SitesBLAST
Comparing GFF3380 FitnessBrowser__psRCH2:GFF3380 to proteins with known functional sites using BLASTp with E ≤ 0.001.
Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures
Found 15 hits to proteins with known functional sites (download)
P77324 Aldehyde oxidoreductase FAD-binding subunit PaoB; EC 1.2.99.6 from Escherichia coli (strain K12) (see paper)
53% identity, 98% coverage: 1:322/328 of query aligns to 1:314/318 of P77324
- 26:34 (vs. 24:32, 78% identical) binding
- T108 (≠ S106) binding
- C119 (= C117) binding
- C129 (= C127) binding
- C138 (= C136) binding
- C157 (= C155) binding
- D164 (= D162) binding
- I213 (= I210) binding
- K230 (= K228) binding
5g5gB Escherichia coli periplasmic aldehyde oxidase (see paper)
53% identity, 98% coverage: 1:322/328 of query aligns to 1:314/316 of 5g5gB
- binding flavin-adenine dinucleotide: K26 (≠ R24), F27 (≠ Y25), A29 (= A27), G30 (= G28), G31 (= G29), T32 (= T30), N33 (= N31), L34 (= L32), G98 (= G96), A99 (= A97), L103 (= L101), A107 (= A105), T108 (≠ S106), A110 (≠ G108), G111 (= G109), N112 (= N110), L114 (= L112), Q115 (= Q113), S163 (= S161), D164 (= D162), L212 (= L209), I213 (= I210), F239 (= F237)
- binding iron/sulfur cluster: C119 (= C117), C129 (= C127), N130 (= N128), K131 (= K129), C138 (= C136), H148 (= H146), C157 (= C155), I158 (≠ V156), A159 (= A157)
5y6qB Crystal structure of an aldehyde oxidase from methylobacillus sp. Ky4400 (see paper)
47% identity, 98% coverage: 1:322/328 of query aligns to 1:326/330 of 5y6qB
- binding flavin-adenine dinucleotide: I26 (≠ Y25), A28 (= A27), G29 (= G28), G30 (= G29), T31 (= T30), T32 (≠ N31), Q33 (≠ L32), A97 (≠ G96), A98 (= A97), I102 (≠ L101), A106 (= A105), T107 (≠ S106), G110 (= G109), N111 (= N110), R113 (≠ L112), Q114 (= Q113), G164 (≠ S161), D165 (= D162), I213 (≠ L209), I214 (= I210), K232 (= K228), F241 (= F237)
- binding iron/sulfur cluster: C118 (= C117), Y121 (≠ F120), C130 (= C127), N131 (= N128), C139 (= C136), A141 (= A138), C158 (= C155), I159 (≠ V156), A160 (= A157)
1rm6B Structure of 4-hydroxybenzoyl-coa reductase from thauera aromatica (see paper)
35% identity, 81% coverage: 1:267/328 of query aligns to 4:263/323 of 1rm6B
- binding flavin-adenine dinucleotide: P29 (≠ Y25), G31 (≠ A27), A32 (≠ G28), G33 (= G29), T34 (= T30), D35 (≠ N31), L36 (= L32), L53 (≠ I49), V101 (≠ G96), A102 (= A97), A110 (= A105), T111 (≠ S106), G114 (= G109), N115 (= N110), C117 (≠ L112), Q118 (= Q113), D162 (= D162), L207 (≠ I210), V231 (≠ Y235), D232 (≠ A236), F233 (= F237)
- binding iron/sulfur cluster: C122 (= C117), F124 (≠ Y119), C138 (≠ S137), C146 (≠ I145), H147 (= H146), V148 (≠ A147), C155 (= C155), Y156 (≠ V156), A157 (= A157)
O33820 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.1.7.1 from Thauera aromatica (see paper)
