Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1fw8a_ | Phosphoglycerate kinase | Phosphoglycerate kinase | Phosphoglycerate kinase | α/β |
| Hit | d1qfja2 | NAD(P)H:flavin oxidoreductase | Ferredoxin reductase-like, C-terminal NADP-linked domain | Ferredoxin reductase-like, C-terminal NADP-linked domain | α/β |
Query <-- 0.733 --> IntermediateDALI alignment (Z-score: 5.0 Raw score:484.70) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 query 1 -------gMENKKMNLLLFS-GDYDKaLASLIIANAAremeiEVTIFCAFWGLL-LLRDp 51 :::::::::::: ::::: :::::::::: :::::::::::: :::: d1fw8a_ 121 kyfgkaleNPTRPFLAILGGaKVADK-IQLIDNLLDK-----VDSIIIGGGMAFtFKKV- 173 query 52 ekasqedkslyeqafSSLTPReAEELplskmnlggigkkmllemmkeekapKLSDLLSGA 111 :::::: :::: ::::::::: d1fw8a_ 174 ----------lenteIGDSIF-DKAG-----------------------aeIVPKLMEKA 199 query 112 RKKEVKFYAXQlsVEIM-------------gFKKE----elfpevqimDVKEYLKNALES 154 ::::::::::: :::: :::: :::::::::::: d1fw8a_ 200 KAKGVEVVLPV--DFIIadafsadantktvtDKEGipagwqgldngpeSRKLFAATVAKA 257 query 155 DLQLFI------------------------------------------------------ 160 :::::: d1fw8a_ 258 KTIVWNgppgvfefekfaagtkalldevvkssaagntviigggdtatvakkygvtdkish 317 query 161 ------------------------------------------------------------ 161 d1fw8a_ 318 vstgggaslellegkelpgvaflsekkslssklsvqdldlkdkrvfirvdfnvpldgkki 377 query 161 -------------------------------------- 161 d1fw8a_ 378 tsnqrivaalptikyvlehhpryvvlashlgrpngern 415 FAST alignment (Normalized score: 2.52 Raw score:648.60) query 1 GM---------------------------------------------------------- 2 d1fw8a_ 1 --SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGS 58 query 3 ------------------------------------------------------------ 3 d1fw8a_ 59 RKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEK 118 query 3 -----------ENKKMNLLLFSGDYDKALASLIIANAAREMEIE---VTIFCAFWGLLLL 48 ::::::::::::::::::::::::: :::::::::: d1fw8a_ 119 ELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLL--------DKVDSIIIGGGMA--- 167 query 49 RDPEKASQEDKSLYEQAF-----------SSLTPREAEELPLSKMNLGGIGKKMLLEMMK 97 ::::: d1fw8a_ 168 ------------------FTFKKVLENTEIGDSI-------------------------- 183 query 98 EEKAP-------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-------- 142 :::::::::::::::::::: d1fw8a_ 184 -----FDKAGAEIVPKLMEKAKAKGVEVVLPV--------------------DFIIADAF 218 query 143 ---------------------------DVKEYLKNALESDLQLFI--------------- 160 :::::::::::::::: d1fw8a_ 219 SADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIV--WNGPPGVFEFEKFAA 276 query 161 ------------------------------------------------------------ 161 d1fw8a_ 277 GTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPG 336 query 161 ------------------------------------------------------------ 161 d1fw8a_ 337 VAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEH 396 query 161 ------------------- 161 d1fw8a_ 397 HPRYVVLASHLGRPNGERN 415 TMalign alignment (TM-score: 0.39 Raw score:62.58) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 query 1 ---------GMENKKMNLLL-----------------------FS--------------- 13 :::::::::: :: d1fw8a_ 121 KYFGKALEN-PTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEI 179 query 14 ------------------------------------------------------------ 14 d1fw8a_ 180 GDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQG 239 query 14 -GD-YDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTP 71 :: ::::::::::::::: :::::::::: : : : ::: d1fw8a_ 240 LDNGPESRKLFAATVAKAK----TIVWNGPPGV-F----------------E--F--EKF 274 query 72 REAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK-EVKFYAXQLSVEIMGF 130 :::::: ::::::::::: :::::::::::: : d1fw8a_ 275 AAGTKA--------------------------LLDEVVKSSAAGNTVIIGGGDTAT---V 305 query 131 KKEELFPE-V--QI-MDVKEYLKNALE--------------------------------- 153 :::::::: : :: :::::::::::: d1fw8a_ 306 AKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIR 365 query 154 --------------------------------------------------SDLQLFI 160 d1fw8a_ 366 VDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERN------- 415 HHsearch alignment (Probability: 0.03 E-value:0.09) query 85 GGIGKKMLLEM---------MKEEKAPKLSDLLSGARKKEVKFY 119 ::::::::::: :::::::::::::::::::::::: d1fw8a_ 164 GGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVV 207
