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 | d1q6oa_ | 3-keto-L-gulonate 6-phosphate 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 <-- 1.326 --> HitDALI alignment (Z-score: 10.8 Raw score:1159.30) d1j93a_ 1 tqpllldavrgkeveRPPVWLmRQAGrymksyqllcekyplfrdrsenvdLVVEISLQPW 60 :::::: :::: :::::::::: d1q6oa_ 1 ---------------LPMLQV-ALDN------------------------QTMDSAYETT 20 d1j93a_ 61 KVFR--PDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvp 118 :::: ::::::::: d1q6oa_ 21 RLIAeeVDIIEVGTI-----------------------------------------lcvg 39 d1j93a_ 119 YVGEALTILRKEVNNqAAVLG-FVGAPftlasyvveggssknftkikrlafaepkvlhal 177 ::::::::::::::: ::::: ::::: d1q6oa_ 40 EGVRAVRDLKALYPH-KIVLAdAKIAD--------------------------------- 65 d1j93a_ 178 lqkfatSMAKYIRYQADSGAQAVQIFDSwatelspvdfeefSLPYLKQIVDSVKltHPNL 237 :::::::::::::::::::::: ::::::::::::: :::: d1q6oa_ 66 ------AGKILSRMCFEANADWVTVICC------------aDINTAKGALDVAK--EFNG 105 d1j93a_ 238 PLILYAS-GSGG-LLERLPLTGVDVVSLDWT-----------vDMADGRRRL-GPNVAIQ 283 ::::::: :::: :::::::::::::::::: ::::::::: ::::::: d1q6oa_ 106 DVQIELTgYWTWeQAQQWRDAGIGQVVYHRSrdaqaagvawgeADITAIKRLsDMGFKVT 165 d1j93a_ 284 GNVDPgvlfgskefITNRINDtVKKAgkGKHILNlgHGIK-vGTPE--ENFAHFFEIAKG 340 ::::: ::::::: :::: :::::: :::: :::: :::::::::::: d1q6oa_ 166 VTGGL---------ALEDLPL-FKGI--PIHVFI--AGRSirDAASpvEAARQFKRSIAE 211 d1j93a_ 341 LRy 343 :: d1q6oa_ 212 LW- 213 FAST alignment (Normalized score: 6.85 Raw score:1852.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL-----VVEI 55 :::::: :::: d1q6oa_ 1 ---------------LPMLQV------------------------------ALDNQTMDS 15 d1j93a_ 56 SLQPWKVF---RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::: ::::::: d1q6oa_ 16 AYETTRL-IAEEVDIIEV------------------------------------------ 32 d1j93a_ 113 PEKSVP-------YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKR 165 ::::::::::::: :::::::::: d1q6oa_ 33 ------GTILCVGEGVRAVRDLKALY-PHKIVLADAK----------------------- 62 d1j93a_ 166 LAFAEPKVLHALLQKFA--TSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF----S 219 :::::::::::::::::::: : d1q6oa_ 63 -----------------IADAGKILSRMCFEANADWVTV----------------ICCAD 89 d1j93a_ 220 LPYLKQIVDSVKLTHPNLPLILYASG---SGGLLERLPLTGVDVVSLDWTV--------- 267 ::::::::::::: :::::::::: ::::::::::::::::::: d1q6oa_ 90 INTAKGALDVAKE--FNGDVQIELT-GYWTWEQAQQWRDAGIGQVVYH---RSRDAQAAG 143 d1j93a_ 268 -----DMADGRRRLG---PNVAIQGNVDPGVLFGSKEF-----ITNRINDTVKKAGKGKH 314 :::::::: :::::: :::::: :::::: d1q6oa_ 144 VAWGEADITAIKR--LSDMGFKVT--------------VTGGLALEDLP----LFKGIP- 182 d1j93a_ 315 ILNLGHGI---------KVGT--PEENFAHFFEIAKGLRY-- 343 :::: :::::::::::::: d1q6oa_ 183 --------IHVFIAGRSIRDAASPVEAARQFKRSIAE---LW 213 TMalign alignment (TM-score: 0.46 Raw score:157.89) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::: ::: : :: ::::::: d1q6oa_ 1 ---------------LPMLQVA-LDN------------------Q-----TM-DSAYETT 20 d1j93a_ 61 KVFR--PDGVIL---FSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEK 115 :::: :::::: :::: : d1q6oa_ 21 RLIAEEVDIIEVGTILCVG-E--------------------------------------- 40 d1j93a_ 116 SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLH 175 : : :::::::::::: :::::::::: d1q6oa_ 41 -G--V-RAVRDLKALYPH-KIVLADAKIA------------------------------- 64 d1j93a_ 176 ALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHP 235 :: :::::::::::::::::: :: : :::::::::::::::: d1q6oa_ 65 -----DA--GKILSRMCFEANADWVTV-IC-C-----------ADINTAKGALDVAKEF- 103 d1j93a_ 236 NLPLILYASGSGGLLERLPLT---GVDVVSLDW----------T--VDMADGRRRLGPNV 280 ::::::::::: ::::::::: ::::::::: : :::::::::::::: d1q6oa_ 104 NGDVQIELTGY-WTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGF 162 d1j93a_ 281 AIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK-VGTPEENFAHFFEIAK 339 ::::: :: :: :: ::::: :::: :::::: ::: :::::::::::::: d1q6oa_ 163 KVTVT-GG-LA------LE-DLPLF-KGIP--IHVFIA--GRSI--RDAASPVEAARQFK 206 d1j93a_ 340 G-LR--Y 343 : :: : d1q6oa_ 207 RSIAELW 213 HHsearch alignment (Probability: 0.94 E-value:0.00) d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 ::::::::: ::::::::: ::::::::: :::::::::: :::::::: :::: d1q6oa_ 14 DSAYETTRL-IAEEVDIIE-VGTILCVGE------GVRAVRDLKA-LYPHKIVL--ADAK 62 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLI 240 ::::::::::::::::::::::::: ::::: :::::::::::::::::: d1q6oa_ 63 IADAGKILSRMCFEANADWVTVICC----ADINT--------AKGALDVAKEFNGDVQIE 110 d1j93a_ 241 LYASGSGGLLERLPLTGVDVVSLDWT------------VDMADGRRRL--GPNVAIQGNV 286 :::::::::::::::::::::::::: :::::::::: :::::::::: d1q6oa_ 111 LTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGL 170 d1j93a_ 287 DPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKV-GTPEENFAHFFEIAKGL 341 ::: :::::::: ::::::::::::: ::::::::::::::::: d1q6oa_ 171 ALE-----------DLPLFKGI---PIHVFIAGRSIRDAASPVEAARQFKRSIAEL 212