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 | d1i4na_ | 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 <-- 1.316 --> HitDALI alignment (Z-score: 10.6 Raw score:1192.00) d1j93a_ 1 --------------------------tqpLLLDAVrGKEVeRPPVWLMrQAGR------Y 28 :::::: :::: ::::::: :::: : d1i4na_ 1 rrlweiveakkkdileidgenlivqrrnhRFLEVL-SGKE-RVKIIAE-FKKAspsagdI 57 d1j93a_ 29 MKSYqllcekyplfrdrsenvdlvveiSLQPWKVFR--PDGVILFSDILTplsgmnipfd 86 :::: ::::::::: :::::::::::: d1i4na_ 58 NADA----------------------sLEDFIRMYDelADAISILTEKHY---------- 85 d1j93a_ 87 iikgkgpvifdplrtaadvekvrefipeksvpyVGEALTILRKEVNnqAAVLGFVGAPft 146 ::::::::::::: :::::::::: d1i4na_ 86 ------------------------------fkgDPAFVRAARNLTC--RPILAKDFYI-- 111 d1j93a_ 147 lasyvveggssknftkikrlafaepkvlhallqkfatsMAKYIRYQADSGAQAVQIFDSW 206 :::::::::::::::::::::: d1i4na_ 112 --------------------------------------DTVQVKLASSVGADAILIIARI 133 d1j93a_ 207 AtelspvdfeefSLPYLKQIVDSVKLThpNLPLILYASgSGGLLERLP-LTGVDVVSLDW 265 : ::::::::::::::: ::::::::: ::::::::: ::::::::::: d1i4na_ 134 L-----------TAEQIKEIYEAAEEL--GMDSLVEVH-SREDLEKVFsVIRPKIIGINT 179 d1j93a_ 266 ---------TVDMADGRRRLGPNVAIQGNVDPGvlfgskefITNRINDtVKKAGkgkHIL 316 :::::::::::::::::::::::: ::::::: ::::: ::: d1i4na_ 180 rdldtfeikKNVLWELLPLVPDDTVVVAESGIK--------DPRELKD-LRGKV---NAV 227 d1j93a_ 317 NlgHGIKvgTPEEnFAHFFEIAKGLRY 343 : :::: :::: ::::::::::::: d1i4na_ 228 L--VGTSimKAEN-PRRFLEEMRAWSE 251 FAST alignment (Normalized score: 6.47 Raw score:1897.00) d1j93a_ 1 TQPLLLDAVRG-----------------------------------KEVERPPVWLMRQA 25 :::::::::: d1i4na_ 1 -----------RRLWEIVEAKKKDILEIDGENLIVQRRNHRFLEVLSGKERVKIIA---- 45 d1j93a_ 26 GRYMKSYQLLCEKYPLFRDRSENVD----------------LVVEISLQPWKVFRPDGVI 69 ::::::::::: :::::: d1i4na_ 46 -------------------------EFKKASPSAGDINADASLEDFIRMYDE--LADAIS 78 d1j93a_ 70 LFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY--------VG 121 :: :: d1i4na_ 79 IL------------------------------------------------TEKHYFKGDP 90 d1j93a_ 122 EALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKF 181 :::::::::: ::::::::: d1i4na_ 91 AFVRAARNLT--CRPILAKDF--------------------------------------- 109 d1j93a_ 182 ATS--MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF--SLPYLKQIVDSVKLTHPNL 237 ::::::::::::::::::::: :::::::::::::: ::: d1i4na_ 110 ---YIDTVQVKLASSVGADAILIIAR-------------ILTAEQIKEIYEAAEE--LGM 151 d1j93a_ 238 PLILYASGSGGLLERLPL-TGVDVVSLDWTV-------------DMADGRRRLGPNVAIQ 283 ::::::: :::::::::: :::::::: :::::::::::::::: d1i4na_ 152 DSLVEVH-SREDLEKVFSVIRPKIIGI----NTRDLDTFEIKKNVLWELLPLVPDDTVVV 206 d1j93a_ 284 GNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI-------------KVGTPEE- 329 :::::: ::::::: :::: d1i4na_ 207 AESGIK--------DPRELKD------------------LRGKVNAVLVGTSIMKA---E 237 d1j93a_ 330 NFAHFFEIAKGLRY---- 343 :::::::::: d1i4na_ 238 NPRRFLEEMR----AWSE 251 TMalign alignment (TM-score: 0.48 Raw score:165.39) d1j93a_ 1 ---------------------------TQPLLLDAVRGKEVERPPVWLMRQAG-----RY 28 :::::::: : :::::::::::::: :: d1i4na_ 1 RRLWEIVEAKKKDILEIDGENLIVQRR-NHRFLEVL-S-GKERVKIIAEFKKASPSAGDI 57 d1j93a_ 29 MKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR--PDGVILFSDILTPLSGMNIPFD 86 :::: :: :::::::: ::::::::: : d1i4na_ 58 NADA---------------------SL-EDFIRMYDELADAISILTE--K---------- 83 d1j93a_ 87 IIKGKGP--VIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAP 144 : :: :: :::::::::: : :::::::::: d1i4na_ 84 H----YFKG-------------------------DP-AFVRAARNLT-C-RPILAKDFYI 111 d1j93a_ 145 FTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFD 204 :::::::::::::::::: : d1i4na_ 112 ----------------------------------------DTVQVKLASSVGADAILI-I 130 d1j93a_ 205 SWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLP-LTGVDVVSL 263 ::: :::::::::::::: :: :::::::: :::::::::: ::::::::: d1i4na_ 131 ARI----------LTAEQIKEIYEAAE-EL-GMDSLVEV-HSREDLEKVFSVIRPKIIGI 177 d1j93a_ 264 DW---------TVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKH 314 :: ::::::::::::::::::::::: : : :: ::::::::: : d1i4na_ 178 NTRDLDTFEIKKNVLWELLPLVPDDTVVVAESGI--K-D----PR-ELKDLRGKV----N 225 d1j93a_ 315 ILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 :::: ::::::::: ::::::::::::: d1i4na_ 226 AVLV--GTSIMKAEN-PRRFLEEMRAWSE 251 HHsearch alignment (Probability: 0.14 E-value:0.01) d1j93a_ 187 KYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGS 246 :::::::::::::::::: ::::::::::: ::::::::::: : ::::: d1i4na_ 114 VQVKLASSVGADAILIIA---RILTAEQIKEI--------YEAAEELGMDS--L-VEVHS 159 d1j93a_ 247 GGLLERLPL-TGVDVVSLD 264 ::::::::: ::::::::: d1i4na_ 160 REDLEKVFSVIRPKIIGIN 178