-pentonate aldolase (PubMed:23233208). Overexpression leads to increased growth (over 2 hours) in the presence of the antibiotics norfloxacin, ampicillin and streptomycin (PubMed:21294156).
catalytic activity: 2-dehydro-3-deoxy-D-gluconate = D-glyceraldehyde + pyruvate (RHEA:35583)
catalytic activity: 2-dehydro-3-deoxy-D-arabinonate = glycolaldehyde + pyruvate (RHEA:20609)
subunit: A dimer of dimers.
disruption phenotype: Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhH-yagE double mutant cannot use D- xylonate as the sole source of carbon.
3nevA / P75682 Crystal structure of yage, a prophage protein from e. Coli k12 in complex with kdgal (see paper)
31% identity, 80% coverage
- Ligand: 3-deoxy-d-lyxo-hexonic acid (3nevA)
b0268 CP4-6 prophage; predicted lyase/synthase from Escherichia coli str. K-12 substr. MG1655
31% identity, 77% coverage
- Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products
Bator, Frontiers in bioengineering and biotechnology 2019 - “...VLB120 was performed using primers IB-68 and IB-124 and the gene for the aldolase yagE (b0268 from E. coli DH5) was amplified using the primers IB-118 and IB-125 to create a synthetic operon. All fragments were assembled via Gibson reactions. In a final step to obtain...”
- In vitro reconstitution and characterisation of the oxidative D-xylose pathway for production of organic acids and alcohols
Boer, AMB Express 2019 - “...E. coli Cc XylD GI: 1043567249 Dehydratase 4.2.1.82 C. crescentus Strep-II_N E. coli Ec YagE b0268 GI: 357529065 Aldolase 4.1.2.20 E. coli Strep-II_N E. coli Ec AldA b1415 GI: 113602 Oxidoreductase 1.2.1.22 E. coli His 6 -tag_N E. coli Ab AraE GI: 40339944 Oxidoreductase 1.2.1.24 1.2.1.26...”
- “...113602, NCBI), and E. coli 2-dehydro-3-deoxy- d -pentonate aldolase encoding gene ( Ec yagE , b0268, Accession: P75682.2, GI: 357529065, NCBI) were purchased as synthetic genes, and codon optimized for E. coli (GenScript, China) in the pBAT4 vector (Pernen et al. 1996 ). The genes encoding...”
- Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b0727 b2744 b0368 b3991 b1323 b4196 b4324 b0422 b0208 b0268 b0357 b0407 b0413 b0447 b0492 b0559 b0597 b0577 b0660 b0736 b0742 COG1519 COG2186 COG1044 COG1522...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...1.00 b0259 yi52_1 1 IS5 transposase 0.61* 0.50* 1.04 b0268 b0269 yagE yagF 2 2 Putative lyase/synthase Putative dehydratase 0.25* 0.33* 0.85 b0306 b0307 b0308...”
DAPAL_RHIML / O69782 Uncharacterized DapA-like lyase; EC 4.-.-.- from Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti) (see paper)
29% identity, 97% coverage
- function: Upon expression in E.coli complements a dapA deletion mutation, but this may not be its physiological function
subunit: Homotetramer.
STM3532 putative dihydrodipicolinate synthetase from Salmonella typhimurium LT2
SL1344_3499 dihydrodipicolinate synthase family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
28% identity, 96% coverage
KZA74_17400 dihydrodipicolinate synthase family protein from Acinetobacter baumannii
28% identity, 94% coverage
Bbr_1740 dihydrodipicolinate synthase family protein from Bifidobacterium breve
30% identity, 96% coverage
BLJ_1832 dihydrodipicolinate synthase family protein from Bifidobacterium longum subsp. longum JDM301
30% identity, 96% 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 - “...in JDM301AR after acid challenge. The l -lysine biosynthesis via DAP pathway (BLJ_0147, BLJ_0149, BLJ_0489, BLJ_1832, BLJ_1564, BLJ_1831, BLJ_1383 and BLJ_1843) was activated in JDM301AR (Additional file 2 ). During the process, the homologs of diaminopimelate decarboxylase (BLJ_1843, Log 2 FC=1.6) were shown to specifically catalyze...”
- Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences
Wei, World journal of gastroenterology 2012 - “...25.8 30.62 28.62 VFG1817 VFG0574 VFG0574 VFG1116 BLJ_1832 BLJ_0490 BLJ_0021 21.89 VFG1109 25.95 VFG1109 26.83 VFG0307 BLJ_1889 24.14 VFG2227 BLJ_1251 BLJ_0214...”
Q8NMD2 N-acetylneuraminate lyase (EC 4.1.3.3) from Corynebacterium glutamicum (see paper)
cg2931 N-acetylneuraminate lyase (aldolase) from Corynebacterium glutamicum ATCC 13032
28% identity, 90% coverage
- Transcription of Sialic Acid Catabolism Genes in Corynebacterium glutamicum Is Subject to Catabolite Repression and Control by the Transcriptional Repressor NanR
Uhde, Journal of bacteriology 2016 - “...N-acetylneuraminic acid lyase NanA (encoded by cg2931 [nanA]), the N-acetylmannosamine kinase NanK (encoded by cg2932 [nanK]), the...”
- “...from C. glutamicum M4 pEPRI containing the nanA (cg2931) promoter fragment pEPRI containing the siaE (cg2937) promoter fragment pEPRI containing the nanH...”
- Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate
Kato, BMC microbiology 2010 - “...system component 7,7 0,7 cg1884 hypothetical protein 1,3 0,2 cg2402 cell wall-associated hydrolase 0,8 0,2 cg2931 putative dihydrodipicolinate synthase 4,4 1,0 cg2937 ABC-type transporter, periplasmic component 4,6 0,9 cg2938 ABC-type transporter, permease component 4,1 1,5 cg3114 sulfate adenylate transferase subunit 1 2,2 0,2 cg3116 phosphoadenosine phosphosulfate...”
5c55A / Q8NMD2 Crystal structure of the y138f mutant of c.Glutamicum n- acetylneuraminic acid lyase in complex with pyruvate
28% identity, 92% coverage
- Ligand: pyruvic acid (5c55A)
ArtHe_16635 dihydrodipicolinate synthase family protein from Arthrobacter sp. Helios
30% identity, 94% coverage
c0761 Putative dihydrodipicolinate synthase from Escherichia coli CFT073
32% identity, 87% coverage
PA14_48000 putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa UCBPP-PA14
28% identity, 94% coverage
Blon_2338 dihydrodipicolinate synthetase from Bifidobacterium longum subsp. infantis ATCC 15697
29% identity, 96% coverage
PA1254 probable dihydrodipicolinate synthetase from Pseudomonas aeruginosa PAO1
28% identity, 94% coverage
Q6NY77 4-hydroxy-2-oxoglutarate aldolase, mitochondrial from Danio rerio
28% identity, 90% coverage
BOV_A0349 dihydrodipicolinate synthase family protein from Brucella ovis ATCC 25840
25% identity, 95% coverage
- Cross-regulation in a three-component cell envelope stress signaling system of <i>Brucella</i>
Chen, mBio 2023 - “...clusters encodes carbohydrate metabolism enzymes (BOV_A0354-A0355), transporter subunits (BOV_A0347-A0348; BOV_A0350-A0352), a DapA-family dihydrodipicolinate synthase/N-acetylneuraminate lyase (BOV_A0349), Gfo/Idh/MocA family oxidoreductases (BOV_A0345-A0346), and a FadR-family transcription regulator (BOV_A0353). Transcription of this entire cluster is significantly reduced following cenR or essRS deletion ( Fig. 4 ; Table S3 )....”
SSO3072 Dihydrodipicolinate synthase (dapA-3) from Sulfolobus solfataricus P2
31% identity, 75% coverage
SSO2274 Dihydrodipicolinate synthase (dapA-1) from Sulfolobus solfataricus P2
27% identity, 98% coverage
PSF113_2126 dihydrodipicolinate synthase family protein from Pseudomonas ogarae
26% identity, 93% coverage
- Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440
Blanco-Romero, Scientific reports 2018 - “...Methyl-accepting chemotaxis protein OTHERS PSF113_0079c Phage-related replication protein-like protein PSF113_1047 Multicopper oxidase PSF113_1201 FerredoxinNADP(+) reductase PSF113_2126 Dihydrodipicolinate synthase PSF113_2158 nuoA NuoA PSF113_2972 Glycosaminoglycan degradation PSF113_3889 Zinc carboxypeptidase domain protein PSF113_3918 tig Tig PSF113_3922 folD FolD PSF113_4083 Sterol desaturase PSF113_4204 Protein binding PSF113_4932 prs Prs PSF113_4978 Pentapeptide...”
rrnAC0960 dihydrodipicolinate synthase from Haloarcula marismortui ATCC 43049
31% identity, 88% coverage
- Metabolism of halophilic archaea
Falb, Extremophiles : life under extreme conditions 2008 - “...lacks all enzyme genes for the ED pathway. In addition to their archaeal KD(P)G aldolase (rrnAC0960, HQ2365A), H. marismortui (rrnAC3121), H. walsbyi (HQ1495A), and Haloferax alicantei (AAB40121, co-located with kdgK , AAB40122) also encode the canonical bacterial-type KDPG aldolase (EC 4.1.2.14, kdgA , COG0800), which is...”
BMEII0862 DIHYDRODIPICOLINATE SYNTHASE from Brucella melitensis 16M
25% identity, 90% coverage
8u8wA / A0A0H3FJT8 Crystal structure of n-acetylneuraminate lyase (nana) from klebsiella aerogenes (pyruvate and halides bound)
26% identity, 95% coverage
- Ligand: pyruvic acid (8u8wA)
Varpa_5951 dihydrodipicolinate synthase family protein from Variovorax paradoxus EPS
29% identity, 95% coverage
Deide_3p01100 putative dihydrodipicolinate synthase from Deinococcus deserti VCD115
27% identity, 94% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...radiodurans DR_1365 DR_2008 DR_1758 Deinococcus geothermalis Dgeo_1127 Dgeo_1782 Dgeo_0790 Deinococcus deserti Deide_11430 Deide_15740 Deide_1p00310, Deide_3p00120, Deide_3p01100 Deide_12830, Deide_21880 Deinococcus maricopensis Deima_1822 Deima_2680 Deima_2660 Deinococcus proteolyticus Deipr_0941 Deipr_0985 Deipr_1377* Deipr_1378* Deipr_1376* Deipr_0627, Deipr_1375* Truepera radiovictrix Trad_0977 Trad_0289 Trad_1893 Trad_0134 *More than 3 genes are clustered....”
A9CFV4 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Agrobacterium tumefaciens (see paper)
25% identity, 93% coverage
- Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks
Zhao, eLife 2014 - “...A3QH73, A3S939, A3SU01, A5VZY6, A6WW16, A6WXX7, A8H392, A9AKG8, A9AKH1, A9AL52, A9ALD3, A9AQW9, A9CFU8, A9CFU9, A9CFV0, A9CFV4, A9CFW8, A9CGZ4, A9CGZ5, A9CGZ9, A9CH01, A9CH04, A9CKB4, B0VB44, B1KJ76, B3D6W2, B4EHE6, B9J8G8, B9JHU6, B9JQV3, B9K4G4, B9R4E3, C5ZMD2, D2AV87, D2QN44, D5SQS4, D6EJK6, D6EJK7, D6EJK8, D6EJK9, D6EJL0, Q0B950, Q0B953, Q0B9R9, Q0B9S2, Q16D96,...”
