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 | d1ht6a2 | Plant 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 <-- 0.966 --> HitDALI alignment (Z-score: 11.0 Raw score:1328.90) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQAGRymksYQLLcekyplfrdrsenvdLVVEISLQPW 60 ::::::::::: :::: :::::::::: d1ht6a2 1 ----------------HQVLFQGFNWE--swKQSG---------------GWYNMMMGKV 27 d1j93a_ 61 KVFR---PDGVILFS--------DILTPLsgmnipfdiikgkgpvifdplrtaadvekvr 109 :::: :::::::: :::::: d1ht6a2 28 DDIAaagVTHVWLPPpshsvsneGYMPGR------------------------------- 56 d1j93a_ 110 efipekSVPY-----vGEALTILRKEV-NNQAAVLGFVGApftLASYV------------ 151 :::: ::::::::::: :::::::::::: ::::: d1ht6a2 57 -----lYDIDaskygnAAELKSLIGALhGKGVQAIADIVI---NHRCAdykdsrgiycif 108 d1j93a_ 152 ---veggssknftkikrLAFA----EPKVLH----------aLLQK--FATSMAKYIRYQ 192 :::: :::::: :::: :::::::::::: d1ht6a2 109 eggtsdgrldwgphmicRDDTkysdGTANLDtgadfaaapdiDHLNdrVQRELKEWLLWL 168 d1j93a_ 193 AD-SGAQAVQIFDSWAtelspvdfeeFSLPYLKQIVDSVKlthpnLPLILYASG------ 245 :: ::::::::::::: :::::::::::::: ::::::::: d1ht6a2 169 KSdLGFDAWRLDFARG----------YSPEMAKVYIDGTS----pSLAVAEVWDnmatgg 214 d1j93a_ 246 ----------sGGLLER-LPLT----GVDVVSLD--WTVD-----------------mAD 271 :::::: :::: :::::::: :::: :: d1ht6a2 215 dgkpnydqdahRQNLVNwVDKVggaaSAGMVFDFttKGILnaavegelwrlidpqgkaPG 274 d1j93a_ 272 GRRRLgpnVAIQGNVD----------pGVLFGskeFITNRINDTVKKAgkgkHILNLghG 321 ::::: :::::::: ::::: ::::::::::::: ::::: : d1ht6a2 275 VMGWW--pAKAVTFVDnhdtgstqamwPFPSD---KVMQGYAYILTHP----GIPCI--F 323 d1j93a_ 322 IKV-gTPEEnFAHFFEIAKGLRY-- 343 ::: :::: ::::::::::::: d1ht6a2 324 YDHffNWGF-KDQIAALVAIRKRng 347 FAST alignment (Normalized score: 4.66 Raw score:1608.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRY----MKSYQLLCEKYPLFRDRSENVD----LV 52 ::::: :::: :: d1ht6a2 1 ----------------HQVLF-------QGFNWESW------------------KQSGGW 19 d1j93a_ 53 VEISLQPWK---VFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVR 109 ::::::::: ::::::::: d1ht6a2 20 YNMMMGKVDDIAAAGVTHVWL--------------------------------------- 40 d1j93a_ 110 E--------------FIPEKSVPY--------VGEALTILRKEVNN----QAAVLGFVGA 143 :::: ::::::::::: ::::::::: d1ht6a2 41 -PPPSHSVSNEGYMPGRLY-----DIDASKYGNAAELKSLIGA---LHGKGVQAIADIV- 90 d1j93a_ 144 PFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL-------------------------- 177 d1ht6a2 91 ----------------------------------INHRCADYKDSRGIYCIFEGGTSDGR 116 d1j93a_ 178 -------------------------------------LQKFATSMAKYIRYQA-DSGAQA 199 :::::::::::::::: :::::: d1ht6a2 117 LDWGPHMICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKSDLGFDA 