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 | d1n7ka_ | Deoxyribose-phosphate aldolase DeoC | 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 <-- 1.441 --> HitDALI alignment (Z-score: 11.0 Raw score:1208.20) d1j93a_ 1 ---tqpllldavrgkeVERP--PVWLMRQAGRymksyqllcekyplfrdrsenVDLVVEI 55 :::: :::::::::: ::::::: d1n7ka_ 1 psardilqqgldrlgsPEDLasRIDSTLLSPR--------------------aTEEDVRN 40 d1j93a_ 56 SLQPWKVFRPDGVILFSdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipek 115 ::::::::::::::::: d1n7ka_ 41 LVREASDYGFRCAVLTP------------------------------------------- 57 d1j93a_ 116 svpyvgeALTILRKEVN-NQAAVLGFVGapFTLAsyvveggssknftkikrlafaepkvl 174 :::::::::: :::::::::: :::: d1n7ka_ 58 ------vYTVKISGLAEkLGVKLCSVIGfpLGQA-------------------------- 85 d1j93a_ 175 hallqkFATSMAKYIRYQADSGAQAVQIFDswATELspvdFEEFSLPYLKQIVDSVKltH 234 :::::::::::::::::::::::: :::: ::::::::::::::::: : d1n7ka_ 86 ------PLEVKLVEAQTVLEAGATELDVVP--HLSL----GPEAVYREVSGIVKLAK--S 131 d1j93a_ 235 PNLPLILYASGSGG----LLERL---PLTGVDVVSLD--------wtVDMADGRRRLGP- 278 :::::::::::::: ::::: ::::::::::: :::::::::::: d1n7ka_ 132 YGAVVKVILEAPLWddktLSLLVdssRRAGADIVKTStgvytkggdpVTVFRLASLAKPl 191 d1j93a_ 279 NVAIQGNVDPgvlfgskefITNRINDTVKKAgkgkHILNLghgikvgtpeenfAHFFEIa 338 :::::::::: :::::::::::: ::::: :::::: d1n7ka_ 192 GMGVKASGGI--------rSGIDAVLAVGAG---aDIIGT----------ssaVKVLES- 229 d1j93a_ 339 kglry 343 d1n7ka_ 230 fkslv 234 FAST alignment (Normalized score: 7.09 Raw score:2009.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----------------------PVWLMRQAGRYMKSYQLLCEK 38 :::: d1n7ka_ 1 -----------------PSARDILQQGLDRLGSPEDLASRIDS----------------- 26 d1j93a_ 39 YPLFRDRS------ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKG 92 :::::::::::::: ::::::::: d1n7ka_ 27 --------TLLSPRATEEDVRNLVREAS-DYGFRCAVL---------------------- 55 d1j93a_ 93 PVIFDPLRTAADVEKVREFIPEKS-VPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASY 150 ::::::::::::: ::::::: d1n7ka_ 56 ------------------------TPVYTVKISGLAEK----LGVKLCSV---------- 77 d1j93a_ 151 VVEGGSSKNFTKIKRLAFAEPKVLHALLQK--------FATSMAKYIRYQADSGAQAVQI 202 :::::::::::::::::::::: d1n7ka_ 78 ------------------------------IGFPLGQAPLEVKLVEAQTVLEAGATELDV 107 d1j93a_ 203 FDSW-ATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG---------SGGLLER 252 : ::::: ::::::::::::::::: ::::::::: ::::::: d1n7ka_ 108 V---PHLSLG----PEAVYREVSGIVKLAKS--YGAVVKVIL--EAPLWDDKTLSLLVDS 156 d1j93a_ 253 LPLTGVDVVSLDWTV-------------DMADGRRRLG---PNVAIQGNVDPGVLFGSKE 296 :::::::::: :::::::: ::::: d1n7ka_ 157 SRRAGADIVK-----TSTGVYTKGGDPVTVFRLASL--AKPLGMGV-------------- 195 d1j93a_ 297 F-------ITNRINDTVKKAGKGKHILNLGHGIKVGTPEE---------NFAHFFEIAKG 340 :::::::::: :::::::::: d1n7ka_ 196 -KASGGIRSGIDAVLAVG----------------------AGADIIGTSSAVKVLESFK- 231 d1j93a_ 341 LRY--- 343 d1n7ka_ 232 ---SLV 234 TMalign alignment (TM-score: 0.47 Raw score:159.86) d1j93a_ 1 -----------------TQPLLLDAVRGKEVER--PPVWLMRQAGRYMKSYQLLCEKYPL 41 :: ::::::::::: :: d1n7ka_ 1 PSARDILQQGLDRLGSP--------------EDLASRIDSTLLSPR---AT--------- 34 d1j93a_ 42 FRDRSENVDLVVEISLQPWKVF--R-PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 : :::::::::: : ::::::::: d1n7ka_ 35 ---------E--EDVRNLVREASDYGFRCAVLTPV------------------------- 58 d1j93a_ 99 LRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGA-PFTLASYVVEGGSS 157 ::: :::::::: :: ::::::::: :::: d1n7ka_ 59 --------------------YTV-KISGLAEK-LG-VKLCSVIGFP-LGQA--------- 85 d1j93a_ 158 KNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEE 217 :::::::::::::::::::::::: :: : :::: d1n7ka_ 86 -----------------------PLEVKLVEAQTVLEAGATELDVVP--HL-S---LGPE 116 d1j93a_ 218 FSLPYLKQIVDSVKLTHPNLPLILYAS-GSGG--LLE-RL--PL-TGVDVVSLD------ 264 :::::::::::::: :: ::::::::: :::: ::: :: :: ::::::::: d1n7ka_ 117 AVYREVSGIVKLAK-SY-GAVVKVILEAPLWDDKTLSLLVDSSRRAGADIVKTSTGVYTK 174 d1j93a_ 265 W-T-VDMADGRRRLGP-NVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHG 321 : : :::::::::::: ::::::: :: :: ::::::::::::: ::::: : d1n7ka_ 175 GGDPVTVFRLASLAKPLGMGVKAS-GG-IR------SGIDAVLAVGAGA---DIIGT--S 221 d1j93a_ 322 IKVGTPEENFAHFFEIAKG--LRY 343 : :::::::::: d1n7ka_ 222 S--------AVKVLESFKSLV--- 234 HHsearch alignment (Probability: 0.78 E-value:0.01) d1j93a_ 294 SKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG 340 :::::::::::::::: ::::::::::::::::::::::::::::: d1n7ka_ 146 DDKTLSLLVDSSRRAG--ADIVKTSTGVYTKGGDPVTVFRLASLAKP 190