BPSS0331 putative dihydrodipicolinate synthase from Burkholderia pseudomallei K96243
BMAA1420 dihydrodipicolinate synthetase family protein from Burkholderia mallei ATCC 23344
27% identity, 84% coverage
BKKJ1_2072 dihydrodipicolinate synthase family protein from Bifidobacterium catenulatum subsp. kashiwanohense
28% identity, 96% coverage
- Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
James, Scientific reports 2019 - “...7.45 6.88 BKKJ1_2070 fumA2 GH29 alpha-1 3/4-fucosidase 11.04 10.43 BKKJ1_2071 fumB L-fucose mutarotase 12.80 12.17 BKKJ1_2072 fumF L-2-keto-3-deoxy-fuconate aldolase 13.14 10.86 BKKJ1_2073 fumD L-fuconolactone hydrolase 14.15 8.21 BKKJ1_2074 fumC L-keto-3-deoxy-fuconate-4-dehydrogenase 15.95 15.37 BKKJ1_2075 fumE L-fuconate dehydratase 17.29 13.90 BKKJ1_2076 fumS ABC transporter solute binding protein 19.68...”
- “...with species ordered by origin of isolation. The products of the genes with locus tags BKKJ1_2072 (designated here as fumF and encoding a putative L2-keto-deoxy-fuconate aldolase), BKKJ1_2073 ( fumD encoding a predicted L-fuconolactone hydrolase), BKKJ1_2074 ( fumC encoding a putative L-fucose dehydrogenase) and BKKJ1_2075 ( fumE...”
CD3000 putative dihydrodipicolinate synthase from Clostridium difficile 630
28% identity, 90% coverage
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...by CcpA; arrow: gene upregulated by CcpA. lysC (CD2054), aspartokinase; asd (CD3224), aspartate-semialdehyde dehydrogenase; dapA1 (CD3000), dihydrodipicolinate synthase 1; dapA2 (CD3223), dihydrodipicolinate synthase 2; dapA3 (CD3225), dihydrodipicolinate synthase 3; dapB1 (CD3226), dihydrodipicolinate reductase; dapH (CD3227), 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate; lysA (CD2053), diaminopimelate decarboxylase; thrC (CD2118), threonine synthase, thrB (CD2119),...”
Q7D3Z9 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Agrobacterium tumefaciens (see paper)
32% identity, 70% coverage
DIP0511 Putative lysine biosynthesis protein from Corynebacterium diphtheriae NCTC 13129
24% identity, 94% coverage
Q9HWJ3 Dihydrodipicolinate synthase family protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4188 hypothetical protein from Pseudomonas aeruginosa PAO1
25% identity, 92% coverage
3na8A / Q9I6R5 Crystal structure of a putative dihydrodipicolinate synthetase from pseudomonas aeruginosa
26% identity, 98% coverage
- Ligand: magnesium ion (3na8A)
PA0223 probable dihydrodipicolinate synthetase from Pseudomonas aeruginosa PAO1
Q9I6R5 Probable dihydrodipicolinate synthetase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
26% identity, 97% coverage
- A Pseudomonas aeruginosa small RNA regulates chronic and acute infection
Cao, Nature 2023 - “...by our proteomic findings showing that sicX exhibited increased levels of two proteins (encoded by PA0223 and PA0224 ) that are biomarkers of dispersed P. aeruginosa 32 (Supplementary Table 2 ). Moreover, ubiUVT showed a similar spatial organization pattern to that of sicX (Fig. 3f )....”
- Toward a Comprehensive Analysis of Posttranscriptional Regulatory Networks: a New Tool for the Identification of Small RNA Regulators of Specific mRNAs
Han, mBio 2021 - “...PA3536 55 4 sr0161 2 sRNA PA1060 opdP 38 5 s0223 2 3 RNA of PA0223 mRNA PA0222 PA0224 St. 5 3 1 ErsA 24 sRNA PA5492 PA5493 37 2 ReaL 15 sRNA PA3535 PA3536 55 3 sRmf 9 3 RNA of rmf mRNA PA3049 PA3050...”
- “...were enriched near the stop codon or the 3 UTR of mRNAs ( PA3661 , PA0223 , Rmf , and AdhC , respectively; Fig.5A ), suggesting that these sRNAs represent the class of sRNAs derived by processing of mRNAs or internal starts within the coding sequences...”
- Species-specific recruitment of transcription factors dictates toxin expression
Trouillon, Nucleic acids research 2020 - “...two-gene operon transcribed in the opposite direction. These two genes ( PA0224 / IHMA87_00214 and PA0223 / IHMA87_00213 ) were also the most upregulated genes in the erfA mutants in RNA-seq, as confirmed by RTqPCR (Figure 3G ,H), and we propose to name them ergA and...”
- Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion
Schnell, PloS one 2012 - “...on the DapA crystal structure determined to 1.6 resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1 dapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA...”
- “...amino acids (Gly-Ser-His) at the N-terminus. The genes coding for DapA (PA1010) and its homologues PA0223 and PA4188 were amplified by PCR and cloned in pNIC28Bsa4 (GenBank Accession No. EF198106) using the LIC method resulting in an N-terminal His6-tag with a TEV protease cleavage site. Similarly,...”
- Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm
Sauer, Journal of bacteriology 2004 - “...Gene ontology Fold changea PA5117 PA3531 PA3525 PA4442 PA0223 PA3635 PA3155 PA1838 PA1338 PA1553 PA4333 PA3621 PA1584 PA1609 PA3806 PA3722 PA1913 PA4852 PA2950...”
- Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion
Schnell, PloS one 2012 - “...of P. aeruginosa identified two other orfs that may represent DapA homologues. PA0223 (Uniprot id: Q9I6R5) is a tetrameric enzyme (PDB:3NA8, unpublished) that shows 30% sequence identity and 1.5 rmsd over 291 aligned C atoms when comparing to Pa DapA (PA1010). PA4188 is an uncharacterized protein...”
Npl / b3225 N-acetylneuraminate lyase (EC 4.1.3.3) from Escherichia coli K-12 substr. MG1655 (see 21 papers)
nanA / P0A6L4 N-acetylneuraminate lyase (EC 4.1.3.3) from Escherichia coli (strain K12) (see 30 papers)
NANA_ECOLI / P0A6L4 N-acetylneuraminate lyase; AcNeu lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; NALase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Escherichia coli (strain K12) (see 8 papers)
P0A6L4 N-acetylneuraminate lyase (EC 4.1.3.3) from Escherichia coli (see 4 papers)
nanA N-acetylneuraminate lyase; EC 4.1.3.3 from Escherichia coli K12 (see 6 papers)
NP_417692 N-acetylneuraminate lyase from Escherichia coli str. K-12 substr. MG1655
b3225 N-acetylneuraminate lyase from Escherichia coli str. K-12 substr. MG1655
S3478 N-acetylneuraminate lyase (aldolase) from Shigella flexneri 2a str. 2457T
Z4583 N-acetylneuraminate lyase (aldolase); catabolism of sialic acid; not K-12? from Escherichia coli O157:H7 EDL933
WP_000224714 N-acetylneuraminate lyase from Escherichia coli
28% identity, 81% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate (PubMed:12711733, PubMed:1646603, PubMed:24521460, PubMed:33895133). Experiments show the true substrate is aceneuramate (linearized Neu5Ac), which forms spontaneously at alkaline pH (PubMed:33895133). Linear aceneuramate can be provided by NanQ (PubMed:33895133). Can also cleave other substrates such as N-glycollylneuraminic acid (GcNeu), but not colominic acid or 2-oxocarboxylic acids such as 2-oxohexanoic acid, 2-oxo-octanoic acid, 2-oxo-3-deoxyoctanoic acid and 2-oxononanoic acid (PubMed:1646603).
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - Toward Single Bacterium Proteomics
Végvári, Journal of the American Society for Mass Spectrometry 2023 - “...P69776 [5359] [R].SDVQAAK.[D] 1176.70 588.85 +2 33.77 4 190.35 25.00% 466 N -acetylneuraminate lyase nanA P0A6L4 [242248] [K].VIDLLIK.[T] 1271.87 636.44 +2 86.04 4 205.75 25.00% 50S ribosomal protein L7/L12 rplL P0A7K2 [110121] [K].ALEEAGAEVEVK.[-] 1702.96 568.33 +3 63.17 16 252.42 93.75% 21 elongation factor Tu2 tufB P0CE48...”
- “...P19934 [118125] [K].KQAEEAAK.[Q] 1333.77 667.39 +2 45.17 1 189.61 6.25% 1001 N -acetylneuraminate lyase nanA P0A6L4 [242248] [K].VIDLLIK.[T] 1271.87 636.44 +2 86.04 1 205.75 6.25% Tat proofreading chaperone DmsD dmsD P69853 [95113] [R].ESVLFGDSTLALRQWMREK.[G] 2725.47 909.17 +3 77.51 1 183.75 6.25% 960 Inner membrane protein YiaV yiaV...”
- Biochemical and structural basis of sialic acid utilization by gut microbes
Bell, The Journal of biological chemistry 2023 - “...113 ) Lp NanA L.plantarum ATCC BAA-793 P59407 ( 110 ) Ec NanA E.coli K12 P0A6L4 1NAL ( 114 ) 4BWL 2WNN 2WNQ 2WPB R.gnavus ATCC29149 A7B555 6RAB ( 15 ) 6RD1 6RB7 Sphingobacterium ( 115 ) Bf NanL B.fragilis NCTC 9343 Q5LEN8 ( 104 )...”
- Magnetization of active inclusion bodies: comparison with centrifugation in repetitive biotransformations
Koszagova, Microbial cell factories 2018 - “...Sigma-Aldrich (St. Louis, Missouri, USA). GFP (FPbase: TurboGFP; GenBank: ASW25889), sialic acid aldolase (SAA, UniProt: P0A6L4; NCBI-GeneID: 947742) and UDPglucose pyrophosphorylase (GalU, UniProt: P0AEP3; NCBI-GeneID: 945730) genes were N -terminally fused with the cellulose-binding domain from Clostridium cellulovorans by cloning into plasmid pET-34b (Additional file 1...”
- Exposure of E. coli to DNA-Methylating Agents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N-Acetylneuraminate Lyase NanA
Di, Frontiers in microbiology 2016 - “...dehydrogenase A, NAD-linked aldA P25553 BIOSYNTHESIS OF SECONDARY METABOLITES 5.78 3272 0.00024 N-acetylneuraminate lyase nanA P0A6L4 1.68 3674 0.000046 Glucosamine-6-phosphate deaminase nagB P0A760 1.72 2441 0.0042 Tryptophanase tnaA P0A853 1.30 1408 0.0029 Polyribonucleotide nucleotidyltransferase pnp P05055 +1.09 2400 0.0063 Glutamate decarboxylase beta gadB P69910 GLYCEROPHOSPHOLIPID METABOLISM...”
- Comprehensively Characterizing the Thioredoxin Interactome In Vivo Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control
Arts, Molecular & cellular proteomics : MCP 2016 - “...P25553 P0A6K6 P0A6L0 P0AAB6 P0ABQ2 B1X7I7 P0C8J8 P0A6F3 P0A6L4 P0A9X4 P0A6F5 dehydratase 1 ATP synthase subunit alpha ATP synthase subunit beta ATP synthase...”
