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 | d1kwga2 | A4 beta-galactosidase | (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 <-- 1.369 --> HitDALI alignment (Z-score: 12.0 Raw score:1455.70) d1j93a_ 1 tqpllldavrgkeverpPVWLMRqagrymksyqllcekyplfrdRSENVDLvVEISLQPW 60 :::::: ::::::: :::::::: d1kwga2 1 -----------------MLGVCY-------------------ypEHWPKER-WKEDARRM 23 d1j93a_ 61 KVFRPDGVIL-fsDILTPLSgmNIPFdiikgkgpvifdplrtaadvekvrefipeKSVPY 119 :::::::::: ::::::: :::: ::::: d1kwga2 24 REAGLSHVRIgefAWALLEP--EPGR-----------------------------LEWGW 52 d1j93a_ 120 VGEALTilRKEVnnqAAVLGFVGApfTLASY-VVEGgssknftkikrLAFA--------- 169 :::::: :::: ::::::::: ::::: :::: :::: d1kwga2 53 LDEAIAtlAAEG---LKVVLGTPT--ATPPKwLVDR-------ypeiLPVDregrrrrfg 100 d1j93a_ 170 ----epkvLHALLQKFATSMAKYIRYQADS-GAQAVQIFDSWAT-ELSP----------- 212 :::::::::::::::::::::: ::::::::::::: :::: d1kwga2 101 grrhycfsSPVYREEARRIVTLLAERYGGLeAVAGFQTDNEYGChDTVRcycprcqeafr 160 d1j93a_ 213 ----------------------------------------------------VDFEEfSL 220 ::::: :: d1kwga2 161 gwlearygtiealneawgtafwsqryrsfaevelphltvaepnpshlldyyrFASDQ-VR 219 d1j93a_ 221 PYLKQIVDSVKLTHPNLPLILYAsgSGGL----LERLPLtGVDVVSLDWT---------- 266 ::::::::::::::::::::::: :::: :::::: :::::::::: d1kwga2 220 AFNRLQVEILRAHAPGKFVTHNF--MGFFtdldAFALAQ-DLDFASWDSYplgftdlmpl 276 d1j93a_ 267 --------------vDMADGRRRLGPNV--AIQG-NVDPGV-------lFGSKefiTNRI 302 ::::::::::::: :::: :::::: :::: :::: d1kwga2 277 ppeeklryartghpdVAAFHHDLYRGVGrgRFWVmEQQPGPvnwaphnpSPAP---GMVR 333 d1j93a_ 303 NDTVKKAGKGKHILNLgHGIKV---------------gtPEEN-FAHFFEIAKGLR---- 342 :::::::::::::::: ::::: :::: :::::::::::: d1kwga2 334 LWTWEALAHGAEVVSY-FRWRQapfaqeqmhaglhrpdsAPDQgFFEAKRVAEELAalal 392 d1j93a_ 343 y 343 d1kwga2 393 p 393 FAST alignment (Normalized score: 5.92 Raw score:2172.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDR-----SENVDLVVEI 55 :::: :::::::::: d1kwga2 1 -----------------MLGV------------------------CYYPEHWPKERWKED 19 d1j93a_ 56 SLQPWKVFRPDGVILF-SDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPE 114 :::::: :::::: ::::::::: d1kwga2 20 ARRMRE-AGLSHV---RIGEFAWALL---------------------------------- 41 d1j93a_ 115 ------KSVPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLA 167 ::::::::::::::: :::::::: d1kwga2 42 EPEPGRLEWGWLDEAIATLAA----EGLKVVLGT-------------------------- 71 d1j93a_ 168 FAEPKVLHAL-------------------------------------LQKFATSMAKYIR 190 ::::::::::::: d1kwga2 72 ----------PTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121 d1j93a_ 191 YQADS-----GAQAVQIFDSWATEL----------------------------------- 210 ::::: :::::: d1kwga2 122 LLAERYGGLEAVAGFQ---------TDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEA 172 d1j93a_ 211 --------------------------------------SPVDFEEFSLPYLKQIVDSVKL 232 ::::: :::::::::::::::: d1kwga2 173 LNEAWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFAS-DQVRAFNRLQVEILRA 231 d1j93a_ 233 THPNLPLILYASGSGG-------LLERLPLTGVDVVSLDWTV------------------ 267 ::::::::::: ::::::: :::::::: d1kwga2 232 HAPGKFVTHNF-----MGFFTDLDAFALAQ-DLDFASWD---SYPLGFTDLMPLPPEEKL 282 d1j93a_ 268 ---------DMADGRRR----LGPNVAIQGNVDPGVLFGSK---------------EFIT 