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 | d1dqwa_ | Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase) | Ribulose-phoshate binding barrel | 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 <-- 0.908 --> HitDALI alignment (Z-score: 8.2 Raw score:1014.80) d1j93a_ 1 ----------------tqpLLLDavrgkeverpPVWLmRQAGrymksyqllcekyplfrd 44 :::: :::: :::: d1dqwa_ 1 mhkatykeraathpspvaaKLFN---imhekqtNLCA-SLDV------------------ 38 d1j93a_ 45 rsENVDLVVEISLQPWkvFRPDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaad 104 :::::::::::::: ::::::::::: d1dqwa_ 39 --RTTKELLELVEALG--PKICLLKTHVD------------------------------- 63 d1j93a_ 105 vekvrefipeksvpYVGE-ALTILRKEVN-nQAAVLGFVGAPftlasyvveggssknftk 162 :::: :::::::::: ::::::::::: d1dqwa_ 64 ----------iltdFSMEgTVKPLKALSAkyNFLLFEDRKFA------------------ 95 d1j93a_ 163 ikrlafaepkvlhallqkFATS-MAKYIR----YQADsGAQAVQIfdswatelspvdfee 217 :::: :::::: :::: ::::::: d1dqwa_ 96 ------------------DIGNtVKLQYSagvyRIAE-WADITNA--------------- 121 d1j93a_ 218 fsLPYLKQIVDSVKLTHP-----NLPLILY-ASGS------gGLLERLPLTG------VD 259 :::::::::::::::: ::::::: :::: :::::::::: :: d1dqwa_ 122 -hGVVGPGIVSGLKQAAEevtkePRGLLMLaELSCkgslstgEYTKGTVDIAksdkdfVI 180 d1j93a_ 260 VVSLDwtvdmadGRRR--lgPNVAIQGNVDPgVLFG-skefitnRINDTVKKAgkgkHIL 316 ::::: :::: ::::::::::: :::: ::::::::: ::: d1dqwa_ 181 GFIAQ------rDMGGrdegYDWLIMTPGVGlDDKGdalgqqyrTVDDVVSTG---sDII 231 d1j93a_ 317 NlgHGIK---VGTP-eENFAHFFEIAKGLRY------- 343 : :::: :::: ::::::::::::::: d1dqwa_ 232 I--VGRGlfaKGRDakVEGERYRKAGWEAYLrrcgqqd 267 FAST alignment (Normalized score: 4.13 Raw score:1251.00) d1j93a_ 1 TQPLLLDAVRGKEVERP------------------------------PVWLMRQAGRYMK 30 :::: d1dqwa_ 1 -----------------MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCA--------- 34 d1j93a_ 31 SYQLLCEKYPLFRDR---SENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDI 87 :::::::::::::::: :::::::: d1dqwa_ 35 ---------------SLDVRTTKELLELVEALGP--KICLLKTH---------------- 61 d1j93a_ 88 IKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV---------GEALTILRKEVNN----Q 134 :::::::::: : d1dqwa_ 62 ---------------------------------VDILTDFSMEGTVKPLKAL---SAKYN 85 d1j93a_ 135 AAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKF----ATSMAKYIR 190 :::::::: :::::::: d1dqwa_ 86 FLLFEDRK---------------------------------------FADIGNTVKLQY- 105 d1j93a_ 191 YQAD--------SGAQAVQIFDSWATELSPVDFEEF----SLPYLKQIVDSVKLTH-PNL 237 :::::::: :::::::::::::::: ::: d1dqwa_ 106 ----SAGVYRIAEWADITNA----------------HGVVGPGIVSGLKQAAEEVTKEPR 145 d1j93a_ 238 PLILYASG--------------SGGLLERLPLT----GVDVVSLDWTVDMADGRRRLG-- 277 ::::: ::::::::: :::::: d1dqwa_ 146 GLLML---AELSCKGSLSTGEYTKGTVDIAK--SDKDFVIGFI---------------AQ 185 d1j93a_ 278 ---------PNVAIQGNVDPGVLFGSKEFITN-------------------RINDTVKKA 309 ::::: ::::::: d1dqwa_ 186 RDMGGRDEGYDWLI------------------MTPGVGLDDKGDALGQQYRTVDDVVS-- 225 d1j93a_ 310 GKGKHILNLGHGI-------------KVGT-PEENFAHFFEIAKGLRY---------- 343 :::: :::::::::::::: d1dqwa_ 226 -------------TGSDIIIVGRGLFAKGRDAKVEGERYRKAGWE---AYLRRCGQQD 267 TMalign alignment (TM-score: 0.45 Raw score:153.38) d1j93a_ 1 ----------TQ----PLLLDAVRGKEVERPP-VWLMRQAGRYMKSY------------- 32 : ::::::: :::::::: :::::::::::::: d1dqwa_ 1 MHKATYKERA-ATHPSPVAAKLF-NIMHEKQTNLCASLDVRTTKELLELVEALGPKICLL 58 d1j93a_ 33 ---QLLCEKYPLFRDRS---ENVDLVVEISLQPWKVF-RP-DGVILFSDILTPLSGMNIP 84 ::: :::::::::::::: :: :::::: ::: :: d1dqwa_ 59 KTH-----------VDILTD---FSMEGTVKPLKALSAKYNFLLFED-RKF-AD------ 96 d1j93a_ 85 FDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV-PYV-GEALTILRKEVNNQAAVLGFVG 142 :::::::: ::: :::::: :::::: d1dqwa_ 97 -------------------------IGNTVKLQYSAGV-YRIAEW---------ADITNA 121 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQAD-SG-AQAV 200 :: : :::::::::::::: :: :::: d1dqwa_ 122 HG---------------------------------V--VGPGIVSGLKQAAEEVTKEPRG 146 d1j93a_ 201 QIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLT---G 257 :::::::::::::::::: :::::::::::: : ::::::: : :: :::: : d1dqwa_ 147 LLMLAELSCKGSLSTGEY-TKGTVDIAKSDK---D-FVIGFIA--Q---RD-MGGRDEGY 195 d1j93a_ 258 VDVVSLD-W------------TVDMADGRRRLGPNVAIQGNVDPGVLF--GS-KEFITNR 301 ::::::: : ::::::::::: :::::::::::: :: ::::::: d1dqwa_ 196 DWLIMTPGVGLDDKGDALGQQYRTVDDVVSTG----SDIIIVGRGLFAKGRDAKVEGERY 251 d1j93a_ 302 INDTVKKAGKGK----HILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 :::::::::::: d1dqwa_ 252 RKAGWEAYLRRCGQQD------------------------------ 267 HHsearch alignment (Probability: 0.06 E-value:0.73) d1j93a_ 250 LERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQ-GNVDPGVLFGSKEFITNRINDTVKK 308 ::::::::::::::: :::::::::::::::::: :::::: :::::::::::::::: d1dqwa_ 168 TVDIAKSDKDFVIGF-IAQRDMGGRDEGYDWLIMTPGVGLD---DKGDALGQQYRTVDDV 223 d1j93a_ 309 AGKGKHILNLGHGIKV--GTPEENFAHFFEI 337 :::::::::::::::: ::::::::::::: d1dqwa_ 224 VSTGSDIIIVGRGLFAKGRDAKVEGERYRKA 254