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 | d1b5ta_ | Methylenetetrahydrofolate reductase | FAD-linked oxidoreductase | 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 <-- 1.403 --> HitDALI alignment (Z-score: 9.1 Raw score:1078.80) d1j93a_ 1 tqpllldavrgkevERPPVWLMRqagrymksyqlLCEKyplfrdrsenvdlvveisLQPW 60 ::::::::: :::: :::: d1b5ta_ 1 --------------GQINVSFEF-------fpprTSEM--------------eqtlWNSI 25 d1j93a_ 61 KVFR---PDGVILFSDiLTPLsgmnipfdiikgkgpvifdplrtaadvekvrefipeksV 117 :::: ::::::::: :::: : d1b5ta_ 26 DRLSslkPKFVSVTYG-ANSG-------------------------------------eR 47 d1j93a_ 118 PYVGEALTILRKEVNnqAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhal 177 ::::::::::::::: :::::::::: d1b5ta_ 48 DRTHSIIKGIKDRTG--LEAAPHLTCI--------------------------------- 72 d1j93a_ 178 lqKFATSMAKYIRYQADSGAQAVQIFDSWatelspvdfeEFSLpyLKQIVDSVKLTHpNL 237 ::::::::::::::::::::::::::: :::: :::::::::::: :: d1b5ta_ 73 -dATPDELRTIARDYWNNGIRHIVALRGD---lppgsgkPEMY--ASDLVTLLKEVA-DF 125 d1j93a_ 238 PLILYASgSGGL---------LERLPLTG---VDVVSLDWT---vDMADGRRRLG---PN 279 ::::::: :::: :::::::: ::::::::: :::::::::: :: d1b5ta_ 126 DISVAAY-PEVHpeaksaqadLLNLKRKVdagANRAITQFFfdveSYLRFRDRCVsagID 184 d1j93a_ 280 VAIQGNVDPgVLFG--------------------------------SKEFITNRINDTVK 307 ::::::::: :::: :::::::::::::: d1b5ta_ 185 VEIIPGILP-VSNFkqakkfadmtnvripawmaqmfdgldddaetrKLVGANIAMDMVKI 243 d1j93a_ 308 K-aGKGKhILNLghgikvgtpeenFAHFFEIAKGLR---y 343 : :::: :::: :::::::::::: d1b5ta_ 244 LsrEGVK-DFHF-------ytlnrAEMSYAICHTLGvrpa 275 FAST alignment (Normalized score: 6.29 Raw score:1933.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSE---------NVDL 51 ::::::: :::: d1b5ta_ 1 --------------GQINVSF--------------------------EFFPPRTSEMEQT 20 d1j93a_ 52 VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF 111 :::::::: ::::::::::: d1b5ta_ 21 LWNSIDRL-SSLKPKFVSVT---------------------------------------- 39 d1j93a_ 112 IPEKS-------VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIK 164 ::::::::::::::: ::::::::: d1b5ta_ 40 -----YGANSGERDRTHSIIKGIKDRT--GLEAAPHLT---------------------- 70 d1j93a_ 165 RLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSL 220 ::::::::::::::::::::::: d1b5ta_ 71 ----------------CIDATPDELRTIARDYWNNGIRHIVAL----------------- 97 d1j93a_ 221 P-------------YLKQIVDSVKLTHPNLPLILYASG-------------SGGLLERLP 254 :::::::::::: ::::::::: ::::::::: d1b5ta_ 98 -RGDLPPGSGKPEMYASDLVTLLKEV-ADFDISVAA--YPEVHPEAKSAQADLLNLKRKV 153 d1j93a_ 255 LTGVDVVSLDWTV------DMADGRRRLG-----PNVAIQGNVDPGVLFG---------- 293 :::::::::: :::::::: ::::: d1b5ta_ 154 DAGANRAITQ---FFFDVESYLRFRDR--CVSAGIDVEI-----------IPGILPVSNF 197 d1j93a_ 294 -------------------------------SKEFITNRINDTVKKAGKGK------HIL 316 ::::::::::::::: ::: d1b5ta_ 198 KQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKI-----LSREGVKDF 252 d1j93a_ 317 NLGHGIKVGT-----PEENFAHFFEIAKGLRY------ 343 : ::::::::::: d1b5ta_ 253 H---------FYTLNRAEMSYAICHT------LGVRPA 275 TMalign alignment (TM-score: 0.50 Raw score:171.04) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::::::::: ::::: ::::::: d1b5ta_ 1 --------------GQINVSFEFFPPR----TSEME-----------------QTLWNSI 25 d1j93a_ 61 KVFR-P-D-GVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV 117 :::: : : :::::::::: :: :: d1b5ta_ 26 DRLSSLKPKFVSVTYGANS---------GE----------------------------RD 48 d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 ::: ::::::::::: :::::::: : :: d1b5ta_ 49 RTH-SIIKGIKDRTG--LEAAPHLT-C--ID----------------------------- 73 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWA-TE---LSPVDFEEFSLPYLKQIVDSVKLT 233 :::::::::::::::::::::::::::: : : :::: ::::::::::: d1b5ta_ 74 --ATPDELRTIARDYWNNGIRHIVALRGDLP-PGSG-----K-PEMY--ASDLVTLLKEV 122 d1j93a_ 234 HPNLPLILYAS-GSG-----G--LLERLPLT--G-VDVVSLDWT-V--DMADGRRRLG-- 277 :: :::::::: ::: : :::::::: : ::::::::: : :::::::::: d1b5ta_ 123 AD-FDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSA 181 d1j93a_ 278 -PNVAIQGNVDPGV---------------------------------LF-GSKEFITNRI 302 ::::::::::::: :: :::::::::: d1b5ta_ 182 GIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMV 241 d1j93a_ 303 NDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGL--RY 343 ::::::::: : ::: :::: : :::::::::::::: d1b5ta_ 242 KILSREGVK--D-FHF--YTLN-R-AEMSYAICHTLGVRPA-- 275 HHsearch alignment (Probability: 0.38 E-value:0.01) d1j93a_ 187 KYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGS 246 ::::::::::::::: : ::: ::::::::::::::::::::::::::::: d1b5ta_ 147 LNLKRKVDAGANRAI---------T-QFF--FDVESYLRFRDRCVSAGIDVEIIPGILPV 194 d1j93a_ 247 GGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLF-GSKEFITNRINDT 305 :::::::::::::::::: ::::::::: : :: :::::: ::::::::::::: d1b5ta_ 195 SNFKQAKKFADMTNVRIP-----AWMAQMFDG---L-DD-DAETRKLVGANIAMDMVKIL 244 d1j93a_ 306 VKKAGKGKHILNLGH 320 ::::::::::::::: d1b5ta_ 245 SREGVKDFHFYTLNR 259