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 | d1izca_ | Macrophomate synthase | Phosphoenolpyruvate/pyruvate domain | 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 <-- 1.122 --> HitDALI alignment (Z-score: 9.8 Raw score:1127.90) d1j93a_ 1 -------------TQPL---------LLDAVRG--KEVERPPVWLMrqagrymksyqllc 36 :::: ::::::: ::::::::::: d1izca_ 1 aksyseqpelhakAPYRsamltypgnLRQALKDamADPSKTLMGVA-------------- 46 d1j93a_ 37 ekyplfrdrsenvdLVVEISLQPWKvFRPDGVILFSdILTPlsgmnipfdiikgkgpvif 96 ::::::::::: :::::::::: :::: d1izca_ 47 -----------hgiPSTFVTKVLAA-TKPDFVWIDV-EHGM------------------- 74 d1j93a_ 97 dplrtaadvekvrefipekSVPYVGEALTILRKEVNNQAAVLGFVGAPftlasyvveggs 156 ::::::::::::::::::::::::::::: d1izca_ 75 ------------------fNRLELHDAIHAAQHHSEGRSLVIVRVPKH------------ 104 d1j93a_ 157 sknftkikrlafaepkvlhallqkfatsMAKYIRYQADSGAQAVQIFDSwatelspvdfe 216 ::::::::::::::::::::: d1izca_ 105 ----------------------------DEVSLSTALDAGAAGIVIPHV----------- 125 d1j93a_ 217 efSLPYLKQIVDSVKL--------------------------------tHPNLPLILYAS 244 :::::::::::::: ::::::::::: d1izca_ 126 -eTVEEVREFVKEMYYgpigrrsfspwtfspgiadaslfpndpynvatsNNHVCIIPQIE 184 d1j93a_ 245 G--SGGLLERLPLT-GVDVVSLDW-----------------------tvdMADGRRRL-G 277 : ::::::::::: ::::::::: :::::::: : d1izca_ 185 SvkGVENVDAIAAMpEIHGLMFGPgdymidagldlngalsgvphptfveaMTKFSTAAqR 244 d1j93a_ 278 PNVAIQGnVDPGvlfgskefitNRINDTVKKAgkgkHILNlghgiKVGTPE--enfahff 335 ::::::: :::: :::::::::: :::: :::::: d1izca_ 245 NGVPIFGgALSV----------DMVPSLIEQG---yRAIAvqfdvWGLSRLvhgslaqar 291 d1j93a_ 336 eiakglry 343 d1izca_ 292 asakqfag 299 FAST alignment (Normalized score: 6.06 Raw score:1939.00) d1j93a_ 1 TQ------------------------PLLLDAV--RGKEVERPPVWLMRQAGRYMKSYQL 34 ::::::: :::::::::::: d1izca_ 1 --AKSYSEQPELHAKAPYRSAMLTYPGNLRQALKDAMADPSKTLMGV------------- 45 d1j93a_ 35 LCEKYPLFRDRSENVDL-----VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIK 89 ::::::::: :::::::::: d1izca_ 46 -----------------AHGIPSTFVTKVLA-ATKPDFVWID------------------ 69 d1j93a_ 90 GKGPVIFDPLRTAADVEKVREFIPEKS-------VPYVGEALTILRKEVNNQAAVLGFVG 142 :::::::::::::::::::::::::: d1izca_ 70 ---------------------------VEHGMFNRLELHDAIHAAQHHSEGRSLVIVRVP 102 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATS--MAKYIRYQADSGAQAV 200 :::::::::::::::: d1izca_ 103 ------------------------------------------KHDEVSLSTALDAGAAGI 120 d1j93a_ 201 QIFDSWATELSPVDFEEF----SLPYLKQIVDSVKLT----------------------- 233 :: :::::::::::: d1izca_ 121 VI----------------PHVETVEEVREFVKEM---YYGPIGRRSFSPWTFSPGIADAS 161 d1j93a_ 234 ------------HPNLPLILYAS---GSGGLLERLPLT-GVDVVSLDWTV---------- 267 :::::::::: :::::::::::: :::::::: d1izca_ 162 LFPNDPYNVATSNNHVCIIPQI-ESVKGVENVDAIAAMPEIHGLMFG---PGDYMIDAGL 217 d1j93a_ 268 ----------------DMADGRRRLG---PNVAIQGNVDPGVLFGSKEF-----ITNRIN 303 :::::::: ::::: :::::: d1izca_ 218 DLNGALSGVPHPTFVEAMTKFSTA--AQRNGVPI---------------FGGALSVDMVP 260 d1j93a_ 304 DTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY-------------------- 343 :::: d1izca_ 261 SLIE------------------------------------QGYRAIAVQFDVWGLSRLVH 284 d1j93a_ 344 --------------- 344 d1izca_ 285 GSLAQARASAKQFAG 299 TMalign alignment (TM-score: 0.47 Raw score:160.02) d1j93a_ 1 --------------TQP--------LLLDAVRGK-EV-ERPPVWLMRQAGRYMKSYQLLC 36 ::: ::::::::: :: :::::::: ::: d1izca_ 1 AKSYSEQPELHAKAPYRSAMLTYPGNLRQALKDAMADPSKTLMGVA-HGI---------- 49 d1j93a_ 37 EKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIF 96 : : ::::::::: ::::::::::::::: d1izca_ 50 ---------P----S-TFVTKVLAA-TKPDFVWIDVEHGMF------------------- 75 d1j93a_ 97 DPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGS 156 ::::::::::::::::::::::::::::: d1izca_ 76 -------------------NRLELHDAIHAAQHHSEGRSLVIVRVPKH------------ 104 d1j93a_ 157 SKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE 216 : :: ::::::::::::::::: : :: d1izca_ 105 ------------------------D--EV--SLSTALDAGAAGIVIPH--V-------ET 127 d1j93a_ 217 EFSLPYLKQIVDSVK----L-T--------------------------HPN-LPLILYAS 244 :::::::::::: : : ::: :::::::: d1izca_ 128 ---VEEVREFVKEMYYGPIGRRSFSPWTFSPGIADASLFPNDPYNVATSNNHVCIIPQIE 184 d1j93a_ 245 G--SGGLLERLPLT-GVDVVSLDW----------------------TVD-MADGRRRL-G 277 : ::::::::::: ::::::::: ::: :::::::: : d1izca_ 185 SVKGVENVDAIAAMPEIHGLMFGPGDYMIDAGLDLNGALSGVPHPTFVEAMTKFSTAAQR 244 d1j93a_ 278 PNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKV-GTPEEN------ 330 ::::::::: : : :: ::::::::: :::::::::::: :::::: d1izca_ 245 NGVPIFGGA-L--S------VD-MVPSLIEQG---YRAIAVQFDVWGLSRLVHGSLAQAR 291 d1j93a_ 331 --------FAHFFEIAKGLRY 343 d1izca_ 292 ASAKQFAG------------- 299 HHsearch alignment (Probability: 0.08 E-value:0.05) d1j93a_ 195 SGAQAVQIF--DSWATELSP-----VDF-EEFSLPYLKQIVDSVKLTHPNLPLILYASGS 246 ::::::::: ::::::::: ::: :::::::::::::::::: :::::::::: d1izca_ 199 PEIHGLMFGPGDYMIDAGLDLNGALSGVPHPTFVEAMTKFSTAAQRN--GVPIFGGALS- 255 d1j93a_ 247 GGLLERLPLTGVDVVSLD 264 :::::::::::::::::: d1izca_ 256 VDMVPSLIEQGYRAIAVQ 273