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 | d1r5ya_ | Queosine tRNA-guanine transglycosylase | tRNA-guanine transglycosylase | 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 <-- 1.035 --> HitDALI alignment (Z-score: 9.2 Raw score:1188.40) d1j93a_ 1 tqpllldaVRGKEVE-----------------rppVWLMR----qAGRYmksyqllceky 39 ::::::: ::::: :::: d1r5ya_ 1 -----rprFSFSIAAregkartgtiemkrgvirtpAFMPVgtaatVKAL----------- 44 d1j93a_ 40 plfrdrsenvdlvveISLQPWKVFrPDGVILfsdILTPLSGmnipfdiikgkgpvifdpl 99 ::::::::: :::::: ::::::: d1r5ya_ 45 ---------------KPETVRATG-ADIILG-ntYHLMLRP------------------- 68 d1j93a_ 100 rtaadvekvrefIPEKSV-PYVGEAlTILRkevnnqAAVLGFVGApfTLASYVVEggssk 158 :::::: :::::: :::: ::::::::: :::::::: d1r5ya_ 69 ------------GAERIAkLGGLHSfMGWD------RPILTDSGG--YQVMLSLT----- 103 d1j93a_ 159 nftkikrlafaepkVLHALL---qKFATSMAKYIRYQAdsgAQAVQIFDsWATE-----l 210 :::::: :::::::::::::: :::::::: :::: d1r5ya_ 104 --------------KQSEEGvtfmLSPERSIEIQHLLG---SDIVMAFD-ECTPypatps 145 d1j93a_ 211 SPVDFEEFSLPYLKQIVDSVKL--THPN-LPLILYAS------gsGGLLERLPLTGVDVV 261 :::::::::::::::::::::: :::: :::::::: ::::::::::::::: d1r5ya_ 146 RAASSMERSMRWAKRSRDAFDSrkEQAEnAALFGIQQgsvfenlrQQSADALAEIGFDGY 205 d1j93a_ 262 SL----------dwtvDMADGRRRLGPNVAIQG-nVDPGvlfgskefitNRINDTVKKAg 310 :: ::::::::::::::::: :::: :::::::::: d1r5ya_ 206 AVgglavgegqdemfrVLDFSVPMLPDDKPHYLmgVGKP----------DDIVGAVERG- 254 d1j93a_ 311 kgkHILNLgHGIK------vGTPE------------------------------------ 328 ::::: :::: :::: d1r5ya_ 255 ---IDMFD-CVLPtrsgrngQAFTwdgpinirnarfsedlkpldsechcavcqkwsrayi 310 d1j93a_ 329 --------------------eNFAHFFEIAKGLRY---------------- 343 :::::::::::::: d1r5ya_ 311 hhlirageilgamlmtehniaFYQQLMQKIRDSISegrfsqfaqdfraryf 361 FAST alignment (Normalized score: 4.49 Raw score:1581.00) d1j93a_ 1 TQPLLLDAVRGKEVE--------------------------------------------- 15 d1r5ya_ 1 ---------------RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALK 45 d1j93a_ 16 ----------------------------------------RPPVWLMRQAGRYMKSYQLL 35 :::::: d1r5ya_ 46 PETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILT-------------- 91 d1j93a_ 36 CEKYPLFRDRS----------------------ENVDLVVEISLQPWKVFRPDGVILFSD 73 :::::::::::: ::::::::::: d1r5ya_ 92 -----------DSGGYQVMLSLTKQSEEGVTFMLSPERSIEIQHL----LGSDIVMAFDE 136 d1j93a_ 74 ILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS--------------VPY 119 ::: d1r5ya_ 137 -------------------------------------------CTPYPATPSRAASSMER 153 d1j93a_ 120 VGEALTILRKEVN--------NQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEP 171 ::::::::::: ::::::::: d1r5ya_ 154 SMRWAKRSRDA--FDSRKEQAENAALFGIQ------------------------------ 181 d1j93a_ 172 KVLHALLQK----FATSMAKYIRYQADSGAQAVQI-FDSWATELSPVDFEEFSLPYLKQI 226 :::::::::::::::::::::: ::: ::::: :::::::::: d1r5ya_ 182 ---------QGSVFENLRQQSADALAEIGFDGYAVGGLA--VGEGQ----DEMFRVLDFS 226 d1j93a_ 227 VDSVKLT-HPNLPLIL-YASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQG 284 ::: :::::::: ::: :::::::::::::::: d1r5ya_ 227 VPM----LPDDKPHYLMGVG-KPDDIVGAVERGIDMF----------------------- 258 d1j93a_ 285 N----VDPGVLFG----------------------------------------------- 293 :::::: d1r5ya_ 259 -DCVLPTRSGR--NGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIR 315 d1j93a_ 294 ------SKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY---- 343 ::::::::::::::: d1r5ya_ 316 AGEILGAMLMTEHNIAFYQQL-----------------------------------MQKI 340 d1j93a_ 344 --------------------- 344 d1r5ya_ 341 RDSISEGRFSQFAQDFRARYF 361 TMalign alignment (TM-score: 0.50 Raw score:171.07) d1j93a_ 1 TQPLLLDAVRGK--------EV------ERP--PVWLMRQAGRYMK-------------- 30 ::: :: :::: :: ::: ::::::::::::: d1r5ya_ 1 RPR--FS-FSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADII 57 d1j93a_ 31 ----SYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFD 86 :::::::::::::::::::::::::::::::::::: d1r5ya_ 58 LGNT----------YHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQ---------- 97 d1j93a_ 87 IIKGKGPVIFDPLRTAADVEKVREF---IPEKSVPYVGEALTILRKEVNNQAAVLGFVGA 143 :: ::::::: :::: :::::::::::::: :::::::: d1r5ya_ 98 VM--LSLTKQS----------EEGVTFM---LSPERSIEIQHLLG-------SDIVMAFD 135 d1j93a_ 144 PFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADS--GA--QA 199 : : : : :: :: : : ::::::::::::::::::::::: :: :: d1r5ya_ 136 E-C--T-------P-YP--AT--P---S-RAASSMERSMRWAKRSRDAFDSRKEQAENAA 176 d1j93a_ 200 VQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG-------SGGLLER 252 :::::: :: : :::: :::::::::::: : ::::::::: ::::::: d1r5ya_ 177 LFGIQQ-GS-V----FENL-RQQSADALAEIG--F--DGYAVGGLAVGEGQDEMFRVLDF 225 d1j93a_ 253 LPLTGV--DVVSL--DWT-VDMADGRRRLGPNVAIQGNVDPG-VLF---G---------- 293 :::::: ::::: ::: :::::::::: :::::::::: ::: : d1r5ya_ 226 SVPMLPDDKPHYLMGVGKPDDIVGAVERG---IDMFDCVLPTRSGRNGQAFTWDGPINIR 282 d1j93a_ 294 ----------S-------KE-------------------------FI-TNRINDTVKKAG 310 : :: :: :::::::::::: d1r5ya_ 283 NARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRD 342 d1j93a_ 311 KGK----------------HILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 ::: d1r5ya_ 343 SISEGRFSQFAQDFRARYF------------------------------ 361 HHsearch alignment (Probability: 0.68 E-value:0.00) d1j93a_ 236 NLPLILYASGSGGLLERLPLTGVDVV 261 :::::::::::::::::::::::::: d1r5ya_ 233 DKPHYLMGVGKPDDIVGAVERGIDMF 258