Intermediate <-- 0.716 --> HitDALI alignment (Z-score: 4.4 Raw score:410.60) d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 d1qfja2 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 d1qfja2 1 ------------------------------------------------------------ 1 d1fw8a_ 121 kyfgkaLENPTRPFLAILGGAkvadkiqlIDNLLDK-------vDSIIIGGgmaFTFKkv 173 ::::::::::::::: ::::::: ::::::: :::: d1qfja2 1 ------RDDEERPMILIAGGT---gfsyaRSILLTAlarnpnrdITIYWGGreeQHLY-- 49 d1fw8a_ 174 lenteigdsifdkagaeivPKLMEKAKAK-GVEVVLPVDFiiadafsadantktvtDKEG 232 :::::::::: :::::::::: :::: d1qfja2 50 -----------------dlCELEALSLKHpGLQVVPVVEQ----------------PEAG 76 d1fw8a_ 233 ipagwqgldngPESRklFAATVA------kaKTIVWNGPpgvfefekfaagTKALLDEVV 286 :::: :::::: :::::::: ::::::::: d1qfja2 77 --------wrgRTGT--VLTAVLqdhgtlaeHDIYIAGR------------FEMAKIARD 114 d1fw8a_ 287 KSSA-AGNT---VIIGggdtatVAKKygvtdkishvstgggaslellegkelpgvaflse 342 :::: :::: :::: :::: d1qfja2 115 LFCSeRNARedrLFGD------AFAF---------------------------------- 134 d1fw8a_ 343 kkslssklsvqdldlkdkrvfirvdfnvpldgkkitsnqrivaalptikyvlehhpryvv 402 d1qfja2 135 ------------------------------------------------------------ 135 d1fw8a_ 403 lashlgrpngern 415 d1qfja2 135 ------------i 135 FAST alignment (Normalized score: 2.48 Raw score:586.40) d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 d1qfja2 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 d1qfja2 1 ------------------------------------------------------------ 1 d1fw8a_ 121 KYFGKALENPT-----RPFLAILGGAKV-ADKIQLIDNLLDKV---------DSIIIGGG 165 ::::::: ::::::::::::: ::::: d1qfja2 1 -----------RDDEERPMILIA-----GGTGFSYARSILLT-ALARNPNRDITIYW--- 40 d1fw8a_ 166 MAFTFKKVLENTEIGDSIFDKAG-------AEIVPKLMEKAKAK-GVEVVLPVDFIIADA 217 :::::::::::::: ::::::: d1qfja2 41 -----------------------GGREEQHLYDLCELEALSLKHPGLQVVPV-------- 69 d1fw8a_ 218 FSADANTKTVTDKEGIPAGWQGLDNGP-------------ESRKLFAATVAKA------K 258 ::::::::: : d1qfja2 70 ---------------------------VEQPEAGWRGRTGTVLTAVLQD----HGTLAEH 98 d1fw8a_ 259 TIVWNGPPGVFEFEKFAA-GTKALLDEVVKSSAAGNTVIIGGGDT----------ATVAK 307 ::::: :::::::::::::: ::::: d1qfja2 99 DIYIA-------------GRFEMAKIARDLFCS------------ERNAREDRLFGDAFA 133 d1fw8a_ 308 KYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVD 367 : d1qfja2 134 F----------------------------------------------------------- 134 d1fw8a_ 368 FNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERN- 415 d1qfja2 135 ------------------------------------------------I 135 TMalign alignment (TM-score: 0.20 Raw score:83.91) d1fw8a_ 1 -----------------SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSV 43 d1qfja2 1 RDDEERPMILIAGGTGF------------------------------------------- 17 d1fw8a_ 44 ILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMV 103 : d1qfja2 18 ----------------------------------------------------S------- 18 d1fw8a_ 104 GFDLPQRAAGFLLEKEL-KYFG-KALENP-TRPFLAILGGAKVADKIQLIDNLL-DK--V 157 :: ::: :::::: :::::::::::::::::: ::::: :: : d1qfja2 19 ---------------YAR-SILLTALARNPNRDITIYWGGREEQHLYD-LCELEALSLKH 61 d1fw8a_ 158 --DSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIA 215 ::::::::: :: :::: :: : d1qfja2 62 PGLQVVPVVEQ-PE-AGWR---------------------------------GR--T--- 81 d1fw8a_ 216 DAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFA 275 : :: d1qfja2 82 -------------------------G-----------------------TV--------- 84 d1fw8a_ 276 AGTKALLDEVVKSSAAGNTVIIGGGD-TATVAKKYGV----TDKISHVSTGGGASLELLE 330 :: ::::::::: : :::::::::: :::::::::: :::::::::: d1qfja2 85 -LT-AVLQDHGTL-A-EHDIYIAGRFEMAKIARDLFCSERNAREDRLFGDA--------- 131 d1fw8a_ 331 GKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTI 390 : ::: d1qfja2 132 ------------------------------------------------F-AFI------- 135 d1fw8a_ 391 KYVLEHHPRYVVLASHLGRPNGERN 415 d1qfja2 136 ------------------------- 136 HHsearch alignment (Probability: 0.30 E-value:0.02) d1fw8a_ 128 ENPTRPFLAILGGAKVADKIQLIDNLLDKVDS--IIIGGGMAFTFKKVLENTEIGDSIFD 185 :::::::::::::::::::::::::::::::: ::: :: ::: : d1qfja2 2 DDEERPMILIAGGTGFSYARSILLTALARNPNRDITI--------YW---GGR------E 44 d1fw8a_ 186 KAGAEIVPKLMEKAKAKGVEVVLPVD 211 :::::::::::::::::::::::::: d1qfja2 45 EQHLYDLCELEALSLKHPGLQVVPVV 70