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 | d1bf6a_ | Phosphotriesterase homology protein | Metallo-dependent hydrolases | 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 <-- 0.768 --> HitDALI alignment (Z-score: 8.3 Raw score:1018.50) d1j93a_ 1 TQPLlldavrgkeverppVWLMRqagrymksyqllcekYPLFrdRSENVDLvVEISLQ-P 59 :::: ::::: :::: ::::::: :::::: : d1bf6a_ 1 SFDP-----------tgyTLAHE-----hlhidlsgfkNNVD-cRLDQYAF-ICQEMNdL 42 d1j93a_ 60 WKVFRPDGVIlfsDILTplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpy 119 :::::::::: :::: d1bf6a_ 43 MTRGVRNVIEmtnRYMG------------------------------------------- 59 d1j93a_ 120 vgeaLTILRKEVN--nqAAVLGFVGApFTLASyvveggssknftkikrlafaepkvlhAL 177 ::::::::: ::::::::: ::::: :: d1bf6a_ 60 --rnAQFMLDVMRetgiNVVACTGYYqDAFFP--------------------------EH 91 d1j93a_ 178 LQ-KFATSMAKYIRYQAD-------SGAQAVQIFDSwATELspvdFEEFSlPYLKQIVDS 229 :: ::::::::::::::: ::::::::::: :::: ::::: ::::::::: d1bf6a_ 92 VAtRSVQELAQEMVDEIEqgidgteLKAGIIAEIGT-SEGK----ITPLE-EKVFIAAAL 145 d1j93a_ 230 VKLTHPnLPLILYASGSGgLLERLPLTG--------vDVVSLDWTVDMADGRRRLGP-NV 280 :::::: ::::::::::: ::::::::: :::::::::::::::::::: :: d1bf6a_ 146 AHNQTG-RPISTHTSFST-MGLEQLALLqahgvdlsrVTVGHCDLKDNLDNILKMIDlGA 203 d1j93a_ 281 AIQGNVDPGVlfgskefITNRINDTVKKA----GKGKHILNLghGIKV---------gtp 327 :::::::::: :::::::::::: ::::::::: :::: d1bf6a_ 204 YVQFDTIGKN----syyPDEKRIAMLHALrdrgLLNRVMLSM--DITRrshlkanggygy 257 d1j93a_ 328 eenFAHFFEIA----kGLRY-------------- 343 :::::::: :::: d1bf6a_ 258 dylLTTFIPQLrqsgfSQADvdvmlrenpsqffq 291 FAST alignment (Normalized score: 3.62 Raw score:1144.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRD---------------- 44 d1bf6a_ 1 --------------------------------------------SFDPTGYTLAHEHLHI 16 d1j93a_ 45 -----------RSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGP 93 :::::::::::::::: ::::::: d1bf6a_ 17 DLSGFKNNVDCRLDQYAFICQEMNDLM-TRGVRNV------------------------- 50 d1j93a_ 94 VIFDPLRTAADVEKVREFIPEKSVPY----------VGEALTILRKEVNNQAAVLGFVGA 143 :::::::::::: :::::::: d1bf6a_ 51 --------------------------IEMTNRYMGRNAQFMLDVMRET--GINVVACT-- 80 d1j93a_ 144 PFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA---------------LLQKFATSMAKY 188 :::::::::::: d1bf6a_ 81 ---------------------------------GYYQDAFFPEHVATRSVQELAQEMVDE 107 d1j93a_ 189 IRYQADS--------GAQA-VQIFDSWATELSPVDF------EEFSLPYLKQIVDSVKLT 233 :: :::: :::: ::::::::: :::::::: d1bf6a_ 108 IE-----QGIDGTELKAGIIAEIG------------TSEGKITPLEEKVFI-AAALAHNQ 149 d1j93a_ 234 HPNLPLILYASGS-GGLLERLPLTGVDVVSLDWTV------------------------D 