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 | d1trba1 | Thioredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1v1aa_ | 2-keto-3-deoxygluconate kinase | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 1.208 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:393.90) query 1 -gmenkKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCafwGLLLlrdpekasqedk 59 :::::: :::::::::::::::::::::: :::: d1trba1 1 gttkhsKLLILG------sGPAGYTAAVYAARANLQPVLIT---GMEK------------ 39 query 60 slyeqafssltpreaeELPLskmnlggigKKMLleMMKEE-----kapKLSDLLSGARKK 114 :::: :::: ::::: :::::::::::: d1trba1 40 -------------ggqLTTT---------TEVE--NWPGDpndltgplLMERMHEHATKF 75 query 115 EVKFY-AXQLsveimgfkkeelfpevqiMDVKEYlknalESDLQLFI------------- 160 ::::: :::: :::::: :::::::: d1trba1 76 ETEIIfDHIN------kvdlqnrpfrlnGDNGEY-----TCDALIIAtgasaryhspnta 124 query 161 ------------------------------------------------------------ 161 d1trba1 125 ifegqlelengyikvqsgihgnatqtsipgvfaagdvmdhiyrqaitsagtgcmaaldae 184 query 161 ----- 161 d1trba1 185 ryldg 189 FAST alignment (Normalized score: 3.91 Raw score:680.70) query 1 GMENK------KMNLLLFSGDYDK---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDP 51 :::: :::::::::::::::::::::::: d1trba1 1 -----GTTKHSKLLI---------LGSGPAGYTAAVYAARANLQPVLITGM--------- 37 query 52 EKASQEDKSLYEQAFSSLTPREAEE---LPLSKMNLGGIGKKM---LLEMMKEEKAP--- 102 :::: ::::: d1trba1 38 -------------------------EKGGQLT-----------TTTEVENW------PGD 55 query 103 --------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNA--- 151 ::::::::::::::::: ::::: d1trba1 56 PNDLTGPLLMERMHEHATKFETEII-------------------FDHIN--------KVD 88 query 152 --------------LESDLQLFI------------------------------------- 160 ::::::: d1trba1 89 LQNRPFRLNGDNGEYTCDALI--IATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGN 146 query 161 ------------------------------------------- 161 d1trba1 147 ATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG 189 TMalign alignment (TM-score: 0.43 Raw score:69.20) query 1 -----GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::: :::::::::::::::::::::::::: :: d1trba1 1 GTTKH----SKLLILG------SGPAGYTAAVYAARANLQPVLITGME--KG-------- 40 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE------EKAPKLSDLLS 109 ::::: : :: : ::: :::: :::::::: d1trba1 41 ------------------GQLTT----T--TE-V-ENW-PGDPNDLTGP---LLMERMHE 70 query 110 GARKKEVKFYAXQLS------------VEIMGFKKEELFPEVQIMDVKEYLKNALESDLQ 157 ::::::::::::::: ::::: :: ::::: d1trba1 71 HATKFETEIIFDHINKVDLQNRPFRLN-----------------GDNGE--YT--CDALI 109 query 158 LFI--------------------------------------------------------- 160 ::: d1trba1 110 IATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGNATQTSIPGVFAAGDVMDHIYRQA 169 query 161 -------------------- 161 d1trba1 170 ITSAGTGCMAALDAERYLDG 189 HHsearch alignment (Probability: 0.05 E-value:0.06) query 1 GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 :::::::::::::: :::::::::::::::::::: d1trba1 1 GTTKHSKLLILGSG-----PAGYTAAVYAARANLQPVLI 34