- First functional and mutational analysis of group 3 N-acetylneuraminate lyases from Lactobacillus antri and Lactobacillus sakei 23K
García-García, PloS one 2014 - “...influenzae, C. perfringens, L. plantarum and E. coli K-12 (Uniprot codes: P44539, Q9S4K9, P59407 and P0A6L4, respectively). The sequences were aligned using ClustalW [22] and ESPript [23] . Automatic homology modeling was performed through the MODWEB modeling server ( http://salilab.org/modweb ) using the E. coli NAL...”
- Requirement of purine and pyrimidine synthesis for colonization of the mouse intestine by Escherichia coli
Vogel-Scheel, Applied and environmental microbiology 2010 - “...in vivo P0A786 P0A7D7 P0AF93 P61889 P77256 Q46856 P0A6L4 P0AEX9 P68066 pyrB purC yjgF mdh ydjG yqhD nanA malE yfiD Aspartate carbamoyltransferase catalytic...”
- Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val-251.
Chou, The Journal of biological chemistry 2011 - GeneRIF: analysis of modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val-251
- Structural insights into substrate specificity in variants of N-acetylneuraminic Acid lyase produced by directed evolution.
Campeotto, Journal of molecular biology 2010 - GeneRIF: A comparison of mutant and wild-type nanA structures, in combination with the specificity profiles of the variants, reveals subtle differences that explain the details of the substrate specificity changes.
- The quaternary structure of Escherichia coli N-acetylneuraminate lyase is essential for functional expression.
Devenish, Biochemical and biophysical research communications 2009 (PubMed)- GeneRIF: the dimer-dimer interface of NAL is intolerant to mutation and essential for functional expression.
- Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 angstrom resolution.
Campeotto, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: Results describe the structure of a mutant variant of Escherichia coli N-acetyl-d-neuraminic acid lyase (NAL), E192N, in complex with pyruvate in a new crystal form.
- Complete nucleotide sequence of the E. coli N-acetylneuraminate lyase.
Ohta, Nucleic acids research 1985 - GeneRIF: N-terminus verified by Edman degradation on complete protein
- The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim
Sangurdekar, BMC genomics 2011 - “...induced by alkali; putative membrane transport or efflux protein ygjU b3089 Na+/serine (threonine) symporter nanA b3225 N-Acetylneuraminate lyase (aldolase) yhiP b3496 Function unknown uhpT b3666 Fosfomycin sensitivity; sugar P transport system; transport protein for hexose P's yiiQ b3920 Function unknown uvrA b4058 Excision nuclease subunit A;...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...protein yhcH nanK nanE nanA c3975 b3222 b3223 b3225 2.6 2.4 2.8 3.6 2.6 1.8 3.0 5.4 (CFT073) hypothetical protein Predicted N-acetylmannosamine kinase Predicted...”
- Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
White-Ziegler, Journal of bacteriology 2007 - “...lysine sensitive lysP b2156 Lysine-specific permease nanA b3225 N-Acetylneuraminate lyase (aldolase) tesA b0494 Acyl-coenzyme A thioesterase I; also functions...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...acid transporter 0.21* 0.15* 0.32 0.26 0.81* 0.67* b3225 nanA 1 N-Acetylneuraminate lyase (aldolase) 0.13* 0.29 0.76* b3418 malT 2 Positive regulator of mal...”
- Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO
Stratmann, Journal of bacteriology 2008 - “...S3346 S3108 S3322 S3375 S3469 S3470 S3472 S3474 S3476 S3478 S3480 S3482 S3484 S3486 S3488 S3494 S3496 S3587 S3588 S3590 S3592 S3594 S3596 S3598 S3600 S3602...”
- “...S3474 hns::kanKD4 S3476 leuO::cat S3476 hns::kanKD4 S3478 leuO::cat S3478 hns::kanKD4 S3480 leuO::cat S3480 hns::kanKD4 S3488 leuO::cat S3482 hns::kanKD4...”
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...Z0826 nagE PTS system N-acetylglucosamine-specific IIABC component 3.31 4.52E-08 4.11 9.49E-12 NDE 2.25 3.91E-04 NDE Z4583 nanA N-acetylneuraminate lyase 7.79 1.62E-18 5.14 2.72E-08 3.55 2.07E-04 5.90 8.61E-11 NDE Z4582 nanT Sialic acid transporter 6.32 1.03E-13 3.85 1.80E-05 2.30 1.71E-02 5.18 2.28E-09 NDE Z3463 napA Nitrate reductase...”
- Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content
Bertin, Environmental microbiology 2013 - “...were designed according to the EDL933 genome sequence (Z4488, Z4117 and Z416, Z0927, Z2616, Z0826, Z4583 and Z4582 respectively). The PCR products were purified using the Qiaquick Purification PCR kit (Qiagen) and digested with the relevant enzymes. The PCR fragments were then ligated into the expression...”
- The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans
Robinson, The Journal of biological chemistry 2017 - “...thetaiotaomicron NanH sialidase (WP_008766031), B. fragilis EstA (WP_005794991), and E. coli NanA sialic acid lyase (WP_000224714). DNA manipulations Primers (Integrated DNA Technologies) used in this study are shown in Table 2 . PCR products for cloning were generated with Phusion polymerase (New England Biolabs). Restriction endonucleases...”
2wpbA / P0A6L4 Crystal structure of the e192n mutant of e. Coli n-acetylneuraminic acid lyase in complex with pyruvate and the inhibitor (2r,3r)-2,3,4- trihydroxy-n,n-dipropylbutanamide in space group p21 crystal form i (see paper)
28% identity, 79% coverage
- Ligand: (2r,3r)-2,3,4-trihydroxy-n,n-dipropylbutanamide (2wpbA)
Afu8g02270 dihydrodipicolinate synthetase family protein from Aspergillus fumigatus Af293
31% identity, 69% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...3.99 [1.95, 0.88] Afu3g01560 1.93 [2.22, 1.55] Afu8g02200 5.98 [1.94, 2.69] Afu2g01230 1.97 [2.22, 1.46] Afu8g02270 4.73 [1.84, 1.78] Afu3g13130 2.00 [2.19, 1.45] Afu8g01530 2.15 [2.21, 1.29] Afu8g04100 2.00 [2.19, 1.45] Afu1g00450 2.27 [2.12, 1.05] Afu4g07330 2.01 [2.19, 1.46] Afu2g11750 2.43 [2.14, 0.87] Afu1g05270 2.02 [2.21,...”
c3979 N-acetylneuraminate lyase subunit from Escherichia coli CFT073
28% identity, 77% coverage
Q8A3Z0 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Bacteroides thetaiotaomicron (see paper)
BT_2814, BT_RS14270 dihydrodipicolinate synthase family protein from Bacteroides thetaiotaomicron VPI-5482
BT2814 dihydrodipicolinate synthase from Bacteroides thetaiotaomicron VPI-5482
25% identity, 94% coverage
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...uptake outer memb. protein, DUF4969 domain-containing protein, nucleoside hydrolase, multidrug DMT transporter permease 4.2 0.352 BT_RS14270 BT2814 Dihydrodipicolinate synthase family protein 11 0.107 BT_RS14485 BT2856 DUF5013 domain-containing protein 4.2 0.353 BT_RS14490 BT2857 DUF4959 domain-containing protein 3.5 0.065 BT_RS14495 BT2858 RagB/SusD family nutrient uptake outer memb. protein...”
- Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals
Severi, Microbial genomics 2021 - “...site identified in P. mirabilis SiaT (Fig. S8). This gene, BT_2813 , sits next to BT_2814 , which encodes a NanA-like protein, and in some other related Bacteroidetes , such as Cyclobacterium marinum ( Fig. 4 ), the same two genes are linked to a sialidase...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...outer memb. protein, DUF4969 domain-containing protein, nucleoside hydrolase, multidrug DMT transporter permease 4.2 0.352 BT_RS14270 BT2814 Dihydrodipicolinate synthase family protein 11 0.107 BT_RS14485 BT2856 DUF5013 domain-containing protein 4.2 0.353 BT_RS14490 BT2857 DUF4959 domain-containing protein 3.5 0.065 BT_RS14495 BT2858 RagB/SusD family nutrient uptake outer memb. protein 3.1...”
ESA_03612 N-acetylneuraminate lyase from Cronobacter sakazakii ATCC BAA-894
25% identity, 94% coverage
IHMA87_00213 dihydrodipicolinate synthase family protein from Pseudomonas aeruginosa
25% identity, 97% coverage
RHE_RS03065 dihydrodipicolinate synthase family protein from Rhizobium etli CFN 42
25% identity, 95% coverage
t3256 N-acetylneuraminate lyase from Salmonella enterica subsp. enterica serovar Typhi Ty2
26% identity, 95% coverage
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021
European, EFSA journal. European Food Safety Authority 2023 - “...years, most isolates were spa types associated with LAMRSA, except for t843 in 2018/2019 and t3256 in 2019; all three isolates were confirmed to belong to CC130 and carry the mecC gene. 6.5 Summary data on the occurrence and susceptibility of MRSA Determination of the susceptibility...”
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019-2020
European, EFSA journal. European Food Safety Authority 2022 - “...2019): spatypes: t011 CC398 (4 isolates), t034 CC398 (6), t1451 CC398 (1), t843 CC130 (1), t3256 CC130 (1). Spatypes t843 and t3256 were confirmed to carry the mecC gene. *: spatypes not reported. Monitoring of MRSA in animals following clinical investigations Typically, clinical investigations differ from...”
- “...etal., 2020 ; Cui etal., 2021 ; Silva etal., 2021 ). mecC MRSA spa type t3256, also CC130 was reported by Denmark in one isolate from horses. Considering the two spa types of CC130 (t843 and t3256), both have previously been observed in humans (Petersen etal.,...”
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019
European, EFSA journal. European Food Safety Authority 2021 - “...398 (4 isolates), t034 CC 398 (6), t1451 CC 398 (1), t843 CC 130 (1), t3256 CC 130 (1). spa types t843 and t3256 were confirmed to carry the mecC gene.18: spa types: t011 CC 398 (3 isolates), t034 CC 398 (6), t843 CC 130 (1)....”
- “...herd and equine premises by Denmark) are summarised below: Denmark reported spa types t843 and t3256 from two equine premises, as well as t843 from a dairy cow herd. All three isolates were confirmed to belong to CC130 and carry the mecC gene. Overall, where molecular...”
ESA_03612 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
25% identity, 95% coverage
Deide_1p00310 putative dihydrodipicolinate synthase (DHDPS) from Deinococcus deserti VCD115
29% identity, 79% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...Marky_1261 Deinococcus radiodurans DR_1365 DR_2008 DR_1758 Deinococcus geothermalis Dgeo_1127 Dgeo_1782 Dgeo_0790 Deinococcus deserti Deide_11430 Deide_15740 Deide_1p00310, Deide_3p00120, Deide_3p01100 Deide_12830, Deide_21880 Deinococcus maricopensis Deima_1822 Deima_2680 Deima_2660 Deinococcus proteolyticus Deipr_0941 Deipr_0985 Deipr_1377* Deipr_1378* Deipr_1376* Deipr_0627, Deipr_1375* Truepera radiovictrix Trad_0977 Trad_0289 Trad_1893 Trad_0134 *More than 3 genes are clustered....”
Cj0481 putative lyase from Campylobacter jejuni subsp. jejuni NCTC 11168
21% identity, 96% coverage
- Activation of the l-fucose utilization cluster in Campylobacter jejuni induces proteomic changes and enhances Caco-2 cell invasion and fibronectin binding
Middendorf, Heliyon 2024 - “...acid and lactic acid via metabolic enzymes Cj0488 , Cj0485 (FucX), Cj0487 , Cj0482/Cj0483 , Cj0481 (DapA) and Cj0489 , respectively [ 28 ]. Both pyruvate and lactate can be further metabolized and support growth of C. jejuni [ 33 , 37 ]. l -fucose is...”
