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 | d1sr9a2 | 2-isopropylmalate synthase LeuA, catalytic domain | Aldolase | 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 <-- 0.657 --> HitDALI alignment (Z-score: 11.5 Raw score:1346.70) d1j93a_ 1 tqpllldavrgkeVERPPVWLM---RQAGRYMKSYqllcekyplfrdrsenvDLVVEISL 57 ::::::::: :::::::::: :::::::: d1sr9a2 1 -----rtwpdrviDRAPLWCAVdlrDGNQALIDPM----------------sPARKRRMF 39 d1j93a_ 58 QPWKVFRPDGVILFSDILTplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksv 117 ::::::::::::::::::: d1sr9a2 40 DLLVRMGYKEIEVGFPSAS----------------------------------------- 58 d1j93a_ 118 PYVGEALTILR--KEVNNQAAVLGFVGApftlasyvveggssknftkikrlafaepkvlh 175 ::::::::::: ::::::::::::::: d1sr9a2 59 QTDFDFVREIIeqGAIPDDVTIQVLTQC-------------------------------- 86 d1j93a_ 176 allqkfATSMAKYIRYQADSG-aQAVQIFDSwATELSP-----VDFEEfSLPYLKQIVDS 229 ::::::::::::::: :::::::: :::::: ::::: ::::::::::: d1sr9a2 87 ------RPELIERTFQACSGAprAIVHFYNS-TSILQRrvvfrANRAE-VQAIATDGARK 138 d1j93a_ 230 VKLTHP-----NLPLILYASGS----GGLLER-LPLTG---------vDVVSLDW----- 265 :::::: ::::::::::: :::::: ::::: ::::::: d1sr9a2 139 CVEQAAkypgtQWRFEYSPESYtgteLEYAKQvCDAVGeviaptperpIIFNLPAtvemt 198 d1j93a_ 266 -----tvDMADGRRRLG--PNVAIQGNVDpgVLFGskeFITNRINDTVKKAgkgkHILN- 317 :::::::::: :::::::::: :::: ::::::::::::: :::: d1sr9a2 199 tpnvyadSIEWMSRNLAnrESVILSLHPH--NDRG---TAVAAAELGFAAG---aDRIEg 250 d1j93a_ 318 -lghgIKVGtpeenfahFFEIAKGLR---------------------------------- 342 :::: ::::::::: d1sr9a2 251 clfgnGERT-----gnvCLVTLGLNLfsrgvdpqidfsnideirrtveycnqlpvherhp 305 d1j93a_ 343 ----y 343 d1sr9a2 306 yggdl 310 FAST alignment (Normalized score: 4.49 Raw score:1465.00) d1j93a_ 1 TQPLLLDAVRGKEV---------ERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS----- 46 ::::::: d1sr9a2 1 --------------RTWPDRVIDRAPLWCA-------------------------VDLRD 21 d1j93a_ 47 --------ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 ::::::::::::::: :::::::: d1sr9a2 22 GNQALIDPMSPARKRRMFDLLVR-MGYKEIEV---------------------------- 52 d1j93a_ 99 LRTAADVEKVREFIPEKS-----VPYVGEALTILR--KEVNNQAAVLGFVGAPFTLASYV 151 :::::::::::: :::::::::::::: d1sr9a2 53 ------------------GFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQ--------- 85 d1j93a_ 152 VEGGSSKNFTKIKRLAFAEPKVLHAL-LQKFATSMAKYIRYQADSGA------QAVQIFD 204 ::::::::::: :::::: d1sr9a2 86 --------------------------CRPELIERTFQA---------CSGAPRAIVHFY- 109 d1j93a_ 205 SWA-----------TELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERL 253 :::::::::::::::::: :::::::::::::: d1sr9a2 110 ---NSTSILQRRVVFRANRAEVQAIATDGARK-CVEQAAKYPGTQWR------------- 152 d1j93a_ 254 PLTGVDVVSL--DWTVDMADGRRRLGP--------------NVAIQGNVDPGV-LFGSKE 296 ::::: :::::::::::: :::: ::::: :::::: d1sr9a2 153 -----FEYSPESYTGTELEYAKQV---CDAVGEVIAPTPERPIIF-NLPAT--VEMTTPN 201 d1j93a_ 297 FITNRINDTVKKAGK---GKHILNLGHGIKVGTPE-------ENFAHFFEIAKGLRY--- 343 ::::::::::::: :::::: ::::::::::: d1sr9a2 202 VYADSIEWMSRNL--ANRESVILS-----------LHPHNDRGTAVAAAELGF----AAG 244 d1j93a_ 344 ------------------------------------------------------------ 344 d1sr9a2 245 ADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQIDFSNIDEIRRTVEYCNQLPVHERH 304 d1j93a_ 344 ------ 344 d1sr9a2 305 PYGGDL 310 TMalign alignment (TM-score: 0.48 Raw score:166.03) d1j93a_ 1 ---------TQPLLLDAVRGKEVERPPVWLMRQA--GR----YMKSYQ------------ 33 ::::::::::: :: :::::: d1sr9a2 1 RTWPDRVID--------------RAPLWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMG 46 d1j93a_ 34 -------LLCEKYPLFRDRSENVDLVVEISLQPW-K-VFR-PDGVILFSDILTPLSGMNI 83 :::::::::::::::: : ::: :::::::: :: : d1sr9a2 47 YKEIEVG-----------FPSASQTDFDFVREIIEQGAIPDDVTIQVLT-QC-R------ 87 d1j93a_ 84 PFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGA 143 : :::::::::::: : : :::::::: d1sr9a2 88 -----------------------------P-ELIERTFQACSG-A---P---RAIVHFYN 110 d1j93a_ 144 PFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQAD-S--GAQAV 200 ::: :::::::: : :::::::::::::::::::::: : ::::: d1sr9a2 111 STS-ILQRRVVF-------R---------ANRAEVQAIATDGARKCVEQAAKYPGTQWRF 153 d1j93a_ 201 QIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS--G------SGGLLER 252 :::::::::: :::: :::::::::::::::::::::::::: : ::::::: d1sr9a2 154 EYSPESYTGT---ELEY-AKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEW 209 d1j93a_ 253 LP-LT--G--VDVVSLD------WTVDMADGRRRLGPNVAIQGNVDPGVL------FGSK 295 :: :: : ::::::: :::::::::::: :::::::::::: d1sr9a2 210 MSRNLANRESVILSLHPHNDRGTAVAAAELGFAAG---ADRIEGCLFGNGERTGNV---- 262 d1j93a_ 296 EFITNRINDTVKKAGKGKHIL---------NLGHGIKVGTPEENF--AHF---------- 334 :::::::::::::::: ::: ::::::: : d1sr9a2 263 -CLVTLGLNLFSRGVDP-QIDFSNIDEIRR--------TVEYCNQLP--VHERHPYGGDL 310 d1j93a_ 335 FEIAKGLRY 343 d1sr9a2 311 --------- 311 HHsearch alignment (Probability: 0.50 E-value:0.00) d1j93a_ 194 DSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHP---NLPLILYASGSGGL 249 :::::::::::::: :::::::::: ::::::::: :::::::::::::: d1sr9a2 183 PERPIIFNLPATVE-MTTPNVYADS--------IEWMSRNLANRESVILSLHPHNDRGT 232