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 | d1geha1 | Ribulose 1,5-bisphosphate carboxylase-oxygenase | RuBisCo, C-terminal domain | 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 <-- 1.074 --> HitDALI alignment (Z-score: 12.5 Raw score:1438.90) d1j93a_ 1 -----------TQPLlldavrgkeVERPPVWLmRQAGrymksyqllcekyplfrDRSEnV 49 :::: :::::::: :::: :::: : d1geha1 1 dgpafgiegvrKMLE--------iKDRPIYGV-VPKP----------------kVGYS-P 34 d1j93a_ 50 DLVVEISLQPWKvFRPDGVIL-fsDILTplsgmnipfdiikgkgpvifdplrtaadvekv 108 :::::::::::: :::::::: :::: d1geha1 35 EEFEKLAYDLLS-NGADYMKDdenLTSP-------------------------------- 61 d1j93a_ 109 refipekSVPYVGEALTILRKEVN----NQAAVLGFVGapftlasyvveggssknftkik 164 ::::::::::::::::: :::::::::: d1geha1 62 ----wynRFEERAEIMAKIIDKVEnetgEKKTWFANIT---------------------- 95 d1j93a_ 165 rlafaepkvlhallqkFATSMAKYIRYQADSGAQAVQIFDSWAtelspvdfeefSLPYLK 224 ::::::::::::::::::::::::::: :::::: d1geha1 96 ---------------aDLLEMEQRLEVLADLGLKHAMVDVVIT-----------GWGALR 129 d1j93a_ 225 QIVDSVKLthPNLPLILYASG-------------SGGLLERLPLTGVDVVSLDW----tv 267 :::::::: ::::::::::: :::::::::::::::::::: d1geha1 130 YIRDLAAD--YGLAIHGHRAMhaaftrnpyhgisMFVLAKLYRLIGIDQLHVGTaeggkw 187 d1j93a_ 268 DMADGRRRLGP---------------------NVAIQGNVDPgvlfgskefITNRINDTV 306 ::::::::::: :::::::::: ::::::::: d1geha1 188 DVIQNARILREshykpdendvfhleqkfysikAAFPTSSGGL---------HPGNIQPVI 238 d1j93a_ 307 KKAGKGkHILNLghgikvgTPEE----NFAHFFEIAKGLR-------------------- 342 :::::: ::::: :::: ::::::::::::: d1geha1 239 EALGTD-IVLQL--gggtlGHPDgpaaGARAVRQAIDAIMqgipldeyakthkelarale 295 d1j93a_ 343 ------y 343 d1geha1 296 kwghvtp 302 FAST alignment (Normalized score: 3.86 Raw score:1242.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD---------- 50 d1geha1 1 --------------------------------------------------DGPAFGIEGV 10 d1j93a_ 51 ------------------------------------------------------LVVEIS 56 :::::: d1geha1 11 RKMLEIKDRPIYGVVPKPKVGYSPEEFEKLAYDLLSNGADYMKDDENLTSPWYNRFEERA 70 d1j93a_ 57 LQPWKVFRP------------DGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAAD 104 ::::: :::::: d1geha1 71 EIMAK----IIDKVENETGEKKTWFAN--------------------------------- 93 d1j93a_ 105 VEKVREFIPEKS----VPYVGEALTILRKEVNNQAA---VLGFVGAPFTLASYVVEGGSS 157 ::::::::::::: :::::: d1geha1 94 ------------ITADLLEMEQRLEVLAD-------LGLKHAMVD--------------- 119 d1j93a_ 158 KNFTKIKRLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQIFDSWATE---L 210 :::::::::::::::: ::::::::::: : d1geha1 120 -----------------------VVITGWGALRYIRDLAADYG-LAIHGHRAMHA-AFTR 154 d1j93a_ 211 SPVDFEE---FSLPYLKQIVDSVKLTHPNLP---LILYASGS---GGLLERLPLTGV--- 258 ::: ::::::::::: ::::: ::::::::: d1geha1 155 NPY----HGISMFVLAKLYRL----------IGIDQLHV---GTAEGGKWDVIQ---NAR 194 d1j93a_ 259 --------------------------DVVSLDWTV-------DMADGRRRLGPNVAIQGN 