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 | d2mnra1 | Mandelate racemase | Enolase C-terminal domain-like | 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 <-- 1.205 --> HitDALI alignment (Z-score: 11.6 Raw score:1248.30) d1j93a_ 1 tqpllldavrgkeveRPPVWLMRqagrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 :::::::: ::::::::::::::: d2mnra1 1 ---------------PVQAYDSH---------------------sLDGVKLATERAVTAA 24 d1j93a_ 61 KVFRPdGVILFSdILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVPYV 120 ::::: :::::: :::: :::: d2mnra1 25 ELGFR-AVKTKI-GYPA---------------------------------------LDQD 43 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGApftlasyvveggssknftkikrlafaepkvlhallqk 180 ::::::::::::::::::::::: d2mnra1 44 LAVVRSIRQAVGDDFGIMVDYNQ-----------------------------------sl 68 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQI-FDSWatelspvdfeefSLPYLKQIVDSVklthpNLPL 239 :::::::::::::::::::::: :::: :::::::::::: :::: d2mnra1 69 DVPAAIKRSQALQQEGVTWIEEpTLQH------------DYEGHQRIQSKL-----NVPV 111 d1j93a_ 240 ILYASGSG-GLLERLP-LTGVDVVSLDWTV-----DMADGRRRLGP-NVAIQGNVDPgvl 291 :::::::: ::::::: ::::::::::::: ::::::::::: :::::::::: d2mnra1 112 QMGENWLGpEEMFKALsIGACRLAMPDAMKiggvtGWIRASALAQQfGIPMSSHLFQ--- 168 d1j93a_ 292 fgskefitnRINDTVKKAGkGKHILNlghGIKVGT-PEENfaHFFE-iAKGL-------- 341 :::::::::: :::::: :::::: :::: :::: :::: d2mnra1 169 --------eISAHLLAATP-TAHWLE--rLDLAGSvIEPT--LTFEggNAVIpdlpgvgi 215 d1j93a_ 342 ----------ry 343 d2mnra1 216 iwrekeigkylv 227 FAST alignment (Normalized score: 6.74 Raw score:1879.00) d1j93a_ 1 TQPLLLDAVRGKEVER-PPVWLMRQAGRYMKSYQLLCEKYPLFRDR---SENVDLVVEIS 56 ::::: ::::::::::: d2mnra1 1 ----------------PVQAYD------------------------SHSLDGVKLATERA 20 d1j93a_ 57 LQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEK- 115 ::::: ::::::::: d2mnra1 21 VTAAE-LGFRAVKTK--------------------------------------------I 35 d1j93a_ 116 ---SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPK 172 ::::::::::::::::::::::::::: d2mnra1 36 GYPALDQDLAVVRSIRQAVGDDFGIMVDYN------------------------------ 65 d1j93a_ 173 VLHALLQK---FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF-------SLPY 222 :::::::::::::::::::: :::: d2mnra1 66 --------QSLDVPAAIKRSQALQQEGVTWI------------------EEPTLQHDYEG 99 d1j93a_ 223 LKQIVDSVKLTHPNLPLILYASGS--GGLLERLPLT-GVDVVSLDWTV-------DMADG 272 ::::::: :::::: ::::: :::::::::: ::::::::: ::::: d2mnra1 100 HQRIQSK-----LNVPVQ-MGENWLGPEEMFKALSIGACRLAMPDA--MKIGGVTGWIRA 151 d1j93a_ 273 RRRLG---PNVAIQGNVDPGVLFGSKEFITN-RINDTVKKAGKGKHILNLGHGI------ 322 ::: :::::::: :::::::: d2mnra1 152 SAL--AQQFGIPMSSH---------------LFQEISAHL--------------LAATPT 180 d1j93a_ 323 ----------KVGTPEENFAHFFEIAKGLRY----------------------------- 343 ::::: d2mnra1 181 AHWLERLDLAGSVIE----------------PTLTFEGGNAVIPDLPGVGIIWREKEIGK 224 d1j93a_ 344 --- 344 d2mnra1 225 YLV 227 TMalign alignment (TM-score: 0.49 Raw score:167.80) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::: :: :: :::::::: :::: d2mnra1 1 ---------------PVQAYDS-HS-------------------LD-GVKLATER-AVTA 23 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 :::::::::::: : :: ::::: d2mnra1 24 AELGFRAVKTKI-G-YP--------------------------------------ALDQD 43 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 ::::::::::::::::::::::: :: d2mnra1 44 LAVVRSIRQAVGDDFGIMVDYNQ---SL-------------------------------- 68 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLI 240 :::::::::::::::::::::::: :: : :::::::::::: : :::: d2mnra1 69 DVPAAIKRSQALQQEGVTWIEEPT-LQ-------H---DYEGHQRIQSKL----N-VPVQ 112 d1j93a_ 241 LYASGSG-GLLERLP-LTGVDVVSLDWT-V--D--MADGRRRLGP-NVAIQGNVDPGVLF 292 ::::::: ::::::: :::::::::::: : : :::::::::: :::::::::: : d2mnra1 113 MGENWLGPEEMFKALSIGACRLAMPDAMKIGGVTGWIRASALAQQFGIPMSSHLFQ-E-- 169 d1j93a_ 293 GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGL----------- 341 : :: ::::::: ::::::: ::::::::::: ::::::::: d2mnra1 170 -----I--SA-HLLAATP-TAHWLER--LDLAGSVIEPT-LTFEGGNAVIPDLPGVGIIW 217 d1j93a_ 342 ----------RY 343 d2mnra1 218 REKEIGKYLV-- 227 HHsearch alignment (Probability: 0.16 E-value:0.01) d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL--L 178 ::::::::::::::::::::::::::::::::: ::::::::::::::::::::: : d2mnra1 44 LAVVRSIRQAVGDDFGIMVDYNQSLDVPAAIKR---SQALQQEGVTWIEEPTLQHDYEGH 100 d1j93a_ 179 QKFATS------------MAKYIRYQADS-GAQAVQIFDSWATELSPVDFEEFSLPYLKQ 225 :::::: ::::::::::: :::::::::::: :::::::: d2mnra1 101 QRIQSKLNVPVQMGENWLGPEEMFKALSIGACRLAMPDAMKI----------GGVTGWIR 150 d1j93a_ 226 IVDSVKLTHPNLPLILYASGSGGLLE 251 :::::::: :::::::::::::::: d2mnra1 151 ASALAQQF--GIPMSSHLFQEISAHL 174