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 | d1f74a_ | N-acetylneuraminate lyase | 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 <-- 1.323 --> HitDALI alignment (Z-score: 11.0 Raw score:1286.30) d1j93a_ 1 tQPLLldavrgkeverpPVWLMRQAGrymksyqllcekyPLFRdrsENVDLVVEISLQPW 60 :::: ::::::::: :::: :::::::::::::: d1f74a_ 1 -MRDL------------KGIFSALLV----------sfnEDGT---INEKGLRQIIRHNI 34 d1j93a_ 61 KVFRPDGVILF---SDILTPLsgmnipfdiikgkgpvifdplrtaadvekvrefipeKSV 117 ::::::::::: ::::::: ::: d1f74a_ 35 DKMKVDGLYVGgstGENFMLS-----------------------------------tEEK 59 d1j93a_ 118 PYVGEALTILRKEVnnqAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhal 177 :::::::::::::: :::::::::: d1f74a_ 60 KEIFRIAKDEAKDQ---IALIAQVGSV--------------------------------- 83 d1j93a_ 178 lqkFATSMAKYIRYQADSGAQAVQIFDSWatelspvDFEEfSLPYLKQIVDSVKlthpnL 237 :::::::::::::::::::::::::: :::: ::::::::::::: : d1f74a_ 84 ---NLKEAVELGKYATELGYDCLSAVTPF---yykfSFPE-IKHYYDTIIAETG-----S 131 d1j93a_ 238 PLILYASG-------SGGLLERLPLT-GVDVVSLDWTVD--MADGRRRlGPNVAIQGNVD 287 :::::::: ::::::::::: :::::::::::: ::::::: ::::::::::: d1f74a_ 132 NMIVYSIPfltgvnmGIEQFGELYKNpKVLGVKFTAGDFylLERLKKA-YPNHLIWAGFD 190 d1j93a_ 288 PgvlfgskefitnRINDTVKKAgkgkHILNlghgikvgtpeeNFAHFFEIAKGLRY---- 343 : ::::::::: :::: :::::::::::::: d1f74a_ 191 E------------MMLPAASLG---vDGAI------gstfnvNGVRARQIFELTKAgklk 229 d1j93a_ 344 ------------------------------------------------------------ 344 d1f74a_ 230 ealeiqhvtndliegilanglyltikellklegvdagycrepmtskataeqvakakdlka 289 d1j93a_ 344 ---- 344 d1f74a_ 290 kfls 293 FAST alignment (Normalized score: 6.60 Raw score:2094.00) d1j93a_ 1 TQPLLLDAVRGKEVERP-----PVWLMRQAGRYMKSYQLLCE------KYPLFRDRS-EN 48 :::: :::: :: d1f74a_ 1 -----------------MRDLKGIFS----------------ALLVSFNEDG-----TIN 22 d1j93a_ 49 VDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKV 108 ::::::::::::::::::::: d1f74a_ 23 EKGLRQIIRHNIDKMKVDGLY--------------------------------------- 43 d1j93a_ 109 REFIPEKS------------VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGS 156 :::::::::::::::::::::::: d1f74a_ 44 --------VGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQ---------------- 79 d1j93a_ 157 SKNFTKIKRLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQIFDSWAT---- 208 :::::::::::::::::::::: d1f74a_ 80 ------------------------VGSVNLKEAVELGKYATELGYDCLSA------VTPF 109 d1j93a_ 209 --ELSPVDFEEFSLPYLKQIVDSVKLTHP-NLPLIL-YASGS-------GGLLERLPLT- 256 :::: ::::::::::::: :::::: :::: :::::::::: d1f74a_ 110 YYKFSF----PEIKHYYDTIIAE------TGSNMIVYSIPF-LTGVNMGIEQFGELYKNP 158 d1j93a_ 257 GVDVVSLDWTV------DMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAG 310 ::::::: :::::::: :::::: :::::: ::::::: d1f74a_ 159 KVLGVKF----TAGDFYLLERLKKA-YPNHLI-WAGFDE-----------MMLPAAS--- 198 d1j93a_ 311 KGKHILNLGHGIKVGTP-----------EENFAHFFEIAKGLRY---------------- 343 ::::::::::::: d1f74a_ 199 -----------------LGVDGAIGSTFNVNGVRARQIFEL---TKAGKLKEALEIQHVT 238 d1j93a_ 344 ------------------------------------------------------- 344 d1f74a_ 239 NDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATAEQVAKAKDLKAKFLS 293 TMalign alignment (TM-score: 0.50 Raw score:171.69) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :::: ::::::::: : : ::: :: :::::::::::::: d1f74a_ 1 -MRDL------------KGIFSALLV-----S---F-NED-GT---INEKGLRQIIRHNI 34 d1j93a_ 61 KVFRPDGVILF---S-DILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS 116 ::::::::::: : :::::: : : d1f74a_ 35 DKMKVDGLYVGGSTGENFMLST----------------------------------E--E 58 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 ::::::::::::: :: ::::::::: : d1f74a_ 59 KKEIFRIAKDEAK--DQ-IALIAQVGS---V----------------------------- 83 d1j93a_ 177 LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 236 ::::::::::::::::::::::::::: :: :::::::::::::::::: d1f74a_ 84 ----NLKEAVELGKYATELGYDCLSAVTPFY-YK---FSFPEIKHYYDTIIAETG----- 130 d1j93a_ 237 LPLILYASGSGG----LLERLPLT--G--VDVVSLDWTVD--MADGRRRLGPNVAIQGNV 286 :::::::::::: :::::::: : ::::::::::: ::::::: ::::::::: d1f74a_ 131 SNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKA-YPNHLIWAG- 188 d1j93a_ 287 DPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG-LRY-- 343 ::::: : :::::: : : ::: ::::: :: :::::::::: ::: d1f74a_ 189 FDEMM------L--PAASLG--V----D-GAI-GSTFN---VN-GVRARQIFELTKAGKL 228 d1j93a_ 344 ------------------------------------------------------------ 344 d1f74a_ 229 KEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATAEQVAKAKDLK 288 d1j93a_ 344 ----- 344 d1f74a_ 289 AKFLS 293 HHsearch alignment (Probability: 0.94 E-value:0.00) d1j93a_ 183 TSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILY 242 :::::::::::::::::::::::::::::: :::::::::::::: ::::::: d1f74a_ 86 KEAVELGKYATELGYDCLSAVTPFYYKFSF----PEIKHYYDTIIAET-----GSNMIVY 136 d1j93a_ 243 AS----G---SGGLLERLPLTGVDVVSL-DWTVDMAD---GRRRLGPNVAIQG 284 :: : ::::::::::: :::::: :::::::: ::::::::::::: d1f74a_ 137 SIPFLTGVNMGIEQFGELYKN-PKVLGVKFTAGDFYLLERLKKAYPNHLIWAG 188