- “...upregulated in all tested conditions; eight of them belonged to the l -fucose utilization cluster (Cj0481, Cj0482, Cj0483, Cj0485, Cj0486, Cj0487, Cj0488, Cj0489), and one was a membrane related protein (Cj0771c). Furthermore, two proteins were downregulated in all tested conditions, namely, the bifunctional protein PutA, and...”
- Campylobacter jejuni uses energy taxis and a dehydrogenase enzyme for l-fucose chemotaxis
Zhou, mBio 2023 - “...the only member found to also play a key role in C. jejuni chemotaxis while cj0481 , cj0483 , cj0484 , cj0486 , cj0487, and cj0488 mutants still showed l -fucose chemotaxis ( 7 , 8 ). Notably, deletion of the l -fucose permease ( fucP,...”
- Phylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni
Hur, Microbiology spectrum 2022 - “...transporter cj1415c cysC Adenylyl-sulfate kinase Amino acid transport and metabolism cj0029 ansA Type II asparaginase cj0481 dapA Dihydrodipicolinate synthase family protein cj0763c hisS Histidine-tRNA ligase cj0817 glnH Transporter substrate-binding domain-containing protein cj1726c metA Homoserine O -succinyltransferase cj1727c metB O -Acetylhomoserine aminocarboxypropyltransferase/cysteine synthase Defense mechanisms cj0139 Hypothetical...”
- Comparative Analysis of L-Fucose Utilization and Its Impact on Growth and Survival of Campylobacter Isolates
Middendorf, Frontiers in microbiology 2022 - “...acid via the metabolic enzymes encoded by C j0488, Cj0485 (FucX), Cj0487 , Cj0482/Cj0483 , Cj0481 (DapA) and Cj0489/Cj0490 ( Stahl et al., 2011 ; Dwivedi et al., 2016 ; Garber et al., 2020 ). Both, pyruvate and lactate can be further metabolized and support growth...”
- Characterization of l-2-keto-3-deoxyfuconate aldolases in a nonphosphorylating l-fucose metabolism pathway in anaerobic bacteria
Watanabe, The Journal of biological chemistry 2020 (secret) - The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus
Garber, Communications biology 2020 - “...but the current homology comparisons suggest a previously unrecognized model based upon the role of Cj0481 as a dihydrodipicolinate synthase. Interestingly, this pathway is identical to one recently described for the archaeon Sulfolobus solfataricus 43 but to our knowledge, this is the first time it has...”
- “...fucX into the parent strain. NMR analysis of cellular metabolites C. jejuni 11168 wild-type, cj0488, cj0481 , and cj0489 mutants were grown on MH plates for two days and subcultured on MH plates for one day further after which 50mL minimal essential medium with glutamine and...”
- Analyses of energy metabolism and stress defence provide insights into Campylobacter concisus growth and pathogenicity
Yeow, Gut pathogens 2020 - “...C. concisus lacks homologs of C. jejuni genes implicated in the catabolism of fucose ( cj0481 , cj0484 , cj0485 , cj0486 , cj0487 ). Genes for the conversion of pyruvate to acetate via acetyl-CoA and acetylphosphate were identified in C. concisus : pyruvate-flavodoxin oxidoreductase (...”
- Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner
Looft, Frontiers in microbiology 2018 - “...NCTC11168, were up regulated (919 fold) for all the mucus cultures. This gene cluster ( Cj0481 - Cj0489 ) includes fucose utilization proteins and a transporter. Figure 3 Transcriptomic profiles (sense) from C. jejuni grown on defined media with and without mucus isolated from avian and...”
- “...was observed with mucus comparisons with the defined media. The eight-gene fucose utilization operon ( Cj0481 - Cj0489 ), upregulated in all mucus cultures, had antisense reads mapping to the adjacent transcriptional regulator for the operon, Cj0480c , in the defined media cultures. Antisense RNA that...”
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Q6KD26 N-acetylneuraminate lyase from Escherichia coli
25% identity, 90% coverage
PPA1998 dihydrodipicolinate synthase from Propionibacterium acnes KPA171202
24% identity, 95% coverage
- Comparative genomics and transcriptomics of Propionibacterium acnes
Brzuszkiewicz, PloS one 2011 - “...process threonine to glycine (PPA0402/403) and to interconvert aspartate, homoserine and lysine (PPA0642, PPA1258, PPA1470, PPA1998) were all upregulated in strain 266. In addition, transcription of genes encoding enzymes that provide the electron acceptor for anaerobic respiration, fumarate, was affected: argininosuccinate lyase (PPA1346) and aspartate-ammonia lyase...”
PP_2036 dihydrodipicolinate synthase, putative from Pseudomonas putida KT2440
26% identity, 96% coverage
A911_02350 dihydrodipicolinate synthase family protein from Campylobacter jejuni subsp. jejuni PT14
21% identity, 96% coverage
- Host adaption to the bacteriophage carrier state of Campylobacter jejuni
Brathwaite, Research in microbiology 2015 - “...strains is further emphasised by 3- to 8-fold downregulation of all the L-fucose utilisation genes (A911_02350 - A911_02390) that are reported to confer a competitive advantage in the colonisation of pigs as a consequence of utilising L-fucose derived from intestinal mucin [50] . The association of...”
BP3687 putative dihydrodipicolinate synthase from Bordetella pertussis Tohama I
27% identity, 98% coverage
BBA_06627 dihydrodipicolinate synthase from Beauveria bassiana ARSEF 2860
30% identity, 64% coverage
SSO3035 Dihydrodipicolinate synthase (dapA-2) from Sulfolobus solfataricus P2
30% identity, 66% coverage
- Appendage-mediated surface adherence of Sulfolobus solfataricus
Zolghadr, Journal of bacteriology 2010 - “...An oxidoreductase (SSO3014) and a dihydrodipicolinate synthase (SSO3035), which is part of the lysine synthesis pathway, were induced as well. DISCUSSION...”
- “...SSO3017 SSO3019 SSO3021 SSO3022 SSO3029 SSO3032 SSO3034 SSO3035 SSO3036 SSO3037 SSO3038 SSO3039 SSO3041 SSO3042 SSO3043 SSO3045 SSO3046 SSO3047 SSO3048...”
Q7D0E8 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) from Agrobacterium tumefaciens (see paper)
Atu0899 dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58 (Cereon)
30% identity, 95% coverage
- A peptidoglycan N-deacetylase specific for anhydroMurNAc chain termini in Agrobacterium tumefaciens
Gilmore, The Journal of biological chemistry 2024 - “...containing a DUF930-containing rhizobiales-specific protein of unknown function (Atu0898), a dihydrodipicolinate synthase ( dapA , Atu0899), and a DNA repair methyltransferase ( ada , Atu0901) ( Fig.2 B ). Furthermore, because of the presence of a putative signal peptide targeting it to the periplasm, Atu0900 represented...”
- In situ proteolysis for protein crystallization and structure determination
Dong, Nature methods 2007 - “...PDB code 2RC3 We repurified the 55 different bacterial Atu0899 1-311 gi|17934807 C C 2.0 A, C Solved: PDB code 2R8W proteins with hexahistidine tags,...”
- “...generate the crystals, and in two instances (HP0029 and Atu0899), we were unable to repeatedly generate crystals of the quality used to determine the structure....”
CH_124068 putative dihydrodipicolinate synthase from Magnaporthe grisea 70-15 (see paper)
30% identity, 64% coverage
PMI1233 dihydrodipicolinate synthase from Proteus mirabilis HI4320
28% identity, 95% coverage
BCAM2771 putative dihydrodipicolinate synthetase from Burkholderia cenocepacia J2315
26% identity, 93% coverage
HOGA1_BOVIN / Q0P5I5 4-hydroxy-2-oxoglutarate aldolase, mitochondrial; Dihydrodipicolinate synthase-like; DHDPS-like protein; Probable 2-keto-4-hydroxyglutarate aldolase; Probable KHG-aldolase; EC 4.1.3.16 from Bos taurus (Bovine) (see 2 papers)
Q0P5I5 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) from Bos taurus (see paper)
29% identity, 65% coverage
HOGA1 / Q86XE5 4-hydroxy-2-ketoglutarate aldolase subunit (EC 4.1.3.16) from Homo sapiens (see 6 papers)
HOGA1_HUMAN / Q86XE5 4-hydroxy-2-oxoglutarate aldolase, mitochondrial; Dihydrodipicolinate synthase-like; DHDPS-like protein; Probable 2-keto-4-hydroxyglutarate aldolase; Probable KHG-aldolase; Protein 569272; EC 4.1.3.16 from Homo sapiens (Human) (see 2 papers)
Q86XE5 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) from Homo sapiens (see 5 papers)
NP_612422 4-hydroxy-2-oxoglutarate aldolase, mitochondrial isoform 1 from Homo sapiens
28% identity, 65% coverage
- function: Catalyzes the final step in the metabolic pathway of hydroxyproline.
catalytic activity: (4S)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate (RHEA:35639)
catalytic activity: (4R)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate (RHEA:30687)
subunit: Homotetramer. - Endoplasmic Reticulum Stress in Bronchopulmonary Dysplasia: Contributor or Consequence?
Wu, Cells 2024 - Identification of perioperative neurocognitive dysfunction biomarkers in cerebrospinal fluid with quantitative proteomic approach in patients undergoing transurethral resection of prostate with combined spinal and epidural analgesia
Luo, Medicine 2022 - “...nuclear ribonucleoprotein A1-like 2 P14927 38 P14927 Down 225 0.35 0.36 Cytochrome b-c1 complex subunit7 Q86XE5 39 Q86XE5 Down 247 0.30 0.29 4-hydroxy-2-oxoglutarate aldolase, mitochondrial P23528 40 P23528 Down 335 0.51 0.49 Cofilin-1 Q96PQ6 41 Q96PQ6 Down 1242 0.43 0.42 Zinc finger protein 317 Q15493 42...”
- Purification, crystallization and preliminary crystallographic analysis of human dihydrodipicolinate synthase-like protein (DHDPSL).
Bunker, Acta crystallographica. Section F, Structural biology and crystallization communications 2012 - Mutations in DHDPSL are responsible for primary hyperoxaluria type III.
Belostotsky, American journal of human genetics 2010 - Kidney cysts in patients with HOGA1 variants.
Patel, Clinical nephrology 2023 (PubMed)- GeneRIF: Kidney cysts in patients with HOGA1 variants.
- HOGA1 variants in Chinese patients with primary hyperoxaluria type 3: genetic features and genotype-phenotype relationships.
Ge, World journal of urology 2023 (PubMed)- GeneRIF: HOGA1 variants in Chinese patients with primary hyperoxaluria type 3: genetic features and genotype-phenotype relationships.
- Extended genetic analysis of exome sequencing for primary hyperoxaluria in pediatric urolithiasis patients with hyperoxaluria.
Zhao, Gene 2022 (PubMed)- GeneRIF: Extended genetic analysis of exome sequencing for primary hyperoxaluria in pediatric urolithiasis patients with hyperoxaluria.
- HOGA1 gene pathogenic variants in primary hyperoxaluria type III: Spectrum of pathogenic sequence variants, and phenotypic association.
Abid, Human mutation 2022 (PubMed)- GeneRIF: HOGA1 gene pathogenic variants in primary hyperoxaluria type III: Spectrum of pathogenic sequence variants, and phenotypic association.
