SitesBLAST
Comparing GFF2454 FitnessBrowser__WCS417:GFF2454 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 13 hits to proteins with known functional sites (download)
Q4U331 Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 from Pseudomonas syringae pv. tomato (see paper)
76% identity, 99% coverage: 1:343/345 of query aligns to 1:341/343 of Q4U331
- HFAAL 126:130 (= HFAAL 128:132) binding in other chain
- DLA 184:186 (= DLA 186:188) binding in other chain
- HK 236:237 (= HK 238:239) binding
- 309:315 (vs. 311:317, 100% identical) binding in other chain
2cwhA Crystal structure of delta1-piperideine-2-carboxylate reductase from pseudomonas syringae complexed with NADPH and pyrrole-2-carboxylate (see paper)
77% identity, 96% coverage: 12:343/345 of query aligns to 1:332/332 of 2cwhA
- active site: H45 (= H56)
- binding nadph dihydro-nicotinamide-adenine-dinucleotide phosphate: H45 (= H56), A119 (= A130), A120 (= A131), L121 (= L132), H148 (= H159), T157 (= T168), P159 (= P170), F174 (= F185), D175 (= D186), L176 (= L187), A177 (= A188), H227 (= H238), K228 (= K239), R300 (= R311), G303 (= G314), R305 (= R316), R306 (= R317)
- binding pyrrole-2-carboxylate: H45 (= H56), R49 (= R60), M142 (= M153), T157 (= T168), H183 (= H194), G184 (= G195)
2cwfB Crystal structure of delta1-piperideine-2-carboxylate reductase from pseudomonas syringae complexed with NADPH (see paper)
77% identity, 96% coverage: 12:343/345 of query aligns to 4:335/337 of 2cwfB
- active site: H48 (= H56)
- binding nadph dihydro-nicotinamide-adenine-dinucleotide phosphate: H48 (= H56), H120 (= H128), A122 (= A130), A123 (= A131), L124 (= L132), T160 (= T168), P162 (= P170), F177 (= F185), D178 (= D186), L179 (= L187), A180 (= A188), H230 (= H238), K231 (= K239), R303 (= R311), G306 (= G314), R308 (= R316), R309 (= R317)
P30178 Hydroxycarboxylate dehydrogenase B; 2-oxoglutarate reductase; Hydroxyphenylpyruvate reductase; Phenylpyruvate reductase; EC 1.1.1.-; EC 1.1.1.237 from Escherichia coli (strain K12)
32% identity, 95% coverage: 17:343/345 of query aligns to 7:342/361 of P30178
2x06A Sulfolactate dehydrogenase from methanocaldococcus jannaschii (see paper)
30% identity, 94% coverage: 23:345/345 of query aligns to 11:334/344 of 2x06A
- active site: H44 (= H56)
- binding nicotinamide-adenine-dinucleotide: F41 (≠ A53), H44 (= H56), H116 (= H128), F117 (= F129), G118 (≠ A130), I119 (≠ A131), A120 (≠ L132), T156 (= T168), P158 (= P170), D173 (= D186), M174 (≠ L187), A175 (= A188), L301 (= L312), I306 (≠ R316), E307 (≠ R317)
2g8yA The structure of a putative malate/lactate dehydrogenase from e. Coli.
32% identity, 95% coverage: 17:343/345 of query aligns to 5:340/359 of 2g8yA
- active site: H46 (= H56)
- binding nicotinamide-adenine-dinucleotide: H43 (≠ A53), H46 (= H56), G120 (≠ A130), I122 (≠ L132), T160 (= T168), P162 (= P170), L176 (≠ V184), L177 (≠ F185), D178 (= D186), Y179 (≠ L187), A180 (= A188), H232 (= H238), Y235 (≠ S241), N268 (≠ T276), G311 (= G314), E314 (≠ R317)
1vbiA Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus hb8
34% identity, 94% coverage: 20:344/345 of query aligns to 8:334/340 of 1vbiA
- active site: H44 (= H56)
- binding nicotinamide-adenine-dinucleotide: H44 (= H56), H115 (= H128), G117 (≠ A130), A119 (≠ L132), T155 (= T168), P157 (= P170), A171 (≠ F185), D172 (= D186), L173 (= L187), A174 (= A188), F301 (vs. gap), P303 (= P313), L306 (≠ R316), E307 (≠ R317)
P77555 Ureidoglycolate dehydrogenase (NAD(+)); EC 1.1.1.350 from Escherichia coli (strain K12) (see paper)
31% identity, 94% coverage: 15:338/345 of query aligns to 3:329/349 of P77555
- S43 (= S55) mutation to A: 4- and 10-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency.
- H44 (= H56) mutation to A: 16-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency.
- R48 (= R60) mutation to A: Loss of dehydrogenase activity.
