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 | d1h3ga3 | Cyclomaltodextrinase, 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 <-- 1.257 --> HitDALI alignment (Z-score: 12.7 Raw score:1534.80) d1j93a_ 1 --tqplLLDAvrgkeverPPVWLMRQAGRYMKSYQLLCE-----KYPL-----FRDRsen 48 :::: ::::::::::::::::::::: :::: :::: d1h3ga3 1 gsaqrqGFGP--------GDAIYQIMPDRFANGDPSNDNvagmrEQADrrhggGRHG--- 49 d1j93a_ 49 vdlVVEISLQPWKVFR---PDGVILFS------------DILTPlsgmnipfdiikgkgp 93 ::::::::::::: :::::::: ::::: d1h3ga3 50 --gDIRGTIDHLDYIAglgFTQLWPTPlvendaaaysyhGYAAT---------------- 91 d1j93a_ 94 vifdplrtaadvekvrefipeKSVPY-----vGEALTILRKEVNN-QAAVLGFVGAP--- 144 ::::: ::::::::::::: ::::::::::: d1h3ga3 92 ---------------------DHYRIdprygsNEDFVRLSTEARKrGMGLIQDVVLShig 130 d1j93a_ 145 --------ftlasyVVEG--------------gssknFTKIKR--lafaepkvlhaLLQK 180 :::: :::::: :::: d1h3ga3 131 khhwwmkdlptpdwINYGgkfvptqhhrvavqdpyaaQADSENftkgwfvegmpdlNQTN 190 d1j93a_ 181 --FATSMAKYIRYQADSG-AQAVQIFDSWAtelspvdfeeFSLPYLKQIVDSVKLTHPNL 237 :::::::::::::::: ::::::::::: :::::::::::::::::::: d1h3ga3 191 plVANYLIQNNIWWIEYAgLSGLRIDTYGY----------SDGAFLTEYTRRLMAEYPRL 240 d1j93a_ 238 PLILYAsGSGG--LLERLPL---------TGVDVVSLD--WTVD---------------- 268 :::::: :::: ::::::: ::::::::: :::: d1h3ga3 241 NMVGEE-WSTRvpVVARWQRgkanfdgytSHLPSLMDFplVDAMrnalsktgeenglnev 299 d1j93a_ 269 --mADGRRRlGPNV-AIQGNVD----pGVLF---GSKEFITNRINDTVKKAgkgkHILNL 318 :::::: :::: ::::::: :::: ::::::::::::::::: ::::: d1h3ga3 300 yetLSLDYL-YPEPqNLVLFGGnhdmaRMFSaagEDFDRWRMNLVFLMTMP----RIPQF 354 d1j93a_ 319 gHGIK-------------------------------------vgtPEENFAHFFEIAKGL 341 :::: ::::::::::::::: d1h3ga3 355 -YSGDeilmtstvkgrddasyrrdfpggwagdkanafsgagltsqQRAAQDLVRKLANWR 413 d1j93a_ 342 RY------- 343 :: d1h3ga3 414 KNqpvihng 422 FAST alignment (Normalized score: 5.01 Raw score:1905.00) d1j93a_ 1 TQPLLLDAVRGKEVER----------PPVWLMRQAGRYMKSYQLLCE------------- 37 ::::: d1h3ga3 1 ----------------GSAQRQGFGPGDAIY----------------QIMPDRFANGDPS 28 d1j93a_ 38 ------------KYPLFRDRS-----ENVDLVVEISLQPWKVFRPDGVILFSDILTPLS- 79 :::: ::::::::::::::: :::::::: d1h3ga3 29 NDNVAGMREQADRRHG-----GGRHGGDIRGTIDHLDYIAG-LGFTQLWP---------T 73 d1j93a_ 80 ---GMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS-------------------- 116 :::: d1h3ga3 74 PLVENDA---------------------------------AAYSYHGYAATDHYRIDPRY 100 d1j93a_ 117 --VPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 ::::::::::::: ::::::::: d1h3ga3 101 GSNEDFVRLSTEARK----RGMGLIQDVV------------------------------- 125 d1j93a_ 174 ------------------------------------------------------------ 174 d1h3ga3 126 LSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPD 185 d1j93a_ 174 ----LHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF------SLPYL 223 :::::::::::::::::: :::::::: ::::: d1h3ga3 186 LNQTNPLVANYLIQNNIWWIEY---AGLSGLRI----------------DTYGYSDGAFL 226 d1j93a_ 224 KQIVDSVKLTHPNLPLILYASGSGG---LLERLPL------------TGVDVVSLDWTVD 268 :::::::::::::::::::: ::::::: :::::::: d1h3ga3 227 TEYTRRLMAEYPRLNMVGEE-----WSTRVPVVARWQRGKANFDGYTSHLPSLMD----- 276 d1j93a_ 269 MADGRRRLGPNVAIQGNV------DPGVLFGSKEF------ITNRINDTVKKAGK----- 311 :::::: ::::::::::: d1h3ga3 277 ------------------FPLVDAMRNALS-----KTGEENGLNEVYETLSL---DYLYP 310 d1j93a_ 312 --GKHILNLGHGIKVG------------TPEENFAHFFEIAKGLRY-------------- 343 :::::::: ::::::::::::::: d1h3ga3 311 EPQNLVLFGG------NHDMARMFSAAGEDFDRWRMNLVFLMT---MPRIPQFYSGDEIL 361 d1j93a_ 344 ------------------------------------------------------------ 344 d1h3ga3 362 MTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHN 421 d1j93a_ 344 - 344 d1h3ga3 422 G 422 TMalign alignment (TM-score: 0.63 Raw score:214.94) d1j93a_ 1 TQ--PLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYP-LFRDR---------SEN 48 :: ::::: : ::::::::::::: :::::::::: ::::: d1h3ga3 1 GSAQ--RQGFG-P-----GDAIYQIMPDRFA-NGDPSNDNVAGMREQADRRHGGGRH--- 48 d1j93a_ 49 VDLVVEISLQPWKVFR---PDGVILFSDILTPLSGMNIPFDIIKGKG-PVI--FDPLRTA 102 ::::::::::::::: :::::::::: : :::::::: ::: d1h3ga3 49 -GGDIRGTIDHLDYIAGLGFTQLWPTPLV-E--------NDAAAYSYHGYAAT------- 91 d1j93a_ 103 ADVEKVREFIPEKSVP---YVGEALTILRKEV-NNQAAVLGFVGAPFTLAS-Y------- 150 ::: ::: ::::::::::::: :::::::::::: ::::: : d1h3ga3 92 --------DHY--RIDPRYGSNEDFVRLSTEARKRGMGLIQDVVL-SHIGKHHWWMKDLP 140 d1j93a_ 151 ----VVEG--GSSKNFTKI-----------KRLAFAEP--------KVLHALLQKFATSM 185 :::: ::::::: :::::::: ::::::::::::: d1h3ga3 141 TPDWINYGGK--FVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMP-DLNQTNPLVANYL 197 d1j93a_ 186 AKYIRYQADS-GAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS 244 :::::::::: :::::::::::: ::::::::::::::::::::::::::: d1h3ga3 198 IQNNIWWIEYAGLSGLRIDTYGY----------SDGAFLTEYTRRLMAEYPRLNMVGEEW 247 d1j93a_ 245 GSG-GLLERLPL---------TGVDVVSLD--WTV----------------D--MADGRR 274 ::: :::::::: ::::::::: ::: : :::::: d1h3ga3 248 STRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDY 307 d1j93a_ 275 RLGPNVAIQGNVDP----GVLF---GSKEFITNRINDTVKKAGKGKHILNLGHGI----- 322 :::::::::::::: :::: ::::::::::::::: :: ::::::::: d1h3ga3 308 LYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMT-MP---RIPQFYSGDEILMT 363 d1j93a_ 323 ----------KVG-TP---------E---------E--NFAHFFEIAKGL--R--Y--- 343 ::: :: : : :::::::::::: : : d1h3ga3 364 STVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNG 422 HHsearch alignment (Probability: 0.10 E-value:0.01) d1j93a_ 280 VAIQGNVDPGVLFGSKE---FITNRINDTVKKAGKGKHILN 317 ::::::::::::::::: ::::::::::::::::::::: d1h3ga3 316 VLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYS 356