- Mutations in HOGA1 do Not Confer a Dominant Phenotype Manifesting as Kidney Stone Disease.
Bar, The Journal of urology 2021 (PubMed)- GeneRIF: Mutations in HOGA1 do Not Confer a Dominant Phenotype Manifesting as Kidney Stone Disease.
- Nine novel HOGA1 gene mutations identified in primary hyperoxaluria type 3 and distinct clinical and biochemical characteristics in Chinese children.
Fang, Pediatric nephrology (Berlin, Germany) 2019 (PubMed)- GeneRIF: Study found that primary hyperoxaluria type 3 (PH3) was significantly diagnosed in Chinese children with urolithiasis. Nine novel HOGA1 mutations were identified in association with PH3, which provide a first-line investigation in Chinese PH3 patients. The eGFR was normal in all children with PH3. This finding contrasts with the early impairment of renal function in PH1 and PH2.
- Mutation Hot Spot Region in the HOGA1 Gene Associated with Primary Hyperoxaluria Type 3 in the Chinese Population.
Wang, Kidney & blood pressure research 2019 (PubMed)- GeneRIF: Potential mutation hot spot region (c.834_834+1) in the Chinese population and two novel mutations were found.
- Regulation of human 4-hydroxy-2-oxoglutarate aldolase by pyruvate and α-ketoglutarate: implications for primary hyperoxaluria type-3.
Huang, The Biochemical journal 2019 (PubMed)- GeneRIF: Biophysical and structural studies showed that pyruvate was a competitive inhibitor of HOGA1 with an inhibition constant in the micromolar range.
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HSERO_RS15785 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Herbaspirillum seropedicae SmR1
27% identity, 75% coverage
- mutant phenotype: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
KDGA_PICTO / Q6KZI8 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; 2-dehydro-3-deoxy-galactonate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase; EC 4.1.2.14; EC 4.1.2.51; EC 4.1.2.-; EC 4.1.2.21 from Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / KAW 2/3) (see paper)
Q6KZI8 2-dehydro-3-deoxy-D-gluconate aldolase (EC 4.1.2.51) from Picrophilus torridus (see paper)
26% identity, 69% coverage
- function: Involved in the degradation of glucose via the Entner- Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy- 6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2- keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3- deoxygalactonate (KDGal). It is equally active with both D- and L- glyceraldehyde.
catalytic activity: 2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3- phosphate + pyruvate (RHEA:17089)
catalytic activity: 2-dehydro-3-deoxy-D-gluconate = D-glyceraldehyde + pyruvate (RHEA:35583)
catalytic activity: 2-dehydro-3-deoxy-6-phospho-D-galactonate = D-glyceraldehyde 3-phosphate + pyruvate (RHEA:24464)
catalytic activity: 2-dehydro-3-deoxy-D-galactonate = D-glyceraldehyde + pyruvate (RHEA:46116)
subunit: Homotetramer; dimer of dimers.
kdgD / Q6FFQ1 5-dehydro-4-deoxyglucarate dehydratase subunit (EC 4.2.1.41) from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (see paper)
KDGD_ACIAD / Q6FFQ1 Probable 5-dehydro-4-deoxyglucarate dehydratase; 5-keto-4-deoxy-glucarate dehydratase; KDGDH; EC 4.2.1.41 from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (see paper)
Q6FFQ1 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Acinetobacter baylyi (see 2 papers)
ACIAD0130 5-dehydro-4-deoxyglucarate dehydratase (5-keto-4-deoxy-glucarate dehydratase) from Acinetobacter sp. ADP1
29% identity, 76% coverage
- catalytic activity: 5-dehydro-4-deoxy-D-glucarate + H(+) = 2,5-dioxopentanoate + CO2 + H2O (RHEA:24608)
- L-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti
Chen, Journal of bacteriology 2016 - “...D-glucarate dehydratase (ACIAD0128) and D-5-keto-4-deoxyglucarate dehydratase (ACIAD0130), which were overexpressed from E. coli as described in the work...”
- “...for clones carrying the A. baylyi proteins ACIAD0128 and ACIAD0130 used for synthesis of -KGSA, and Seiya Watanabe for clones carrying the P. putida and P....”
- New insights into the alternative D-glucarate degradation pathway
Aghaie, The Journal of biological chemistry 2008 - “...D-glucarate Gene ID ACIAD0127 ACIAD0128 ACIAD0130 ACIAD0131 ACIAD0244 ACIAD2275 ACIAD2417 ACIAD2876 Function D-Glucarate/D-Galactarate D-Glucarate dehydratase...”
- “...co-located on the genome (ACIAD0127, ACIAD0128, ACIAD0130, and ACIAD0131) and are respectively annotated as D-glucarate/D-galactarate permease, D-glucarate...”
Q9DCU9 4-hydroxy-2-oxoglutarate aldolase, mitochondrial from Mus musculus
28% identity, 75% coverage
HF996_00605 N-acetylneuraminate lyase from Mycoplasma sp. 1654_15
26% identity, 72% coverage
- Swine Conjunctivitis Associated with a Novel Mycoplasma Species Closely Related to Mycoplasma hyorhinis
Hennig-Pauka, Pathogens (Basel, Switzerland) 2020 - “...( nanE , HF996_00590), a sialic acid transporter (HF996_00595), a N-acetylneuraminate lyase ( nanA , HF996_00605), and a N-acetylmannosamine kinase ( nanK , locus tag HF996_00610), a predicted immunoglobuline A1 proteases (HF99600875), a glycosyl transferase (HF996_02470) possibly contributing to capsule formation [ 35 ], as well...”
Ta1157 dihydrodipicoline synthase related protein from Thermoplasma acidophilum DSM 1728
23% identity, 80% coverage
- Cell-Free Enzymatic Conversion of Spent Coffee Grounds Into the Platform Chemical Lactic Acid
Kopp, Frontiers in bioengineering and biotechnology 2019 - “...aldohexose dehydrogenase, AldT) and pProEx HTc-Ta1157 (encoding the 2-keto-3-deoxygluconate aldolase, KDGA), the genes Ta0754 and Ta1157 were amplified directly from Thermoplasma acidophilum DSM 1728 (DSMZ, Braunschweig, Germany) genomic DNA using the primers in Table S1 . The amplified Ta0754 DNA fragment was digested with BamHI/EcoRI and...”
- “...a KDG aldolase from Picrophilus torridus (Reher et al., 2010 ). Accordingly, the gene locus Ta1157 was recombinantly-produced in E. coli and the purified enzyme was shown to successfully cleave KDG to pyruvate and glyceraldehyde. Since this enzyme is also derived from the same organism as...”
- The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase
Reher, Journal of bacteriology 2010 - “...putative homologs from Thermoplasma species, T. acidophilum (Ta1157), and T. volcanium (TVN1228), suggesting the presence of functional KDG-specific aldolases...”
- “...Pto-KDGA in T. acidophilum and T. volcanii Ta1157 and TVN1228; Sso-KD(P)GA, S. solfataricus gi:2879782; Tte-KD(P)GA, T. tenax gi:41033593; Eco-NAL, gi:128526;...”
SSA_0078 / A3CK37 N-acetylneuraminate lyase subunit (EC 4.1.3.3) from Streptococcus sanguinis (strain SK36) (see 3 papers)
SSA_0078 N-acetylneuraminate lyase, putative from Streptococcus sanguinis SK36
24% identity, 93% coverage
SXYL_02665 dihydrodipicolinate synthase family protein from Staphylococcus xylosus
24% identity, 94% coverage
- Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro
Leroy, Microorganisms 2021 - “...hydrolase 12.1 7.6 SXYL_01476-78 dapHBA 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N -acetyltransferase, 4.1 * 2.5 * 4-hydroxy-tetrahydrodipicolinate reductase, synthase SXYL_02665 Dihydrodipicolinate synthase 2.0 3.2 SXYL_00325 ldhD d -lactate dehydrogenase 10.3 11.9 COFACTOR, VITAMIN SYNTHESIS SXYL_01097-100 ribDEBAH Riboflavin biosynthesis 2.8 * 3.7 * SXYL_00734-35 ecfA2T Energy-coupling factor transporter 2.2 * SXYL_01194...”
A1VMN2 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Polaromonas naphthalenivorans CJ2 (see paper)
31% identity, 58% coverage
CLP_0032 N-acetylneuraminate lyase from Clostridium butyricum E4 str. BoNT E BL5262
26% identity, 77% coverage
WP_005948757 N-acetylneuraminate lyase from Fusobacterium varium
26% identity, 77% coverage
- Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma.
Wang, Marine drugs 2018 - “...(WP_033546508.1), Clostridium perfringens (Q9S4K9), Lactobacillus plantarum (P59407), Staphylococcus carnosus (B9DIJ2), Haemophilus influenza (P44539), Fusobacterium varium (WP_005948757), Staphylococcus simulans (WP_002480218), Clostridium colicanis (WP_002599534.1), Aggregatibacter actinomycetemcomitans (WP_005566544.1), Haemophilus haemolyticus (WP_046942498.1), Actinobacillus suis (WP_015674266.1), Gallibacterium genomosp (WP_039135793.1), Clostridium butyricum (WP_058229325.1), Clostridium hiranonis (WP_040410204.1), Leclercia adecarboxylata (WP_039030055.1), Peptoclostridium difficile (WP_044213638.1),...”
Q27818 N-acetylneuraminate lyase from Trichomonas vaginalis
26% identity, 71% coverage
- Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison
Singh, Bioinformation 2012 - “...screened against the Database of Essential Genes. BLASTP search for N-acetylneuraminate lyase of T. vaginalis (Q27818) was performed to select the related sequences in different organisms. Four other N-acetylneuraminate lyase sequences in Haemophilus parainfluenzae (E1W1D4), Pasteurella dagmatis (C9PLY8), Haemophilus influenza (A4N656) and Aggregatibacter actinomycetemcomitans (G4B7P9) were...”
XP_001323296 dihydrodipicolinate synthase from Trichomonas vaginalis G3
26% identity, 71% coverage
- Trichomonas vaginalis virulence factors: an integrative overview
Hirt, Sexually transmitted infections 2013 - “...3.2.1.24 -mannosidase XP_001579222 Prokaryotes 3.2.1.25 -mannosidase XP_001322689 Proteobacteria 3.2.1.51 -fucosidase XP_001316088 Bacteria 4.1.3.3 N-acetylneuraminate lyase XP_001323296 Pasteurellaceae (-proteobacteria) 5.1.3.8 Acylglucosamine 2-epimerase XP_001308218 Bacteroidetes 3.2.1.45 Glucosylceramidase XP_001279673 Bacteroidetes *For details about inference of LGT methodology and gene and enzyme characteristics see ref. 26. Note that some of...”
D4A2K1 4-hydroxy-2-oxoglutarate aldolase, mitochondrial from Rattus norvegicus
27% identity, 88% coverage
CTL0615 dihydrodipicolinate synthase from Chlamydia trachomatis 434/Bu
28% identity, 91% coverage
Q1QUM4 Probable 5-dehydro-4-deoxyglucarate dehydratase from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)
31% identity, 58% coverage
BCAM2512 putative 5-dehydro-4-deoxyglucarate dehydratase from Burkholderia cenocepacia J2315
26% identity, 75% coverage
- Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms
Slachmuylders, PloS one 2018 - “...gudD ) Glucarate dehydratase 2.6 1.5 BCAM2511 ( garD ) Putative galactarate dehydratase 2.3 1.6 BCAM2512 5-dehydro-4-deoxyglucarate dehydratase 2.2 2.9 BCAM2514* Putative fatty aldehyde dehydrogenase 2.0 1.6 Quorum sensing BCAM1870 ( cepI ) N-acylhomoserine lactone synthase CepI - 1.5 BCAM0239a ( cciI ) N-acylhomoserine lactone synthase...”
