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 | d1qopa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | 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 <-- 1.513 --> HitDALI alignment (Z-score: 10.7 Raw score:1227.50) d1j93a_ 1 TQPLLLDAvrgKEVE---RPPVWLMRqagrymksyqllcekyplfrdRSENVDLVVEISL 57 :::::::: :::: :::::::: ::::::::::::: d1qopa_ 1 MERYENLF---AQLNdrrEGAFVPFV-------------------tlGDPGIEQSLKIID 38 d1j93a_ 58 QPWKVFrPDGVILFSDILtplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksV 117 :::::: ::::::::::: : d1qopa_ 39 TLIDAG-ADALELGVPFS-------------------dpladgptiqnanlrafaagvtP 78 d1j93a_ 118 PYVGEALTILRKEVNNqAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhal 177 :::::::::::::::: :::::::::: d1qopa_ 79 AQCFEMLAIIREKHPT-IPIGLLMYAN--------------------------------- 104 d1j93a_ 178 lqkFATSMAKYIRYQADSGAQAVQIFDswatelspvdfeefSLPYLKQIVDSVKLTHpnL 237 :::::::::::::::::::::::: :::::::::::::::: : d1qopa_ 105 -lvFNNGIDAFYARCEQVGVDSVLVAD-------------vPVEESAPFRQAALRHN--I 148 d1j93a_ 238 PLILYASGSGG--LLERLPlTGVD-VVSLDWT---------vDMADGRRRLG--PNVAIQ 283 ::::::::::: :::::: :::: ::::::: :::::::::: :::::: d1qopa_ 149 APIFICPPNADddLLRQVA-SYGRgYTYLLSRsgvtgaenrgPLHHLIEKLKeyHAAPAL 207 d1j93a_ 284 GNVDPgvlfgskefITNRINDTVKKAgkgkHILNLghGIKVG-------------tpeEN 330 ::::: :::::::::::: ::::: ::::: :: d1qopa_ 208 QGFGI--------sSPEQVSAAVRAG---aAGAISgsAIVKIieknlaspkqmlaelrSF 256 d1j93a_ 331 FAHFFEIAKglry 343 ::::::::: d1qopa_ 257 VSAMKAASR---- 265 FAST alignment (Normalized score: 6.29 Raw score:1898.00) d1j93a_ 1 TQPLLLDAVRGKE-------------VERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS- 46 :::::::: d1qopa_ 1 -------------MERYENLFAQLNDRREGAFVP-------------------------F 22 d1j93a_ 47 -----ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRT 101 ::::::::::::::: ::::::::::: d1qopa_ 23 VTLGDPGIEQSLKIIDTLID-AGADALELGVP---------------------------- 53 d1j93a_ 102 AADVEKVREFIPEKS------------------------VPYVGEALTILRKEVNNQAAV 137 ::::::::::::::: ::::: d1qopa_ 54 ---------------FSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKH-PTIPI 97 d1j93a_ 138 LGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFAT-------SMAKYIR 190 ::::: ::::::: d1qopa_ 98 GLLMY-----------------------------------------ANLVFNNGIDAFYA 116 d1j93a_ 191 YQADSGAQAVQIFDSWATELSPVDFEEF---SLPYLKQIVDSVKLTHPNLPLILY-ASGS 246 :::::::::::: :::::::::::::: :::::::: :::: d1qopa_ 117 RCEQVGVDSVLV----------------ADVPVEESAPFRQAALR--HNIAPIFICPPNA 158 d1j93a_ 247 G-GLLERLPLT-GVDVVSLDWT-----------VDMADGRRRLGPNVAIQGNVDPGVLFG 293 : :::::::: :::::::: ::::::::: d1qopa_ 159 DDDLLRQVAS-YGRGYTYLL--SRSGVTGAENRGPLHHLIEK------------------ 197 d1j93a_ 294 SKEF----------------ITNRINDTVKKAGKGKHILNLGHGIKVGT----------- 326 :::::::::: d1qopa_ 198 ----LKEYHAAPALQGFGISSPEQVSAAVR-------------------AGAAGAISGSA 234 d1j93a_ 327 --------------PEENFAHFFEIAKGLRY---- 343 ::::::::::::: d1qopa_ 235 IVKIIEKNLASPKQMLAELRSFVSAMK----AASR 265 TMalign alignment (TM-score: 0.51 Raw score:173.61) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::: :::::::::::::::::::::: :: : : : ::::::::::: d1qopa_ 1 MER-YENLFAQLNDRREGAFVPFVTL----GD---P-------G---I-EQSLKIIDTLI 41 d1j93a_ 61 KVFRPDGVILFSDILT--------PLSGMNIPFDIIKGKGP------VIFDPLRTAADVE 106 : :::::::::::::: :::::: d1qopa_ 42 D-AGADALELGVPFSDPLADGPTI-----------QNANLRAFAAGV------------- 76 d1j93a_ 107 KVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRL 166 :::::::::::::::::: ::::::::: :: d1qopa_ 77 ---------TPAQCFEMLAIIREKHPT-IPIGLLMYA---NL------------------ 105 d1j93a_ 167 AFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQI 226 :::::::::::::::::: :::::: :: :::::::: d1qopa_ 106 -------------VFNNGIDAFYARCEQVGV-DSVLVA-DV-----------PVEESAPF 139 d1j93a_ 227 VDSVKLTHPNLPLILYASGSGGLLE-RLPLT--GVD-VVSLDWT---------VDMADGR 273 ::::: :: :::::::: :::::: ::::: ::: ::::::: ::::::: d1qopa_ 140 RQAAL-RH-NIAPIFIC--PPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGPLHHLI 195 d1j93a_ 274 RRL-GPNV-AIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK-VG--T-- 326 ::: :::: ::::::::: : :: :::::::::: : :::::::: :: : d1qopa_ 196 EKLKEYHAAPALQGFGIS-S------PE-QVSAAVRAGA---A-GAISGSAIVKIIEKNL 243 d1j93a_ 327 --------PE-ENFAHFFEIAKGLRY 343 :: :::::::::: : d1qopa_ 244 ASPKQMLAELRSFVSAMKAAS--R-- 265 HHsearch alignment (Probability: 0.96 E-value:0.00) d1j93a_ 82 NIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFV 141 ::::::::::::::: :::::::::: :::::::::::::::: ::::::: d1qopa_ 51 GVPFSDPLADGPTIQ-----NANLRAFAAG---VTPAQCFEMLAIIREK-HPTIPIG--- 98 d1j93a_ 142 GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQ 201 ::::: :::::: ::: ::::::::::::::: d1qopa_ 99 -----LLMYA------------------NLVFNN-GID-------AFYARCEQVGVDSVL 127 d1j93a_ 202 IFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYA--SGSGGLLERL------ 253 ::: :::::::::::::::: :::::::: :::::::::: d1qopa_ 128 VAD-----VPVEESAPFRQAALRH----------NIAPIFICPPNADDDLLRQVASYGRG 172 d1j93a_ 254 -----PLTGVDVVSL--DWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTV 306 :::::::::: :::::::::::::::::::::::: ::::::: :: d1qopa_ 173 YTYLLSRSGVTGAENRGPLHHLIEKLKEYHAAPALQGFGIS------SPEQVSA----AV 222 d1j93a_ 307 KKAGKGKHILNLG-------HGIKVGTPEENFAHFFEIAKG 340 :::: :::::::: ::::::::::::::::::::: d1qopa_ 223 RAGA-AGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKA 262