268 : ::::::::: ::::::::: : d1bf6a_ 150 T-GRPISTHTS--FSTMGLEQLA------------LLQAHGVDLSRVTVGHCDLKDNLDN 194 d1j93a_ 269 MADGRRRLGPNVAIQGNVDPGVL---------FGSKEFITNRINDTVKKA--GKGKHILN 317 :::::: ::::: :::::::::::::::: :::::::: d1bf6a_ 195 ILKMID---LGAYV---------QFDTIGKNSYYPDEKRIAMLHALRD--RGLLNRVMLS 240 d1j93a_ 318 LGHGIKVGTPEEN-------------------FAHFFEIAKGLRY--------------- 343 : :::::::::: d1bf6a_ 241 M------------DITRRSHLKANGGYGYDYLLTTFIPQLRQ---SGFSQADVDVMLREN 285 d1j93a_ 344 ------ 344 d1bf6a_ 286 PSQFFQ 291 TMalign alignment (TM-score: 0.51 Raw score:174.72) d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGR-------YMKSYQLLC--EKYPLFRDRSENVD 50 ::::: ::::::::::: : : ::: d1bf6a_ 1 SFDPTG-----------YTLAHEHLHIDLSGFKNN--------VDC-----R-LDQ---- 31 d1j93a_ 51 LVVEISLQPWKVFR---PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEK 107 : ::::::::::: :::::::::::::: d1bf6a_ 32 Y--AFICQEMNDLMTRGVRNVIEMTNRYMGR----------------------------- 60 d1j93a_ 108 VREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLA 167 :::: :::::::::: :::::::::::: :::: : d1bf6a_ 61 ---------NAQF-MLDVMRETGI----NVVACTGYYQDA-FFPE----------H---- 91 d1j93a_ 168 FAEPKVLHALLQKFATSMAKYIRYQA---DSGAQAVQIFDSWATELSPVDFEEFSLPYLK 224 ::::::::::::::::::::: :::: ::::::: :::::: : :::::::: d1bf6a_ 92 -----VATRSVQELAQEMVDEIEQGIDGTELKA-GIIAEIG-TSEGKI--T-PLEEKVFI 141 d1j93a_ 225 QIVDSVKLTHPNLPLILYASGSGGLLERLP-LT----G---VDVVSLDWTVDMADGRRRL 276 ::::::::: : ::::::::::: :::::: :: : ::::::::::::::::::: d1bf6a_ 142 AAALAHNQT-G-RPISTHTSFST-MGLEQLALLQAHGVDLSRVTVGHCDLKDNLDNILKM 198 d1j93a_ 277 GP-NVAIQGNVDPGVLFGSKEFITNRINDTVKKA----GKGKHILNLGHGI-KV----GT 326 :: ::::::::::::::: :: :::::::::: ::::::::::::: :: :: d1bf6a_ 199 IDLGAYVQFDTIGKNSYY---PD-EKRIAMLHALRDRGLLNRVMLSMDITRRSHLKANGG 254 d1j93a_ 327 PEENF--AHFFEIAK----GLRY-------------- 343 ::::: :::::::: :::: d1bf6a_ 255 YGYDYLLTTFIPQLRQSGFSQADVDVMLRENPSQFFQ 291 HHsearch alignment (Probability: 0.93 E-value:0.00) d1j93a_ 178 LQKFATSMAKYIRYQA-DSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 236 :::::::::::::::: :::::::::::::::::::::::::::::::::: ::: : d1bf6a_ 97 VQELAQEMVDEIEQGIDGTELKAGIIAEIGTSEGKITPLEEKVFIAAALAH---NQT--G 151 d1j93a_ 237 LPLILYASGSG---GLLERLPLTGVD----VV-SLDWTVDMADGRRRLGPNVAIQGNVDP 288 ::::::::::: :::::::::::: :: ::::::::::::::::::::::::::: d1bf6a_ 152 RPISTHTSFSTMGLEQLALLQAHGVDLSRVTVGHCDLKDNLDNILKMIDLGAYVQFDTIG 211 d1j93a_ 289 GVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI 322 :::::::::::::::::::::::::::::::::: d1bf6a_ 212 KNSYYPDEKRIAMLHALRDRGLLNRVMLSMDITR 245