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 | d1pbga_ | 6-phospho-beta-D-galactosidase, PGAL | (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 <-- 1.287 --> HitDALI alignment (Z-score: 12.9 Raw score:1569.50) d1j93a_ 1 tqpllldavrgkeVERPPVWLMRqagrymksyqllcekypLFRD---------------- 44 :::::::::: :::: d1pbga_ 1 --------mtktlPKDFIFGGAT----------aayqaegATHTdgkgpvawdkyledny 42 d1j93a_ 45 ------rseNVDLvVEISLQPWKVFRPDGVILFSDILTPLSGMnipfdiikgkgpvifdp 98 :::: ::::::::::::::::::::::::::::: d1pbga_ 43 wytaepasdFYHK-YPVDLELAEEYGVNGIRISIAWSRIFPTG----------------- 84 d1j93a_ 99 lrtaadvekVREFIpEKSVPYVGEALTILRKEVnnqAAVLGFVGapfTLASY-VVEGgss 157 ::::: :::::::::::::::::: :::::::: ::::: :::: d1pbga_ 85 ---------YGEVN-EKGVEFYHKLFAECHKRH---VEPFVTLH--hFDTPEaLHSN--- 126 d1j93a_ 158 knftkikrlafaepkvLHALLQKFATSMAKYIRYQAdsGAQAVQIFDSWATELS------ 211 :::::::::::::::::::: :::::::::::::::: d1pbga_ 127 ------------gdflNRENIEHFIDYAAFCFEEFP--EVNYWTTFNEIGPIGDgqylvg 172 d1j93a_ 212 ------------PVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG-------------- 245 :::::::::::::::::::::::::::::::::: d1pbga_ 173 kfppgikydlakVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALptkypydpenpadv 232 d1j93a_ 246 ---------SGGL-LERLP------------------------------------LTGVD 259 :::: ::::: ::::: d1pbga_ 233 raaelediiHNKFiLDATYlghysdktmegvnhilaenggeldlrdedfqaldaaKDLND 292 d1j93a_ 260 VVSLDWT------------------------------------vDMADGRRRL---GPNV 280 ::::::: ::::::::: :::: d1pbga_ 293 FLGINYYmsdwmqafdgeteikyqikgvgrrvapdyvpwiiypeGLYDQIMRVkndYPNY 352 d1j93a_ 281 -AIQG-NVDPG------vlfgSKEFITNRINDTVKKAG------kGKHILNLghgIKVG- 325 :::: ::::: ::::::::::::::::: ::::::: :::: d1pbga_ 353 kKIYItENGLGykdefvdntvYDDGRIDYVKQHLEVLSdaiadgaNVKGYFIwslMDVFs 412 d1j93a_ 326 ---------------------tpEENFAHFFEIAKGLR-y 343 ::::::::::::::: d1pbga_ 413 wsngyekryglfyvdfdtqerypKKSAHWYKKLAETQVie 452 FAST alignment (Normalized score: 3.99 Raw score:1570.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWL--------------------------------------- 21 d1pbga_ 1 ---------------------MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLE 39 d1j93a_ 22 ---------------------------------MRQAGRYMKS----------------- 31 ::::::: d1pbga_ 40 DNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSR---IFPTGYGEVNEKGVEFY 96 d1j93a_ 32 -----------------------YQLLCEKYPLFR-DRSE---NVDLVVEISLQPWKVF- 63 :::::: :::: :::::::::::::::: d1pbga_ 97 HKLFAECHKRHVEPFVTLHHFDTPEALHS------NGDFLNRENIEHFIDYAAFCFEEFP 150 d1j93a_ 64 RPDGVILFS---DILTPLSGM----NIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS 116 ::::::: ::::: :::: d1pbga_ 151 EVNYWTT--FNEIGPIG----DGQYLVGK------------------------------- 173 d1j93a_ 117 ---------------VPYVGEALTILRKE---VNNQAAVLGFVGAPFTLASYVVEGGSSK 158 :::::::::::::: :::::::::::: d1pbga_ 174 FPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHA---------------- 217 d1j93a_ 