35% identity, 81% coverage: 1:267/328 of query aligns to 4:263/324 of O33820
- 29:36 (vs. 25:32, 38% identical) binding
- T111 (≠ S106) binding
- N115 (= N110) binding
- Q118 (= Q113) binding
- D162 (= D162) binding
- K224 (= K228) binding
4zohB Crystal structure of glyceraldehyde oxidoreductase (see paper)
29% identity, 96% coverage: 4:319/328 of query aligns to 6:273/274 of 4zohB
- active site: Y256 (vs. gap)
- binding flavin-adenine dinucleotide: R28 (= R24), P29 (≠ Y25), A31 (= A27), G32 (= G28), G33 (= G29), H34 (≠ T30), S35 (≠ N31), L36 (= L32), H77 (≠ N73), I95 (≠ G96), G96 (≠ A97), V100 (≠ L101), T105 (≠ S106), G108 (= G109), S109 (≠ N110), S111 (≠ L112), A117 (vs. gap), D118 (= D162), L160 (= L209), V161 (≠ I210), D185 (≠ A236), F186 (= F237)
1ffuC Carbon monoxide dehydrogenase from hydrogenophaga pseudoflava which lacks the mo-pyranopterin moiety of the molybdenum cofactor (see paper)
28% identity, 80% coverage: 4:264/328 of query aligns to 6:220/287 of 1ffuC
- binding flavin-adenine dinucleotide: K29 (≠ R24), L30 (≠ Y25), A32 (= A27), G33 (= G28), G34 (= G29), H35 (≠ T30), S36 (≠ N31), L37 (= L32), I54 (= I49), I101 (≠ G96), A102 (= A97), G110 (≠ A105), T111 (≠ S106), G114 (= G109), D115 (≠ N110), A117 (≠ L112), N123 (≠ S134), D124 (≠ G135), L161 (= L204), V166 (≠ L209), M167 (≠ I210), W193 (≠ F237)
Q0QLF4 Nicotinate dehydrogenase FAD-subunit; NDH; Nicotinic acid hydroxylase FAD-subunit; NAH; EC 1.17.1.5 from Eubacterium barkeri (Clostridium barkeri) (see paper)
25% identity, 85% coverage: 1:279/328 of query aligns to 1:239/296 of Q0QLF4
- 29:36 (vs. 25:32, 75% identical) binding
- G101 (≠ A97) binding
- TIGGN 110:114 (≠ STGGN 106:110) binding
- D123 (≠ S134) binding
- R160 (≠ D201) binding
- M169 (≠ I210) binding
- K187 (= K228) binding
3hrdG Crystal structure of nicotinate dehydrogenase (see paper)
25% identity, 85% coverage: 1:279/328 of query aligns to 1:239/292 of 3hrdG
- binding flavin-adenine dinucleotide: I29 (≠ Y25), A31 (= A27), G32 (= G28), G33 (= G29), T34 (= T30), D35 (≠ N31), F77 (≠ N73), V100 (≠ G96), G101 (≠ A97), I105 (≠ L101), T110 (≠ S106), G113 (= G109), N114 (= N110), S116 (≠ C127), T117 (≠ N128), G122 (= G133), D123 (≠ S134), I168 (≠ L209), M169 (≠ I210)
1n5wC Crystal structure of the cu,mo-co dehydrogenase (codh); oxidized form (see paper)
28% identity, 84% coverage: 4:279/328 of query aligns to 6:235/287 of 1n5wC
P19920 Carbon monoxide dehydrogenase medium chain; CO dehydrogenase subunit M; CO-DH M; EC 1.2.5.3 from Afipia carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5) (Oligotropha carboxidovorans) (see 2 papers)
28% identity, 84% coverage: 4:279/328 of query aligns to 6:235/288 of P19920
1t3qC Crystal structure of quinoline 2-oxidoreductase from pseudomonas putida 86 (see paper)
