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 | d1u1ja2 | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE | UROD/MetE-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 <-- 2.107 --> HitDALI alignment (Z-score: 21.3 Raw score:2391.90) d1j93a_ 1 ------------------------------TQPLlldavrgkevERPPVWLMRQAGrymk 30 :::: :::::::::::: d1u1ja2 1 egvqkaaaalkgsdhrratnvsarldaqqkKLNL----------PILPTTTIGSFP---- 46 d1j93a_ 31 sYQLLceKYPLfrdrseNVDLvVEISL-QPWKVFRPDGVILFS-----DILTPLSGMN-I 83 :::: :::: :::: ::::: ::::::::::::::: :::::::::: : d1u1ja2 47 -QTVE--LRED---yvkAIKE-EIKKVvDLQEELDIDVLVHGEperndMVEYFGEQLSgF 99 d1j93a_ 84 PFD-------iikGKGPVIfdPLRTaadvekVREFIPEksvpyVGEALTILRKEVNnqAA 136 ::: :::::: :::: ::::::: ::::::::::::: :: d1u1ja2 100 AFTangwvqsygsRCVKPP--VIYG------DVSRPKA----mTVFWSAMAQSMTS--RP 145 d1j93a_ 137 VLGFVGAPFTLASYVVEggssknftkikrlafaEPKVLHALLQKFATSMAKYIRYQADSG 196 ::::::::::::::::: ::::::::::::::::::::::::::: d1u1ja2 146 MKGMLTGPVTILNWSFV---------------rNDQPRHETCYQIALAIKDEVEDLEKGG 190 d1j93a_ 197 AQAVQIFDSWATELS------PVDFEEFSLPYLKQIVDSVkltHPNLPLILYASGSGG-- 248 ::::::::::::::: ::::::::::::::::::: ::::::::::::::: d1u1ja2 191 IGVIQIDEAALREGLplrkseHAFYLDWAVHSFRITNCGV---QDSTQIHTHMCYSHFnd 247 d1j93a_ 249 LLERLPLTGVDVVSLDW-TVDMADgRRRL----GPNVAIQGNV-DPGV-lFGSKEFITNR 301 ::::::::::::::::: :::::: :::: :::::::::: :::: :::::::::: d1u1ja2 248 IIHSIIDMDADVITIENsRSDEKL-LSVFregvKYGAGIGPGVyDIHSprIPSSEEIADR 306 d1j93a_ 302 INDTVKKAGKGKHILNLGHGI--KVGTP-EENFAHFFEIAKGLR-y 343 ::::::::::::::::::::: ::::: ::::::::::::::: d1u1ja2 307 VNKMLAVLEQNILWVNPDCGLktRKYTEvKPALKNMVDAAKLIRsq 352 FAST alignment (Normalized score: 12.14 Raw score:4218.00) d1j93a_ 1 TQPLLLDAVRGKEVE-----------------------------------RPPVWLMRQA 25 :::::: d1u1ja2 1 ---------------EGVQKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTT---- 41 d1j93a_ 26 GRYMKSYQLLCEKYPLFRDRSE------------NVDLVVEISLQPWKV----FRPDGVI 69 ::::::::::::::: ::::::: d1u1ja2 42 ----------------------IGSFPQTVELREDYVKAIKEEIKKVVDLQEELDIDVLV 79 d1j93a_ 70 LFSD--------ILTPLSGMNIPFDIIKG------------KGPVIFDPLRTAADVEKVR 109 : ::::::::: :::::: :::::: ::: d1u1ja2 80 H---GEPERNDMVEYFGEQLS-GFAFTA-NGWVQSYGSRCVKPPVIY----------GDV 124 d1j93a_ 110 EFIPEKSVP---YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRL 166 :: ::::::::::::: ::::::::::::::::: d1u1ja2 125 SR-------PKAMTVFWSAMAQSMT--SRPMKGMLTGPVTILNW---------------- 159 d1j93a_ 167 AFAEPK-------VLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATEL--------S 211 ::::::::::::::::::::::::::::::::::::: : d1u1ja2 160 ------SFVRNDQPRHETCYQIALAIKDEVEDLEKGGIGVIQIDEAALRE-GLPLRKSEH 212 d1j93a_ 212 PVDFEEFSLPYLKQIVDSVKLT-HPNLPLILYA--SGSGGLLERLPLTGVDVVSL-DWTV 267 ::::: :::::::::::: :::::::::: :::::::::::::::::::: :::: d1u1ja2 213 AFYLD-WAVHSFRITNCG----VQDSTQIHTHMCYSHFNDIIHSIIDMDADVITIENSRS 267 d1j93a_ 268 DMADGRRRLG---------PNVAIQG---NVDPGVL---FGSKEFITNRINDTVKKAGKG 312 :::: ::::: ::::: ::::::::::::::::::::: d1u1ja2 268 DEKL------LSVFREGVKYGAGI--GPGVYDIH--SPRIPSSEEIADRVNKMLAVLEQN 317 d1j93a_ 313 KHILNLGHGIKVGTP----EENFAHFFEIAKGLRY---- 343 ::::::::: ::::: ::::::::::::: d1u1ja2 318 ILWVNPDCG-LKTRKYTEVKPALKNMVDAAKL---IRSQ 352 TMalign alignment (TM-score: 0.72 Raw score:245.64) d1j93a_ 1 -----------------------TQPLLLDAVRGK--EVERPPVWLMRQAGRYMKSYQLL 35 ::::::: ::::::::::::: : ::: d1u1ja2 1 EGVQKAAAALKGSDHRRATNVSA-----RLDAQQKKLNLPILPTTTIGSF-P----QTV- 49 d1j93a_ 36 CEKYPLFRDRSENVDLVVEISLQPWKVF-RPDGVIL-F--S--DILTPLSGMN-IPFDII 88 : :: :: :::::::::::::::::: ::::::: : : :::::::::: :::::: d1u1ja2 50 E--LR--ED-YVKAIKEEIKKVVDLQEELDIDVLVHGEPERNDMVEYFGEQLSGFAFTAN 104 d1j93a_ 89 -K------GKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFV 141 : :::::: :: ::: : ::::: : ::::::::::::: ::::::: d1u1ja2 105 GWVQSYGSRCVKPP--VI----YGD-V-SRPKA--M--TVFWSAMAQSMTS--RPMKGML 150 d1j93a_ 142 GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQ 201 :::::::::::: : : : :::::::::::::::::::::::::::::: d1u1ja2 151 TGPVTILNWSFV---------R--N---D-QPRHETCYQIALAIKDEVEDLEKGGIGVIQ 195 d1j93a_ 202 IFDSWATELS------PVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG-SG-GLLERL 253 :::::::::: ::::::::::::::::: :: :::::::::::: :: :::::: d1u1ja2 196 IDEAALREGLPLRKSEHAFYLDWAVHSFRITNC-GV--QDSTQIHTHMCYSHFNDIIHSI 252 d1j93a_ 254 PLTGVDVVSLDW--TVDM-ADGRRR-LGPNVAIQGNVDPG-V-LFGSKEFITNRINDTVK 307 :::::::::::: :::: :::::: :::::::::::::: : ::::::::::::::::: d1u1ja2 253 IDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSSEEIADRVNKMLA 312 d1j93a_ 308 KAGKGKHILNLGHGI-KVG--TPEENFAHFFEIAKGLR-Y 343 ::::::::::::::: ::: ::::::::::::::::: : d1u1ja2 313 VLEQNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLIRSQ 352 HHsearch alignment (Probability: 0.99 E-value:0.00) d1j93a_ 18 PVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVI-------- 69 ::::::::::: ::::::::::: : ::::::::::::: ::::::::: d1u1ja2 35 PILPTTTIGSF-PQTVELREDYV---K-AIKEEIKKVVDLQ--EELDIDVLVHGEPERND 87 d1j93a_ 70 LFSDILTPLSGMNIPFDIIKGKGPVIF---DPLRTAADVEKVREFIPEKSVPYVGEALTI 126 ::::::::::: :::::: ::::: ::::::::::::: :::::::::::: d1u1ja2 88 MVEYFGEQLSG----FAFTAN-GWVQSYGSRCVKPPVIYGDVS-----RPKAMTVFWSAM 137 d1j93a_ 127 LRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMA 186 :::: :::::::::::::::::::::: ::::: :::::::::::: d1u1ja2 138 AQSM--TSRPMKGMLTGPVTILNWSFVR------------NDQPR---HETCYQIALAIK 180 d1j93a_ 187 KYIRYQADSGAQAVQIFDSW-ATEL-----SPVDFEEFSLPYLKQIVDSVKLTHPNLPLI 240 :::::::::::::::::::: :::: :::::::::::::::::::::: ::::: d1u1ja2 181 DEVEDLEKGGIGVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQD---STQIH 237 d1j93a_ 241 LYAS--GSGGLLERLPLTGVDVVSLDWTVD----MADGRRRLG-PNVAIQGNVDPGV-LF 292 :::: :::::::::::::::::::::::: ::::::::: ::::::::::::: :: d1u1ja2 238 THMCYSHFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRI 297 d1j93a_ 293 GSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTP---EENFAHFFEIAKGLR 342 ::::::::::::::::::::::::::::::::::: ::::::::::::::: d1u1ja2 298 PSSEEIADRVNKMLAVLEQNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLIR 350