- “...of BH vs. Ctrl / TOB+BH vs TOB). The involved enzymes are gudD (glucarate dehydratase), BCAM2512 (5-keto-4-deoxyglutarate dehydratase) and BCAM2514 (-ketoglutarate semialdehyde dehydrogenase). For the reactions depicted in grey no significant differential expression in either BH vs. Ctrl or TOB+BH vs TOB was observed. The expression...”
Pf1N1B4_1110 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Pseudomonas fluorescens FW300-N1B4
27% identity, 93% coverage
- mutant phenotype: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
B7WZA5 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Comamonas testosteroni (see paper)
29% identity, 61% coverage
RHE_RS14280 dihydrodipicolinate synthase family protein from Rhizobium etli CFN 42
30% identity, 75% coverage
HOGA1_EMENI / Q5BD77 Probable 4-hydroxy-2-oxoglutarate aldolase, mitochondrial; Dihydrodipicolinate synthase-like; DHDPS-like protein; Probable 2-keto-4-hydroxyglutarate aldolase; Probable KHG-aldolase; EC 4.1.3.16 from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
AN1503 dihydrodipicolinate synthase-like protein AN1503; EC 4.-.-.- from Emericella nidulans (see paper)
28% identity, 94% coverage
- function: Catalyzes the final step in the metabolic pathway of hydroxyproline (By similarity). Involved in osmoadaptation.
catalytic activity: (4S)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate (RHEA:35639)
catalytic activity: (4R)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate (RHEA:30687) - CharProtDB Description: 0; Source:AspGD
NANA_LACPL / P59407 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (Lactobacillus plantarum) (see paper)
lp_3568 N-acetylneuraminate lyase from Lactobacillus plantarum WCFS1
27% identity, 76% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - Role of the luxS gene in bacteriocin biosynthesis by Lactobacillus plantarum KLDS1.0391: A proteomic analysis.
Jia, Scientific reports 2017 - “...0.018 18 A0A0P7HQL7 NADH oxidase 0.374619026 0.019 19 Q88WV2 nrdR Transcriptional regulator 0.391799787 0.025 20 P59407 E4.1.3.3, nanA, NPL N-acetylneuraminate lyase 0.169766187 0.027 21 A0A0G9FD31 E2.4.1.8, mapA Maltose phosphorylase 0.127697815 0.030 22 A0A0R2GC45 alsD, budA, aldC Alpha-acetolactate decarboxylase 0.42085536 0.046 23 A0A0G9F7H9 Malolactic regulator 0.423614866 0.046...”
- First functional and mutational analysis of group 3 N-acetylneuraminate lyases from Lactobacillus antri and Lactobacillus sakei 23K.
García-García, PloS one 2014 - “...from H. influenzae, C. perfringens, L. plantarum and E. coli K-12 (Uniprot codes: P44539, Q9S4K9, P59407 and P0A6L4, respectively). The sequences were aligned using ClustalW [22] and ESPript [23] . Automatic homology modeling was performed through the MODWEB modeling server ( http://salilab.org/modweb ) using the E....”
- The Lp_3561 and Lp_3562 Enzymes Support a Functional Divergence Process in the Lipase/Esterase Toolkit from Lactobacillus plantarum
Esteban-Torres, Frontiers in microbiology 2016 - “...involved in the catabolism of N -acetyl- D -neuraminic acid, a sialic acid (Lp_3566 to Lp_3568). Discussion In fermented foods, microorganisms are in contact with food substrates and their metabolic activities influence food aroma. Numerous ORFs encoding putative esterases/lipases have been found in the genome of...”
- “...these genes are inserted as a 8903 bp region contiguous to the genes nanAKE ( lp_3568 , lp_3576 , and lp_3566 ) that encode proteins involved in the catabolism of N -acetyl- D -neuraminic acid, the most abundant and widely studied sialic acid ( Tanner, 2005...”
SH0282 N-acetylneuraminate lyase subunit from Staphylococcus haemolyticus JCSC1435
27% identity, 78% coverage
Deide_3p00120 putative dihydrodipicolinate synthase from Deinococcus deserti VCD115
29% identity, 64% coverage
- Evolution of lysine biosynthesis in the phylum deinococcus-thermus
Nishida, International journal of evolutionary biology 2012 - “...Deinococcus radiodurans DR_1365 DR_2008 DR_1758 Deinococcus geothermalis Dgeo_1127 Dgeo_1782 Dgeo_0790 Deinococcus deserti Deide_11430 Deide_15740 Deide_1p00310, Deide_3p00120, Deide_3p01100 Deide_12830, Deide_21880 Deinococcus maricopensis Deima_1822 Deima_2680 Deima_2660 Deinococcus proteolyticus Deipr_0941 Deipr_0985 Deipr_1377* Deipr_1378* Deipr_1376* Deipr_0627, Deipr_1375* Truepera radiovictrix Trad_0977 Trad_0289 Trad_1893 Trad_0134 *More than 3 genes are clustered....”
SCO6292 dihydropicolinate synthase from Streptomyces coelicolor A3(2)
26% identity, 96% coverage
- A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2)
Kotowska, Frontiers in microbiology 2019 - “...(pfam13510) SCO6291 511 D-hydroxyproline dehydrogenase subunit (oxidoreductase) FadH2 (COG0446), soxA (TIGR01372), gltD (PRK12810), Fer2_BFD (pfam04324) SCO6292 298 1 -pyrroline-4-hydroxy-2-carboxylate deaminase DHDPS-like (cd00408), DapA (COG0329), dapA (TIGR00674) SCO6293 333 L-hydroxyproline epimerase (proline racemase, 4-hydroxyproline epimerase) Pro_racemase (pfam05544) SCO5912 865 Class M9 secreted zinc metallopeptidase, collagenase Peptidase_M9_N (pfam08453),...”
- “...LhpE, LhpB, and LhpF ( Watanabe et al., 2012 ; Figure 6A ). SCO6293 and SCO6292 are homologs of L-Hyp epimerase and Pyr4H2C deaminase, respectively, with amino acid sequence identity 37 and 33% to respective proteins LhpA and LhpC from P. aeruginosa . L-Hyp catabolic pathway...”
nanA / Q9S4K9 N-acetylneuraminate lyase (EC 4.1.3.3) from Clostridium perfringens (strain 13 / Type A) (see 6 papers)
NANA_CLOPE / Q9S4K9 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Clostridium perfringens (strain 13 / Type A) (see 3 papers)
nanA / GB|CAA73375.1 N-acetylneuraminate lyase; EC 4.1.3.3 from Clostridium perfringens (see 4 papers)
CPE0185 acylneuraminate lyase from Clostridium perfringens str. 13
CPF_0178 N-acetylneuraminate lyase from Clostridium perfringens ATCC 13124
25% identity, 76% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - RNA-seq analysis of virR and revR mutants of Clostridium perfringens
Low, BMC genomics 2016 - “...lower level in the revR mutant [ 15 ]. Other genes, including nanI, ccp and cpe0185, which were previously found to be expressed at a higher level in the revR mutant [ 15 ], showed no significant change in their expression levels in the current study....”
- Regulation of virulence by the RevR response regulator in Clostridium perfringens
Hiscox, Infection and immunity 2011 - “...tag Fold ratiob P valuec Function nanI CPE0725 CPE0185 CPE0173 CPE0846 23.9 16.9 7.02 6.1 1.8E05 8.5E06 4.1E04 5.0E03 Sialidase (NanI) Acylneuraminate lyase...”
- Biochemical and structural basis of sialic acid utilization by gut microbes
Bell, The Journal of biological chemistry 2023 - “...P.multocida Q9CKB0 4IMD ( 112 ) 4IMG 4IMC 4IME 4IMF Cp NanA C.perfringens str 13 Q9S4K9 ( 111 , 113 ) Lp NanA L.plantarum ATCC BAA-793 P59407 ( 110 ) Ec NanA E.coli K12 P0A6L4 1NAL ( 114 ) 4BWL 2WNN 2WNQ 2WPB R.gnavus ATCC29149 A7B555...”
- Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma.
Wang, Marine drugs 2018 - “...sugar-binding domain GXDE of N -acetylneuraminate lyases. Pasteurella multocida (WP_046339671.1), Escherichia coli (WP_033546508.1), Clostridium perfringens (Q9S4K9), Lactobacillus plantarum (P59407), Staphylococcus carnosus (B9DIJ2), Haemophilus influenza (P44539), Fusobacterium varium (WP_005948757), Staphylococcus simulans (WP_002480218), Clostridium colicanis (WP_002599534.1), Aggregatibacter actinomycetemcomitans (WP_005566544.1), Haemophilus haemolyticus (WP_046942498.1), Actinobacillus suis (WP_015674266.1), Gallibacterium genomosp (WP_039135793.1),...”
- First functional and mutational analysis of group 3 N-acetylneuraminate lyases from Lactobacillus antri and Lactobacillus sakei 23K
García-García, PloS one 2014 - “...NALs from H. influenzae, C. perfringens, L. plantarum and E. coli K-12 (Uniprot codes: P44539, Q9S4K9, P59407 and P0A6L4, respectively). The sequences were aligned using ClustalW [22] and ESPript [23] . Automatic homology modeling was performed through the MODWEB modeling server ( http://salilab.org/modweb ) using the...”
- Molecular characterization of a novel N-acetylneuraminate lyase from Lactobacillus plantarum WCFS1
Sánchez-Carrón, Applied and environmental microbiology 2011 - “...and E. coli K-12 (GenBank accession numbers Q9S4K9, AAB42182, P44539, and AAC76257), respectively. LpNAL is more closely related to Haemophilus influenzae...”
- Pasteurella multocida sialic acid aldolase: a promising biocatalyst
Li, Applied microbiology and biotechnology 2008 - “...and E. coli K-12 (GenBank accession nos. P44539, AAB42182, Q9S4K9, and AAC76257). The optimal expression condition for PmNanA was incubation at 20C for 24 h...”
- Molecular identification of hyaluronate lyase, not hyaluronidase, as an intrinsic hyaluronan-degrading enzyme in Clostridium perfringens strain ATCC 13124
Kumon, Scientific reports 2024 (no snippet)
WP_002480218 N-acetylneuraminate lyase from Staphylococcus simulans
27% identity, 78% coverage
- Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma.
Wang, Marine drugs 2018 - “...(Q9S4K9), Lactobacillus plantarum (P59407), Staphylococcus carnosus (B9DIJ2), Haemophilus influenza (P44539), Fusobacterium varium (WP_005948757), Staphylococcus simulans (WP_002480218), Clostridium colicanis (WP_002599534.1), Aggregatibacter actinomycetemcomitans (WP_005566544.1), Haemophilus haemolyticus (WP_046942498.1), Actinobacillus suis (WP_015674266.1), Gallibacterium genomosp (WP_039135793.1), Clostridium butyricum (WP_058229325.1), Clostridium hiranonis (WP_040410204.1), Leclercia adecarboxylata (WP_039030055.1), Peptoclostridium difficile (WP_044213638.1), Planomicrobium glaciei (WP_053167706.1),...”