299 :::::::: ::::::: :::: :::: d1kwga2 283 RYARTGHPDVAAFHHDLYRGVGRGRFWV-MEQQ--------PGPVNWAPHNPSPAPGMVR 333 d1j93a_ 300 NRINDTVKKAGKGK---HILNLGHGIKVGT--------------------------PEEN 330 :::::::: ::::: :::: d1kwga2 334 LWTWEALA------HGAEVVSY--------FRWRQAPFAQEQMHAGLHRPDSAPDQGFFE 379 d1j93a_ 331 FAHFFEIAKGLRY--- 343 ::::::::::: d1kwga2 380 AKRVAEELAAL--ALP 393 TMalign alignment (TM-score: 0.60 Raw score:207.30) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :::::::::: : : ::::::::::: d1kwga2 1 -----------------MLGVCYYPEH----W--P--------------KERWKEDARRM 23 d1j93a_ 61 KVFRPDGVILF-SDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 ::::::::::: ::::::::: : : : : :::: d1kwga2 24 REAGLSHVRIGEFAWALLEPE-P--------------------------G-R-L--EWGW 52 d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLAS-YV-----VE---------GGSSKNFTKIK 164 ::::::::: ::: ::::::::: ::::: :: :: ::::::: :: d1kwga2 53 LDEAIATLA-AEG--LKVVLGTPT-ATPPKWLVDRYPEILPVDREGRRRRFGGRRH--YC 106 d1j93a_ 165 RLAFAEPKVLHALLQKFATSMAKYIRYQADS-GAQAVQIFDSWAT--ELS---------- 211 : : :::::::::::::::::::::: ::::::::::::: ::: d1kwga2 107 --F---S--SPVYREEARRIVTLLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAF 159 d1j93a_ 212 ---------------------------------------------------P-VDFEEFS 219 : ::::: : d1kwga2 160 RGWLEARYGTIEALNEAWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQ-V 218 d1j93a_ 220 LPYLKQIVDSVKLTHPNLPLILYASGSGG-L-LERLPLTGVDVVSLDW----T------- 266 ::::::::::::::::::::::::::::: : :::::: ::::::::: : d1kwga2 219 RAFNRLQVEILRAHAPGKFVTHNFMGFFTDLDAFALAQ-DLDFASWDSYPLGFTDLMPLP 277 d1j93a_ 267 ---------------V--DMADGRRRLGPNVAIQGNVDPGV-------LFGSKEFITNRI 302 : ::::::: ::::::::::::::: :::::::::::: d1kwga2 278 PEEKLRYARTGHPDVAAFHHDLYRG-VGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWT 336 d1j93a_ 303 NDTVKKAGKGKHILNLGHGI----------KVGT------PEENFAHFFEIAKGL--R-Y 343 :::::: : :::::: ::: :::: ::::::::::::::: : : d1kwga2 337 WEALAH-G--AEVVSY-FRWRQAPFAQEQMHAGLHRPDSAPDQGFFEAKRVAEELAALAL 392 d1j93a_ 344 - 344 d1kwga2 393 P 393 HHsearch alignment (Probability: 0.31 E-value:0.01) d1j93a_ 115 KSVPYVGEALTILRKEVNNQAAVLGFV-------------GAPFTLASYVVEGGSSKNFT 161 ::::::::::::::::::::::::::: :::::::: :: d1kwga2 111 VYREEARRIVTLLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEA----------FR 160 d1j93a_ 162 KIKRLAFAEPKVLHALLQKFATSMAKYI-RYQADSGAQAVQIFDSWATELSPVD-FEEFS 219 ::::::::::::::::::::: :::::: ::::::::::: ::::::::::::: ::::: d1kwga2 161 GWLEARYGTIEALNEAWGTAF-WSQRYRSFAEVELPHLTV-AEPNPSHLLDYYRFASDQV 218 d1j93a_ 220 LPYLKQIVDSVKLTHPNLPLILYASGSGGLLER-LPLTGVDVVSLDWTVDM--------- 269 ::::::::::::::::::::::::::::::::: ::::::::::::::::: d1kwga2 219 RAFNRLQVEILRAHAPGKFVTHNFMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPP 278 d1j93a_ 270 ------------------ADGRRRL-GPNVA------IQGNVDPGVLFGSKEFITNRIND 304 ::::::: ::::: ::::::::::::::::::::::: d1kwga2 279 EEKLRYARTGHPDVAAFHHDLYRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWE 338 d1j93a_ 305 TVKKAGKGKHILNL----------GHGI--KVGTPEENFAHFFEIAKGLR 342 :::::::::::::: :::: :::::::::::::::::::: d1kwga2 339 ALAHGAEVVSYFRWRQAPFAQEQMHAGLHRPDSAPDQGFFEAKRVAEELA 388