- Y52 (= Y64) mutation to F: 2- and 16-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency.
- H116 (= H128) mutation to A: Loss of dehydrogenase activity.
- S140 (= S152) mutation to A: 2- and 12-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency.
- D141 (≠ M153) mutation to A: 5-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency.; mutation to E: 14-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency.; mutation to N: 6-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency.
- M251 (vs. gap) mutation to A: 2- and 13-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Slight decrease of the catalytic efficiency.
- R259 (= R272) mutation to A: 2- and 12-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Slight decrease of the catalytic efficiency.
4fjuA Crystal structure of ureidoglycolate dehydrogenase in ternary complex with nadh and glyoxylate (see paper)
31% identity, 94% coverage: 15:338/345 of query aligns to 3:329/338 of 4fjuA
- binding glyoxylic acid: R48 (= R60), H116 (= H128), S140 (= S152), D141 (≠ M153)
- binding 1,4-dihydronicotinamide adenine dinucleotide: I41 (≠ A53), H44 (= H56), H116 (= H128), G118 (≠ A130), I120 (≠ L132), S140 (= S152), F147 (≠ H159), T156 (= T168), P158 (= P170), F173 (= F185), D174 (= D186), M175 (≠ L187), A176 (= A188), P223 (≠ H238), K224 (= K239), Y303 (vs. gap), G306 (= G314), D308 (≠ R316), Q309 (≠ R317)
1v9nA Structure of malate dehydrogenase from pyrococcus horikoshii ot3
27% identity, 93% coverage: 23:344/345 of query aligns to 22:341/348 of 1v9nA
- active site: H55 (= H56)
- binding nadph dihydro-nicotinamide-adenine-dinucleotide phosphate: H55 (= H56), H127 (= H128), G129 (≠ A130), I130 (≠ A131), A131 (≠ L132), T167 (= T168), P169 (= P170), L183 (≠ F185), D184 (= D186), M185 (≠ L187), A186 (= A188), P191 (≠ A193), W308 (vs. gap), H310 (vs. gap), G311 (= G314), K313 (≠ R316), G314 (≠ R317)
Sites not aligning to the query:
1z2iA Crystal structure of agrobacterium tumefaciens malate dehydrogenase, new york structural genomics consortium
31% identity, 95% coverage: 18:344/345 of query aligns to 7:340/350 of 1z2iA
- active site: H45 (= H56)
- binding nicotinamide-adenine-dinucleotide: V42 (≠ A53), H45 (= H56), H117 (= H128), F118 (= F129), G119 (≠ A130), P120 (≠ A131), A121 (≠ L132), T157 (= T168), P159 (= P170), D175 (= D186), M176 (≠ L187), A177 (= A188), P182 (≠ A193), F227 (vs. gap), K228 (= K239), M307 (vs. gap), R312 (= R316), E313 (≠ R317)
3i0pA Crystal structure of malate dehydrogenase from entamoeba histolytica
24% identity, 96% coverage: 12:343/345 of query aligns to 2:352/361 of 3i0pA
- active site: H46 (= H56)
- binding nicotinamide-adenine-dinucleotide: M43 (≠ A53), H46 (= H56), H119 (= H128), I122 (≠ A131), A123 (≠ L132), T159 (= T168), P161 (= P170), F176 (= F185), D177 (= D186), G178 (≠ L187), A179 (= A188), P184 (≠ A193), R187 (≠ D196), Y320 (vs. gap), A322 (vs. gap), G323 (= G314), K325 (≠ R316), E326 (≠ R317)
1s20G A novel NAD binding protein revealed by the crystal structure of e. Coli 2,3-diketogulonate reductase (yiak) northeast structural genomics consortium target er82 (see paper)
27% identity, 71% coverage: 14:257/345 of query aligns to 2:243/335 of 1s20G
Sites not aligning to the query:
Query Sequence
>GFF2454 FitnessBrowser__WCS417:GFF2454
MSASPLDHAPSTTHLSYEALTLLLQRIFIRQGTSESVAQVLAENCASAERDGAHSHGVFR
VPGYVSTLNSGWVDGKAVPIVEDVASGFVRVDAVNGFAQPALAAARSLLVDKARSAGIAL
LAIHNSHHFAALWPDVEPFAEEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRADG
PPIVFDLATSAIAHGDVQIAARKGERLPPGMGVDSLGQPTQDPKAILEGGALLPFGGHKG
SALSMMVELLAAALTGGNFSFEFNWSDHPGARTPWTGQLVILIDPSKTTGQNFAERSQEL
VRQMHAAGLRRLPGDRRHRSRAKSQEIGIEINAQDLKQLQELAED
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SitesBLAST's Database
SitesBLAST's database includes
(1) SwissProt
entries with experimentally-supported functional features;
and (2) protein structures with bound ligands, from the
BioLip database.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory