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 | d1v93a_ | 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 <-- 1.388 --> HitDALI alignment (Z-score: 10.8 Raw score:1265.60) d1j93a_ 1 tqplLLDAVrgKEVERPPVWLMRqagrymKSYQllcekyplfrdrsenvdlvveisLQPW 60 ::::: :::::::::::: :::: :::: d1v93a_ 1 --mkIRDLL--KARRGPLFSFEFfppkdpEGEE---------------------alFRTL 35 d1j93a_ 61 KVFR---PDGVILFSDILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipeksV 117 :::: ::::::::::::: : d1v93a_ 36 EELKafrPAFVSITYGAMGS--------------------------------------tR 57 d1j93a_ 118 PYVGEALTILRKEVnnqAAVLGFVGAPFtlasyvveggssknftkikrlafaepkvlhal 177 :::::::::::::: ::::::::::: d1v93a_ 58 ERSVAWAQRIQSLG---LNPLAHLTVAG-------------------------------- 82 d1j93a_ 178 lqkFATSMAKYIRYQADSGAQAVQIFDSW-atelspvdfeefslPYLKQIVDSVKLTHPN 236 :::::::::::::::::::::::::: :::::::::::::::: d1v93a_ 83 --qSRKEVAEVLHRFVESGVENLLALRGDpprgervfrphpegfRYAAELVALIRERYGD 140 d1j93a_ 237 -LPLILYAsGSGG---------LLERLPLTG---VDVVSLDWT---vDMADGRRRLG--- 277 ::::::: :::: ::::::::: ::::::::: :::::::::: d1v93a_ 141 rVSVGGAA-YPEGhpesesleaDLRHFKAKVeagLDFAITQLFfnnaHYFGFLERARrag 199 d1j93a_ 278 PNVAIQGNVDPG----------------------------------vlFGSKEFITNRIN 303 :::::::::::: :::::::::::: d1v93a_ 200 IGIPILPGIMPVtsyrqlrrftevcgasipgpllaklerhqddpkavlEIGVEHAVRQVA 259 d1j93a_ 304 DTVKKAGkgkHILNLghgikvgtpEENFAHFFEIAkglry 343 ::::::: ::::: ::::::::::: d1v93a_ 260 ELLEAGV---EGVHF----ytlnkSPATRMVLERLglrpa 292 FAST alignment (Normalized score: 6.50 Raw score:2058.00) d1j93a_ 1 TQPLLLDAVR------GKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSE------- 47 ::::::::::: d1v93a_ 1 ----------MKIRDLLKARRGPLFSF--------------------------EFFPPKD 24 d1j93a_ 48 --NVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADV 105 :::::::::::: ::::::::::: d1v93a_ 25 PEGEEALFRTLEEL-KAFRPAFVSIT---------------------------------- 49 d1j93a_ 106 EKVREFIPEKS-------VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 ::::::::::::: :::::::::: d1v93a_ 50 -----------YGAMGSTRERSVAWAQRIQS---LGLNPLAHLT---------------- 79 d1j93a_ 159 NFTKIKRLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQIFDSWATELSPVD 214 :::::::::::::::::::::::: d1v93a_ 80 ----------------------VAGQSRKEVAEVLHRFVESGVENLLALR---------- 107 d1j93a_ 215 FEEFSLP------------------YLKQIVDSVKLTH-PNLPLILYASG---------- 245 ::::::::::::: ::::::::: d1v93a_ 108 -------GDPPRGERVFRPHPEGFRYAAELVALIRERYGDRVSVGGAA--YPEGHPESES 158 d1j93a_ 246 ---SGGLLERLPLTGVDVVSLDWTV------DMADGRRRLG-----PNVAIQGNVDPGVL 291 ::::::::::::::::::: :::::::: ::::: d1v93a_ 159 LEADLRHFKAKVEAGLDFAITQ---LFFNNAHYFGFLER--ARRAGIGIPI--------- 204 d1j93a_ 292 FG-----------------------------------------SKEFITNRINDTVKKAG 