27% identity, 99% coverage: 4:327/328 of query aligns to 6:284/285 of 1t3qC
- binding flavin-adenine dinucleotide: I29 (≠ Y25), A31 (= A27), G32 (= G28), G33 (= G29), Q34 (≠ T30), S35 (≠ N31), L36 (= L32), V100 (≠ G96), A101 (= A97), V105 (≠ L101), T110 (≠ S106), G113 (= G109), S114 (≠ N110), A116 (≠ I145), A122 (= A151), E123 (≠ D162), L166 (≠ I210), Y190 (≠ F237)
7dqxE Crystal structure of xanthine dehydrogenase family protein
27% identity, 97% coverage: 4:322/328 of query aligns to 6:283/293 of 7dqxE
- binding flavin-adenine dinucleotide: K29 (≠ R24), I30 (≠ Y25), I31 (= I26), G33 (= G28), G34 (= G29), Q35 (≠ T30), S36 (≠ N31), L37 (= L32), H78 (≠ N73), I101 (≠ G96), A102 (= A97), I106 (≠ L101), G110 (≠ A105), T111 (≠ S106), G113 (= G108), G114 (= G109), S115 (≠ N110), A117 (≠ I145), A123 (= A151), E124 (≠ D162), I167 (= I210), Y193 (= Y235)
2w54A Crystal structure of xanthine dehydrogenase from rhodobacter capsulatus in complex with bound inhibitor pterin-6-aldehyde (see paper)
26% identity, 94% coverage: 21:327/328 of query aligns to 185:443/450 of 2w54A
- binding flavin-adenine dinucleotide: L189 (≠ Y25), A191 (= A27), G192 (= G28), G193 (= G29), T194 (= T30), D195 (≠ N31), V196 (≠ L32), W199 (≠ M36), L213 (= L52), F258 (≠ G96), A259 (= A97), A267 (= A105), T268 (≠ S106), G271 (= G109), N272 (= N110), A274 (≠ L112), N275 (≠ Q113), G280 (≠ N128), D281 (≠ K129), R318 (≠ N202), V324 (≠ I210), Q347 (≠ Y235)
Sites not aligning to the query:
- binding flavin-adenine dinucleotide: 42
- binding fe2/s2 (inorganic) cluster: 38, 39, 40, 42, 44, 45, 47, 63, 103, 104, 106, 134, 135, 136
- binding {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum: 102, 136
1jroA Crystal structure of xanthine dehydrogenase from rhodobacter capsulatus (see paper)
26% identity, 94% coverage: 21:327/328 of query aligns to 185:443/450 of 1jroA
- binding flavin-adenine dinucleotide: L189 (≠ Y25), A191 (= A27), G192 (= G28), G193 (= G29), T194 (= T30), D195 (≠ N31), V196 (≠ L32), F258 (≠ G96), A259 (= A97), T268 (≠ S106), G271 (= G109), N272 (= N110), A274 (≠ L112), G280 (≠ N128), D281 (≠ K129), R318 (≠ N202), V324 (≠ I210)
Sites not aligning to the query:
- binding flavin-adenine dinucleotide: 42, 43
- binding fe2/s2 (inorganic) cluster: 37, 38, 39, 40, 42, 44, 45, 47, 63, 103, 106, 134, 136
Query Sequence
>GFF3380 FitnessBrowser__psRCH2:GFF3380
MTPFSYQRPERIDQAIALHGPQSRYIAGGTNLLDLMKENVLQPGQLIDINGLPLRDIEQT
AEGGLRIGALVSNADLAWHPQIEQRYPLLSKAILAGASPQLRNMASTGGNLLQRTRCYYF
YDTATPCNKREPGSGCSARDGRNRIHAILGASEHCVAVHPSDMCVALAALDARVHVEGPH
GQRRLELVDFHRLPGDQPQQDNVLVEGELITAIELPVEGFASHCAYLKVRDRASYAFALV
SVAAALEMDGDIIRRARIALGGVAHKPWRLEEAEELLSGKRAKPECFAAAADRLLQGAQP
LADNAFKVDLARRAIVRALTEAAGGTVR
Or try a new SitesBLAST search
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