SitesBLAST
Comparing GFF685 FitnessBrowser__psRCH2:GFF685 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 20 (the maximum) hits to proteins with known functional sites (download)
6a2fA Crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa (see paper)
70% identity, 99% coverage: 1:356/358 of query aligns to 1:356/358 of 6a2fA
- active site: K34 (= K34), R130 (= R130), H159 (= H159), R209 (= R209), Y254 (= Y254), S301 (= S301), D303 (= D303)
- binding acetate ion: Y254 (= Y254), R279 (= R279), L340 (≠ I340), Y342 (= Y342)
- binding d-lysine: Y254 (= Y254), Y273 (= Y273), S301 (= S301), M302 (= M302), D303 (= D303), M304 (= M304)
- binding malonate ion: K123 (= K123), R130 (= R130), L131 (= L131)
1rcqA The 1.45 a crystal structure of alanine racemase from a pathogenic bacterium, pseudomonas aeruginosa, contains both internal and external aldimine forms (see paper)
50% identity, 100% coverage: 1:358/358 of query aligns to 1:356/357 of 1rcqA
- active site: K33 (= K34), R129 (= R130), H158 (= H159), R208 (= R209), Y253 (= Y254), S300 (= S301), D302 (= D303)
- binding d-lysine: K33 (= K34), R129 (= R130), Y341 (= Y342)
- binding pyridoxal-5'-phosphate: V31 (= V32), K33 (= K34), Y37 (= Y38), H158 (= H159), N192 (= N193), S193 (= S194), R208 (= R209), G210 (= G211), I211 (= I212), Y341 (= Y342)
Q9HTQ2 Alanine racemase, catabolic; EC 5.1.1.1 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
50% identity, 100% coverage: 1:358/358 of query aligns to 1:356/357 of Q9HTQ2
- K33 (= K34) modified: N6-(pyridoxal phosphate)lysine
- K122 (= K123) modified: N6-carboxylysine
2rjhA Crystal structure of biosynthetic alaine racemase in d-cycloserine- bound form from escherichia coli (see paper)
43% identity, 100% coverage: 1:357/358 of query aligns to 1:358/359 of 2rjhA
- active site: K34 (= K34), R129 (= R130), H159 (= H159), R209 (= R209), Y255 (= Y254), A302 (≠ S301), D304 (= D303)
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K34 (= K34), Y38 (= Y38), R129 (= R130), H159 (= H159), A193 (≠ N193), S194 (= S194), R209 (= R209), G211 (= G211), I212 (= I212), Y255 (= Y254), A302 (≠ S301), M303 (= M302), Y343 (= Y342)
P0A6B4 Alanine racemase, biosynthetic; EC 5.1.1.1 from Escherichia coli (strain K12) (see paper)
43% identity, 100% coverage: 1:357/358 of query aligns to 1:358/359 of P0A6B4
- K34 (= K34) modified: N6-(pyridoxal phosphate)lysine
- K122 (= K123) modified: N6-carboxylysine
- D164 (= D164) mutation to A: Slightly reduces affinity for D-Ala and L-Ala.; mutation to K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala.
- E165 (= E165) mutation to A: Slightly reduces affinity for D-Ala and L-Ala.; mutation to K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala.
- P219 (= P219) mutation to A: No effect on catalytic activity. No effect on affinity for D-Ala and L-Ala.
- E221 (≠ A221) mutation E->A,K,P: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala.
