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 | d1vc4a_ | 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 <-- 1.358 --> HitDALI alignment (Z-score: 11.0 Raw score:1233.40) d1j93a_ 1 --------------------------------tQPLLLDAVRgkeVERPPVWLMrQAGR- 27 ::::::::: ::::::::: :::: d1vc4a_ 1 mrpdlsrvpgvlgeiarkrasevapyplpeppsVPSFKEALL---RPGLSVIAE-VKRQs 56 d1j93a_ 28 -----YMKSyqllcekyplfrdrsenvdlvveISLQPWKVFR---PDGVILFSDILTpls 79 :::: :::::::::: :::::::::::: d1vc4a_ 57 pseglIREV-----------------------DPVEAALAYArggARAVSVLTEPHR--- 90 d1j93a_ 80 gmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyVGEALTILRKEVnnQAAVLG 139 :::::::::::: :::::: d1vc4a_ 91 -------------------------------------fggSLLDLKRVREAV--DLPLLR 111 d1j93a_ 140 FVGAPftlasyvveggssknftkikrlafaepkvlhallqkfatsMAKYIRYQADSGAQA 199 ::::: ::::::::::::::: d1vc4a_ 112 KDFVV----------------------------------------DPFMLEEARAFGASA 131 d1j93a_ 200 VQIFDSWatelspvdfeefSLPYLKQIVDSVKLTHpnLPLILYASgSGGLLERLPLTGVD 259 ::::::: :::::::::::::::: :::::::: :::::::::::::: d1vc4a_ 132 ALLIVAL------------LGELTGAYLEEARRLG--LEALVEVH-TERELEIALEAGAE 176 d1j93a_ 260 VVSLDW---------TVDMADGRRRLG---PNVAIQGNVDPGvlfgskefITNRINDTVK 307 :::::: :::::::::::: :::::::::::: :::::::::: d1vc4a_ 177 VLGINNrdlatlhinLETAPRLGRLARkrgFGGVLVAESGYS--------RKEELKALEG 228 d1j93a_ 308 KAgkgkHILNLghGIKVgTPEEnFAHFFEIAKGlry 343 :: ::::: :::: :::: :::::::::: d1vc4a_ 229 LF----DAVLI--GTSLmRAPD-LEAALRELVG--- 254 FAST alignment (Normalized score: 6.61 Raw score:1951.00) d1j93a_ 1 TQPLLLDAVRGK-----------------------------------------EVERPPV 19 ::::::: d1vc4a_ 1 ------------MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPSVPSFKEALLRPGLSV 48 d1j93a_ 20 WLMRQAGRYMKSYQLLCEKYPLFRDRSENVD-----------LVVEISLQPWKVFRPDGV 68 :: :::: :::::::::::: ::::: d1vc4a_ 49 IA-EVKR------------------------QSPSEGLIREVDPVEAALAYARG-GARAV 82 d1j93a_ 69 ILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY--------V 120 ::: : d1vc4a_ 83 SVL------------------------------------------------TEPHRFGGS 94 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 ::::::::::: ::::::::: d1vc4a_ 95 LLDLKRVREAV--DLPLLRKDF-------------------------------------- 114 d1j93a_ 181 FATS--MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFS-LPYLKQIVDSVKLTHPNL 237 :::::::::::::::::::::: ::::::::::::: ::: d1vc4a_ 115 ----VVDPFMLEEARAFGASAALLIVAL-------------LGELTGAYLEEARR--LGL 155 d1j93a_ 238 PLILYASGSGGLLERLPLTGVDVVSLDWTV------------DMADGRRRLG-----PNV 280 ::::::: ::::::::::::::::::: :::::::: ::: d1vc4a_ 156 EALVEVH-TERELEIALEAGAEVLGIN---NRDLATLHINLETAPRLGRL--ARKRGFGG 209 d1j93a_ 281 AIQGNVDPGVLFGSKEF-------ITNRINDTVKKAGKGKHILNLGHGI---------KV 324 :: ::::::::::: :: d1vc4a_ 210 VL---------------VAESGYSRKEELKALEGL--------------FDAVLIGTSLM 240 d1j93a_ 325 GT--PEENFAHFFEIAKGLRY-- 343 :: :::::::: d1vc4a_ 241 RAPDLEAALREL---------VG 254 TMalign alignment (TM-score: 0.48 Raw score:163.98) d1j93a_ 1 ---------------------------------TQPLLLDAVRGKEVERPPVWLMRQAGR 27 :::::::: : ::::::::: :::: d1vc4a_ 1 MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPS-VPSFKEAL-L--RPGLSVIAE-VKRQ 55 d1j93a_ 28 -----YMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR---PDGVILFSDILTPLS 79 ::::: : ::::::::: ::::::::: : d1vc4a_ 56 SPSEGLIREV---------------------D-PVEAALAYARGGARAVSVLTE--P--- 88 d1j93a_ 80 GMNIPFDIIKGKGP--VIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAV 137 : :: :: :::::::::: : ::: d1vc4a_ 89 -------H----RFGG-------------------------SL-LDLKRVREAV-D-LPL 109 d1j93a_ 138 LGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGA 197 ::::::: ::::::::::::: d1vc4a_ 110 LRKDFVV----------------------------------------DPFMLEEARAFGA 129 d1j93a_ 198 QAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTG 257 :::::::: : :::::::::::::::: ::::::: ::::::::::::: d1vc4a_ 130 SAALLIVA-L-----------LGELTGAYLEEARRLG--LEALVEV-HTERELEIALEAG 174 d1j93a_ 258 VDVVSL-D---------W-TVDM-ADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDT 305 :::::: : : :::: ::::::::::::::::::: : :::::::: d1vc4a_ 175 AEVLGINNRDLATLHINLETAPRLGRLARKRGFGGVLVAESGY--S------RKEELKAL 226 d1j93a_ 306 VKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 :::: ::::: :::: ::::::::::::::: d1vc4a_ 227 EGLF----DAVLI--GTSL-MRAPDLEAALRELVG--- 254 HHsearch alignment (Probability: 0.58 E-value:0.01) d1j93a_ 246 SGGLLERLPLTGVDVVSL 263 :::::::::::::::::: d1vc4a_ 163 TERELEIALEAGAEVLGI 180