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 | d1km4a_ | 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 <-- 1.021 --> HitDALI alignment (Z-score: 10.6 Raw score:1128.50) d1j93a_ 1 tqpllldavrgkeveRPPVWLMRQAGRymksyqllcekyplfrdrsenvdlvVEISLQPW 60 :::::::::::: :::::::: d1km4a_ 1 --------------vMNRLILAMDLMN-------------------------RDDALRVT 21 d1j93a_ 61 KVFR--PDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvp 118 :::: ::::::::: d1km4a_ 22 GEVReyIDTVKIGYP-----------------------------------------lvls 40 d1j93a_ 119 YVGEALTILRKEVNnqAAVLG-FVGAPftlasyvveggssknftkikrlafaepkvlhal 177 :::::::::::::: ::::: ::::: d1km4a_ 41 EGMDIIAEFRKRFG--CRIIAdFAVAD--------------------------------- 65 d1j93a_ 178 lqkFATSMAKYIRYQADSGAQAVQIFDSwatelspvdfeefSLPYLKQIVdSVKLTHpNL 237 ::::::::::::::::::::::::: ::::::::: :::::: :: d1km4a_ 66 ---IPETNEKICRATFKAGADAIIVHGF------------pGADSVRACL-NVAEEM-GR 108 d1j93a_ 238 PLILYASG------------SGGLLERLPLTGVDVVSLDWTVD--MADGRRRLGPNVAIQ 283 :::::::: ::::::::::::::::::::::: ::::::::::::::: d1km4a_ 109 EVFLLTEMshpgaemfiqgaADEIARMGVDLGVKNYVGPSTRPerLSRLREIIGQDSFLI 168 d1j93a_ 284 GNVDPGVlfgskefitnRINDTVKKAgkgkHILNLghgikvgTPEEnFAHFFEIAKGLRy 343 ::::::: ::::::::: ::::: :::: :::::::::::: d1km4a_ 169 SPGVGAQ--------ggDPGETLRFA----DAIIV--grsiyLADN-PAAAAAGIIESI- 212 FAST alignment (Normalized score: 7.20 Raw score:1943.00) d1j93a_ 1 TQPLLLDAVRGKEVERP---PVWLMRQAGRYMKSYQLLCEKYPLFRDR---SENVDLVVE 54 :::: ::::::::: d1km4a_ 1 -----------------VMNRLIL------------------------AMDLMNRDDALR 19 d1j93a_ 55 ISLQPWKVF-RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIP 113 :::::: ::::::: d1km4a_ 20 VTGEVR---EYIDTVKI------------------------------------------- 33 d1j93a_ 114 EKSVP-------YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRL 166 ::::::::::::: ::::::::: d1km4a_ 34 -----GYPLVLSEGMDIIAEFRKRF--GCRIIADFA------------------------ 62 d1j93a_ 167 AFAEPKVLHALLQK---FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF-SLPY 222 ::::::::::::::::::::::::: :::: d1km4a_ 63 --------------VADIPETNEKICRATFKAGADAIIVHGF-------------PGADS 95 d1j93a_ 223 LKQIVDSVKLTHPNLPLILYAS--------------GSGGLLERLPLTGVDVVSLDWTV- 267 :::::::::: :::::::: :::::::::::::::::::::: d1km4a_ 96 VRACLNVAEE--MGREVFLL--TEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPST-R 150 d1j93a_ 268 --DMADGRRRLGPNVAIQGNVDPGVLFGSKEFITN------RINDTVKKAGKGKHILNLG 319 ::::::::::::::: :::: :::::::: d1km4a_ 151 PERLSRLREIIGQDSFL-ISPG-------------VGAQGGDPGETLRF----------- 185 d1j93a_ 320 HGIKVGT---------------PEENFAHFFEIAKGLRY- 343 ::::::::::: d1km4a_ 186 -------ADAIIVGRSIYLADNPAAAAAGIIES------I 212 TMalign alignment (TM-score: 0.42 Raw score:143.23) d1j93a_ 1 TQPLL-LDAV---------------------RGKEVERPPVWLMR-QAGRYMKSYQLLCE 37 :: :: :::::::: ::::: :: d1km4a_ 1 ---VMN--RLILAMDLMNRDDALRVTGEVRE------YIDTVKIGYPLVLS--EG----- 42 d1j93a_ 38 KYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFD 97 :::::::::::::::::: :::: : d1km4a_ 43 ---------------MDIIAEFRKRFGCRIIAD-FAVA-D-------------------- 65 d1j93a_ 98 PLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSS 157 : : ::::::::::::: :: :::::::: d1km4a_ 66 -------------I-P-ETNEKICRATFKA--GA-----DAIIVHGF------------- 90 d1j93a_ 158 KNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSG----AQAVQIFDSWATELSPV 213 : : ::::::::::: :::::::::::::: d1km4a_ 91 -----------------------P--G-ADSVRACLNVAEEMGREVFLLTEMSHPGA--- 121 d1j93a_ 214 DFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTG--V-----DVVSLDWT 266 : ::::::::::::::::::: ::::: : :: ::::::::: : :::::::: d1km4a_ 122 -E-MFIQGAADEIARMGVDLGV-KNYVG-P--ST-RPERLSRLREIIGQDSFLISPGVGA 174 d1j93a_ 267 VDMADGRRRLGPNVAIQGNV-D-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKV 324 ::: :::: ::::::::::: : ::: : ::::::::::::: d1km4a_ 175 QGG-DPGE-TLRFADAIIVGRSIYLA--D---NPAAAAAGIIESI--------------- 212 d1j93a_ 325 GTPEENFAHFFEIAKGLRY 343 d1km4a_ 213 ------------------- 213 HHsearch alignment (Probability: 0.40 E-value:0.01) d1j93a_ 182 ATSMAKYIRYQADSGAQAVQIF 203 :::::::::::::::::::::: d1km4a_ 67 PETNEKICRATFKAGADAIIVH 88