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 | d1d3ga_ | Dihydroorotate dehydrogenase | FMN-linked oxidoreductases | 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 <-- 1.462 --> HitDALI alignment (Z-score: 12.6 Raw score:1504.00) d1j93a_ 1 -------------------------------------------tqplllDAVRGKeverp 17 :::::: d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevRVLGHK--frn 58 d1j93a_ 18 PVWLMRQAgrymksyqllcekyplfrdrsenvdlVVEISLQPWKVFrPDGVILFSDIlTP 77 :::::::: :::::::::::: :::::::::: :: d1d3ga_ 59 PVGIAAGF------------------------dkHGEAVDGLYKMG-FGFVEIGSVT-PK 92 d1j93a_ 78 LSgmnipFDIIKGKgpvifdplrtaadvekvrefipeksVPYVGEALTilRKEVNNQ--- 134 :: ::::::: ::::::::: ::::::: d1d3ga_ 93 PQ-----EGNPRPR-----vfrlpedqavinrygfnshgLSVVEHRLRarQQKQAKLted 142 d1j93a_ 135 -AAVLGFVGapftlasYVVEggssknftkikrlafaepkvlhallqKFATSMAKYIRYQA 193 :::::::: :::: :::::::::::::: d1d3ga_ 143 gLPLGVNLG-----knKTSV--------------------------DAAEDYAEGVRVLG 171 d1j93a_ 194 DsGAQAVQIFDSWatelspvDFEEfSLPYLKQIVDSVKLTHP--NLPLILYASG-----S 246 : ::::::::::: :::: ::::::::::::::::: :::::::::: : d1d3ga_ 172 P-LADYLVVNVSS-pntaglGKAE-LRRLLTKVLQERDGLRRvhRPAVLVKIAPdltsqD 228 d1j93a_ 247 GGL-LERLPLTGVDVVSLD-----------------------------WTVDMADGRRRL 276 ::: ::::::::::::::: :::::::::::: d1d3ga_ 229 KEDiASVVKELGIDGLIVTnttvsrpaglqgalrsetgglsgkplrdlSTQTIREMYALT 288 d1j93a_ 277 GPNVAIQGNVDPgvlfgskefITNRINDTVKKAgkgkHILNLghGIKVGTPE-ENFAHFF 335 :::::::::::: :::::::::::: ::::: :::::::: ::::::: d1d3ga_ 289 QGRVPIIGVGGV--------sSGQDALEKIRAG---aSLVQL--YTALTFWGpPVVGKVK 335 d1j93a_ 336 EIAK---------GLRY-------- 343 :::: :::: d1d3ga_ 336 RELEallkeqgfgGVTDaigadhrr 360 FAST alignment (Normalized score: 5.70 Raw score:2004.00) d1j93a_ 1 TQPLLLDAVR-------------------------------------------------- 10 d1d3ga_ 1 ----------MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVR 50 d1j93a_ 11 --GKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL----------VVEISLQ 58 :::::: ::::::: d1d3ga_ 51 VLGHKFRN-----------------------------------PVGIAAGFDKHGEAVDG 75 d1j93a_ 59 PWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEK--- 115 ::: :::::::: d1d3ga_ 76 LYK-MGFGFVEI---------------------------------------------GSV 89 d1j93a_ 116 -------------------------------SVPYVGEALTILRKEVNN-------QAAV 137 ::::::::::::::: :::: d1d3ga_ 90 TPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQK---QAKLTEDGLPL 146 d1j93a_ 138 LGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ-------KFATSMAKYIR 190 :::: ::::::::::: d1d3ga_ 147 GVNL--------------------------------------GKNKTSVDAAEDYAEGVR 168 d1j93a_ 191 YQADSGAQAVQIFDSWATELSPVD--------FEEFSLPYLKQIVDSVKLTHP------N 236 :::: ::::::::: ::::::::::::::::: : d1d3ga_ 169 VLGP-LADYLVVNV----------SSPNTAGLGKAELRRLLTKVLQERD----GLRRVHR 213 d1j93a_ 237 LPLILYASG----SGGLLERL----PLTGVDVVSLDWTV--------------------- 267 ::::::: :::::::: ::::::::: d1d3ga_ 214 PAVLVKI--APDLTSQDKEDIASVVKELGIDGLI-----VTNTTVSRPAGLQGALRSETG 266 d1j93a_ 268 -------------DMADGRRRLGPNVAIQGNVDPGVLFGSKEF------ITNRINDTVKK 308 :::::::::::::::: :::::::::: d1d3ga_ 267 GLSGKPLRDLSTQTIREMYALTQGRVPII--------------GVGGVSSGQDALEKIR- 311 d1j93a_ 309 AGKGK---HILNLGHGIKVGT--------PEENFAHFFEIAKGLRY-------------- 343 :::: :::::::::::::: d1d3ga_ 312 -----AGASLVQ---------LYTALTFWGPPVVGKVKRELEA---LLKEQGFGGVTDAI 354 d1j93a_ 344 ------ 344 d1d3ga_ 355 GADHRR 360 TMalign alignment (TM-score: 0.56 Raw score:193.78) d1j93a_ 1 ----------------------------------------------TQPLLLDAVRGKEV 14 ::: :::: : : d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDM--LEV-RVLG-H-K 55 d1j93a_ 15 ERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDI 74 :::::::::::: :: :: ::::::::: :::::: ::: d1d3ga_ 56 FRNPVGIAAGFD------------------KH-----GE-AVDGLYKMG-FGFVEI-GSV 89 d1j93a_ 75 LTPLSGMNIPFDIIKGK--------------GPVI--FDPLRTAADVEKVREFIPEKSVP 118 : ::: ::::::: :::: :: :::: d1d3ga_ 90 T-PKP-----QEGNPRPRVFRLPEDQAVINRYGFNSH----------------GL-SVVE 126 d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL 178 ::::::::::::::::::::::::: :: ::: : :: d1d3ga_ 127 HRLRARQQKQAKLTEDGLPLGVNLG---KN-KTS---------------------V--DA 159 d1j93a_ 179 QKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHP--N 236 :::::::::: :::: ::::::::::::::::: :::::::::::::::::::: : d1d3ga_ 160 AEDYAEGVRV---LGPL-ADYLVVNVSSPNTAGLG--KAELRRLLTKVLQERDGLRRVHR 213 d1j93a_ 237 LPLILYASGSGG--LLERLP-LT---GVDVVSLD-------------------------- 264 :::::::::::: :::::: :: :::::::: d1d3ga_ 214 PAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPL 273 d1j93a_ 265 W-TV-D-MADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHG 321 : :: : ::::::::::::::::: :: :: :::::::::::: :::::: : d1d3ga_ 274 RDLSTQTIREMYALTQGRVPIIGV-GG-VS------SGQDALEKIRAG---ASLVQL--Y 320 d1j93a_ 322 IKVGTPE-ENFAHFFEIAKG-L------R--Y-------- 343 ::::::: :::::::::::: : : : d1d3ga_ 321 TALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 360 HHsearch alignment (Probability: 0.79 E-value:0.00) d1j93a_ 43 RDRSENVDLVVEISLQPWKVF 63 ::::::::::::::::::::: d1d3ga_ 17 LQGLLDPESAHRLAVRFTSLG 37