Intermediate <-- 1.399 --> HitDALI alignment (Z-score: 4.6 Raw score:556.40) d1trba1 1 gttkHSKLLILG-----------------------sGPAGYTAAVYAARANLQPVLITGm 37 :::::::: ::::::::::::::::::::::: d1v1aa_ 1 ----MLEVVTAGeplvalvpqepghlrgkrllevyvGGAEVNVAVALARLGVKVGFVGR- 55 d1trba1 38 ekggqlttttevenwpgdpndltGPLLMERMHEHATKFETEIIF---------------- 81 ::::::::::::::::::::: d1v1aa_ 56 ---------------------vgEDELGAMVEERLRAEGVDLTHfrrapgftglylreyl 94 d1trba1 82 -----------------dHINKvdlqnrpfrlnGDNGEYT--CDALIIA--TGASaryhs 120 :::: ::::::: ::::::: :::: d1v1aa_ 95 plgqgrvfyyrkgsagsaLAPG-----------AFDPDYLegVRFLHLSgiTPAL---sp 140 d1trba1 121 pNTAIFE------------------------gqleLENGY--------ikVQSG------ 142 :::::: ::::: :::: d1v1aa_ 141 eARAFSLwameeakrrgvrvsldvnyrqtlwspeeARGFLeralpgvdllFLSEeeaell 200 d1trba1 143 --------------iHGNA---tqtsipgvfaagdvmdhiyrqaitsAGTGCMAALDAER 185 :::: ::::::::::::: d1v1aa_ 201 fgrveealralsapeVVLKrgakgawafvdgrrvegsafaveavdpvGAGDAFAAGYLAG 260 d1trba1 186 YLDG------------------------------------- 189 :::: d1v1aa_ 261 AVWGlpveerlrlanllgasvaasrgdhegapyredlevll 301 FAST alignment (Normalized score: 4.16 Raw score:993.10) d1trba1 1 GTTKHSKLLILGSG--------------------------PAGYTAAVYAARANLQPVLI 34 ::::::: ::::::::::::::::::: d1v1aa_ 1 ----MLEVVTA---GEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGF- 52 d1trba1 35 TGMEKGGQLTTTTEVENWPGDPNDLTG------PLLMERMHEHATKFETEIIFDHINKVD 88 :::::::::::::::::: d1v1aa_ 53 ---------------------------VGRVGEDELGAMVEERLRAEGVDL--------- 76 d1trba1 89 LQNRPFRLNGDNGE---------------------------------------------- 102 d1v1aa_ 77 --------------THFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDY 122 d1trba1 103 -YTCDALIIATGASARYHSP---------NTAIFEGQLELENGYIKVQSGIHGNATQTSI 152 ::::::::: ::::::: d1v1aa_ 123 LEGVRFLHLS----------GITPALSPEARAFSLW------------------------ 148 d1trba1 153 P----------GVFAAGDVMDHIYRQAITS------------------------------ 172 :::: d1v1aa_ 149 -AMEEAKRRGVRVSL---------------DVNYRQTLWSPEEARGFLERALPGVDLLFL 192 d1trba1 173 -------------------------------------------------------AGTGC 177 ::::: d1v1aa_ 193 SEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDA 252 d1trba1 178 MAALDAERYLDG--------------------------------------- 189 :::::::::: d1v1aa_ 253 FAAGYLAGAV--WGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301 TMalign alignment (TM-score: 0.50 Raw score:94.64) d1trba1 1 GTTKHSKLLILGSG-----------------------PAGYTAAVYAARANLQPVLITGM 37 :::::::::: ::::::::::::::::::::: d1v1aa_ 1 ----MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVG-- 54 d1trba1 38 EKGGQLT-TTTEVENWPGDPNDLTGPLLMERMHEHATKFETEIIFD-------------- 82 :: : ::: :::::::::::::::::: d1v1aa_ 55 -RV---GE----------------DEL-GAMVEERLRAEGVDLTHFRRAPGFTGLYLREY 93 d1trba1 83 -------------------HINKVDLQNRPFRLNGDNGEYT-CDALIIA-TG-ASARYHS 120 :::: :::::::: ::::::: :: :::: :: d1v1aa_ 94 LPLGQGRVFYYRKGSAGSALAPG----------AFDPDYLEGVRFLHLSGITPALSP-EA 142 d1trba1 121 PN-TAI-FE--GQ-----L-E-------------LENGY--IK-----VQSGI------- 143 :: ::: :: : : : ::::: :: ::::: d1v1aa_ 143 RAFSLWAMEEA-KRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLF 201 d1trba1 144 ---------HGNATQTSIPG-----------------------------VFAAGDVMDHI 165 :::::: d1v1aa_ 202 GRVEEALRA-----LSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVD----------- 245 d1trba1 166 YRQAITSAGTGCMAALDAERYLD-G----------------------------------- 189 :: :::::::::::::::: : d1v1aa_ 246 ----PV-GAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVL 300 d1trba1 190 - 190 d1v1aa_ 301 L 301 HHsearch alignment (Probability: 0.46 E-value:0.00) d1trba1 16 AGYTAAVYAARANLQPVLITG 36 ::::::::::::::::::::: d1v1aa_ 35 AEVNVAVALARLGVKVGFVGR 55