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 | d1jpdx1 | L-Ala-D/L-Glu epimerase | 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 <-- 0.896 --> HitDALI alignment (Z-score: 9.8 Raw score:1054.10) d1j93a_ 1 tqpllldavrgkeVERPPVWlMRQAgrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 ::::::: :::: ::::::::::::::: d1jpdx1 1 -----------tlPETVITA-QTVV--------------------IGTPDQMANSASTLW 28 d1j93a_ 61 KVFRPdGVILFsDILTplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpYV 120 ::::: ::::: :::: :: d1jpdx1 29 QAGAK-LLKVK-LDNH------------------------------------------LI 44 d1j93a_ 121 GEALTILRKEVNNqAAVLGFVGApftlasyvveggssknftkikrlafaepkvlhallqk 180 ::::::::::::: ::::::::: d1jpdx1 45 SERMVAIRTAVPD-ATLIVDANE-----------------------------------sw 68 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIF-DSWAtelspvdfeefsLPYLKQivDSVKlthpnLPL 239 ::::::::::::::::::::::: :::: :::::: :::: ::: d1jpdx1 69 RAEGLAARCQLLADLGVAMLEQPlPAQD------------DAALEN--FIHP-----LPI 109 d1j93a_ 240 ILYASGSG-GLLERLPLTgVDVVSLD-WTVD----MADGRRRLGP-NVAIQGNVDPGvlf 292 :::::::: ::::::::: ::::::: :::: :::::::::: ::::::::::: d1jpdx1 110 CADESCHTrSNLKALKGR-YEMVNIKlDKTGglteALALATEARAqGFSLMLGCMLC--- 165 d1j93a_ 293 gskefITNRINDTVKkAGKGKHILNLghgikvgTPEEN--faHFFE-iAKGLry 343 :::::::::: :::::::::: ::::: :::: :::: d1jpdx1 166 -----TSRAISAALP-LVPQVSFADL---dgptWLAVDvepaLQFTtgELHL-- 208 FAST alignment (Normalized score: 3.39 Raw score:905.30) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1jpdx1 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 d1jpdx1 1 ------------------------------------------------------------ 1 d1j93a_ 121 GEALTILRKEVNN----QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 ::::::::: d1jpdx1 1 -------------TLPETVITAQTVV---------------------------------- 13 d1j93a_ 177 LLQK--FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEE--FSLPYLKQIVDSVKL 232 ::::::::::::::::::::::::: :::::::::::: d1jpdx1 14 ----IGTPDQMANSASTLWQAGAKLLKVKLD------------NHLISERMVAIRTA--- 54 d1j93a_ 233 THPNLPLILYASGS--------GGLLERLPLTGVDVVSLDWTVDMADGRRRLG------- 277 ::::::::::: ::::::::::::::: d1jpdx1 55 -VPDATLIVDAN--ESWRAEGLAARCQLLADLGVAML----------------EQPLPAQ 95 d1j93a_ 278 ---------PNVA----------------------------------------------- 281 :::: d1jpdx1 96 DDAALENFIHPLPICADESCHTRSNLKALKGRYEMVNIKLDKTGGLTEALALATEARAQG 155 d1j93a_ 282 --IQGNVDPGVLFGSKEF--ITNRINDTVKKAGKGKHILNLGHG--------------IK 323 :::::: :::::::::: :: d1jpdx1 156 FSLMLGCM----------LCTSRAISAALP--------------LVPQVSFADLDGPTWL 191 d1j93a_ 324 VGTPEENFAHFFEIAKGLRY--------------- 343 :: d1jpdx1 192 AV------------------DVEPALQFTTGELHL 208 TMalign alignment (TM-score: 0.46 Raw score:157.68) d1j93a_ 1 --TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQ 58 :::::::: ::: ::: :::::::::: d1jpdx1 1 TL--------------PETVITAQ-TVV------------------IGT-PDQMANSAST 26 d1j93a_ 59 PWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP 118 ::::::: :::::: :::: :: d1jpdx1 27 LWQAGAK-LLKVKL-DNHL---------------------------------------IS 45 d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL 178 ::::::::::: : ::::::::: :: d1jpdx1 46 ERMVAIRTAVP--D--ATLIVDANE--SW------------------------------- 68 d1j93a_ 179 QKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLP 238 :::::::::::::::::::::::: :: : :: ::::: ::: : :: d1jpdx1 69 --RAEGLAARCQLLADLGVAMLEQPL-PA-------Q--DD-AALEN---FIH--P--LP 108 d1j93a_ 239 LILYASGSGGLLERLPLTGVDVVSLDWT-V-DMADGRRR--LGP--NVAIQGNVDPGVLF 292 :::::::::::::::::::::::::::: : :::::::: ::: ::::::::::::: d1jpdx1 109 ICADESCHTRSNLKALKGRYEMVNIKLDKTGGLTEALALATEARAQGFSLMLGCMLCTS- 167 d1j93a_ 293 GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTP---EENFAH--FFEIAKGLRY 343 :: :: :::: ::::::::::::::::::: ::::: :::: d1jpdx1 168 ----RA--IS-AALP-LVPQVSFADLDGPTWLAVDVEP-ALQFTTGELHL------ 208 HHsearch alignment (Probability: 0.02 E-value:0.12) d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLAS 149 :::::::::::::::::::: ::::::::: d1jpdx1 44 ISERMVAIRTAVPDATLIVD-ANESWRAEG 72