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 | d1vyra_ | Pentaerythritol tetranirate reductase | FMN-linked oxidoreductases | 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 <-- 1.467 --> HitDALI alignment (Z-score: 11.9 Raw score:1429.40) d1j93a_ 1 -tqplllDAVRgkeverPPVWLMRQAGrymksyqllcekyplfrdRSEN------VDLVV 53 :::: :::::::::: :::: ::::: d1vyra_ 1 aeklftpLKVG-avtapNRVFMAPLTR------------------LRSIepgdipTPLMG 41 d1j93a_ 54 EISLQPWkvfRPDGVILFSDIlTPLSgmnipfdiikgkgpvifdplrtaadvekvrefiP 113 ::::::: ::::::::::: :::: : d1vyra_ 42 EYYRQRA---SAGLIISEATQ-ISAQ-----------------------akgyagapglH 74 d1j93a_ 114 EKSvpyVGEALTILRKE-VNNQAAVLGFVGapftLASYV-------veGGSSkNFTKI-- 163 ::: ::::::::::: :::::::::::: ::::: :::: ::::: d1vyra_ 75 SPE---QIAAWKKITAGvHAEDGRIAVQLW---hTGRIShssiqpggqAPVSaSALNAnt 128 d1j93a_ 164 -------------krlafaepkVLHAlLQKFATSMAKYIRYQADSGAQAVQIFDS----- 205 :::: :::::::::::::::::::::::::::: d1vyra_ 129 rtslrdengnairvdtttpralELDE-IPGIVNDFRQAVANAREAGFDLVELHSAhgyll 187 d1j93a_ 206 -WATELS--------pVDFEEFsLPYLKQIVDSVKLTHPNLPLILYASGS---------- 246 :::::: :::::: ::::::::::::::::::::::::::: d1vyra_ 188 hQFLSPSsnqrtdqygGSVENR-ARLVLEVVDAVCNEWSADRIGIRVSPIgtfqnvdngp 246 d1j93a_ 247 --GGLLE-RLPLTG---VDVVSLDWT------vdmADGRRRLGP--NVAIQGNVDPgvlf 292 ::::: :::::: ::::::::: ::::::::: :::::::::: d1vyra_ 247 neEADALyLIEELAkrgIAYLHMSETdlaggkpysEAFRQKVRErfHGVIIGAGAY---- 302 d1j93a_ 293 gskefITNRINDTVKKAGkgkHILNlgHGIKvgtpeenFAHFFEI--------------- 337 ::::::::::::: :::: :::: ::::::: d1vyra_ 303 -----TAEKAEDLIGKGL--iDAVA--FGRDyianpdlVARLQKKaelnpqrpesfyggg 353 d1j93a_ 338 ----akglry 343 d1vyra_ 354 aegytdypsl 363 FAST alignment (Normalized score: 6.21 Raw score:2190.00) d1j93a_ 1 TQPLLLDAVRG------------KEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSEN 48 ::::: :::::::: d1vyra_ 1 -----------AEKLFTPLKVGAVTAPN-RVFMAPLT----------------------- 25 d1j93a_ 49 -----------VDLVVEISLQPWKVF--RPDGVILFSDILTPLSGMNIPFDIIKGKGPVI 95 :::::::::: ::::::: d1vyra_ 26 RLRSIEPGDIPTPLMGEYYRQ-----RASAGLIIS------------------------- 55 d1j93a_ 96 FDPLRTAADVEKVREFIPEKS-----------------------VPYVGEALTILRKEVN 132 ::::::::::::: d1vyra_ 56 ---------------------EATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHA--- 91 d1j93a_ 133 N-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV------------------ 173 :::::::: d1vyra_ 92 -EDGRIAVQL--------------------------------WHTGRISHSSIQPGGQAP 118 d1j93a_ 174 --------------------------------LHALLQKFATSMAKYIRYQADSGAQAVQ 201 :::::::::::::::::::::::::::: d1vyra_ 119 VSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVE 178 d1j93a_ 202 IF------DSWATELSPV--------------DFEEFSLPYLKQIVDSVKLT-HPNLPLI 240 :: :::: :::: ::::::::::::::: ::: ::: d1vyra_ 179 LHSAHGYLLHQF------LSPSSNQRTDQYGGSVEN-RARLVLEVVDAVCNEWSAD-RIG 