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 | d1a53a_ | Indole-3-glycerophosphate synthase, IPGS | 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 <-- 1.548 --> HitDALI alignment (Z-score: 11.1 Raw score:1241.20) d1j93a_ 1 ---------------------------tqplLLDAVrGKEV--ERPPVWLMrQAGR---- 27 ::::: :::: :::::::: :::: d1a53a_ 1 prylkgwlkdvvqlslrrpsfrasrqrpiisLNERI-LEFNkrNITAIIAE-YKRKspsg 58 d1j93a_ 28 YMKSYqllcekyplfrdrsenvdlvveISLQPWKVFR--PDGVILFSDiltplsgmnipf 85 ::::: :::::::::: ::::::::: d1a53a_ 59 LDVER----------------------DPIEYSKFMEryAVGLSILTE------------ 84 d1j93a_ 86 diikgkgpvifdplrtaadvekvrefipeksvpyVGEALTILRKEVnnQAAVLGFVGAPf 145 :::::::::::: ::::::::::: d1a53a_ 85 ----------------------------ekyfngSYETLRKIASSV--SIPILMKDFIV- 113 d1j93a_ 146 tlasyvveggssknftkikrlafaepkvlhallqkfatsMAKYIRYQADSGAQAVQIFDS 205 ::::::::::::::::::::: d1a53a_ 114 ---------------------------------------KESQIDDAYNLGADTVLLIVK 134 d1j93a_ 206 WAtelspvdfeefSLPYLKQIVDSVKLthPNLPLILYAsgSGGL-LERLPLTGVDVVSLD 264 :: :::::::::::::: ::::::::: :::: ::::::::::::::: d1a53a_ 135 IL-----------TERELESLLEYARS--YGMEPLIEI--NDENdLDIALRIGARFIGIN 179 d1j93a_ 265 W---------TVDMADGRRRLGPNVAIQGNVDPGvlfgskefITNRINDTVKKAGkgkHI 315 : :::::::::::::::::::::::: ::::::::::::: :: d1a53a_ 180 SrdletleinKENQRKLISMIPSNVVKVAESGIS--------ERNEIEELRKLGV---NA 228 d1j93a_ 316 LNlgHGIKvgtpeeNFAHfFEIAKGlry 343 :: :::: :::: :::::: d1a53a_ 229 FL--IGSS---lmrNPEK-IKEFIL--- 247 FAST alignment (Normalized score: 6.60 Raw score:1920.00) d1j93a_ 1 TQPLLLDAVRGK----------------------------------------EVERPPVW 20 :::::::: d1a53a_ 1 ------------PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAII 48 d1j93a_ 21 LMRQAGRYMKSYQLLCEKYPLFRDRSENVD----------LVVEISLQPWKVF-RPDGVI 69 : :::: :::::::::: :::::: d1a53a_ 49 A-EYKR------------------------KSPSGLDVERDPIEYSKFME---RYAVGLS 80 d1j93a_ 70 LFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY--------VG 121 :: :: d1a53a_ 81 IL------------------------------------------------TEEKYFNGSY 92 d1j93a_ 122 EALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKF 181 :::::::::: ::::::::: d1a53a_ 93 ETLRKIASSV--SIPILMKDF--------------------------------------- 111 d1j93a_ 182 ATS--MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF--SLPYLKQIVDSVKLTHPNL 237 ::::::::::::::::::::: :::::::::::::: ::: d1a53a_ 112 ---IVKESQIDDAYNLGADTVLLIVK-------------ILTERELESLLEYARS--YGM 153 d1j93a_ 238 PLILYASGSGGLLERLPLTGVDVVSLDWTV------------DMADGRRRLGPNVAIQGN 285 ::::::: ::::::::::::::::::: ::::::::::::::: d1a53a_ 154 EPLIEIN-DENDLDIALRIGARFIGIN---SRDLETLEINKENQRKLISMIPSNVVK--- 206 d1j93a_ 286 VDPGVLFGSKEF-------ITNRINDTVKKAGKGKHILNLGHGIKVG------------- 325 :::::::::: d1a53a_ 207 ------------VAESGISERNEIEELRK------------------LGVNAFLIGSSLM 236 d1j93a_ 326 TPEENFAHFFEIAKGLRY- 343 :::::::::: d1a53a_ 237 RNPEKIKEFI--------L 247 TMalign alignment (TM-score: 0.48 Raw score:164.01) d1j93a_ 1 ----------------------------TQPLLLDAVRGK-EVE-RPPVWLMRQAGR--- 27 :::::::: :: ::: ::::::: :::: d1a53a_ 1 PRYLKGWLKDVVQLSLRRPSFRASRQRP-IISLNERI-LEFNKRNITAIIAE-YKRKSPS 57 d1j93a_ 28 -YMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR--PDGVILFSDILTPLSGMNIP 84 ::::: :: :::::::: ::::::::: : d1a53a_ 58 GLDVER---------------------DP-IEYSKFMERYAVGLSILTE--E-------- 85 d1j93a_ 85 FDIIKGKGP--VIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVG 142 : :: :: :::::::::: : :::::::: d1a53a_ 86 --K----YFNG-------------------------SY-ETLRKIASSV-S-IPILMKDF 111 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQI 202 :: :::::::::::::::::: d1a53a_ 112 IV----------------------------------------KESQIDDAYNLGADTVLL 131 d1j93a_ 203 FDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVS 262 ::: : :::::::::::::: :: :::::::: :::::::::::::::::: d1a53a_ 132 IVK-I----------LTERELESLLEYAR-SY-GMEPLIEI-NDENDLDIALRIGARFIG 177 d1j93a_ 263 LDW---------T-VDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKG 312 ::: : ::: ::::::::::::::: :: :: ::::::::::::: d1a53a_ 178 INSRDLETLEINKENQR-KLISMIPSNVVKVAE-SG-IS------ERNEIEELRKLGV-- 226 d1j93a_ 313 KHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 ::::: ::: :::: ::: :::::: d1a53a_ 227 -NAFLI--GSS--LMRN-PEK-IKEFIL--- 247 HHsearch alignment (Probability: 0.19 E-value:0.01) d1j93a_ 142 GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKF------ATSMAK--YIRYQA 193 :::::::::::::::::::::::::::::::::::::::: :::::: :::::: d1a53a_ 63 RDPIEYSKFMERYAVGLSILTEEKYFNGSYETLRKIASSVSIPILMKDFIVKESQIDDAY 122 d1j93a_ 194 DSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERL 253 :::::::::: ::::::::::: :::::::::::: ::::::::::::: d1a53a_ 123 NLGADTVLLI---VKILTERELES--------LLEYARSYGMEP---LIEINDENDLDIA 168 d1j93a_ 254 PLTGVDVVSLDWT------VDMAD---GRRRLGPNVA-IQ-GNVDPGVLFGSKEFITNRI 302 ::::::::::::: ::::: :::::::::: :: :::: ::::: d1a53a_ 169 LRIGARFIGINSRDLETLEINKENQRKLISMIPSNVVKVAESGIS------ERNEI---- 218 d1j93a_ 303 NDTVKKAGKGKHILNLGHGIK 323 :: ::::::::::: ::::: d1a53a_ 219 EE-LRKLGVNAFLI--GSSLM 236