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 | d1nara_ | Seed storage protein | (Trans)glycosidases | 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 <-- 1.055 --> HitDALI alignment (Z-score: 10.2 Raw score:1202.10) d1j93a_ 1 tqpllldavrgkevERPPVWLMR-QAGRYMKSYqllcekyplfrdrsenvdlvveislQP 59 ::::::::: ::::::::: :: d1nara_ 1 --------------PKPIFREYIgVKPNSTTLH-------------------------DF 21 d1j93a_ 60 WKVFR-----pDGVILFSDILTplsgmnipfdiikgkgpvIFDPlrtaadvekvrefipe 114 ::::: ::::::::::: :::: d1nara_ 22 PTEIIntetleFHYILGFAIES-----------------yYESG---------kgtgtfe 55 d1j93a_ 115 ksvpyvgeALTILrKEVN---NQAAVLGFVG---apfTLASyvveggssknftkikrlaf 168 ::::: :::: :::::::::: :::: d1nara_ 56 eswdvelfGPEKV-KNLKrrhPEVKVVISIGgrgvntPFDP------------------- 95 d1j93a_ 169 aepkvlhALLQKFATSMAKYIRYQADSG-------AQAVQIFDSWAtelspvDFEEFSLP 221 ::::::::::::::::::::: ::::::::::: :::::::: d1nara_ 96 -------AEENVWVSNAKESLKLIIQKYsddsgnlIDGIDIHYEHI------RSDEPFAT 142 d1j93a_ 222 YLKQIVDSVKLT--HPNLPLILYASG-SGGLLER-LPLT--GVDVVSLDWT--------- 266 :::::::::::: :::::::::::: ::::::: :::: :::::::::: d1nara_ 143 LMGQLITELKKDddLNINVVSIAPSEnNSSHYQKlYNAKkdYINWVDYQFSnqqkpvstd 202 d1j93a_ 267 ----vDMADGRRRLGPnvAIQGNVDPG-----vlfgSKEFITNRINDTVKkaGKGKhILN 317 ::::::::::: ::::::::: :::::::::::::: :::: ::: d1nara_ 203 dafveIFKSLEKDYHP-hKVLPGFSTDpldtkhnkiTRDIFIGGCTRLVQ-tFSLP-GVF 259 d1j93a_ 318 LgHGIK--VGTP--eenfAHFFEIAKGLRY- 343 : :::: :::: :::::::::::: d1nara_ 260 F-WNANdsVIPKrdgdkpFIVELTLQQLLAa 289 FAST alignment (Normalized score: 5.71 Raw score:1797.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMR---QAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 57 ::::::: :::: d1nara_ 1 --------------PKPIFRE--YIGVKPN------------------------------ 14 d1j93a_ 58 QPWKVFRP------------------DGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPL 99 :::: d1nara_ 15 --------STTLHDFPTEIINTETLEFHYI------------------------------ 36 d1j93a_ 100 RTAADVEKVREFIPEKSVPY---------------------------VGEALTILRKEVN 132 :::::::::::: d1nara_ 37 --------------------LGFAIESYYESGKGTGTFEESWDVELFGPEKVKNLKRRH- 75 d1j93a_ 133 NQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA-------------LLQ 179 :::::::: ::: d1nara_ 76 PEVKVVIS------------------------------------IGGRGVNTPFDPAEEN 99 d1j93a_ 180 KFATSMAKYIRYQAD-------SGAQAVQIFDSWATELSPVD---FEEFSLPYLKQIVDS 229 ::::::::::::::: ::::::::::: ::::::::::::::: d1nara_ 100 VWVSNAKESLKLIIQKYSDDSGNLIDGIDIHYE---------HIRSDEPFATLMGQLITE 150 d1j93a_ 230 VKLTHPN-------LPLILYASGSGGLLERLPLT-------GVDVVSLDWTV-------- 267 :: ::::::: :::::::::: ::::::: d1nara_ 151 