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 | d1ua7a2 | Bacterial alpha-amylase | (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 <-- 0.839 --> HitDALI alignment (Z-score: 10.9 Raw score:1319.20) d1j93a_ 1 tqPLLLdavrgkeverPPVWLMRQAGrymksyqllcekyplfrdrsenvdlVVEISLQPW 60 :::: :::::::::: ::::::::: d1ua7a2 1 --PSIK----------SGTILHAWNW-------------------------SFNTLKHNM 23 d1j93a_ 61 KVFR---PDGVILFSDilTPLSgmnipfDIIKgkgpvifdplrtaadvekvrefipekSV 117 :::: ::::::::: :::: :::: :: d1ua7a2 24 KDIHdagYTAIQTSPI--NQVK------EGNQ----------gdksmsnwywlyqptsYQ 65 d1j93a_ 118 PY-----VGEALTILRKEVN-NQAAVLGFVGApfTLAS--------------yvveggsS 157 :: ::::::::::::: ::::::::::: :::: : d1ua7a2 66 IGnrylgTEQEFKEMCAAAEeYGIKVIVDAVI--NHTTfdyaaisnevksipnwthgntQ 123 d1j93a_ 158 KNF--TKIKrlafaepkvlhaLLQK--FATSMAKYIRYQADSGAQAVQIFDSWAtelspv 213 ::: :::: :::: ::::::::::::::::::::::::::: d1ua7a2 124 IKNwsDRWDvtqnsllglydwNTQNtqVQSYLKRFLERALNDGADGFRFDAAKH------ 177 d1j93a_ 214 dFEEF----slPYLKQIVDsvklthPNLP-LILYASG-sgGLLERLPLTgvDVVSLD--W 265 :::: :::::::: :::: ::::::: ::::::::: :::::: : d1ua7a2 178 iELPDdgsygsQFWPNITN------TSAEfQYGEILQdsaSRDAAYANY--MDVTASnyG 229 d1j93a_ 266 TVD-------------mADGRRRLGpnVAIQGNVDP---------gvlFGSKEFITNRIN 303 ::: :::::::: ::::::::: :::::::::::: d1ua7a2 230 HSIrsalknrnlgvsniSHYASDVS-aDKLVTWVEShdtyanddeestWMSDDDIRLGWA 288 d1j93a_ 304 DTVKKagkGKHILNLghGIKVGTP----------------EENFAH--FFEIAKGLRY-- 343 ::::: ::::::: ::::::: :::::: :::::::::: d1ua7a2 289 VIASR---SGSTPLF--FSRPEGGgngvrfpgksqigdrgSALFEDqaITAVNRFHNVma 343 d1j93a_ 344 - 344 d1ua7a2 344 g 344 FAST alignment (Normalized score: 5.18 Raw score:1780.00) d1j93a_ 1 TQPLLLDAVRGKEVER----PPVWLMRQAGRYMKSYQLLCEKYPLFRDRS----ENVDLV 52 ::::: :::::: d1ua7a2 1 ----------------PSIKSGTIL-------------------------HAWNWSFNTL 19 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKV---- 108 :::::::: ::::::::: d1ua7a2 20 KHNMKDIH-DAGYTAIQT--------------------------------------SPIN 40 d1j93a_ 109 ---------------------REFIPEKS-------VPYVGEALTILRKEVNN-QAAVLG 139 ::::: ::::::::::::: :::::: d1ua7a2 41 QVKEGNQGDKSMSNWYWLYQPTSYQI---GNRYLGTEQEFKEMCAAAEE----YGIKVIV 93 d1j93a_ 140 FVGAPFTLASY--------------------VVEGGSSKNFTKIKRLAFAEPKVLHAL-- 177 ::: :::: d1ua7a2 94 DAV--------INHTTFDYAAISNEVKSIPNWTHG-----------------------NT 122 d1j93a_ 178 -------------------------LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSP 212 ::::::::::::::::::::::::: ::::::: d1ua7a2 123 