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 | d1tqja_ | D-ribulose-5-phosphate 3-epimerase | 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 <-- 0.786 --> HitDALI alignment (Z-score: 9.7 Raw score:1098.00) d1j93a_ 1 tqpllldavrgkeveRPPVWLM-RQAGryMKSYqllcekyplfrdrsenvdlvveislQP 59 ::::::: :::: :::: :: d1tqja_ 1 --------------kNIVVAPSiLSAD--FSRL-----------------------geEI 21 d1j93a_ 60 WK--VFRPDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksv 117 :: :::::::::::: d1tqja_ 22 KAvdEAGADWIHVDVM------------------------------------dgrfvpni 45 d1j93a_ 118 pYVGEALTILRKEVnnQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhal 177 ::::::::::::: ::::::::::: d1tqja_ 46 tIGPLIVDAIRPLT--KKTLDVHLMIV--------------------------------- 70 d1j93a_ 178 lqkfatSMAKYIRYQADSGAQAVQIFDSWAtelspvdfeefslPYLKQIVDSVKltHPNL 237 :::::::::::::::::::::::: ::::::::::: :::: d1tqja_ 71 ------EPEKYVEDFAKAGADIISVHVEHN-----------asPHLHRTLCQIR--ELGK 111 d1j93a_ 238 PLILYASGSGgLLERLPLT--GVDVVSLDW------TVDMADGRRRLGP-------NVAI 282 :::::::::: :::::::: ::::::::: ::::::::::::: :::: d1tqja_ 112 KAGAVLNPST-PLDFLEYVlpVCDLILIMSvnpqsfIPEVLPKIRALRQmcderglDPWI 170 d1j93a_ 283 QGNVDpgvlfgskefITNRINDTVKKAgkgkHILNlghgikvgTPEEnFAHFFEIAKGLR 342 ::::: :::::::::::: :::: :::: :::::::::::: d1tqja_ 171 EVDGG---------lKPNNTWQVLEAG---aNAIV--agsavfNAPN-YAEAIAGVRNSK 215 d1j93a_ 343 y 343 d1tqja_ 216 r 216 FAST alignment (Normalized score: 6.31 Raw score:1716.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD--------LV 52 ::::::: :: d1tqja_ 1 --------------KNIVVAP-----------------------------SILSADFSRL 17 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::::: ::::::::: d1tqja_ 18 GEEIKAVDE-AGADWIHVD----------------------------------------- 35 d1j93a_ 113 PEKSVPY------------VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNF 160 :::::::::::: ::::::::: d1tqja_ 36 -------VMDGRFVPNITIGPLIVDAIRPLT--KKTLDVHLM------------------ 68 d1j93a_ 161 TKIKRLAFAEPKVLHALLQKFAT--SMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF 218 ::::::::::::::::::::: d1tqja_ 69 -----------------------IVEPEKYVEDFAKAGADIISVHV-------------- 91 d1j93a_ 219 SL-----PYLKQIVDSVKLTHPNLPLILYASGS------GGLLERLPLTGVDVVSLDWTV 267 :::::::::::: :::::::: ::::::::: :::::::: d1tqja_ 92 --EHNASPHLHRTLCQIRE--LGKKAGAV----LNPSTPLDFLEYVLP-VCDLILIM--- 139 d1j93a_ 268 -------------DMADGRRRLG-----PNVAIQGNVDPGVLFGSKEF------ITNRIN 303 :::::::: ::::: :::::: d1tqja_ 140 SVNPQSFIPEVLPKIRALRQM--CDERGLDPWI---------------EVDGGLKPNNTW 182 d1j93a_ 304 DTVKKAGKGKHILNLGHGIKVGTPE---------------ENFAHFFEIAKGLRY-- 343 :::: ::::::::::::: d1tqja_ 183 QVLE---------------------AGANAIVAGSAVFNAPNYAEAIAGVRNS--KR 216 TMalign alignment (TM-score: 0.45 Raw score:153.67) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : ::::::::::: :: : : : ::::: d1tqja_ 1 -------K-------NIVVAPSILSA----DF--S---------------R--L-GEEIK 22 d1j93a_ 61 KV--FRPDGVILFSDILTPL-SGMNIPFDIIKGKGP-VIFDPLRTAADVEKVREFIPEKS 116 :: :::::::::::::: : ::: d1tqja_ 23 AVDEAGADWIHVDVMDGR-FV------------PNIT----------------------- 46 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 : :: :::::::::: : ::::::::: : d1tqja_ 47 I-GP-LIVDAIRPLT-K-KTLDVHLMI---V----------------------------- 70 d1j93a_ 177 LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 236 : :::::::::::::::::::: : : :::::::::::::: :: : d1tqja_ 71 ----E---PEKYVEDFAKAGADIISVHV--E-------H--NASPHLHRTLCQIR-EL-G 110 d1j93a_ 237 LPLILYASGSGGLLERLPLT--GVDVVSLDW--------TVD--MADGRRRLG--PN-VA 281 :::::::::: ::::::::: ::::::::: ::: ::::::::: :: :: d1tqja_ 111 KKAGAVLNPS-TPLDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPW 169 d1j93a_ 282 IQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK-VGTPEENFAHFFEIAKG 340 :::: :: :: : : :::::::::: ::::: ::: ::::::::::::::: d1tqja_ 170 IEVD-GG-LK---P--N--NTWQVLEAGA---NAIVA--GSAV--FNAPNYAEAIAGVRN 213 d1j93a_ 341 L--RY 343 : d1tqja_ 214 SKR-- 216 HHsearch alignment (Probability: 0.83 E-value:0.00) d1j93a_ 187 KYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGS 246 ::::::::::::::::: :::::::::::::::::::::::::::::::: d1tqja_ 74 KYVEDFAKAGADIISVH-----------VEHNASPHLHRTLCQIRELGKKAGAVLNPSTP 122 d1j93a_ 247 GGLLERL-------PLTGVDVVSLDWTV--DMADGRRRLG-----PNVAIQGNVDPGVLF 292 ::::::: :::::::::::::: :::::::::: :::::::::::: d1tqja_ 123 LDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGLKPN--- 179 d1j93a_ 293 GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGT-PEENFAHFFEIAK 339 ::::::: : ::::::::::::::: ::::::::::::: d1tqja_ 180 --------NTWQVLE-A--GANAIVAGSAVFNAPNYAEAIAGVRNSKR 216