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 | d1vm7a_ | Ribokinase | 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 <-- 1.291 --> HitDALI alignment (Z-score: 5.0 Raw score:565.40) d1trba1 1 gttkhsKLLILGSG----------------------------PAGYTAAVYAARA-NLQP 31 :::::::: ::::::::::::: :::: d1vm7a_ 1 ---mflVISVVGSSnidivlkvdhftkpgetqkaiemnvfpgGKGANQAVTVAKIgEKGC 57 d1trba1 32 VLITGmekggqlttttevenwpgdpndltgPLLMERMHEHATKFETEIIF---------- 81 ::::: :::::::::::::::::::: d1vm7a_ 58 RFVTC----------------------ignDDYSDLLIENYEKLGITGYIrvslptgraf 95 d1trba1 82 -------------------dHINKvdlqnrpfrlNGDNGEYT-CDALIIATGasaryhsp 121 :::: :::::::: ::::::::: d1vm7a_ 96 ievdktgqnriiifpganaeLKKE----------LIDWNTLSeSDILLLQNE-------i 138 d1trba1 122 NTAI---------------------fEGQLELengyiKVQS------------------- 141 :::: :::::: :::: d1vm7a_ 139 PFETtlecakrfngivifdpapaqgiNEEIFQ-yldyLTPNekeiealskdffgefltve 197 d1trba1 142 ---------------------GIHGnatqtsipgvfaagdvmdhiyrqaitsAGTGCMAA 180 :::: :::::::: d1vm7a_ 198 kaaekflelgvknvivklgdkGVLL-------vnknekkhfptfkvkavdttAAGDVFNG 250 d1trba1 181 LDAERYLDG---------------------------------------- 189 ::::::::: d1vm7a_ 251 AFAVALSEGknpeeavifgtaaaaisvtrlgaqssipareeveaflknl 299 FAST alignment (Normalized score: 3.84 Raw score:912.30) d1trba1 1 GTTKHS---KLLILGSG-------------------------------PAGYTAAVYAAR 26 ::::: :::::::::::: d1vm7a_ 1 ------MFLVISVV---GSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAK 51 d1trba1 27 -ANLQPVLITGMEKGGQLTTTTEVENWPGDPNDLTG----PLLMERMHEHATKFETEIIF 81 ::::::::: :::::::::::::::: d1vm7a_ 52 IGEKGCRFVT--------------------------CIGNDDYSDLLIENYEKLGI---- 81 d1trba1 82 DHINKVDLQNRPFRLNGDNGE--------------------------------------- 102 d1vm7a_ 82 ---------------------TGYIRVSLPTGRAFIEVDKTGQNRIIIFPGANAELKKEL 120 d1trba1 103 ------YTCDALIIATGASARYHSP---NTAIFEGQLELENGYIKVQSGIHGNATQTSIP 153 ::::::::: ::::::: d1vm7a_ 121 IDWNTLSESDILLLQ----------NEIPFETTLE------------------------- 145 d1trba1 154 -------GVFAAGDVMDHIYRQAITS---------------------------------- 172 :::: d1vm7a_ 146 CAKRFNGIVIF---------------DPAPAQGINEEIFQYLDYLTPNEKEIEALSKDFF 190 d1trba1 173 ----------------------------------------------------AGTGCMAA 180 :::::::: d1vm7a_ 191 GEFLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAAGDVFNG 250 d1trba1 181 LDAERYLDG------------------------------------------ 189 ::::::: d1vm7a_ 251 AFAVALS--EGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFLKNL 299 TMalign alignment (TM-score: 0.48 Raw score:90.60) d1trba1 1 --GTTKHSKLLILGSG----------------------------PAGYTAAVYAAR-ANL 29 ::::::::: :::::::::::: ::: d1vm7a_ 1 MF-----LVISVVGSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKIGEK 55 d1trba1 30 QPVLITGMEKGGQLT-TTTEVENWPGDPNDLTGPLLMERMHEHATKFETEIIF------- 81 :::::: :: : :::::::::::::::::::: d1vm7a_ 56 GCRFVT---CI---GN-----------------DDYSDLLIENYEKLGITGYIRVSLPTG 92 d1trba1 82 -----------------------DHINKVDLQNRPFRLNGDNGE-YT-CDALIIATGAS- 115 :::: ::::: :: ::::::::::: d1vm7a_ 93 RAFIEVDKTGQNRIIIFPGANAELKKE------------LIDWNTLSESDILLLQNEIPF 140 d1trba1 116 ---------------------ARYHSPNTAIFEGQL--E------L--E--NG------- 135 ::: :::::::: : : : :: d1vm7a_ 141 ETTLECAKRFNGIVIFDPAPA---QGI-NEEIFQYLDYLTPNEKEIEALSKDFFGEFLTV 196 d1trba1 136 ------Y----I--KVQSG--IHGNATQTSI---------------PGVFAAGDVMDHIY 166 : : ::::: ::: : :::: d1vm7a_ 197 EKAAEKFLELGVKNVIVKLGDKGV-L-LVNKNEKKHFPTFKVKAVD-------------- 240 d1trba1 167 RQAITSAGTGCMAALDAERYLD-G------------------------------------ 189 :: :::::::::::::::: : d1vm7a_ 241 ---TT-AAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFL 296 d1trba1 190 --- 190 d1vm7a_ 297 KNL 299 HHsearch alignment (Probability: 0.02 E-value:0.07) d1trba1 16 AGYTAAVYAARANLQ-PVLIT 35 ::::::::::::::: ::::: d1vm7a_ 41 KGANQAVTVAKIGEKGCRFVT 61