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 | d1dxea_ | 2-dehydro-3-deoxy-galactarate aldolase | 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 <-- 1.261 --> HitDALI alignment (Z-score: 10.1 Raw score:1152.30) d1j93a_ 1 --TQPLLLDAVRGkeveRPPVWLMRQAgrymksyqllcekyplfrdrsenvdlVVEISLQ 58 ::::::::::: :::::::::: ::::::: d1dxea_ 1 dvFPNKFKAALAA---kQVQIGCWSAL-------------------------sNPISTEV 32 d1j93a_ 59 PWKvFRPDGVILfSDILtplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVP 118 ::: :::::::: :::: :: d1dxea_ 33 LGL-AGFDWLVL-DGEH--------------------------------------apnDI 52 d1j93a_ 119 YVGEALTILRKEVnnQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhall 178 ::::::::::::: ::::::::::: d1dxea_ 53 STFIPQLMALKGS--ASAPVVRVPTN---------------------------------- 76 d1j93a_ 179 qkfatsMAKYIRYQADSGAQAVQIFDswatelspvdfeefSLPYLKQIVDSVKL------ 232 :::::::::::::::::::: :::::::::::::: d1dxea_ 77 ------EPVIIKRLLDIGFYNFLIPF------------veTKEEAELAVASTRYppegir 118 d1j93a_ 233 --------------------tHPNLPLILYASG--SGGLLERLPLT-GVDVVSLDWT--- 266 :::::::::::: ::::::::::: :::::::::: d1dxea_ 119 gvsvshranmfgtvadyfaqsNKNITILVQIESqqGVDNVDAIAATeGVDGIFVGPSdla 178 d1j93a_ 267 ---------------vDMADGRRRL-GPNVAIQGNVDpgvlfgskefITNRINDTVKKAg 310 ::::::::: ::::::::::: :::::::::::: d1dxea_ 179 aalghlgnashpdvqkAIQHIFNRAsAHGKPSGILAP----------VEADARRYLEWG- 227 d1j93a_ 311 kgkHILNL-ghgIKVGTPEenfahffeiakglry 343 ::::: ::::::: d1dxea_ 228 --aTFVAVgsdlGVFRSAT------qkladtfkk 253 FAST alignment (Normalized score: 6.17 Raw score:1819.00) d1j93a_ 1 T---QPLLLDAVRGKEVE---RPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL--- 51 :::::::: :::::: d1dxea_ 1 -DVFPNKFKAAL------AAKQVQIGC------------------------------WSA 23 d1j93a_ 52 --VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVR 109 :::::::::: ::::::::: d1dxea_ 24 LSNPISTEVLGL-AGFDWLVLD-------------------------------------- 44 d1j93a_ 110 EFIPEKSVPY------VGEALTILRKEVN---NQAAVLGFVGAPFTLASYVVEGGSSKNF 160 ::::::::::: ::::::::: d1dxea_ 45 ----------GEHAPNDISTFIPQLMA--LKGSASAPVVRV------------------- 73 d1j93a_ 161 TKIKRLAFAEPKVLHALLQKFATS---MAKYIRYQADSGAQAVQIFDSWATELSPVDFEE 217 :::::::::::::::::: d1dxea_ 74 ------------------------PTNEPVIIKRLLDIGFYNFLI--------------- 94 d1j93a_ 218 F----SLPYLKQIVDSVKLT-----------------------------HPNLPLILYAS 244 :::::::::::: :::::::::: d1dxea_ 95 -PFVETKEEAELAVAST---RYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQI- 149 d1j93a_ 245 ---GSGGLLERLPLT-GVDVVSLDWTV---------------------DMADGRRRLG-- 277 :::::::::::: :::::::: :::::::: d1dxea_ 150 ESQQGVDNVDAIAATEGVDGIFVG---PSDLAAALGHLGNASHPDVQKAIQHIFNR--AS 204 d1j93a_ 278 -PNVAIQGNVDPGVLFGSKEF-----ITNRINDTVKKAGKGKHILNLGHGIKVGTPEENF 331 ::::: :::::::::: d1dxea_ 205 AHGKPS---------------GILAPVEADARRYLE------------------------ 225 d1j93a_ 332 AHFFEIAKGLRY---------------------------- 343 d1dxea_ 226 ------------WGATFVAVGSDLGVFRSATQKLADTFKK 253 TMalign alignment (TM-score: 0.39 Raw score:132.48) d1j93a_ 1 --TQPLLLDAV--RGK--------------------EVERPPVWLMRQA--GRYMKS--- 31 ::::::::: ::: :::::::::: :::::: d1dxea_ 1 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLA---GFDWLVLDGEHAPNDISTFIP 57 d1j93a_ 32 ----------------YQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDIL 75 ::: ::::::::::: ::::::: : : d1dxea_ 58 QLMALKGSASAPVVRV-------------PTN----EPVIIKRLLDI-GFYNFLI-P-F- 96 d1j93a_ 76 TPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRK-----E 130 :: :: :::::::::::: : d1dxea_ 97 VE-----------------------------------TK---EEAELAVASTRYPPEGIR 118 d1j93a_ 131 --------------------VNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAE 170 :::::::::::: :: d1dxea_ 119 GVSVSHRANMFGTVADYFAQSNKNITILVQIE----SQ---------------------- 152 d1j93a_ 171 PKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSW-A-----TELSPVDFEEFSLPYLK 224 ::: ::::::: :::::::::::::: : ::: ::::::::::: d1dxea_ 153 ---------QGV-DNVDAIA--ATEGVDGIFVGPSDLAAALGHLGN---ASHPDVQKAIQ 197 d1j93a_ 225 QIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQG 284 :::::::: :: ::::::: ::::::::::::::::::::: d1dxea_ 198 HIFNRASA-HG-KPSGILA-PVEADARRYLEWGATFVAVGS------------------- 235 d1j93a_ 285 NVDPGV-------------LFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENF 331 ::::: d1dxea_ 236 -DLGVFRSATQKLADTFKK----------------------------------------- 253 d1j93a_ 332 AHFFEIAKGLRY 343 d1dxea_ 254 ------------ 254 HHsearch alignment (Probability: 0.35 E-value:0.01) d1j93a_ 178 LQKFATSMAKYIRYQAD-SGAQAVQIF--DSWATE-LSPVDFEEFSLPYLKQIVDSVKLT 233 ::::::::::::::::: ::::::::: :::::: :::::::::::::::::::::::: d1dxea_ 147 VQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAH 206 d1j93a_ 234 HPNLPLILYASGSGGLLERLPLTGVDVVSLDWTV 267 ::::::::::: :::::::::::::::::::: d1dxea_ 207 --GKPSGILAPVE-ADARRYLEWGATFVAVGSDL 237