4xbjA Y274f alanine racemase from e. Coli inhibited by l-ala-p (see paper)
43% identity, 98% coverage: 8:357/358 of query aligns to 6:356/357 of 4xbjA
- active site: K32 (= K34), R127 (= R130), H157 (= H159), R207 (= R209), Y253 (= Y254), A300 (≠ S301), D302 (= D303)
- binding {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid: V30 (= V32), K32 (= K34), Y36 (= Y38), R127 (= R130), H157 (= H159), A191 (≠ N193), S192 (= S194), R207 (= R209), G209 (= G211), I210 (= I212), Y253 (= Y254), A300 (≠ S301), M301 (= M302), Y341 (= Y342)
3b8tA Crystal structure of escherichia coli alaine racemase mutant p219a (see paper)
42% identity, 100% coverage: 1:357/358 of query aligns to 1:358/359 of 3b8tA
- active site: K34 (= K34), R129 (= R130), H159 (= H159), R209 (= R209), Y255 (= Y254), A302 (≠ S301), D304 (= D303)
- binding pyridoxal-5'-phosphate: V32 (= V32), K34 (= K34), Y38 (= Y38), L78 (= L79), H159 (= H159), A193 (≠ N193), S194 (= S194), R209 (= R209), G211 (= G211), I212 (= I212), Y343 (= Y342)
5fagA Alanine racemase from streptomyces coelicolor a3(2) with bound propionate inhibitor (see paper)
38% identity, 98% coverage: 6:357/358 of query aligns to 17:388/390 of 5fagA
- active site: I19 (≠ V8), K45 (= K34), A46 (= A35), R147 (= R130), H180 (= H159), R236 (= R209), Y282 (= Y254), A329 (≠ S301), D331 (= D303)
- binding pyridoxal-5'-phosphate: K45 (= K34), Y49 (= Y38), W95 (≠ L79), W178 (≠ I157), H180 (= H159), N220 (= N193), S221 (= S194), R236 (= R209), G238 (= G211), I239 (= I212), Y373 (= Y342)
5fajA Alanine racemase from streptomyces coelicolor a3(2) in complex with d- cycloserine (see paper)
38% identity, 98% coverage: 6:357/358 of query aligns to 12:383/385 of 5fajA
- active site: I14 (≠ V8), K40 (= K34), A41 (= A35), R142 (= R130), H175 (= H159), R231 (= R209), Y277 (= Y254), A324 (≠ S301), D326 (= D303)
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K40 (= K34), Y44 (= Y38), W90 (≠ L79), W173 (≠ I157), H175 (= H159), N215 (= N193), S216 (= S194), R231 (= R209), P232 (= P210), G233 (= G211), I234 (= I212), Y277 (= Y254), Y296 (= Y273), M325 (= M302), Y368 (= Y342)
6q70A Crystal structure of the alanine racemase bsu17640 from bacillus subtilis in the presence of hepes (see paper)
35% identity, 98% coverage: 8:357/358 of query aligns to 12:379/386 of 6q70A
- active site: K39 (= K34), R139 (= R130), H169 (= H159), R225 (= R209), Y272 (= Y254), T319 (≠ S301), D321 (= D303)
- binding pyridoxal-5'-phosphate: V37 (= V32), K39 (= K34), Y43 (= Y38), L85 (= L79), R139 (= R130), H169 (= H159), T210 (≠ S194), R225 (= R209), G227 (= G211), I228 (= I212), Y364 (= Y342)
5irpA Crystal structure of the alanine racemase bsu17640 from bacillus subtilis (see paper)
35% identity, 98% coverage: 8:357/358 of query aligns to 12:379/386 of 5irpA
- active site: K39 (= K34), R139 (= R130), H169 (= H159), R225 (= R209), Y272 (= Y254), T319 (≠ S301), D321 (= D303)
- binding magnesium ion: L155 (= L145), K156 (= K146), S158 (≠ K148), L161 (≠ V151)
- binding 2-amino-2-hydroxymethyl-propane-1,3-diol: D174 (= D164), P235 (= P219), Y364 (= Y342)
- binding (5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate: Y43 (= Y38), L85 (= L79), R139 (= R130), H169 (= H159), N209 (= N193), T210 (≠ S194), R225 (= R209), G227 (= G211), I228 (= I212), Y364 (= Y342)
4y2wA Crystal structure of a thermostable alanine racemase from thermoanaerobacter tengcongensis mb4 (see paper)
31% identity, 100% coverage: 1:357/358 of query aligns to 6:375/388 of 4y2wA
- active site: K40 (= K34), R138 (= R130), H168 (= H159), R224 (= R209), Y268 (= Y254), C315 (≠ S301), D317 (= D303)
- binding alanine: Y268 (= Y254), Y287 (= Y273), C315 (≠ S301), M316 (= M302)
- binding phosphate ion: N208 (= N193), A209 (≠ S194), I227 (= I212)
5yycA Crystal structure of alanine racemase from bacillus pseudofirmus (of4) (see paper)
35% identity, 99% coverage: 1:356/358 of query aligns to 6:366/368 of 5yycA
