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 | d1q7za1 | Cobalamin-dependent methionine synthase MetH, C-terminal domain | Dihydropteroate synthetase-like | 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 <-- 1.022 --> HitDALI alignment (Z-score: 11.0 Raw score:1239.60) d1j93a_ 1 -------TQPLLldavrgkeveRPPVWLMRQagrymksyqllcekyPLFRDRS--ENVDL 51 ::::: ::::::::: ::::::: ::::: d1q7za1 1 favsspsKLVTF---------dHFVVIGERI----------npagrKKLWAEMqkGNEEI 41 d1j93a_ 52 VVEISLQPWKvFRPDGVILFSDiLTPLsgmnipfdiikgkgpvifdplrtaadvekvref 111 :::::::::: ::::::::::: :::: d1q7za1 42 VIKEAKTQVE-KGAEVLDVNFG-IESQ--------------------------------- 66 d1j93a_ 112 ipekSVPYVGEALTILRKEVNnqAAVLGFVGapftlasyvveggssknftkikrlafaep 171 ::::::::::::::::: :::::::: d1q7za1 67 ---iDVRYVEKIVQTLPYVSN--VPLSLDIQ----------------------------- 92 d1j93a_ 172 kvlhallqkfatsMAKYIRYQADSG--aQAVQIFDswatelspvdfeefsLPYLKQIVDS 229 :::::::::::: ::::::: :::::::::: d1q7za1 93 -------------NVDLTERALRAYpgrSLFNSAK--------------vDEEELEMKIN 125 d1j93a_ 230 VKLTHpNLPLILYAS---------gSGGLLERLPLTG-------VDVVSLDWT------- 266 ::::: ::::::::: :::::::::::: ::::::::: d1q7za1 126 LLKKY-GGTLIVLLMgkdvpksfeeRKEYFEKALKILerhdfsdRVIFDPGVLplgaegk 184 d1j93a_ 267 -vDMADGRRRL-GPNVAIQGNV-DPGV-lFGSKEFITNRINDTVKKAgkgkHILNLghgi 322 ::::::::: :::::::::: :::: :::::::::::::::::: ::::: d1q7za1 185 pvEVLKTIEFIsSKGFNTTVGLsNLSFglPDRSYYNTAFLVLGISKG---lSSAIM---- 237 d1j93a_ 323 kvgtpeenFAHFFEIAKGLRY------ 343 ::::::::::::: d1q7za1 238 -----nplDETLMKTLNATLVilekke 259 FAST alignment (Normalized score: 5.39 Raw score:1606.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1q7za1 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 d1q7za1 1 ------------------------------------------------------------ 1 d1j93a_ 121 GEALTILRKEVNN-------------QAAVLGFVGAPFT--LASYVVEGGSSKNFTKIKR 165 ::::::: :::: d1q7za1 1 -------------FAVSSPSKLVTFDHFVVIGE------RINPAG--------------- 26 d1j93a_ 166 LAFAEPKVLHALLQK-----------FATSMAKYIRYQADSGAQAVQIFDSWATELSPVD 214 ::::::::::::::::::::::::: :::: d1q7za1 27 ---------------RKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFG-----IESQ 66 d1j93a_ 215 FEEF-SLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDV--------VSLDW 265 :::::::::::::::: ::::::::: :::::::::: ::::: d1q7za1 67 ----IDVRYVEKIVQTLPYVS-NVPLSLDIQ-NVDLTERALR-----AYPGRSLFNSAKV 115 d1j93a_ 266 TV---DMADGRRRLG---PNVAIQGNVDPGVLF-------GSKEFITNRINDTVKKA--- 309 :::::::: :::::::: :::::::::::::::: d1q7za1 116 --DEEELEMKINL--LKKYGGTLIVL-------LMGKDVPKSFEERKEYFEKALKI-LER 163 d1j93a_ 310 --GKGKHILNLGHGIK------VGTPEENFAHFFEIAKGLRY------------------ 343 ::::::::: ::::::::::::::::: d1q7za1 164 HDFSDRVIFDP-----GVLPLGAEGKPVEVLKTIEFISS---KGFNTTVGLSNLSFGLPD 215 d1j93a_ 344 -------------------------------------------- 344 d1q7za1 216 RSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKE 259 TMalign alignment (TM-score: 0.50 Raw score:171.90) d1j93a_ 1 -TQP---LLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEIS 56 ::: ::::: : ::::::::::::: :: :: : :::::::::::::: d1q7za1 1 FAVSSPSKLVTF-----D-HFVVIGERINPAG---RK-KL----W-AEMQKGNEEIVIKE 45 d1j93a_ 57 LQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS 116 ::::::::::::::::: :: ::: : d1q7za1 46 AKTQVEKGAEVLDVNFG-IE-SQI-----------------------------------D 68 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 :::::::::::::::: :::::::: d1q7za1 69 VRYVEKIVQTLPYVSN--VPLSLDIQ---------------------------------- 92 d1j93a_ 177 LLQKFATSMAKYIRYQADSGA--QAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTH 234 :: ::::::::::: ::::::: :::::::::::::::: d1q7za1 93 -------NV-DLTERALRAYPGRSLFNSAK--------------VDEEELEMKINLLKKY 130 d1j93a_ 235 PNLPLILYAS---GSG---GLLERL--PL-TG-------VDVVSLDW--------T-VDM 269 ::::::::: ::: :::::: :: :: :::::::: : ::: d1q7za1 131 -GGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVL 189 d1j93a_ 270 ADGRRRLGPNVAIQGNV--DP----GVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI- 322 ::::::::::::::::: :: ::::: :: ::::::::::: ::::: : d1q7za1 190 KTIEFISSKGFNTTVGLSNLSFGLPDRSYY---NT-AFLVLGISKGL---SSAIM---NP 239 d1j93a_ 323 KVGTPEENFAHFFEIAKG--LRY- 343 :::::::::::::: ::: d1q7za1 240 ----LDETLMKTLNATLVILEKKE 259 HHsearch alignment (Probability: 0.96 E-value:0.00) d1j93a_ 173 VLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKL 232 ::::::::::::::::::::::::::::::: ::::::::::: :::::::::: d1q7za1 30 LWAEMQKGNEEIVIKEAKTQVEKGAEVLDVN----FGIESQIDVRY----VEKIVQTLPY 81 d1j93a_ 233 THPNLPLILYASGSGGLLERLPL-TGVDVVS---LD-WTV-DMADGRRRLGPNVAIQGNV 286 :: :::::::::::::::::::: ::::::: :: ::: :::::::::::::::::: d1q7za1 82 VS-NVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLM- 139 d1j93a_ 287 DPGVLFGSKEFITNRINDTVKKAGKGK----HILNLGHGIKVGTPEENFAHFFEIAKGL 341 :::::::::::::::::::::::::: :::::::::: :::::::: :::::::: d1q7za1 140 -GKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPL-GAEGKPVE-VLKTIEFI 195