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 | d1gzga_ | 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) | 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 <-- 1.943 --> HitDALI alignment (Z-score: 12.6 Raw score:1451.20) d1j93a_ 1 -------------tqpllldavrgkeveRPPVWLMRqagrymksyqllcekyplfrdrSE 47 :::::::: :: d1gzga_ 1 nraypytrlrrnrrddfsrrlvrenvltVDDLILPV---------------------fVL 39 d1j93a_ 48 NVD--------------LVVEISLQPWKVFR---PDGVILFSDiltplSGMNipfdiikg 90 ::: :::::::::::::: ::::::::: :::: d1gzga_ 40 DGVnqresipsmpgverLSIDQLLIEAEEWValgIPALALFPV-tpveKKSL-------- 90 d1j93a_ 91 kgpvifdplrtaadvekvREFI-PEKSVpYVGEALTILRKEVNNqAAVLGFVG------a 143 :::: ::::: ::::::::::::::: :::::::: d1gzga_ 91 ------------------DAAEaYNPEG-IAQRATRALRERFPE-LGIITDVAldpftth 130 d1j93a_ 144 pFTLAsyvveggssknftkikrlafaePKVLhALLQKFATSMAKYIRYQADSGAQAVQIF 203 :::: :::: :::::::::::::::::::::::::::: d1gzga_ 131 gQNGI--------------------ldDDGY-VLNDVSIDVLVRQALSHAEAGAQVVAPS 169 d1j93a_ 204 DSwatelspvdfeefSLPYLKQIVDSVKLT-HPNLPLILY-ASGS--------------- 246 :: ::::::::::::::: ::::::::: :::: d1gzga_ 170 DM-------------MDGRIGAIREALESAgHTNVRVMAYsAKYAsayygpfrdavgsas 216 d1j93a_ 247 -------------------GGLL-ERLPLTGVDVVSLD--WTVD--MADGRRRLGpnVAI 282 :::: :::::::::::::: :::: ::::::::: ::: d1gzga_ 217 nlgkgnkatyqmdpansdeALHEvAADLAEGADMVMVKpgMPYLdiVRRVKDEFR--APT 274 d1j93a_ 283 QGNVDP-GVLFG---------SKEFITNRINDTVKKAgkgkHILNLghgikvgtpeenFA 332 :::::: ::::: :::::::::::::::: ::::: :: d1gzga_ 275 FVYQVSgEYAMHmgaiqngwlAESVILESLTAFKRAG---aDGILT----------yfAK 321 d1j93a_ 333 HFFEIAKGlry 343 :::::::: d1gzga_ 322 QAAEQLRR--- 329 FAST alignment (Normalized score: 7.04 Raw score:2367.00) d1j93a_ 1 TQPLLLDAVRGKEVERP------------------------------PVWLMRQAGRYMK 30 :::: d1gzga_ 1 -----------------NRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLIL--------- 34 d1j93a_ 31 SYQLLCEKYPLFRDRS----------------------ENVDLVVEISLQPWKVFRPDGV 68 :::::::::::::: ::::::: d1gzga_ 35 ----------------PVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWV-ALGIPAL 77 d1j93a_ 69 ILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV----------- 117 :::: d1gzga_ 78 ALFP---------------------------------------------VTPVEKKSLDA 92 d1j93a_ 118 -------PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAE 170 :::::::::::::: :::::::: d1gzga_ 93 AEAYNPEGIAQRATRALRERF-PELGIITD------------------------------ 121 d1j93a_ 171 PKVLHA---------------------LLQKFATSMAKYIRYQADSGAQAVQIFDSWATE 209 ::::::::::::::::::::::::::::: d1gzga_ 122 ------VALDPFTTHGQNGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDM---- 171 d1j93a_ 210 LSPVDFEEFSLPYLKQIVDSVKL-THPNLPLILYASG----------------------- 245 :::::::::::::: :::::::::: d1gzga_ 172 ---------MDGRIGAIREALESAGHTNVRVMAY---SAKYASAYYGPFRDAVGSASNLG 219 d1j93a_ 246 ----------------SGGLLERLPLTGVDVVSLDWTV--------DMADGRRRLGP-NV 280 :::::::::::::::::: :::::::: :: d1gzga_ 220 KGNKATYQMDPANSDEALHEVAADLAEGADMVMV----KPGMPYLDIVRRVKDE---FRA 272 d1j93a_ 281 AIQG--NVDPGVLF----------GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPE 328 :: :::::::: ::::::::::::::: d1gzga_ 273 PT--FVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKR--------------------- 309 d1j93a_ 329 E---------NFAHFFEIAKGLRY- 343 :::::::::: d1gzga_ 310 -AGADGILTYFAKQAAEQLR----R 329 TMalign alignment (TM-score: 0.54 Raw score:186.90) d1j93a_ 1 --------------------------TQPLLLDAVRGKEVERPPVWLMRQAGR--YMKSY 32 :::::::::::::: ::: d1gzga_ 1 NRAYPYTRLRRNRRDDFSRRLVRENV-------------LTVDDLILPVFVLDGV--NQR 45 d1j93a_ 33 QL--------LCEKYPLFRDRSENVDLVVEISLQPWKVFR---PDGVILFSDILTPLSGM 81 :: :: : :::::::::::: ::::::::: : d1gzga_ 46 ESIPSMPGVE----------RL----S-IDQLLIEAEEWVALGIPALALFPV--T----- 83 d1j93a_ 82 NIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY-VGEALTILRKEVNNQAAVLGF 140 ::: ::: : :::::: :::: :::::::::::::: :::::: d1gzga_ 84 ----PVE----KKS--L---------DAAEAY--NPEGIAQRATRALRERFPE-LGIITD 121 d1j93a_ 141 VGAPFTLASYVVEGGSS-KNF-TKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQ 198 ::: :: :: :::: : :::::: :: ::::::::::::::::::::: d1gzga_ 122 VAL--DP--FT--THGQN--GI-LDDDGY------VL--NDVSIDVLVRQALSHAEAGAQ 164 d1j93a_ 199 AVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKL-THPNLPLILY--ASG---------- 245 :::::: : :::::::::::::: :::::::::: ::: d1gzga_ 165 VVAPSD--M-----------MDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDA 211 d1j93a_ 246 ----------------S-G-G--LLERLP-LT--G-VDVVSL-DWTVDMADGRRRL-GPN 279 : : : :::::: :: : :::::: ::::::::::::: ::: d1gzga_ 212 VGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFR 271 d1j93a_ 280 VAIQGNV---DP-GVL--F----GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEE 329 ::::::: :: ::: : :::::::::::::::::: ::::: : d1gzga_ 272 APTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGA---DGILT---Y------- 318 d1j93a_ 330 NFAHFFEIAKGLRY 343 ::::::::::: d1gzga_ 319 FAKQAAEQLRR--- 329 HHsearch alignment (Probability: 0.55 E-value:0.00) d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 ::::::::::::::::::::::::::::::::: ::: ::::::: : d1gzga_ 100 GIAQRATRALRERFPELGIITDVALDPFTTHGQ----------NGI---LDDDGYV---L 143 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 ::::::::::::::::::::::::::::::: :::::::::::: ::::: d1gzga_ 144 NDVSIDVLVRQALSHAEAGAQVVAPSDMMDG----------RIGAIREALESA--GHTNV 191 d1j93a_ 238 PLILYA-SGSGGL 249 :::::: :::::: d1gzga_ 192 RVMAYSAKYASAY 204