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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1bf2a3 | Isoamylase, central domain | (Trans)glycosidases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 1.216 --> HitDALI alignment (Z-score: 10.3 Raw score:1325.40) d1j93a_ 1 ------tqpllLDAVrgkeverPPVWLMRQAGRYmkSYQL--LCEKyplfrdrsenvdLV 52 :::: :::::::::::: :::: :::: :: d1bf2a3 1 pstqstgtkptRAQK-------DDVIYEVHVRGF--TEQDtsIPAQ---------yrgTY 42 d1j93a_ 53 VEISLQpWKVFR---PDGVILFS----------------------DILTPLsgmnipfdi 87 :::::: ::::: :::::::: :::::: d1bf2a3 43 YGAGLK-ASYLAslgVTAVEFLPvqetqndandvvpnsdanqnywGYMTEN--------- 92 d1j93a_ 88 ikgkgpvifdplrtaadvekvrefipekSVPY-----------vgEALTILRKEV-NNQA 135 :::: :::::::::: :::: d1bf2a3 93 ---------------------------yFSPDrryaynkaaggptAEFQAMVQAFhNAGI 125 d1j93a_ 136 AVLGFVGApfTLASyVVEG------------------------gssknfTKIKrlafaep 171 :::::::: :::: :::: :::: d1bf2a3 126 KVYMDVVY--NHTA-EGGTwtssdpttatiyswrgldnatyyeltsgnqYFYD----ntg 178 d1j93a_ 172 kvlhaLLQK--FATSMAKYIRYQAD-SGAQAVQIFDSwatelspvdfeeFSLP------- 221 :::: :::::::::::::: ::::::::::: :::: d1bf2a3 179 iganfNTYNtvAQNLIVDSLAYWANtMGVDGFRFDLA-----------sVLGNsclngay 227 d1j93a_ 222 ---------------------YLKQIVDSVK----lthpNLPLILYA---sgsgGLLERL 253 :::::::::: :::::::: :::::: d1bf2a3 228 tasapncpnggynfdaadsnvAINRILREFTvrpaaggsGLDLFAEPwaiggnsYQLGGF 287 d1j93a_ 254 pLTGVdVVSLD--WTVD--------------------MADGRRRL--GPNV--AIQGNVD 287 :::: ::::: :::: :::::::: :::: ::::::: d1bf2a3 288 -PQGW-SEWNGlfRDSLrqaqnelgsmtiyvtqdandFSGSSNLFqsSGRSpwNSINFID 345 d1j93a_ 288 P----GVLFG----------------------------------------SKEFITNRIN 303 : ::::: :::::::::: d1bf2a3 346 VhdgmTLKDVyscngannsqawpygpsdggtstnyswdqgmsagtgaavdQRRAARTGMA 405 d1j93a_ 304 DTVKKAgkgkHILNLgHGIK--------------------------vgtPEENFAHFFEI 337 :::::: ::::: :::: ::::::::::: d1bf2a3 406 FEMLSA----GTPLM-QGGDeylrtlqcnnnaynldssanwltyswttdQSNFYTFAQRL 460 d1j93a_ 338 AKGLRY--------- 343 :::::: d1bf2a3 461 IAFRKAhpalrpssw 475 FAST alignment (Normalized score: 4.13 Raw score:1669.00) d1j93a_ 1 TQPLLLDAVRGKEVER---------------PPVWLMRQAGRYMKSYQLLCEKYPLFRDR 45 ::::: :::: d1bf2a3 1 ----------------PSTQSTGTKPTRAQKDDVIY-EVHV------------------- 24 d1j93a_ 46 S---------------ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFD---- 86 ::::::::::::: :::::::::: d1bf2a3 25 -RGFTEQDTSIPAQYRGTYYGAGLKASYL-ASLGVTAVEF----------------LPVQ 66 d1j93a_ 87 --------IIKGKGPVIFDPLRTAADVEKVREFIPEKS---------------------- 116 :::: d1bf2a3 67 ETQNDANDVVPN--------------------------SDANQNYWGYMTENYFSPDRRY 100 d1j93a_ 117 ---------VPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRL 166 ::::::::::::: :::::::: d1bf2a3 101 AYNKAAGGPTAEFQAMVQAFHN----AGIKVYMDV------------------------- 131 d1j93a_ 167 AFAEPKVLHAL------------------------------------------------- 177 d1bf2a3 132 -----------VYNHTAEGGTWTSSDPTTATIYSWRGLDNATYYELTSGNQYFYDNTGIG 180 d1j93a_ 178 ------LQKFATSMAKYIRYQA-DSGAQAVQIF--DSWATELSPVDFEEFSL-------- 220 :::::::::::::::: ::::::::: :::: d1bf2a3 181 ANFNTYNTVAQNLIVDSLAYWANTMGVDGFRF-DLASVL-------------GNSCLNGA 226 d1j93a_ 221 ---------------------PYLKQIVDSVKLTHP----------NLPLILYASGSG-- 247 ::::::::: ::::::: d1bf2a3 227 YTASAPNCPNGGYNFDAADSNVAINRILRE------FTVRPAAGGSGLDLFAE-----PW 275 d1j93a_ 248 ------GLLERLPLTGV----DVVSLDWTVD----------------------------- 268 ::::: ::::: d1bf2a3 276 AIGGNSYQLGG------FPQGWSEWN-----GLFRDSLRQAQNELGSMTIYVTQDANDFS 324 d1j93a_ 269 -MADGRRRLGPNV------AIQGNVDPGVLFG---------------------------- 293 ::::::: :::::: d1bf2a3 325 GSSNLFQS-----SGRSPWNSINFI-------DVHDGMTLKDVYSCNGANNSQAWPYGPS 372 d1j93a_ 294 -----------------------SKEFITNRINDTVKKAGKGK--HILNLGHGIKVGT-- 326 :::::::::::::: :::: d1bf2a3 373 DGGTSTNYSWDQGMSAGTGAAVDQRRAARTGMAFEML------SAGTPL---------MQ 417 d1j93a_ 327 -----------------------------------PEENFAHFFEIAKGLRY------- 343 :::::::::::::::: d1bf2a3 418 GGDEYLRTLQCNNNAYNLDSSANWLTYSWTTDQSNFYTFAQRLIAFRKAHP-ALRPSSW 475 TMalign alignment (TM-score: 0.60 Raw score:207.07) d1j93a_ 1 --------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLV 52 :: ::::: ::::::::::::::::::::::: ::: :::: d1bf2a3 1 PSTQSTGT-KP-TRAQK-------DDVIYEVHVRGFTEQDTSIPAQY----RGT--YYGA 45 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIK--------GKG--PVIFDPLRTA 102 :: :::::::::::::: :::::: : ::::: ::: :::: : d1bf2a3 46 GL-KASYLASLGVTAVE-FLPVQE-T------QNDANDVVPNSDANQNYWGYMT-E---- 91 d1j93a_ 103 ADVEKVREFIP----------EK-SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYV 151 ::::: : :::::::::::::: : : :::::::::: :::: d1bf2a3 92 ------NYFSPDRRYAYNKAA-GGPTAEFQAMVQAFHN-A-G--IKVYMDVVYN--HTAE 138 d1j93a_ 152 VEGG-------SSKNFTK---------I---KRLAFA-E---P------KVLHALLQKFA 182 :::: : : ::::: : : ::::::::::: d1bf2a3 139 GGTWTSSDPTT------ATIYSWRGLDNATY-YELTSGNQYFYDNTGIGANFNTYNTVAQ 191 d1j93a_ 183 TSMAKYIRYQADSGAQAVQIFDSWATELSP----------------VDFEEF-S-LPYLK 224 :::::::::::::::::::::::::::::: :::::: : ::::: d1bf2a3 192 NLIVDSLAYWANTMGVDGFRFDLASVLGNSCLNGAYTASAPNCPNGGYNFDAADSNVAIN 251 d1j93a_ 225 QIVDSVKLTH---PNLPLILYASGS----GGLLERLPLTGVDVVSLD--WTVD------- 268 :::::::::: :::::::::::: ::::::: : :::::::: :::: d1bf2a3 252 RILREFTVRPAAGGSGLDLFAEPWAIGGNSYQLGGF-P-QGWSEWNGLFRDSLRQAQNEL 309 d1j93a_ 269 ---------M-AD---GRRRLG--PNV--AIQGNVDP----GVLF-G------------- 293 : :: :::::: ::: :::::::: :::: : d1bf2a3 310 GSMTIYVTQDANDFSGSSNLFQSSGRSPWNSINFIDVHDGMTLKDVYSCNGANNSQAWPY 369 d1j93a_ 294 --------------------------SKEFITNRINDTVKKAGKGKHILNLGHGIK---V 324 :::::::::::::: :: ::::: :::: : d1bf2a3 370 GPSDGGTSTNYSWDQGMSAGTGAAVDQRRAARTGMAFEML-SA---GTPLM-QGGDEYLR 424 d1j93a_ 325 GT-------------------P---EE-NFAHFFEIAKGL--R-Y------ 343 :: : :: :::::::::::: : : d1bf2a3 425 TLQCNNNAYNLDSSANWLTYSWTTDQSNFYTFAQRLIAFRKAHPALRPSSW 475 HHsearch alignment (Probability: 0.07 E-value:0.01) d1j93a_ 302 INDTVKKAGKGKHILN 317 :::::::::::::::: d1bf2a3 403 GMAFEMLSAGTPLMQG 418