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 | d1ub3a_ | 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 <-- 1.785 --> HitDALI alignment (Z-score: 12.6 Raw score:1310.50) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQAgrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 ::::::::: ::::::::::::::: d1ub3a_ 1 -------------dlaAHIDHTLLK--------------------PTATLEEVAKAAEEA 27 d1j93a_ 61 KVFRPDGVILFsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 ::::::::::: d1ub3a_ 28 LEYGFYGLCIP------------------------------------------------- 38 d1j93a_ 121 gEALTILRKEV-NNQAAVLGFVGapFTLAsyvveggssknftkikrlafaepkvlhallq 179 :::::::::: ::::::::::: :::: d1ub3a_ 39 pSYVAWVRARYpHAPFRLVTVVGfpLGYQ------------------------------- 67 d1j93a_ 180 kFATSMAKYIRYQADSGAQAVQIFDSW-ATELSpvDFEEfSLPYLKQIVDSVKlthpNLP 238 :::::::::::::::::::::::::: ::::: :::: ::::::::::::: ::: d1ub3a_ 68 -EKEVKALEAALACARGADEVDMVLHLgRAKAG--DLDY-LEAEVRAVREAVP----QAV 119 d1j93a_ 239 LILYASG-------SGGLLERLPLTGVDVVSLD-------WTVD-MADGRRRLGPNVAIQ 283 ::::::: ::::::::::::::::::: :::: ::::::::::::::: d1ub3a_ 120 LKVILETgyfspeeIARLAEAAIRGGADFLKTStgfgprgASLEdVALLVRVAQGRAQVK 179 d1j93a_ 284 GNVDPgvlfgskefITNRINDTVKKAgkgkHILNLghgikvgtpeenfAHFFEiakglry 343 ::::: :::::::::::: ::::: ::::: d1ub3a_ 180 AAGGI--------rDRETALRMLKAG---aSRLGT----------ssgVALVA------- 211 FAST alignment (Normalized score: 7.79 Raw score:2096.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----PVWLMRQAGRYMKSYQLLCEKYPLFRDRS------ENVD 50 :::: :::: d1ub3a_ 1 -----------------DLAAHIDH-------------------------TLLKPTATLE 18 d1j93a_ 51 LVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 ::: :::::::::::::::: d1ub3a_ 19 EVA-KAAEEALEYGFYGLCI---------------------------------------- 37 d1j93a_ 111 FIPEKSVPYVGEALTILRKEVN-NQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFA 169 ::::::::::::: :::::::: d1ub3a_ 38 ---------PPSYVAWVRARYPHAPFRLVTV----------------------------- 59 d1j93a_ 170 EPKVLHALLQK--------FATSMAKYIRYQADSGAQAVQI-FDSWATELSPVDFEEF-S 219 :::::::::::::::::::::: :::::::: : d1ub3a_ 60 -----------VGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKA--------GD 100 d1j93a_ 220 LPYLKQIVDSVKLTHPNLPLILYASG---------SGGLLERLPLTGVDVVSLDWTV--- 267 :::::::::::::::::::::::: ::::::::::::::::: d1ub3a_ 101 LDYLEAEVRAVREAVPQAVLKVIL--ETGYFSPEEIARLAEAAIRGGADFLK-----TST 153 d1j93a_ 268 ----------DMADGRRRLGPNVAIQGNVDPGVLFGSKEF-------ITNRINDTVKKAG 310 ::::::::::::::: :::::::::: d1ub3a_ 154 GFGPRGASLEDVALLVRVAQGRAQV---------------KAAGGIRDRETALRMLK--- 195 d1j93a_ 311 KGKHILNLGHGIKVGTPEEN----------FAHFFEIAKGLRY-- 343 :::: d1ub3a_ 196 --------------------AGASRLGTSSGVAL---------VA 211 TMalign alignment (TM-score: 0.47 Raw score:160.95) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :::::::::::::: : : :::::::: d1ub3a_ 1 -------------DLAAHIDHTLLKPT----A------------------T-LEEVAKAA 24 d1j93a_ 61 KVFR---PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV 117 :::: :::::::: d1ub3a_ 25 EEALEYGFYGLCIPP--------------------------------------------- 39 d1j93a_ 118 PYVGEALTILRKEV-NNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 : ::::::::: ::::::::::::::::: d1ub3a_ 40 --S--YVAWVRARYPHAPFRLVTVVGFPLGYQ---------------------------- 67 d1j93a_ 177 LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 236 :::::::::::::::::::::::: :::::: : :: ::::::::::::::::: d1ub3a_ 68 ----EKEVKALEAALACARGADEVDMVL-HLGRAK--A-GD--LDYLEAEVRAVREAVPQ 117 d1j93a_ 237 LPLILYAS-G-SGG-LLER-LPLT--G-VDVVSL-------DWTVD-MADGRRRLGPNVA 281 :::::::: : ::: :::: :::: : :::::: ::::: ::::::::::::: d1ub3a_ 118 AVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQ 177 d1j93a_ 282 IQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGL 341 ::::::: : ::::::::::::: ::::: :: :::::: d1ub3a_ 178 VKAAGGI--R------DRETALRMLKAGA---SRLGT--SS--------GVALVA----- 211 d1j93a_ 342 RY 343 d1ub3a_ 212 -- 212 HHsearch alignment (Probability: 0.77 E-value:0.00) d1j93a_ 185 MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS 244 :::::::::::::::::::::::: :::::::::::: ::::::::: d1ub3a_ 20 VAKAAEEALEYGFYGLCIPPSYVA-------------WVRARYPHAPFR--LVTVVGFPL 64 d1j93a_ 245 GSGGLLERL------PLTGVDVV----------SLDWT---VDMADGRRRLGP---NVAI 282 ::::::::: :::::::: ::::: :::::::::::: :::: d1ub3a_ 65 GYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVIL 124 d1j93a_ 283 QGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG 340 ::::: :::::::::::::::: ::::::::::::::::::::::::::::: d1ub3a_ 125 ETGYF------SPEEIARLAEAAIRGG--ADFLKTSTGFGPRGASLEDVALLVRVAQG 174