310 ::::::::::::::: d1v93a_ 205 --LPGIMPVTSYRQLRRFTEVCGASIPGPLLAKLERHQDDPKAVLEIGVEHAVRQVAE-- 260 d1j93a_ 311 KGK------HILNLGHGIKVGTP------EENFAHFFEIAKGLRY------ 343 :::: :::::::::: d1v93a_ 261 ---LLEAGVEGVH----------FYTLNKSPATRMVLER------LGLRPA 292 TMalign alignment (TM-score: 0.48 Raw score:165.93) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRY--MKSYQL--------------------LCEK 38 :: :::::: : ::::::::: ::::: :::::: d1v93a_ 1 -MK-IRDLLK-A-RRGPLFSFE-FFPPKDPEGEEALFRTLEELKAFRPAFVSITYG---- 51 d1j93a_ 39 YPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 :::::: : :::::::::::::: :::::::::: ::: d1v93a_ 52 --AMGSTR-E--RSVAWAQRIQSLGL--NPLAHLTVAG-QSR------------------ 85 d1j93a_ 99 LRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 : :::::::::::::: ::::::: :: : :::: d1v93a_ 86 --------------K-EVAEVLHRFVESGV--------ENLLALR--GD--P----PRGE 114 d1j93a_ 159 NFTKIKRLAFAEPKVL--HALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE 216 : :: : : ::::::::::::::::::::::::::::::::::: :::: d1v93a_ 115 -R-VF--R-------PHP--EGFRYAAELVALIRERYGDRVSVGGAAYPEGHPES-ESLE 160 d1j93a_ 217 EFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRL 276 : :::::::::::: :::: :::::: ::::::::: d1v93a_ 161 A-DLRHFKAKVEAG------LDFA--------------------ITQLFF-NNAHYFGFL 192 d1j93a_ 277 G--P----NVAIQGNVDPGVL--------------------------------FGSKEFI 298 : : ::::::::::::: ::: ::: d1v93a_ 193 ERARRAGIGIPILPGIMPVTSYRQLRRFTEVCGASIPGPLLAKLERHQDDPKAVLE-IGV 251 d1j93a_ 299 TNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGL--RY 343 :::::::::::::::::::: :::: : :::::::::::::: d1v93a_ 252 EHAVRQVAELLEAGVEGVHF--YTLN-K-SPATRMVLERLGLRPA-- 292 HHsearch alignment (Probability: 0.32 E-value:0.02) d1j93a_ 57 LQPWKVFRPDGVILFSD----------ILTPLSGMNIPFDI-IKGKGPVIFDPLRTAADV 105 ::::::::::::::::: :::::::::::::: :::::::::::: d1v93a_ 64 AQRIQSLGLNPLAHLTVAGQSRKEVAEVLHRFVESGVENLLALRGDPPRGERVF------ 117 d1j93a_ 106 EKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKR 165 : :::::::::::::::::::::::: ::::::::::: ::: d1v93a_ 118 R-----PHPEGFRYAAELVALIRERYGDRV-SVGGAAYPEGH-------------PES-- 156 d1j93a_ 166 LAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQ 225 :::: :: :::::::::::::::: : ::: :::::::: d1v93a_ 157 ---ESLE---AD--------LRHFKAKVEAGLDFAI---------T-QLF--FNNAHYFG 190 d1j93a_ 226 IVDSVKLTHPNLPLILYA--SGSGGLLERLP-LTGVDVVSLDWTVDMADGRRRLGPNVAI 282 :::::::::::::::::: ::::::::::: :::: :: : ::::::::: : d1v93a_ 191 FLERARRAGIGIPILPGIMPVTSYRQLRRFTEVCGA---SI----P-GPLLAKLER-H-- 239 d1j93a_ 283 QGNVDPGVLF-GSKEFITNRINDTVKKAGKGKHILNLGH 320 :: :::::: :::::::::::::::::::::::::::: d1v93a_ 240 -QD-DPKAVLEIGVEHAVRQVAELLEAGVEGVHFYTLNK 276