285 ::::: ::::::::::::::: d1geha1 195 ILRESHYKPDENDVFHLEQKFYSIKAAFPTS----SGGLHPGNIQPVIEALGTDIVL--- 247 d1j93a_ 286 VDP----GVLFG---SKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIA 338 ::::: ::::::::::::::: d1geha1 248 ---QLGGGTLGHPDGPAAGARAVRQAIDAI------------------------------ 274 d1j93a_ 339 KGLRY---------------------------- 343 d1geha1 275 -----MQGIPLDEYAKTHKELARALEKWGHVTP 302 TMalign alignment (TM-score: 0.46 Raw score:159.35) d1j93a_ 1 ----TQPLLLDAVR---GKEVERPPVWLMRQAGRY-MKSYQLLC---------------- 36 :::::::: ::::::::::::::: ::::::: d1geha1 1 DGPA--FGIEGVRKMLE---IKDRPIYGVVPKPKVG-YSPEEFEKLAYDLLSNGADYMKD 54 d1j93a_ 37 -----EKYPLFRDRSENVDLVVEISLQPW-KV--FRPDGVILFSDILTPLSGMNIPFDII 88 :::::::: ::::::::::: :: :::::::::::: : : d1geha1 55 DENLT----SPWYNRFE-ERAEIMAKIIDKVENETGEKKTWFANIT-A-D---------- 97 d1j93a_ 89 KGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLA 148 ::: ::::::::::::: :::::::: :: d1geha1 98 ----------------------LLE--MEQRLEVLADLGL--------KHAMVDVV--IT 123 d1j93a_ 149 SYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWAT 208 :::::::::::::::::: ::::::::: d1geha1 124 --------------------------------GWGALRYIRDLAADYGLA-IHGHRAMHA 150 d1j93a_ 209 EL--SPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGS--GG-LLERLPLTGVDV--- 260 :: ::::::: :::::::::::: ::::::::: :: ::::::: :::: d1geha1 151 AFTRNPYHGIS-MFVLAKLYRLIG-------IDQLHVGTAEGGKWDVIQNAR-ILRESHY 201 d1j93a_ 261 --------VSLDWTVDMADGRRR-LGP------NVAIQGNVDPGVLFGSKEFITNRINDT 305 : :: :::::::::: : : :::::: d1geha1 202 KPDENDVF--------------HL-EQKFYSIKAAFPTSSGGL-H-------P-GNIQPV 237 d1j93a_ 306 VKKAGKGKHILNLGHGIKVGT---PE-ENFAHFFEIAKG-LRY----------------- 343 ::::: :::: :: ::::::: :: :::::::::::: ::: d1geha1 238 IEALG-TDIV-LQ-LGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARAL 294 d1j93a_ 344 -------- 344 d1geha1 295 EKWGHVTP 302 HHsearch alignment (Probability: 0.39 E-value:0.02) d1j93a_ 113 PEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPK 172 :::::::::::::::::::::: ::: ::: :::::: d1geha1 66 FEERAEIMAKIIDKVENETGEK-KTW------------FAN-------------ITADLL 99 d1j93a_ 173 VLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKL 232 ::: :::::::::::::::::::::::::::::::: :: d1geha1 100 ---EME--------QRLEVLADLGLKHAMVDVVITGWGALRYIRDL--------AA---- 136 d1j93a_ 233 THPNLPLILYASGSGG-------------LLERLPLTGVDVVSLDWTVDMA----D---- 271 ::::::::::::::: :::::::::::::::::::::: : d1geha1 137 -DYGLAIHGHRAMHAAFTRNPYHGISMFVLAKLYRLIGIDQLHVGTAEGGKWDVIQNARI 195 d1j93a_ 272 GRRR-LGP--NVA-----IQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI- 322 :::: ::: ::: :::::::::::::::::::::::::::::: :::::::::: d1geha1 196 LRESHYKPDENDVFHLEQKFYSIKAAFPTSSGGLHPGNIQPVIEALGT-DIVLQLGGGTL 254 d1j93a_ 323 -KVGTPEENFAHFFEIAK 339 ::::::::::::::::: d1geha1 255 GHPDGPAAGARAVRQAID 272