QIKNWSDRWDVTQNSLLGLYDWNTQNTQVQSYLKRFLERALNDGADGFRF--DAAKHIE- 179 d1j93a_ 213 VDFEEFS--------LPYLKQIVDSVKLTHPN---LPLILYASGSG-----GLLERLPLT 256 ::::::::: ::::::: :::::::: d1ua7a2 180 -------LPDDGSYGSQFWPNITN--------TSAEFQYGEI----LQDSASRDAAYAN- 219 d1j93a_ 257 GV-DVVSLDWTVDMADGR-------------------------RRLGPNVAIQGNVDPGV 290 ::::: :::::: :::::: d1ua7a2 220 --YMDVTA----------SNYGHSIRSALKNRNLGVSNISHYASDVSAD-KLVTWV---- 262 d1j93a_ 291 LF---------------GSKEFITNRINDTVKKAG-KGKHILNLGHGIKVGTP------- 327 :::::::::::::: ::::::: d1ua7a2 263 --ESHDTYANDDEESTWMSDDDIRLGWAVIA----SRSGSTPL----------FFSRPEG 306 d1j93a_ 328 -----------------EENF--AHFFEIAKGLRY------ 343 :::: ::::::::: d1ua7a2 307 GGNGVRFPGKSQIGDRGSALFEDQAITAVNRF---HNVMAG 344 TMalign alignment (TM-score: 0.56 Raw score:193.36) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::: : :::::::::: ::::::::: d1ua7a2 1 ---PSI--K-------SGTILHAWNW-------------------------SFNTLKHNM 23 d1j93a_ 61 KVFR---PDGVILFSDILTPLSGMNIPFDIIK-G----K-GPVIF-DPLRTAADVEKVRE 110 :::: :::::::::: : : ::::: : : ::::: : d1ua7a2 24 KDIHDAGYTAIQTSPIN-Q-V------KEGNQGDKSMSNWYWLYQP-----------T-- 62 d1j93a_ 111 FIPEKSVP----YVGEALTILRKEV-NNQAAVLGFVGAPFTLASYVVEGG---------- 155 : : ::: ::::::::::::: ::::::::::::: ::::::::: d1ua7a2 63 S-Y--QIGNRYLGTEQEFKEMCAAAEEYGIKVIVDAVIN--HTTFDYAAISNEVKSIPNW 117 d1j93a_ 156 --SSKNFTKIKRL----AFA-EPKV----LHALLQK--FATSMAKYIRYQADSGAQAVQI 202 ::::::: ::: ::: ::::::: :::::::::::::::::::::: d1ua7a2 118 TH----GNTQIKNWSDRWDVT-QNSLLGLYDWNTQNTQVQSYLKRFLERALNDGADGFRF 172 d1j93a_ 203 FDSWATELSPV-DFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVV 261 :::::: :: :::: ::: :: :::::: :::::::::: ::::::::::::::::: d1ua7a2 173 DAAKHI---ELP-DDGS-YGS-QF-WPNITN-TSAEFQYGEI-LQDSASRDAAYANYMDV 223 d1j93a_ 262 SLD--WTVD-------------MADGRRRLGPNVAIQGNVDP----------GVLFGSKE 296 ::: :::: :::::::::::: ::::::: ::::::: d1ua7a2 224 TASNYGHSIRSALKNRNLGVSNISHYASDVSADK-LVTWVESHDTYANDDEESTWMSDD- 281 d1j93a_ 297 FITNRINDTVKKAGKGKHILNLGHGIKV-GTP--------------EENF-AHFFEIAKG 340 ::::::::::: :: : ::::: ::::: ::: :::: ::::::::: d1ua7a2 282 DIRLGWAVIAS-RS-G-STPLF-FSRPEGGGNGVRFPGKSQIGDRGSALFEDQAITAVNR 337 d1j93a_ 341 L--RY-- 343 : :: d1ua7a2 338 FHNVMAG 344 HHsearch alignment (Probability: 0.09 E-value:0.02) d1j93a_ 166 LAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQ 225 :::::::::::: :::::::::::::::: ::: ::::::::::::::::::: d1ua7a2 144 WNTQNTQVQSYL--------KRFLERALNDGADGFR-FDA-AKHIELPDDGSYGSQFWPN 193 d1j93a_ 226 IVD 228 ::: d1ua7a2 194 ITN 196