4woqC / D5Q364 Crystal structures of cdnal from clostridium difficile in complex with ketobutyric
24% identity, 94% coverage
- Ligand: 2-ketobutyric acid (4woqC)
nanA sialic acid lyase from Clostridium perfringens (see paper)
25% identity, 76% coverage
CD2240 N-acetylneuraminate lyase from Clostridium difficile 630
24% identity, 94% coverage
NANA_PASMU / Q9CKB0 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetyl-D-neuraminic acid lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Pasteurella multocida (strain Pm70) (see paper)
Q9CKB0 N-acetylneuraminate lyase (EC 4.1.3.3) from Pasteurella multocida (see 2 papers)
PM1715 NanA from Pasteurella multocida subsp. multocida str. Pm70
26% identity, 77% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - Biochemical and structural basis of sialic acid utilization by gut microbes
Bell, The Journal of biological chemistry 2023 - “...) Bf NanU B.fragilis NCTC 9343 Q5LEN2 4L7T ( 102 ) Aldolases Pm NanA P.multocida Q9CKB0 4IMD ( 112 ) 4IMG 4IMC 4IME 4IMF Cp NanA C.perfringens str 13 Q9S4K9 ( 111 , 113 ) Lp NanA L.plantarum ATCC BAA-793 P59407 ( 110 ) Ec NanA...”
- Pasteurella multocida sialic acid aldolase: a promising biocatalyst
Li, Applied microbiology and biotechnology 2008 - “...gene sequence encoding NanA (Pm1715, GenBank accession no. Q9CKB0) has been identified (Steenbergen et al. 2005). Previously, we reported the cloning of a NanA...”
- “...for P. multocida genomic strain PM70 (GenBank accession no. Q9CKB0), the DNA sequence of the cloned gene differs on six bases: T228C, T303C, C624T, G777A,...”
- A glyco-engineering approach for site-specific conjugation to Fab glycans
Jaramillo, mAbs 2023 - “...The synthesis of N -azidoacetylneuraminic acid (Neu5NAz) was performed using a recombinant form of the Pm1715 sialic acid aldolase from Pasteurella multocida . The reaction mix with the Pm1715 sialic acid aldolase included 20mM ManNAz, 100mM sodium pyruvate and 100mM Tris pH 8.6, and was incubated...”
- PmST2: a novel Pasteurella multocida glycolipid α2-3-sialyltransferase
Thon, Glycobiology 2011 - “...Vinogradov, Li, et al. 2005), a sialic acid aldolase/lyase (Pm1715) (Li et al. 2008) and two sialidases NanB (cleaves both 2-3- and 2-6-linked sialyl lactose)...”
- “...al. 2000), one sialic acid aldolase/lyase (encoded by gene Pm1715) (Li et al. 2008), at least one CMP-sialic acid synthetase (encoded by gene Pm0187) (gene...”
- Pasteurella multocida sialic acid aldolase: a promising biocatalyst
Li, Applied microbiology and biotechnology 2008 - “...1972), and a hypothetic gene sequence encoding NanA (Pm1715, GenBank accession no. Q9CKB0) has been identified (Steenbergen et al. 2005). Previously, we...”
- “...protein in a pET22b (+) vector. Compared to the Pm1715 gene sequence reported for P. multocida genomic strain PM70 (GenBank accession no. Q9CKB0), the DNA...”
- Sialic Acid metabolism and systemic pasteurellosis
Steenbergen, Infection and immunity 2005 - “...acid cytidylyltransferase in P. multocida. A sialate aldolase (pm1715) mutant unable to initiate dissimilation of internalized sialic acid was not attenuated in...”
- “...an 500-bp internal fragment of pm1715 using the gene-specific forward (5-GGATGGTCTTTAC GTTGGCGGCAGTAC-3) and reverse (5-GATTTGACGAGCGCGCACAC CATTGAC-3)...”
C9PLY8 N-acetylneuraminate lyase from Pasteurella dagmatis ATCC 43325
26% identity, 77% coverage
- Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison
Singh, Bioinformation 2012 - “...sequences in different organisms. Four other N-acetylneuraminate lyase sequences in Haemophilus parainfluenzae (E1W1D4), Pasteurella dagmatis (C9PLY8), Haemophilus influenza (A4N656) and Aggregatibacter actinomycetemcomitans (G4B7P9) were selected. The physicochemical properties were calculated by ProtParam, motif prediction by motif search ( www.genome.jp/tools/motif/ ), secondary structures prediction by GOR IV...”
ACICU_00871 dihydrodipicolinate synthase/N-acetylneuraminate lyase from Acinetobacter baumannii ACICU
ACICU_RS04560 dihydrodipicolinate synthase family protein from Acinetobacter baumannii ACICU
25% identity, 90% coverage
A1S_0203 hypothetical protein from Acinetobacter baumannii ATCC 17978
27% identity, 71% coverage
NANA_HAEIN / P44539 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see 2 papers)
HI0142 N-acetylneuraminate lyase (nanA) from Haemophilus influenzae Rd KW20
26% identity, 79% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma.
Wang, Marine drugs 2018 - “...(WP_046339671.1), Escherichia coli (WP_033546508.1), Clostridium perfringens (Q9S4K9), Lactobacillus plantarum (P59407), Staphylococcus carnosus (B9DIJ2), Haemophilus influenza (P44539), Fusobacterium varium (WP_005948757), Staphylococcus simulans (WP_002480218), Clostridium colicanis (WP_002599534.1), Aggregatibacter actinomycetemcomitans (WP_005566544.1), Haemophilus haemolyticus (WP_046942498.1), Actinobacillus suis (WP_015674266.1), Gallibacterium genomosp (WP_039135793.1), Clostridium butyricum (WP_058229325.1), Clostridium hiranonis (WP_040410204.1), Leclercia adecarboxylata (WP_039030055.1),...”
- First functional and mutational analysis of group 3 N-acetylneuraminate lyases from Lactobacillus antri and Lactobacillus sakei 23K
García-García, PloS one 2014 - “...characterized NALs from H. influenzae, C. perfringens, L. plantarum and E. coli K-12 (Uniprot codes: P44539, Q9S4K9, P59407 and P0A6L4, respectively). The sequences were aligned using ClustalW [22] and ESPript [23] . Automatic homology modeling was performed through the MODWEB modeling server ( http://salilab.org/modweb ) using...”
- Molecular characterization of a novel N-acetylneuraminate lyase from Lactobacillus plantarum WCFS1
Sánchez-Carrón, Applied and environmental microbiology 2011 - “...coli K-12 (GenBank accession numbers Q9S4K9, AAB42182, P44539, and AAC76257), respectively. LpNAL is more closely related to Haemophilus influenzae NAL (Protein...”
- The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase
Reher, Journal of bacteriology 2010 - “...sapiens (gi:13540533), Haemophilus influenzae (Swiss Prot P44539), and Escherichia coli (Swiss Prot P06995); for KD(P)GA, Sulfolobus solfataricus (gi:2879782),...”
- Pasteurella multocida sialic acid aldolase: a promising biocatalyst
Li, Applied microbiology and biotechnology 2008 - “...perfringens, and E. coli K-12 (GenBank accession nos. P44539, AAB42182, Q9S4K9, and AAC76257). The optimal expression condition for PmNanA was incubation at 20C...”
- An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates
Buchanan, The Biochemical journal 1999 - “...2022 NAL from E. coli (P06995) and H. influenzae (P44539), and DHDPS from E. coli (P05640), H. influenzae (P43797) and B. subtilis (Q04796) were aligned with S....”
- Sialic acid mediated transcriptional modulation of a highly conserved sialometabolism gene cluster in Haemophilus influenzae and its effect on virulence
Jenkins, BMC microbiology 2010 - “...independently by insertion of kan R at NruI and BglII sites respectively. For nanA ( HI0142 ), insertion of kan R was achieved following partial digestion with Mfe1 and siaR ( HI0143 ) was inactivated by inserting kan R at an MfeI site. Table 1 Oligonucleotide...”
- “...The genes for sialic acid catabolism ( HI0140 ( nagA ), HI0141 ( nagB ), HI0142 ( nanA ), HI0144 ( nanK ), HI0145 ( nanE ) and including HI0143 ( siaR )) and procurement ( HI0146 ( siaP ), HI1047 ( siaQM ), HI0148 )...”
- Pasteurella multocida sialic acid aldolase: a promising biocatalyst
Li, Applied microbiology and biotechnology 2008 - “...perfringens A99 (Traving et al. 1997), Haemophilus influenzae (HI0142; Lilley et al. 1998), and Trichomonas vaginalis (Meysick et al. 1996). The X-ray...”
- “...identity, respectively, with the NanAs from H. influenzae (HI0142), T. vaginalis, C. perfringens, and E. coli K-12 (GenBank accession nos. P44539, AAB42182,...”
- Nontypeable Haemophilus influenzae strain 2019 produces a biofilm containing N-acetylneuraminic acid that may mimic sialylated O-linked glycans
Greiner, Infection and immunity 2004 - “...lyase gene, nanA (The Institute for Genome Research locus HI0142), was generated. The DNA sequence of H. influenzae Rd KW20 was used to construct two primers,...”
- Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
Gmuender, Genome research 2001 - “...hi0008 hi1133 hi0140 hi0117 hi1154 hi1218 hi0537 hi0373 hi0142 hi1227 hi0505 hi0544 hi1167 hi0536 hi0087 hi0089 hi1367 hi1511 hi0447 hi1172 hi0564 hi0088 hi1545...”
- Sialic acid metabolism's dual function in Haemophilus influenzae
Vimr, Molecular microbiology 2000 (PubMed)- “...infant-rat infection model. The predicted H. influenzae homologue (HI0142) of the E. coli sialic acid aldolase structural gene, nanA, was subcloned and...”
- “...resulting H. influenzae aldolase mutants showed that: (i) HI0142 is essential for sialic acid degradation; (ii) the products of the open reading frames (ORFs)...”
C8P490 N-acetylneuraminate lyase (EC 4.1.3.3) from Limosilactobacillus antri (see paper)
22% identity, 93% coverage
NANA_STAA8 / Q2G160 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see 4 papers)
NANA_STAAR / Q6GK01 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Staphylococcus aureus (strain MRSA252) (see paper)
Q2G160 N-acetylneuraminate lyase (EC 4.1.3.3) from Staphylococcus aureus (see 2 papers)
Q6GK01 N-acetylneuraminate lyase (EC 4.1.3.3) from Staphylococcus aureus (see paper)
MW0292 N-acetylneuraminate lyase subunit from Staphylococcus aureus subsp. aureus MW2
SAOUHSC_00295 N-acetylneuraminate lyase subunit, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0315 N-acetylneuraminate lyase subunit from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL0312 N-acetylneuraminate lyase from Staphylococcus aureus subsp. aureus COL
YP_498885 N-acetylneuraminate lyase from Staphylococcus aureus subsp. aureus NCTC 8325
26% identity, 77% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate (PubMed:23418011, PubMed:27943302). In vitro, catalyzes the reaction between fluoropyruvate and ManNAc, albeit much less efficiently than with pyruvate as donor, leading to the synthesis of fluorinated analogs of N-acetylneuraminic acid (PubMed:26537532). Variants are useful catalysts of reactions between fluoropyruvate and unnatural aldehyde substrates (PubMed:26537532).
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer. - The SaeR/S gene regulatory system is essential for innate immune evasion by Staphylococcus aureus
Voyich, The Journal of infectious diseases 2009 - “...2.89 ME & ES MW0239 lrgB antiholin-like protein LrgB 2.57 & 1.92 ME & ES MW0292 nanA N-acetylneuraminate lyase 2.19 ME MW0297 geh glycerol ester hydrolase 4.09 & 3.00 ME & ES MW0394 set26 exotoxin homolog 16.46 ME MW0568 adh1 alcohol dehydrogenase 1.65 & 4.34 ME...”
- Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy
Timms, Chembiochem : a European journal of chemical biology 2013 - “...natural, cysteine-free, NAL enzymes. A putative sequence from S. aureus was identified (Uniprot accession number Q2G160) and we amplified the gene ( nan A) by PCR (Table S2) and cloned it into the expression vector pKK223-3. After induction of protein expression with IPTG, a band of...”
- Modulation of cell wall synthesis and susceptibility to vancomycin by the two-component system AirSR in Staphylococcus aureus NCTC8325
Sun, BMC microbiology 2013 - “...Cap8M 2.02 SAOUHSC_00127 cap5N Cap5N protein/UDP-glucose 4-epimerase, putative 2.14 SAOUHSC_00222 tagB TagB protein, putative 2.24 SAOUHSC_00295 nanA N-acetylneuraminate lyase 2.02 SAOUHSC_00469 spoVG Regulatory protein SpoVG 2.51 SAOUHSC_00545 sdrD sdrD protein, putative 3.68 SAOUHSC_00640 tagA Teichoic acid biosynthesis protein 2.08 SAOUHSC_00812 clfA Clumping factor, ClfA 4.72 SAOUHSC_00918...”
- Sialic acid catabolism in Staphylococcus aureus
Olson, Journal of bacteriology 2013 - “...(NC_000907). This cluster included putative nanA (ORF SAUSA300_0315) and nanT (ORF SAUSA300_0314) genes that appeared to be cotranscribed in a two-gene...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...putative 28.3 (2.1) 32.0 (1.7) SACOL0311 nanT Sodium:solute symporter family protein 38.1 (1.7) 13.2 (1.7) SACOL0312 nanA N-acetylneuraminate lyase 54.8 (1.7) 3.5 (1.3) 14.4 (1.7) SACOL0400 ( ulaA ) Transport protein SgaT, putative 13.7 (1.4) 12.6 (1.4) SACOL0401 ( ulaB ) Conserved hypothetical protein 20.7 (1.4)...”
- “...meshwork, lens, VH and retina, and its concentration seems to increase with aging [37] . SACOL0312 and SACOL0311 encode a putative sodium:solute symporter protein (NanT) and N-acetylneuraminate lyase (NanA), respectively. NanA converts N-acetylneuraminate to N-acetylmannosamine and pyruvate [38] . Recently, it was shown that nanA and...”
- Response of Staphylococcus aureus to salicylate challenge
Riordan, Journal of bacteriology 2007 - “...D D D D D SACOL1734 SACOL0311 SACOL0312 SACOL0204 SACOL2386 SACOL0746 SACOL2287 SACOL0557 SACOL0211 SACOL0224 SACOL0314 SACOL0966 SACOL1838 SACOL0214 SACOL0200...”
- Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy.
Timms, Chembiochem : a European journal of chemical biology 2013 - GeneRIF: Solved is the X-ray crystal structures of the wild-type S. aureus N-acetylneuraminate lyase, both in the absence of, and in complex with, pyruvate.
NANA_FUSNN / Q8RDN6 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355) (see paper)
25% identity, 77% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer.
SA0304 N-acetylneuraminate lyase from Staphylococcus aureus subsp. aureus N315
SAV0315 N-acetylneuraminate lyase from Staphylococcus aureus subsp. aureus Mu50
26% identity, 77% coverage
BPHYT_RS24155 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Burkholderia phytofirmans PsJN
26% identity, 92% coverage
- mutant phenotype: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
PFLU0849 5-dehydro-4-deoxyglucarate dehydratase from Pseudomonas fluorescens SBW25
29% identity, 58% coverage
NANA_MEDG7 / A7B555 N-acetylneuraminate lyase; NAL; Neu5Ac lyase; N-acetylneuraminate pyruvate-lyase; N-acetylneuraminic acid aldolase; Sialate lyase; Sialic acid aldolase; Sialic acid lyase; EC 4.1.3.3 from Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9) (Ruminococcus gnavus) (see paper)
RUMGNA_02692 hypothetical protein from Ruminococcus gnavus ATCC 29149
22% identity, 90% coverage
- function: Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate (PubMed:31636419). Cannot use 2,7-anhydro-Neu5Ac (PubMed:31636419). Involved in the degradation of sialic acid, which is present in the host mucus layer and represents a much-coveted source of nutrients for R.gnavus, a prevalent member of the normal gut microbiota (PubMed:31636419).
catalytic activity: aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)
subunit: Homotetramer.
disruption phenotype: Deletion of the nan cluster abolishes the ability to grow on sialylated substrates (PubMed:31636419). The fitness of the nan mutant is significantly impaired, with a reduced ability to colonize the mucus layer in monocolonized mice (PubMed:31636419). - Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut
Bell, Nature microbiology 2019 - “...for proteins encoding RUMGNA_02698, the predicted solute binding protein (SBP) giving specificity to ABC transporters, RUMGNA_02692 (sialic acid aldolase), the first protein of the canonical Neu5Ac metabolism, and RUMGNA_02695, a putative oxidoreductase, suggesting that these proteins may be associated with 2,7-anhydro-Neu5Ac metabolism ( Supplementary Figure 1...”
- “...R. gnavus sialic acid aldolase for Neu5Ac The substrate specificity of recombinant sialic acid aldolase (RUMGNA_02692; Rg NanA), was determined using a coupled activity assay where pyruvate released during the conversion of Neu5Ac to ManNAc is converted to lactate by a lactate dehydrogenase and the subsequent...”
- Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent
Crost, PloS one 2013 - “...which encodes a predicted ManNAc-6-P epimerase converting ManNAc-6-P into N -acetylglucosamine-6-P (GlcNAc-6-P) followed by nanA (RUMGNA_02692) encoding a putative Neu5Ac lyase involved in the breaking down of Neu5Ac into N -acetylmannosamine (ManNAc) and phosphoenolpyruvate (PEP). nanK (RUMGNA_02691) is the last gene of the cluster, coding for...”
- Biochemical and structural basis of sialic acid utilization by gut microbes.
Bell, The Journal of biological chemistry 2023 - “...Ec NanA E.coli K12 P0A6L4 1NAL ( 114 ) 4BWL 2WNN 2WNQ 2WPB R.gnavus ATCC29149 A7B555 6RAB ( 15 ) 6RD1 6RB7 Sphingobacterium ( 115 ) Bf NanL B.fragilis NCTC 9343 Q5LEN8 ( 104 ) Anomerase Ec NanQ (YhcH) E.coli K12 P45424 ( 99 ) Oxidoreductase...”
B9DIJ2 N-acetylneuraminate lyase (EC 4.1.3.3) from Staphylococcus carnosus (see paper)
26% identity, 97% coverage
SCO2543 5-dehydro-4-deoxyglucarate dehydratase from Streptomyces coelicolor A3(2)
29% identity, 55% coverage
- Genome-wide identification and characterization of reference genes with different transcript abundances for Streptomyces coelicolor
Li, Scientific reports 2015 - “...polymerase specialized sigma subunit, sigma 24homolog 0.62 SCO1519 [L] Holliday junction resolvasome, DNA-binding subunit 0.93 SCO2543 [M] Dihydrodipicolinate synthase/N-acetylneuraminate lyase 0.49 SCO6185 [M] Glycosyltransferase 0.80 SCO1544 [O] Protein-disulfide isomerase 1.97 SCO1962 [P] Ca 2+ /H + antiporter 0.68 SCO1596 [T] Osmosensitive K + channel histidine kinase...”
- “...8 SCO1596 0.779 SCO1596 0.53 SCO4758 0.64 SCO0301 9 SCO1519 0.803 SCO6218 0.859 SCO2742 0.72 SCO2543 10 SCO2543 0.838 SCO2543 0.885 SCO1962 0.75 SCO1596 11 SCO0301 0.882 SCO1519 0.918 hrdB 0.86 SCO6218 12 SCO6218 0.926 SCO0301 0.928 SCO1519 0.92 SCO1519 13 SCO2742 0.97 SCO2742 0.98 SCO1453...”
1f74A / P44539 Crystal structure analysis of n-acetylneuraminate lyase from haemophilus influenzae: crystal form ii complexed with 4-deoxy-sialic acid (see paper)
26% identity, 79% coverage
- Ligand: 6,7,8,9-tetrahydroxy-5-methylcarboxamido-2-oxononanoic acid (1f74A)
4imgA / Q9CKB0 Crystal structure of pasteurella multocida n-acetyl-d-neuraminic acid lyase k164 mutant complexed with n-glycolylneuraminic acid (see paper)
25% identity, 97% coverage
- Ligand: 3,5-dideoxy-5-[(hydroxyacetyl)amino]-d-glycero-d-galacto-non-2-ulosonic acid (4imgA)
SP_1676 N-acetylneuraminate lyase, putative from Streptococcus pneumoniae TIGR4
22% identity, 93% coverage
A4N656 N-acetylneuraminate lyase from Haemophilus influenzae R3021
26% identity, 77% coverage
- Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison
Singh, Bioinformation 2012 - “...organisms. Four other N-acetylneuraminate lyase sequences in Haemophilus parainfluenzae (E1W1D4), Pasteurella dagmatis (C9PLY8), Haemophilus influenza (A4N656) and Aggregatibacter actinomycetemcomitans (G4B7P9) were selected. The physicochemical properties were calculated by ProtParam, motif prediction by motif search ( www.genome.jp/tools/motif/ ), secondary structures prediction by GOR IV method, predicting Pfam...”
PS417_04195 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Pseudomonas simiae WCS417
PS417_04195 5-dehydro-4-deoxyglucarate dehydratase from Pseudomonas simiae
29% identity, 58% coverage
- mutant phenotype: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
- Genome-wide identification of bacterial plant colonization genes
Cole, PLoS biology 2017 - “...on single carbon sources ( Fig 4 ). Some of these genes (e.g. PS417_00160 , PS417_04195 , operon 1751 comprising genes PS417_22130 22145 ) appear to be involved in the metabolism of specific sugars (galactose, galacturonate, and glucose, respectively), suggesting a role for these carbohydrate sources...”
PAAG_03793 dihydrodipicolinate synthase from Paracoccidioides lutzii Pb01
27% identity, 66% coverage
- Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
Freitas, Journal of fungi (Basel, Switzerland) 2020 - “...PAAG_02682 fructose-1,6-bisphosphatase * 0.933 PAAG_08203 phosphoenolpyruvate carboxykinase # 0.926 PAAG_07725 peroxisomal (S)-2-hydroxy-acid oxidase & 0.911 PAAG_03793 dihydrodipicolinate synthase & 0.900 PAAG_08075 citrate synthase * 0.899 PAAG_04550 2-methylcitrate synthase * 0.858 PAAG_06563 succinate/fumarate mitochondrial transporter & 0.835 PAAG_02653 acetyl-coenzyme A synthetase & 0.827 PAAG_04549 mitochondrial 2-methylisocitrate lyase...”
6rb7A / A7B555 Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant (see paper)
22% identity, 93% coverage
- Ligand: magnesium ion (6rb7A)
PP_3599 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) from Pseudomonas putida KT2440
26% identity, 76% coverage
- mutant phenotype: Specifically important for utilizing D-Glucuronic Acid. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 784,739 different protein sequences to 1,253,012 scientific articles. Searches against EuropePMC were last performed on November 25 2024.
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