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 | d1piia1 | Indole-3-glycerophosphate synthase, IPGS | 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 <-- 1.788 --> HitDALI alignment (Z-score: 10.1 Raw score:1126.10) d1j93a_ 1 -----------------------------------tqpllLDAVrgkeVERPPVWLMrQA 25 :::: ::::::::: :: d1piia1 1 mqtvlakivadkaiwvearkqqqplasfqnevqpstrhfyDALQ----GARTAFILEcKK 56 d1j93a_ 26 GR-----YMKSyqllcekyplfrdrsenvdlvveislqpWKVF--RPDGVI-LFSDiltp 77 :: :::: :::: :::::: :::: d1piia1 57 ASpskgvIRDD----------------------fdpariAAIYkhYASAISvLTDE---- 90 d1j93a_ 78 lsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyVGEALTILRKEVnnQAAV 137 :::::::::::: :::: d1piia1 91 -------------------------------------kyfqgSFNFLPIVSQIA--PQPI 111 d1j93a_ 138 LGFVGapftlasyvveggssknftkikrlafaepkvlhallqkfatSMAKYIRYQADSGA 197 ::::: :::::::::::::: d1piia1 112 LCKDF----------------------------------------iIDPYQIYLARYYQA 131 d1j93a_ 198 QAVQIFDSWAtelspvdfeefSLPYLKQIVDSVKLthPNLPLILYASgSGGLLERLPLTG 257 :::::::::: :::::::::::::: :::::::::: :::::::::::: d1piia1 132 DACLLMLSVL-----------DDDQYRQLAAVAHS--LEMGVLTEVS-NEEEQERAIALG 177 d1j93a_ 258 VDVVSLDWT---------vDMADGRRRLGPNVAIQGNVDPGvlfgskefITNRINDTVKK 308 ::::::::: :::::::::::::::::::::: ::::::::::: d1piia1 178 AKVVGINNRdlrdlsidlnRTRELAPKLGHNVTVISESGIN--------TYAQVRELSHF 229 d1j93a_ 309 AgkgkHILNL-ghgikvgtpeENFAHFFEiakglry 343 : ::::: :::::::: d1piia1 230 A----NGFLIgsalmahddlhAAVRRVLL------- 254 FAST alignment (Normalized score: 6.81 Raw score:2010.00) d1j93a_ 1 TQPLLLDAVRGKEV---------------------------------------------E 15 : d1piia1 1 --------------MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGA 46 d1j93a_ 16 RPPVWLMRQAG----------RYMKSYQLLCEKYPLFRDRSENVD--LVVEISLQPWKVF 63 :::::: :::: :::::::::: d1piia1 47 RTAFIL-----ECKKASPSKGVIRD--------------------DFDPARIAAIYK--- 78 d1j93a_ 64 -RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY--- 119 :::::::: d1piia1 79 HYASAISVL------------------------------------------------TDE 90 d1j93a_ 120 -----VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVL 174 :::::::::::: ::::::::: d1piia1 91 KYFQGSFNFLPIVSQIA--PQPILCKDF-------------------------------- 116 d1j93a_ 175 HALLQKFATS--MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF--SLPYLKQIVDSV 230 ::::::::::::::::::::: :::::::::::: d1piia1 117 ----------IIDPYQIYLARYYQADACLLMLS-------------VLDDDQYRQLAAVA 153 d1j93a_ 231 KLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTV------------DMADGRRRLGP 278 :: :::::::::: ::::::::::::::::::: ::::::::::: d1piia1 154 HS--LEMGVLTEVS-NEEEQERAIALGAKVVGIN---NRDLRDLSIDLNRTRELAPKLGH 207 d1j93a_ 279 NVAIQGNVDPGVLFGSKEF--ITNRINDTVKKAGKGKHILNLGHGIKVGT---------- 326 :::: ::::: ::::::::::: d1piia1 208 NVTV--ISESG--------INTYAQVRELSHF------------------ANGFLIGSAL 239 d1j93a_ 327 -----PEENFAHFFEIAKGLRY- 343 ::::::::: d1piia1 240 MAHDDLHAAVRRVL--------L 254 TMalign alignment (TM-score: 0.47 Raw score:162.17) d1j93a_ 1 -----------------------------------TQPLLLDAVRGKEVERPPVWLMRQA 25 :::::::: : :: :::::::::: d1piia1 1 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPS-TRHFYDAL-Q-GA-RTAFILECKK 56 d1j93a_ 26 G-----RYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR-PD-GVILFSDILTPL 78 : :::::: : ::::::::: :: :::::::: d1piia1 57 ASPSKGVIRDDF---------------------D-PARIAAIYKHYASAISVLTDE---- 90 d1j93a_ 79 SGMNIPFDIIKGKGP--VIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAA 136 : :: :: :::::::::: : :: d1piia1 91 --------K----YFQG-------------------------SF-NFLPIVSQIA-P-QP 110 d1j93a_ 137 VLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSG 196 :::::::: :::::::::::: d1piia1 111 ILCKDFII----------------------------------------DPYQIYLARYYQ 130 d1j93a_ 197 AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLT 256 ::::::::: : :::::::::::::: :: :::::::: :::::::::::: d1piia1 131 ADACLLMLS-V----------LDDDQYRQLAAVAH-SL-EMGVLTEV-SNEEEQERAIAL 176 d1j93a_ 257 GVDVVSLDW--------T-VDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVK 307 ::::::::: : :::::::::::::::::::::: : :::::::::: d1piia1 177 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGI--N------TYAQVRELSH 228 d1j93a_ 308 KAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 :: ::::: :::::: ::::::::::::: d1piia1 229 FA----NGFLI--GSALMA-HDDLHAAVRRVLL--- 254 HHsearch alignment (Probability: 0.20 E-value:0.01) d1j93a_ 189 IRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGG 248 :::::::::::::: ::::::::::::: ::::::::::::: :::::: d1piia1 123 IYLARYYQADACLL---MLSVLDDDQYRQL--------AAVAHSLEMGVLT---EVSNEE 168 d1j93a_ 249 LLERLPLTGVDVVSLDWT------VDMADGR---RRLGPNVAIQGNVDPGVLFGSKEFIT 299 :::::::::::::::::: ::::::: :::::::::::: :::::::::: d1piia1 169 EQERAIALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISE----SGINTYAQVR 224 d1j93a_ 300 NRINDTVKKAGKGKHILNLGHGIKVGT-PEENFAHF 334 : :::: :::::: :::::::: :::::::: d1piia1 225 E-----LSHF-ANGFLI--GSALMAHDDLHAAVRRV 252