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 | d1cqxa3 | Flavohemoglobin, C-terminal domain | 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 <-- 1.129 --> HitDALI alignment (Z-score: 4.5 Raw score:436.40) d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 d1cqxa3 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 d1cqxa3 1 ------------------------------------------------------------ 1 d1fw8a_ 121 kyfgkalENPTRPFLAILGGakvadKIQLIDNLLDKV-------DSIIIGggMAFTfkkv 173 ::::::::::::: :::::::::::: :::::: :::: d1cqxa3 1 ------dVDAKTPIVLISGG----vGLTPMVSMLKVAlqapprqVVFVHG--ARNS---- 44 d1fw8a_ 174 lenteigdsifdKAGAeiVPKLMEKAKAK-GVEVVL---------------PVDFiiada 217 :::: ::::::::::: :::::: :::: d1cqxa3 45 ------------AVHA-mRDRLREAAKTYeNLDLFVfydqplpedvqgrdyDYPG----- 86 d1fw8a_ 218 fsadantktvtdkegipagwqgldngpeSRKLFAATVAK-aKTIVWNGppgvfefekfaa 276 ::::::::::: ::::::: d1cqxa3 87 --------------------------lvDVKQIEKSILLpdADYYICG---------pip 111 d1fw8a_ 277 gtkaLLDEVV--KSSAagNTVIIGGgdtatvakkygvtdkishvstgggasLELLegkel 334 :::::: :::: ::::::: :::: d1cqxa3 112 fmrmQHDALKnlGIHE--ARIHYEV--------------------------FGPD----- 138 d1fw8a_ 335 pgvaflsekkslssklsvqdldlkdkrvfirvdfnvpldgkkitsnqrivaalptikyvl 394 d1cqxa3 139 ------------------------------------------------------------ 139 d1fw8a_ 395 ehhpryvvlashlgrpngern 415 d1cqxa3 139 -----------------lfae 142 FAST alignment (Normalized score: 2.90 Raw score:704.20) d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 d1cqxa3 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 d1cqxa3 1 ------------------------------------------------------------ 1 d1fw8a_ 121 KYFGKALENPTRPFLAILGGAKV-----ADKIQLIDNLLDKV-------DSIIIGGGMAF 168 :::::::::::: :::::::::: :::::: d1cqxa3 1 ------DVDAKTPIVLIS-----GGVGLTPMVSMLKVA----LQAPPRQVVFVHG----- 40 d1fw8a_ 169 TFKKVLENTEIGDSIFDKAG------AEIVPKLMEKAKAK-GVEVVLPVDFIIADAFSAD 221 :::::::::::::: ::::::: d1cqxa3 41 --------------------ARNSAVHAMRDRLREAAKTYENLDLFVF------------ 68 d1fw8a_ 222 ANTKTVTDKEGIPAGWQGLDNGPE--------------------SRKLFAATVAKA---- 257 ::::::::: d1cqxa3 69 ------------------------YDQPLPEDVQGRDYDYPGLVDVKQIEKSI---LLPD 101 d1fw8a_ 258 KTIVWNGPPGVFEFEK-FAAGTKALLDEVVKSSAAGN------TVIIGGGDTATVAKKYG 310 :::::: :::::::::::::: :::: d1cqxa3 102 ADYYIC----------GPIPFMRMQHDALKN------LGIHEARIHY------------- 132 d1fw8a_ 311 VTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNV 370 d1cqxa3 133 ------------------------------------------------------------ 133 d1fw8a_ 371 PLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERN---------- 415 d1cqxa3 133 ---------------------------------------------EVFGPDLFAE 142 TMalign alignment (TM-score: 0.21 Raw score:88.33) d1fw8a_ 1 -----------------SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSV 43 d1cqxa3 1 DVDAKTPIVLISGGVGL------------------------------------------- 17 d1fw8a_ 44 ILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMV 103 : d1cqxa3 18 ----------------------------------------------------T------- 18 d1fw8a_ 104 GFDLPQRAAGFLLEKELKYFGKALEN--PTRPFLAILGGAKVADKIQLIDNLLDKV---- 157 : :::::::: :: ::: :::::::::::: ::::::::::: d1cqxa3 19 ------------P--MVSMLKVA-LQAPPRQ-VVFVHGARNSAV-HAMRDRLREAAKTYE 61 d1fw8a_ 158 -DSIIIGGGMAF--TFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFII 214 ::::::::::: :::: : : ::: d1cqxa3 62 NLDLFVFYDQPLPEDVQG-R-----------------D--------------YDY----- 84 d1fw8a_ 215 ADAFSADANTKTVTDKEGIPAGWQGLDNG-PESRKLFAATVAKAKTIVWNGPPGVFEFEK 273 ::::: :: :::::: d1cqxa3 85 ------------------------PGLVDV--KQ--IEKSIL------------------ 98 d1fw8a_ 274 FAAGTKALLDEVVKSSAAGNTVIIGGG-DTATVAKKYGV----TDKISHVSTGGGASLEL 328 : :::::::::: ::::::::::: :::::::::::::::: d1cqxa3 99 --------------L--PDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFA- 141 d1fw8a_ 329 LEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALP 388 : d1cqxa3 142 -E---------------------------------------------------------- 142 d1fw8a_ 389 TIKYVLEHHPRYVVLASHLGRPNGERN 415 d1cqxa3 143 --------------------------- 143 HHsearch alignment (Probability: 0.13 E-value:0.01) d1fw8a_ 129 NPTRPFLAILGGAKVADKIQLIDNLLDKVDS 159 ::::::::::::::::::::::::::::::: d1cqxa3 3 DAKTPIVLISGGVGLTPMVSMLKVALQAPPR 33