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 | d1q7za2 | Cobalamin-dependent methionine synthase MetH, N-terminal domain | Homocysteine S-methyltransferase | 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 <-- 1.562 --> HitDALI alignment (Z-score: 16.7 Raw score:1861.30) d1j93a_ 1 tqpllLDAVRGKeVERPPVWLMRqAGRYMKSyQLLCekyplfRDRSENV----DLVVEIs 56 ::::::: :::::::::: ::::::: :::: ::::::: :::::: d1q7za2 1 --mrnRREVSKLlSERVLLLDGA-YGTEFMK-YGYD------DLPEELNikapDVVLKV- 49 d1j93a_ 57 LQPWKVFRPDGVILFSDILTPLSGmnIPFDiikgkgpvifdplrtaadvekvrefipeKS 116 :::::::::::::::::::::::: :::: :: d1q7za2 50 HRSYIESGSDVILTNTFGATRMKL--RKHG-------------------------ledKL 82 d1j93a_ 117 VPYVGEALTILRKEVNNqAAVLGFVGApfTLASyvveggssknftkikrlafaePKVLHA 176 ::::::::::::::::: ::::::::: :::: :::::: d1q7za2 83 DPIVRNAVRIARRAAGE-KLVFGDIGP--TGEL--------------------pYPLGST 119 d1j93a_ 177 LLQKFATSMAKYIRYQADSGAQAVQIFDSWAtelspvdfeefsLPYLKQIVDSVKLTHPN 236 ::::::::::::::::::::::::::::::: ::::::::::::::::: d1q7za2 120 LFEEFYENFRETVEIMVEEGVDGIIFETFSD------------ILELKAAVLAAREVSRD 167 d1j93a_ 237 LPLILYASG-----------SGGLLERLPLTGVDVVSLD-------WTVDMADGRRRLGp 278 ::::::::: ::::::::::::::::::: ::::::::::::: d1q7za2 168 VFLIAHMTFdekgrsltgtdPANFAITFDELDIDALGINcslgpeeILPIFQELSQYTD- 226 d1j93a_ 279 nVAIQGnvDPGV-----------lFGSKeFITNRINDTVKKAgkgkHILNlgHGIKvgtp 327 ::::: :::: :::: ::::::::::::: :::: :::: d1q7za2 227 -KFLVV-ePNAGkpivengktvypLKPH-DFAVHIDSYYELG---vNIFG--GCCG--tt 276 d1j93a_ 328 eENFAHFFEIAKGLRY-------- 343 ::::::::::::::: d1q7za2 277 pEHVKLFRKVLGNRKPlqrkkkri 300 FAST alignment (Normalized score: 9.30 Raw score:2985.00) d1j93a_ 1 TQPLLLDAVRGKE-----------VERPPVWLMRQAGRYMKSYQLLCEKYPLFR-----D 44 :::::::: ::::: :::: : d1q7za2 1 -------------MRNRREVSKLLSERVLLLD--GAYGT--EFMK---------YGYDDL 34 d1j93a_ 45 RSE----NVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLR 100 ::: :::::::::::::: ::::::::: :::: d1q7za2 35 PEELNIKAPDVVLKVHRSYIE-SGSDVILTN-TFGA------------------------ 68 d1j93a_ 101 TAADVEKVREFIPEKS--------------VPYVGEALTILRKEVNNQAAVLGFVGAPFT 146 :::::::::::::::: :::::::::: d1q7za2 69 ----------------TRMKLRKHGLEDKLDPIVRNAVRIARRAAG-EKLVFGDIGP--- 108 d1j93a_ 147 LASYVVEGGSSKNFTKIKRLAFAEPKVLHA-----------LLQKFATSMAKYIRYQADS 195 ::::::::::::::::::: d1q7za2 109 ------------------------------TGELPYPLGSTLFEEFYENFRETVEIMVEE 138 d1j93a_ 196 GAQAVQIFDSWATELSPVDFEEF----SLPYLKQIVDSVKLTHPNLPLILYAS------- 244 ::::::: ::::::::::::::::::::::::: d1q7za2 139 GVDGIIF----------------ETFSDILELKAAVLAAREVSRDVFLIAHM-TFDEKGR 181 d1j93a_ 245 -----GSGGLLERLPLTGVDVVSLDWTV----------DMADGRRRLGP-NVAIQGNVDP 288 :::::::::::::::::::: :::::::: :::: :::: d1q7za2 182 SLTGTDPANFAITFDELDIDALGIN---CSLGPEEILPIFQELSQY---TDKFL-VVEP- 233 d1j93a_ 289 GVL--------------FGSKEFITNRINDTVKKAGKGK---HILNLGHGIKVGT----- 326 :::::::::::::::: :::: d1q7za2 234 ---NAGKPIVENGKTVYPLKPHDFAVHIDSYYE------LGVNIFG---------GCCGT 275 d1j93a_ 327 PEENFAHFFEIAKGLRY-------------- 343 ::::::::::: d1q7za2 276 TPEHVKLFRKV------LGNRKPLQRKKKRI 300 TMalign alignment (TM-score: 0.62 Raw score:213.60) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSEN-VDLVVEISLQP 59 ::: ::: :::::::::::::: ::::: ::::::: :::::::: ::::::::::: d1q7za2 1 MRN-RRE-VSKLLSERVLLLDG-AYGTE--FMKYGYD---DLPEELNIKAPDVVLKVHRS 52 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 ::::::::::::::::::::: : ::: : :: ::::: d1q7za2 53 YIESGSDVILTNTFGATRMKL--R-KHG-------L---------------ED--KLDPI 85 d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 :::::::::::::: :::::::: :: :: :: ::: : ::: :: d1q7za2 86 VRNAVRIARRAAGE-KLVFGDIG---PT-GE------------LP-YPL--G-STL--FE 122 d1j93a_ 180 KFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPL 239 :::::::::::::::::::::::::::: : ::::::::::::: :::::: d1q7za2 123 EFYENFRETVEIMVEEGVDGIIFETFSD-------I--LELKAAVLAAREV---SRDVFL 170 d1j93a_ 240 ILYASG----------SG-GLLERLPLTGVDVVSLD-------WTVDMADGRRRLGPNVA 281 :::::: :: ::::::::::::::::: :::::::::::: : :: d1q7za2 171 IAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYT-D-KF 228 d1j93a_ 282 IQGNVDPGV----------LFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENF 331 ::::::::: ::::::::: :::::::::: ::::: :::: : :::: d1q7za2 229 LVVEPNAGKPIVENGKTVYPLKPHDFAV-HIDSYYELGV---NIFGG--CCGT-T-PEHV 280 d1j93a_ 332 AHFFEIAKGLRY-------- 343 :::::::::::: d1q7za2 281 KLFRKVLGNRKPLQRKKKRI 300 HHsearch alignment (Probability: 0.97 E-value:0.00) d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 :::::::::::::: :::::::::: ::::::::: ::: : d1q7za2 84 PIVRNAVRIARRAA-GEKLVFGDIG-PTGELPYPL---GST------------------L 120 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 ::::::::::::::::::::::: ::::::::: :::::::::::::::: d1q7za2 121 FEEFYENFRETVEIMVEEGVDGI-IFETFSDIL-----------ELKAAVLAAREVSRDV 168 d1j93a_ 238 PLILYAS-----------GSGGLLERLPLTGVDVVSLDWTVD-------MADGRRRLGPN 279 ::::::: :::::::::::::::::::::::: ::::::::::: d1q7za2 169 FLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKF 228 d1j93a_ 280 VAIQGNVDP-GVL------FGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFA 332 ::::::::: ::: ::::::::::::::::: :::::::::: ::::::: d1q7za2 229 LVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYEL---GVNIFGGCCG----TTPEHVK 281 d1j93a_ 333 HFFEIAKGLR 342 :::::::::: d1q7za2 282 LFRKVLGNRK 291