230 d1j93a_ 241 LYASG------------------SGGLLERLPLTGVDVVSLDWTV-------------DM 269 ::: ::::::::::::::::::: :: d1vyra_ 231 IRV--SPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMS---ETDLAGGKPYSEAFR 285 d1j93a_ 270 ADGRRRLGPNVAIQGN-VDPGVLFGSKEF-ITNRINDTVKKAGKGKHILNLGHGIKVGTP 327 ::::::: :::: :::: :::::::::: d1vyra_ 286 QKVRERF--HGVI---IGAGA--------YTAEKAEDLIG-------------------- 312 d1j93a_ 328 EENFAHFFEIAKGLRY-------------------------------------------- 343 d1vyra_ 313 ----------------KGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEG 356 d1j93a_ 344 ------- 344 d1vyra_ 357 YTDYPSL 363 TMalign alignment (TM-score: 0.57 Raw score:195.80) d1j93a_ 1 -----TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCE------------------ 37 ::::::::::::::::::::: :: :: ::::: d1vyra_ 1 AEKLF----TPLKVGAVTAPNRVFMAPLTR-LR-SI-EPGDIPTPLMGEYYRQRASAGLI 53 d1j93a_ 38 -------KYPLFRDR----SENVD-LVVEISLQPWKVFR---PDGVILFSDILT------ 76 :::::: ::::: :::::::::::::: :::::::::::: d1vyra_ 54 ISEATQI--SAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRISHSSI 111 d1j93a_ 77 ------PLSGMNIPFD----IIK---------GKGPVIFDPLRTAADVEKVREFIPEKSV 117 :: :::::: ::: :::::::: ::::::: ::: d1vyra_ 112 QPGGQA-PV-SASALNANTRTSLRDENGNAIRVDTTTPRA---------LELDEIP-GIV 159 d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPF---TLASYVVEGGSSKNFTKIKRL-----AFA 169 :::::::::::::: ::::::::::: ::::::::: : d1vyra_ 160 NDFRQAVANAREAG---FDLVELHSAHGYLLHQFLSPSSN-----------QRTDQY--- 202 d1j93a_ 170 EPKVLHALLQKFATSMAKYIRYQADSGA--QAVQIFDSWATEL---SPVDFEEFSLPYLK 224 ::::::::::::::::::::::: :::::::: :::: ::::::::::: d1vyra_ 203 -----GGSVENRARLVLEVVDAVCNEWSADRIGIRVSP-IGTFQNV---DNGPNEEADAL 253 d1j93a_ 225 QIVDSVKLTHPNLPLILYASG---SGGLLE-RLPLT--GV--DVVSLDWTVDMADGRRRL 276 :::::::: :::::::::::: :::::: ::::: :: :::::: ::::::::::: d1vyra_ 254 YLIEELAK-RGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAG-AYTAEKAEDLI 311 d1j93a_ 277 -GPNVAIQGNVDPGVLFGSKEFITNRINDTVKK-----AGKGKHILNL-GH-GIKV---- 324 ::::::::::::::: : :: :::::::: : : ::: d1vyra_ 312 GKGLIDAVAFGRDYIA---N--PD-LVARLQKKAELNP---------QR-PE-SFYGGGA 354 d1j93a_ 325 GTPEENFAHFFEIAKGLRY 343 ::::::: : : d1vyra_ 355 EGYTDYP-S---L------ 363 HHsearch alignment (Probability: 0.92 E-value:0.00) d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPY--------------- 222 :::::::::::::::::::::::::::::::::: :::::: d1vyra_ 155 IPGIVNDFRQAVANAREAGFDLVELHSAHGYLLH-----QFLSPSSNQRTDQYGGSVENR 209 d1j93a_ 223 ---LKQIVDSVKLTHPNLPLILYA----------------SGSGGLLERLPLTGVDVVSL 263 ::::::::::::::::::::: :::::::::::::::::::: d1vyra_ 210 ARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHM 269 d1j93a_ 264 DWTV----------DMADGRRRLGPNVAIQGNVDPG 289 :::: :::::::::::::::::::::: d1vyra_ 270 SETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAE 305