LK-----KDDDLNINVVSIAP--SENNSSHYQK-LYNAKKDYINWVDY----QFSNQQKP 198 d1j93a_ 268 ---------DMADGRRRLGPNVAIQGNVDPGVLF-----------------GSKEFITNR 301 :::::::::::: ::::::::: d1nara_ 199 VSTDDAFVEIFKSLEKDYHPH-------------KVLPGFSTDPLDTKHNKITRDIFIGG 245 d1j93a_ 302 INDTVKKAGKGKHILNLGHGIKVGT------------------------PEENFAHFFEI 337 :::::: ::::::::::: d1nara_ 246 CTRLVQ-------------------TFSLPGVFFWNANDSVIPKRDGDKPFIVELTLQQL 286 d1j93a_ 338 AKGLRY- 343 :: d1nara_ 287 LA----A 289 TMalign alignment (TM-score: 0.54 Raw score:186.71) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : : :::::::::::::::: : : :: : d1nara_ 1 ------P------K--PIFREYIGVKPNSTTL------------------H--D--FP-T 23 d1j93a_ 61 KVFRP---D-GVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIP--- 113 : ::: : ::::::::: : : : ::::: :: :::: : d1nara_ 24 E-IINTETLEFHYILGFAI--E----S-----------Y--YESGK-GT--GTFE-ESWD 59 d1j93a_ 114 EKSVP-YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPK 172 :: ::::::::::::::: ::::::: :: : ::::: :: : : d1nara_ 60 ---VELFGPEKVKNLKRRHPE--VKVVISI---GG--R-----GVNTP--FD--P---A- 96 d1j93a_ 173 VLHALLQKFATSMAKYIRYQA---DSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDS 229 ::::::::::::::::::::: :::: :::::::: :::::::::::::::::::: : d1nara_ 97 EENVWVSNAKESLKLIIQKYSDDSGNLI-DGIDIHYE-HIRSDEPFATLMGQLITELK-K 153 d1j93a_ 230 VKLTHPNLPLILYAS-GSGG-LLERLPLT--GVDVVSLDW--T---------V--DMADG 272 : ::::::::::::: :::: :::::::: ::::::::: : : ::::: d1nara_ 154 D-DDLNINVVSIAPSENNSSHYQKLYNAKKDYINWVDYQFSNQQKPVSTDDAFVEIFKSL 212 d1j93a_ 273 RRRLGPNVAIQGNVDP----G--VLFGSKEFITNRINDTVKKAGKGKHILNLGHG--IK- 323 :::::: ::::::::: : :::::: ::::::::::::::: ::::: :: :: d1nara_ 213 EKDYHP-HKVLPGFSTDPLDTKHNKITRD-IFIGGCTRLVQTFSL--PGVFF-WNANDSV 267 d1j93a_ 324 VGTP--EENFAHFFEIAKGLRY 343 :::: :::::::::::::::: d1nara_ 268 IPKRDGDKPFIVELTLQQLLAA 289 HHsearch alignment (Probability: 0.19 E-value:0.03) d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 ::::::::::::::::::: ::: ::::: ::::: :::::::::::: d1nara_ 65 PEKVKNLKRRHPEVKVVIS-IGG-RGVNT---------PFDPA-----EENVWVSNAKES 108 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN---- 236 :::::::::: ::::::::::: ::::::::::::: ::::::::::::::: d1nara_ 109 LKLIIQKYSD-DSGNLIDGIDI--HYEHIRSDEPFAT----LMGQLITELKKDDDLNINV 161 d1j93a_ 237 LPLILYASGSGGLLERLPLTG--VDVVSLDW------------TVDMA-DGRRRLGPNVA 281 ::::::::::::::::::::: :::::::: ::::: ::::::::::: d1nara_ 162 VSIAPSENNSSHYQKLYNAKKDYINWVDYQFSNQQKPVSTDDAFVEIFKSLEKDYHPHKV 221 d1j93a_ 282 IQGNV----DPGVLFGSKEFITNRINDTVKKAG-KGKHILNLGHGIKVGT 326 ::::: :::::::::::::::::::::::: :::::::::::::::: d1nara_ 222 LPGFSTDPLDTKHNKITRDIFIGGCTRLVQTFSLPGVFFWNANDSVIPKR 271