176 d1j93a_ 200 VQI-FDSWATELSPVDFEEF-SLPYLKQIVDSVKLTHPN---LPLILYASG--------- 245 ::: :::: ::::::::::: ::::::: d1ht6a2 177 WRLDFARG------------YSPEMAKVYIDG-------TSPSLAVAEV--WDNMATGGD 215 d1j93a_ 246 -------------SGGLLER--LPLTGV-DVVSLDWTVDMA------------------- 270 ::::::: :::: ::::: d1ht6a2 216 GKPNYDQDAHRQNLVNWVDKVGGAAS--AGMVFD-------FTTKGILNAAVEGELWRLI 266 d1j93a_ 271 -------DGRRRLGPNV----AIQGNVDPGVLFGSK----------------EFITNRIN 303 :::: :::::: :::::::: d1ht6a2 267 DPQGKAPGVMG------WWPAKAVTFV---------DNHDTGSTQAMWPFPSDKVMQGYA 311 d1j93a_ 304 DTVKKAGKGK--HILNLGHGIKVGT----------PEENFAHFFEIAKGLRY--- 343 :::: :::: ::::::::::::: d1ht6a2 312 YILT------HPGIPC---------IFYDHFFNWGFKDQIAALVAIRK----RNG 347 TMalign alignment (TM-score: 0.55 Raw score:188.39) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : :::: ::::::: ::::: :::::::::: d1ht6a2 1 -------------H--QVLF-QGFNWES--WKQSG---------------GWYNMMMGKV 27 d1j93a_ 61 KVFR-P-D-GVILFSDILTPLSGMNIPFDIIK-GKGPVIFDPLRTAADVEKVREFIPEKS 116 :::: : : :::::::: : ::::: :::: : : : : d1ht6a2 28 DDIAAAGVTHVWLPPPS-H--------SVSNEG--YMPG-------------R-L-Y--D 59 d1j93a_ 117 VP----YVGEALTILRKEV-NNQAAVLGFVGAPFTLASYVV------EGG---------- 155 :: ::::::::::::: :::::::::::: ::: ::: ::: d1ht6a2 60 IDASKYGNAAELKSLIGALHGKGVQAIADIVI--NHR-CADYKDSRGIYCIFEGGTSDGR 116 d1j93a_ 156 -------SSKNFTKIKRLA--F-AEPKVLH---------ALL-Q-KFATSMAKYIRYQAD 194 :::::: : ::::::: ::: : ::::::::::::::: d1ht6a2 117 LDWGPHM------ICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKS 170 d1j93a_ 195 -SGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSG------ 247 ::::::::::::: :::::::::::::: :::::::::::: d1ht6a2 171 DLGFDAWRLDFARG----------YSPEMAKVYIDGTS----PSLAVAEVWDNMATGGDG 216 d1j93a_ 248 --------G--LLERLP-LT----GVDVVSLD--WTVD-----------------MADGR 273 : :::::: :: :::::::: :::: ::::: d1ht6a2 217 KPNYDQDAHRQNLVNWVDKVGGAASAGMVFDFTTKGILNAAVEGELWRLIDPQGKAPGVM 276 d1j93a_ 274 RRLGPNVAIQGNVD----P------GVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK 323 :: :: :::::::: : ::::: ::::::::::: :: :::::: ::: d1ht6a2 277 GW-WP-AKAVTFVDNHDTGSTQAMWPFPSD---KVMQGYAYILT-HP--GIPCIF--YDH 326 d1j93a_ 324 VGTPEENFAHFFEIAKGLR--Y- 343 ::::::::::::::::: : d1ht6a2 327 --FFNWGFKDQIAALVAIRKRNG 347 HHsearch alignment (Probability: 0.09 E-value:0.02) d1j93a_ 280 VAIQGNVDPGV---LFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFE 336 ::::::::::: ::::::::::::::::::::::::::: ::::: :::::::::::: d1ht6a2 284 VTFVDNHDTGSTQAMWPFPSDKVMQGYAYILTHPGIPCIFY-DHFFN-WGFKDQIAALVA 341 d1j93a_ 337 IA 338 :: d1ht6a2 342 IR 343