- active site: K41 (= K34), R139 (= R130), H169 (= H159), R225 (= R209), Y269 (= Y254), C316 (≠ S301), D318 (= D303)
- binding pyridoxal-5'-phosphate: K41 (= K34), Y45 (= Y38), R139 (= R130), H169 (= H159), N209 (= N193), S210 (= S194), R225 (= R209), G227 (= G211), I228 (= I212), Y352 (= Y342)
1vfsA Crystal structure of d-cycloserine-bound form of alanine racemase from d-cycloserine-producing streptomyces lavendulae (see paper)
36% identity, 99% coverage: 4:358/358 of query aligns to 6:375/383 of 1vfsA
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K36 (= K34), Y40 (= Y38), W82 (≠ L79), R134 (= R130), H166 (= H159), S207 (= S194), R222 (= R209), G224 (= G211), Y268 (= Y254), Y287 (= Y273), M316 (= M302), Y359 (= Y342)
1vfhA Crystal structure of alanine racemase from d-cycloserine producing streptomyces lavendulae (see paper)
36% identity, 99% coverage: 4:358/358 of query aligns to 6:375/382 of 1vfhA
- active site: K36 (= K34), R134 (= R130), H166 (= H159), R222 (= R209), Y268 (= Y254), A315 (≠ S301), D317 (= D303)
- binding pyridoxal-5'-phosphate: K36 (= K34), Y40 (= Y38), W82 (≠ L79), H166 (= H159), S207 (= S194), R222 (= R209), G224 (= G211), L225 (≠ I212), Y359 (= Y342)
P0A2W8 Alanine racemase; EC 5.1.1.1 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (see paper)
34% identity, 99% coverage: 2:356/358 of query aligns to 7:366/367 of P0A2W8
- K129 (= K123) modified: N6-carboxylysine
3e6eA Crystal structure of alanine racemase from e.Faecalis complex with cycloserine (see paper)
33% identity, 99% coverage: 2:356/358 of query aligns to 6:369/370 of 3e6eA
- active site: K39 (= K34), R138 (= R130), H168 (= H159), R221 (= R209), Y266 (= Y254), C312 (≠ S301), D314 (= D303)
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K39 (= K34), Y43 (= Y38), L85 (= L79), R138 (= R130), H168 (= H159), S206 (= S194), R221 (= R209), G223 (= G211), V224 (≠ I212), Y266 (= Y254), Y285 (= Y273), M313 (= M302), Y355 (= Y342)
6g59A Structure of the alanine racemase from staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative (see paper)
34% identity, 99% coverage: 2:356/358 of query aligns to 12:373/387 of 6g59A
- active site: K44 (= K34), R143 (= R130), H173 (= H159), R224 (= R209), Y270 (= Y254), C316 (≠ S301), D318 (= D303)
- binding (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate: K44 (= K34), Y48 (= Y38), L90 (= L79), H173 (= H159), S209 (= S194), R224 (= R209), G226 (= G211), I227 (= I212), Y359 (= Y342)
3e5pB Crystal structure of alanine racemase from e.Faecalis (see paper)
33% identity, 99% coverage: 2:356/358 of query aligns to 7:370/371 of 3e5pB
- active site: K40 (= K34), R139 (= R130), H169 (= H159), R222 (= R209), Y267 (= Y254), C313 (≠ S301), D315 (= D303)
- binding pyridoxal-5'-phosphate: K40 (= K34), Y44 (= Y38), R139 (= R130), H169 (= H159), S207 (= S194), G224 (= G211), V225 (≠ I212), Y356 (= Y342)
6g58A Structure of the alanine racemase from staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative (see paper)
34% identity, 99% coverage: 2:356/358 of query aligns to 7:368/382 of 6g58A
- active site: K39 (= K34), R138 (= R130), H168 (= H159), R219 (= R209), Y265 (= Y254), C311 (≠ S301), D313 (= D303)
- binding (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate: K39 (= K34), Y43 (= Y38), L85 (= L79), K131 (= K123), R138 (= R130), H168 (= H159), S204 (= S194), R219 (= R209), G221 (= G211), I222 (= I212), Y354 (= Y342)
Query Sequence
>GFF685 FitnessBrowser__psRCH2:GFF685
MRPLVATVDLTALRHNYLLAKQCAPQRKAFAVVKANAYGHGACEAVTALREIADGFAVAC
LEEAEDIRRSAPDARILLLEGCFEPAEYLRAAELGLDVAVQDQRQADWLLAANISRPLNV
WLKLDSGMHRLGFTLEGLRDCHERLKGKAQVGELNLISHFACADERGHPLTELQLERYAE
LLSLEFDNCSLANSAAVLTLPQAHMAWIRPGIMLYGATPFAELSAQELGLRPVMTLTGAL
IAVRDVSEGESVGYGASWVAQRASRIGTVSCGYADGYPRTAPSGTSVVIHGQRVPLAGRV
SMDMLAVDLTDLPQAQLGDAVELWGAQMPIDELAQACGTIGYELLTKVTGRVPRRYIG
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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