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 | d1dqua_ | Isocitrate lyase | 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 <-- 1.184 --> HitDALI alignment (Z-score: 10.3 Raw score:1259.00) d1j93a_ 1 -----------------------------------------------------tqPLLLD 7 ::::: d1dqua_ 1 syieeedqrywdevaavknwwkdsrwrytkrpftaeqivakrgnlkieypsnvqaKKLWG 60 d1j93a_ 8 AvrGKEV---eRPPVWlMRQAgrymksyqllcekyplfrdrsenvdlvVEISLQPWKVFr 64 : :::: ::::: :::: ::::::::::: d1dqua_ 61 I--LERNfknkEASFT-YGCL---------------------------DPTMVTQMAKY- 89 d1j93a_ 65 PDGVILFSD--------------iLTPLsgmnipfdiikgkgpvifdplrtaadvekvre 110 ::::::::: :::: d1dqua_ 90 LDTVYVSGWqssstasstdepspdLADY-------------------------------- 117 d1j93a_ 111 fipekSVPYVGEALTILRKEVN-------------------------nQAAVLGFVGApf 145 ::::::::::::::::: :::::::::: d1dqua_ 118 -----PMNTVPNKVNHLWMAQLfhdrkqreermttpkdqrhkvanvdyLRPIIADADT-- 170 d1j93a_ 146 tlasyvveggssknftkikrlafaepkvlhallqKFATSMAKYIRYQADSGAQAVQIFDS 205 :::::::::::::::::::::::::: d1dqua_ 171 --------------------------------ghGGLTAVMKLTKLFVERGAAGIHIEDQ 198 d1j93a_ 206 W--atELSPvdfeeFSLPYLKQIVDSVKLTHP----NLPLILYASGS------------- 246 : :::: :::::::::::::::::: ::::::::::: d1dqua_ 199 ApgtkGKVL-----VPISEHINRLVAIRAQADimgtDLLAIARTDSEaatlitstidhrd 253 d1j93a_ 247 ------------------------------------------------------------ 247 d1dqua_ 254 hpfiigstnpdiqplndlmvmaeqagkngaelqaiedewlakaglklfndavvdainnsp 313 d1j93a_ 247 ------------------------------------------------------GGLLE- 251 ::::: d1dqua_ 314 lpnkkaaiekyltqskgksnlearaiakeiagtdiyfdweaprtregyyryqggTQCAIn 373 d1j93a_ 252 RLPLT--GVDVVSLDWT----vDMADGRRRLG---PNVAIQGNVDP-GVLF--GSKEFIT 299 ::::: :::::::::: :::::::::: ::::::::::: :::: ::::::: d1dqua_ 374 RAVAYapFADLIWMESKlpdykQAKEFADGVHavwPEQKLAYNLSPsFNWKkaMPRDEQE 433 d1j93a_ 300 NRINDTVKKAgkgkHILNlgHGIK------------------------------------ 323 :::::::::: :::: :::: d1dqua_ 434 TYIKRLGALG---yAWQF--ITLAglhttalisdtfakayakqgmraygelvqepemang 488 d1j93a_ 324 -----vgtpeenfahffeiakglry 343 d1dqua_ 489 vdvvthqkwsganyvdnmlkmitgg 513 FAST alignment (Normalized score: 5.30 Raw score:2222.00) d1j93a_ 1 TQ-------------------------------------------------------PLL 5 ::: d1dqua_ 1 --SYIEEEDQRYWDEVAAVKNWWKDSRWRYTKRPFTAEQIVAKRGNLKIEYPSNVQAKKL 58 d1j93a_ 6 LDAVRGKEV------ERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL----VVEI 55 :::: :::::: :::: d1dqua_ 59 WGIL-----ERNFKNKEASFT-------------------------------YGCLDPTM 82 d1j93a_ 56 SLQPWKVFRPDGVILF----------------SDILTPLSGMNIPFDIIKGKGPVIFDPL 99 :::::: :::::::: :::: d1dqua_ 83 VTQMAK--YLDTVYVSGWQSSSTASSTDEPSPDLAD------------------------ 116 d1j93a_ 100 RTAADVEKVREFIPEK-SVPYVGEALTILRKEVNN------------------------- 133 ::::::::::::::: d1dqua_ 117 ----------------YPMNTVPNKVNHLWMA---QLFHDRKQREERMTTPKDQRHKVAN 157 d1j93a_ 134 ---QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK-----FATSM 185 :::::::: ::::: d1dqua_ 158 VDYLRPIIADA---------------------------------------DTGHGGLTAV 178 d1j93a_ 186 AKYIRYQADSGAQAVQIFDSWATELSPVDFEEF-----------SLPYLKQIVDSVKLTH 234 ::::::::::::::::::: ::::::::::::::: d1dqua_ 179 MKLTKLFVERGAAGIHIED--------------QAPGTKGKVLVPISEHINRLVAIRAQ- 223 d1j93a_ 235 -----PNLPLILYASG-------------------------------------------- 245 ::::::::: d1dqua_ 224 ADIMGTDLLAIART--DSEAATLITSTIDHRDHPFIIGSTNPDIQPLNDLMVMAEQAGKN 281 d1j93a_ 246 ------------------------------------------------------------ 246 d1dqua_ 282 GAELQAIEDEWLAKAGLKLFNDAVVDAINNSPLPNKKAAIEKYLTQSKGKSNLEARAIAK 341 d1j93a_ 246 -----------------------------SGGLLERLPLTGVDVVSLDWTV-------DM 269 :::::::::: :::::::: :: d1dqua_ 342 EIAGTDIYFDWEAPRTREGYYRYQGGTQCAINRAVAYAP-FADLIWME---SKLPDYKQA 397 d1j93a_ 270 ADGRRRL----GPNVAIQ-GNVDP--GVL-FGSKEFITNRINDTVKKAGKGK---HILNL 318 :::::: :::::: ::::: ::: :::::::::::::::: :::: d1dqua_ 398 KEFADG-VHAVWPEQKL-AYNLSPSFNWKKAMPRDEQETYIKRLGA------LGYAWQF- 448 d1j93a_ 319 GHGIKVGTPEENFAHFFEIAKGLRY----------------------------------- 343 d1dqua_ 449 -------------------------ITLAGLHTTALISDTFAKAYAKQGMRAYGELVQEP 483 d1j93a_ 344 ------------------------------ 344 d1dqua_ 484 EMANGVDVVTHQKWSGANYVDNMLKMITGG 513 TMalign alignment (TM-score: 0.47 Raw score:161.24) d1j93a_ 1 ------------------------T------------------------------QPLLL 6 : ::::: d1dqua_ 1 SYIEEEDQRYWDEVAAVKNWWKDSRWRYTKRPFTAEQIVAKRGNLKIEYPSNVQAKKLWG 60 d1j93a_ 7 DAVRGKEVERPPVWLM-------------------RQ-AGRYMKSYQLLCEKYPLFRDRS 46 :::::::::::::::: :: :::: ::: :::::::::::: d1dqua_ 61 ILERNFKNKEASFTYGCLDPTMVTQMAKYLDTVYVSGWQSSS-TAS--STDEPSPDLADY 117 d1j93a_ 47 ENVDLVVEISLQPW-KV--------------------------FRPDGVILFSDILTPLS 79 :: ::::::::::: :: :::::::::: :::: d1dqua_ 118 PM-NTVPNKVNHLWMAQLFHDRKQREERMTTPKDQRHKVANVDYLRPIIADAD-TGHG-- 173 d1j93a_ 80 GMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLG 139 ::: : :::::::::::: ::::: d1dqua_ 174 --------------------------------GLT--A--VMKLTKLFVERG---AAGIH 194 d1j93a_ 140 FVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSG--- 196 :::: : :: ::: : : : ::::::::::::::::: d1dqua_ 195 IEDQ---A--PG---TKG--K--V--------------L-VPISEHINRLVAIRAQADIM 227 d1j93a_ 197 ---AQAVQIFDSWATEL-----------SP-V---------------------------- 213 :::::::::::::: : : d1dqua_ 228 GTDLLAIARTDSEAATLITSTIDHRDHP-FIIGSTNPDIQPLNDLMVMAEQAGKNGAELQ 286 d1j93a_ 214 ------------DF--E------------------------------------------- 216 :: : d1dqua_ 287 AIEDEWLAKAGLKLFNDAVVDAINNSPLPNKKAAIEKYLTQSKGKSNLEARAIAKEIAGT 346 d1j93a_ 217 -----------------EFS-LPYLKQIVDSVKLTHPNLPLILYASGSG-GLLERLPLTG 257 ::: ::::::::::::: : :::::::::::: :::::::::: d1dqua_ 347 DIYFDWEAPRTREGYYRYQGGTQCAINRAVAYAP-F-ADLIWMESKLPDYKQAKEFADGV 404 d1j93a_ 258 VD--VVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFG----SKEFITNRINDTVKKAGK 311 :: :::::::::::::::: ::::::::::::: d1dqua_ 405 HAVW------------------PEQKLAYNLSPSFNWKKAMP-----RDEQETYIKRLGA 441 d1j93a_ 312 -GKHILNLGHGIKVGTPEEN--------------------------FAH--FFE------ 336 ::::::: ::::::::::: : : d1dqua_ 442 LGYAWQFI-TLAGLHTTALISDTFAKAYAKQGMRAYGELVQEPEMA--NGV--DVVTHQK 496 d1j93a_ 337 -----------------IAKGLRY 343 d1dqua_ 497 WSGANYVDNMLKMITGG------- 513 HHsearch alignment (Probability: 0.03 E-value:0.05) d1j93a_ 257 GVDVVSLDWT-VDMAD-------GRRRLGPNVAIQGNVDPGV---LFGSKEFITNRINDT 305 :::::::::: ::::: ::::::::: ::::::::: :::::::: ::: d1dqua_ 381 FADLIWMESKLPDYKQAKEFADGVHAVWPEQK-LAYNLSPSFNWKKAMPRDEQ----ETY 435 d1j93a_ 306 VKKAGKGKHILNL 318 ::::::::::::: d1dqua_ 436 IKRLGALGYAWQF 448