159 NFTKIKRLAFA-------------EPKVLHALLQKFATSMAKYIRYQAD----------- 194 :::::::::::: ::::::::: d1pbga_ 218 -----------LPTKYPYDPENPADVRAAELEDIIH---NKFILDATY-LGHYSDKTMEG 262 d1j93a_ 195 --------------------------SGAQAVQIFDSWATELSPVDFEEF---------- 218 ::::::::::: d1pbga_ 263 VNHILAENGGELDLRDEDFQALDAAKDLNDFLGINYY-------------MSDWMQAFDG 309 d1j93a_ 219 ------------------------SLPYLKQIVDSVKLTHPN-LPLILYASG-------- 245 :::::::::::::::::: ::::: d1pbga_ 310 ETEIKYQIKGVGRRVAPDYVPWIIYPEGLYDQIMRVKNDYPNYKKIYI----TENGLGYK 365 d1j93a_ 246 ------------SGGLLERLPLT----------GVDVVSLDWTVDMADGRRRLGPNVAIQ 283 :::::::::: ::::::: d1pbga_ 366 DEFVDNTVYDDGRIDYVKQHLE-VLSDAIADGANVKGYFI-------------------- 404 d1j93a_ 284 GNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 d1pbga_ 405 ------------------------------------------------------------ 405 d1j93a_ 344 ------------------------------------------------ 344 d1pbga_ 405 WSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 452 TMalign alignment (TM-score: 0.58 Raw score:200.44) d1j93a_ 1 ----TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFR------------- 43 :::::::::::::::: :: ::::::::: d1pbga_ 1 MTKT------------LPKDFIFGGATAAYQA---EG-ATHTDGKGPVAWDKYLEDNYWY 44 d1j93a_ 44 --------D----------------------RS--E-----------NVDLVVEISLQPW 60 : :: : ::::::::::::: d1pbga_ 45 TAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECH 104 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 :: :: :::::::::: :: :: :::::: ::::::::::::::::: d1pbga_ 105 KR-HV-EPFVTLHHFD-TP-----EA-------LHSNGD----FLNRENIEHFIDYAAFC 145 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 :::::::: ::::::::::::::::: :::::::::: :: : :::::::: d1pbga_ 146 FEEFPEVN--------YWTTFNEIGPIGDGQYL-VGKFPPGIKY-DL---A-KVFQSHHN 191 d1j93a_ 181 FATSMAKYIRYQA--DSGAQAVQIFDSWAT------------ELSPVDFEEFSLPYLKQI 226 ::::::::::::: ::::::::::::::: ::::::::::::::::: d1pbga_ 192 MMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADVR-AAELEDIIHNKFILDAT 250 d1j93a_ 227 VDS------------------------------VKLT-HPNLPLILYASGSGGLL----- 250 ::: :::: ::::::::: ::::::: d1pbga_ 251 YLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGIN-YYMSDWMQAFDG 309 d1j93a_ 251 ---------------------ERLPLTGVDVVSLDWTVDMADGRRRLGPNV--------A 281 :::::::::::::::: : d1pbga_ 310 ETEIKYQIKGVGRRVAPDYVP--------------WIIYPEGLYDQIMRVKNDYPNYKKI 355 d1j93a_ 282 IQ-GNVDPGVL-----FGSKEFITNRINDTVKKAGK-G-----KHILNLGHGIKV----- 324 :: :::::::: :::::::::::::::::::: : :::::::::::: d1pbga_ 356 YITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSN 415 d1j93a_ 325 ---------GT------PEEN-FAHFFEIAKGLRY-- 343 :: :::: ::::::::::::: d1pbga_ 416 GYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 452 HHsearch alignment (Probability: 0.12 E-value:0.02) d1j93a_ 293 GSKEFITNRINDTVKKAGK--GKHILNLGHGIK 323 ::::::::::::::::::: :::::::::::: d1pbga_ 333 IYPEGLYDQIMRVKNDYPNYKKIYITENGLGYK 365