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 | d1i60a_ | Hypothetical protein IolI | Xylose isomerase-like | 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 <-- 1.154 --> HitDALI alignment (Z-score: 10.7 Raw score:1239.10) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQ-AGRYMksyqllcekyplfrdrsenvdlvveISLQP 59 :::::::: ::::: ::::: d1i60a_ 1 ----------------MKLCFNEAtTLENS-------------------------NLKLD 19 d1j93a_ 60 WKVFR---PDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeks 116 ::::: ::::::::: d1i60a_ 20 LELCEkhgYDYIEIRTM---------------------------------------dklp 40 d1j93a_ 117 vpyvgEALTILRKEVN-NQAAV-LGFV-GAPFtlasyvveggssknftkikrlafaepkv 173 ::::::::::: ::::: :::: :::: d1i60a_ 41 eylkdHSLDDLAEYFQtHHIKPlALNAlVFFN---------------------------n 73 d1j93a_ 174 LHALLQKFATSMAKYIRYQADSG-AQAVQIFDSW-ateLSPVDFEEFSLPYLKQIVDSVk 231 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::::: d1i60a_ 74 RDEKGHNEIITEFKGMMETCKTLgVKYVVAVPLVteqkIVKEEIKKSSVDVLTELSDIA- 132 d1j93a_ 232 LTHPnLPLILYAS-------GSGGL-LERLPLT--GVDVVSLD-WTVD-----mADGRRR 275 :::: :::::::: ::::: ::::::: :::::::: :::: :::::: d1i60a_ 133 EPYG-VKIALEFVghpqctvNTFEQaYEIVNTVnrDNVGLVLDsFHFHamgsniESLKQA 191 d1j93a_ 276 lGPNVA-IQGNVD-------------PGVLfgskefitNRINDTVKKAG--KGKHILNLg 319 ::::: :::::: :::: ::::::::::: :::::::: d1i60a_ 192 -DGKKIfIYHIDDtedfpigfltdedRVWP----gqgaIDLDAHLSALKeiGFSDVVSV- 245 d1j93a_ 320 HGIKVGT----pEENFAHFFEIAK-GLRY---- 343 ::::::: :::::::::::: :::: d1i60a_ 246 ELFRPEYykltaEEAIQTAKKTTVdVVSKyfsm 278 FAST alignment (Normalized score: 3.29 Raw score:1015.00) d1j93a_ 1 TQPLLLDAVRGKEVERP-PVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVE----- 54 :::: d1i60a_ 1 -----------------MKLCF---------------------------------NEATT 10 d1j93a_ 55 ----ISLQPWK---VFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEK 107 ::::::: :::::::::: d1i60a_ 11 LENSNLKLDLELCEKHGYDYIEIR------------------------------------ 34 d1j93a_ 108 VREFIPEKS-------------VPYVGEALTILRKEVN-NQAAVLGFVGAPFTLASYVVE 153 ::::::::: ::::: d1i60a_ 35 ---------TMDKLPEYLKDHSLDDLAEYFQ-------THHIKP---------------- 62 d1j93a_ 154 GGSSKNFTKIKRLAFAE------------PKVLHALLQKFATSMAKYIRYQADSGAQAVQ 201 ::::::::::::::::::::: ::::::: d1i60a_ 63 -----------------LALNALVFFNNRDEKGHNEIITEFKGMMETCKT---LGVKYVV 102 d1j93a_ 202 IFDSWAT-------ELSPVDFEEFSLPYLKQIVDSVKLTH---PNLPLILYASGSGG--- 248 : :::::: ::::::::::::::: ::::::::: d1i60a_ 103 A------VPLVTEQKIVKEE----IKKSSVDVLTELSDI-AEPYGVKIALEF-----VGH 146 d1j93a_ 249 ------LLERLPLTG------------------------------------VDVVSLD-- 264 ::::::: ::::::: d1i60a_ 147 PQCTVNTFEQAYE--IVNTVNRDNVGLVLDSFHFHAMGSNIESLKQADGKKIFIYHIDDT 204 d1j93a_ 265 ------------------WTVDMADGRRRLGPN-------VAIQGN-VDPGVLFGSKEFI 298 ::::::::::: :::::: :::::::: :: d1i60a_ 205 EDFPIGFLTDEDRVWPGQGAIDLDAHLSA----LKEIGFSDVVSVELFRPEYYKL---TA 257 d1j93a_ 299 TNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY----------- 343 :::::::::: d1i60a_ 258 EEAIQTAKKT-----------------------------------TVDVVSKYFSM 278 TMalign alignment (TM-score: 0.54 Raw score:184.59) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLM-RQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 :::::: ::::: ::: ::::::: d1i60a_ 1 ----------------MKLCFNEATTLE--NSN--------------------LKLDLEL 22 d1j93a_ 60 WKVFRPDGVILFSDILTP--LSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV 117 :::::::::::::::::: :: d1i60a_ 23 CEKHGYDYIEIRTMDKLPEY--------------------------------------LK 44 d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 ::::::::::::::: ::::::::::::: : : : :: d1i60a_ 45 DHSLDDLAEYFQTHH-IKPLALNALVFFN-----------------N--R------D-EK 77 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATE--LSPVDFEEFSLPYLKQIVDSVKLTHP 235 :::::::::::::::::::::::::::::::: :::::::::::::::::::::: ::: d1i60a_ 78 GHNEIITEFKGMMETCKTLGVKYVVAVPLVTEQKIVKEEIKKSSVDVLTELSDIAE-PYG 136 d1j93a_ 236 NLPLILYASG------SG-GLL-ERLPLT-G-VDVVSL---DWT---VDMADGRRRLGPN 279 ::::::::: :: ::: :::::: : :::::: ::: :::::::: :::: d1i60a_ 137 -VKIALEFVGHPQCTVNTFEQAYEIVNTVNRDNVGLVLDSFHFHAMGSNIESLKQ-ADGK 194 d1j93a_ 280 VAIQGNVDPGV-----------LFGSKEFITNRINDTVKKAGK-GKH-ILNLGHGIKVGT 326 ::::::::::: ::::: ::::::::::::::: ::: :::: ::::::: d1i60a_ 195 KIFIYHIDDTEDFPIGFLTDEDRVWPG-QGAIDLDAHLSALKEIGFSDVVSV-ELFRPEY 252 d1j93a_ 327 --P----E-ENFAHFFEI-AKG-LRY 343 : : ::::::::: ::: ::: d1i60a_ 253 YKLTAEEAIQTAKKTTVDVVSKYFSM 278 HHsearch alignment (Probability: 0.83 E-value:0.00) d1j93a_ 186 AKYIRYQADSGAQAVQIFDS-WATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS 244 :::::::::::::::::::: :::::::::::::::::::::::::::: ::::::::: d1i60a_ 87 KGMMETCKTLGVKYVVAVPLVTEQKIVKEEIKKSSVDVLTELSDIAEPY--GVKIALEFV 144 d1j93a_ 245 G--------SGGLLERLPLTGVDVVSL--D------WTVDMADGRRRLGPNVAIQ---GN 285 : :::::::::::::::::: : ::::::::::::::::::: :: d1i60a_ 145 GHPQCTVNTFEQAYEIVNTVNRDNVGLVLDSFHFHAMGSNIESLKQADGKKIFIYHIDDT 204 d1j93a_ 286 V---------DPGVLFGSKEFITNRINDTVKKAGKGKHILN--LGHGIKVGTPEENFAHF 334 : ::::::::::::::::::::::::::::::: ::::::::::::::::: d1i60a_ 205 EDFPIGFLTDEDRVWPGQGAIDLDAHLSALKEIGFSDVVSVELFRPEYYKLTAEEAIQTA 264 d1j93a_ 335 FEIAKGL 341 ::::::: d1i60a_ 265 KKTTVDV 271