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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1nyta1 | Shikimate 5-dehydrogenase AroE | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1edza1 | Methylenetetrahydrofolate dehydrogenase/cyclohydrolase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 0.853 --> IntermediateDALI alignment (Z-score: 3.8 Raw score:453.70) query 1 dadeevYSALVVGL--rAYVAkngfRSVLIGLSgGIDSALVAAIACDALGaqNVYGVSMp 58 :::::::: :::: :::::::: :::::::::::::::: ::::::: d1nyta1 1 -----dGVGLLSDLerlSFIR--pgLRILLIGA-GGASRGVLLPLLSLDC--AVTITNR- 49 query 59 skyssdhSKGDAAELARRTG----LNFRTVSiepmfdaymaslgltglaeenlqsrlrgt 114 ::::::::::::: ::::::: d1nyta1 50 -------TVSRAEELAKLFAhtgsIQALSMD----------------------------- 73 query 115 tlmaisNQEGH-IVLAPgnkselavGYSTLY-------gdsvgAYGPikdvyktsifrla 166 ::::: ::::: :::::: :::: d1nyta1 74 ----elEGHEFdLIINA----tssgISGDIPaipsslihpgiyCYDM------------- 112 query 167 ewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktl 226 d1nyta1 113 ------------------------------------------------------------ 113 query 227 rmvdtaeyKRRQY-------------PPGTK-------------------iSAKGFG-KD 253 ::::: ::::: :::::: :: d1nyta1 113 ------fyQKGKTpflawceqrgskrNADGLgmlvaqaahafllwhgvlpdVEPVIKqLQ 166 query 254 RRlpitnrwregh 266 :: d1nyta1 167 EE---------ls 170 FAST alignment (Normalized score: 2.78 Raw score:591.60) query 1 DADEEV-YSALVVGLRAYVAKNGF-------RSVLIGLSGGIDSALVAAIACDALGAQ-N 51 :::::::::: ::::: :::::::::::::::: : d1nyta1 1 ------DGVGLLSDLER-------LSFIRPGLRILL-IGAGGASRGVLLPLLS-----LD 41 query 52 VYGVSMPSKYSSDH--SKGDAAELARRTG----LNFRTVSIEPMFDAYMASLGLTGLAEE 105 :::::: ::::::::::: :::::: d1nyta1 42 CAVTIT--------NRTVSRAEELAKL--FAHTGSIQAL--------------------- 70 query 106 NLQSRLRGTTLMAISNQEG---HIVLAPGNK-SELAVGYSTLYGDSVGAYGPIKDVYKTS 161 ::::::: :::::: :::::::::: d1nyta1 71 ------SMDELEG------HEFDLIINA---TSSGISGDIPA------------------ 97 query 162 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 221 d1nyta1 98 ------------------------------------------------------------ 98 query 222 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 266 d1nyta1 98 ---------------------------------------------IPSSLIHPGIYCYDM 112 query 267 ---------------------------------------------------------- 267 d1nyta1 113 FYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 TMalign alignment (TM-score: 0.35 Raw score:94.08) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :: :::::::::::::: :::::::::::::::::::::::: : :::::::: d1nyta1 1 --DG-VGLLSDLERLSFIR---PGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNR-- 49 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE-PM-------------FDAYMASLGLTGL-AEE 105 ::: :::::::::::::::::::::: : : :: d1nyta1 50 -TVS-RAEELAKLFAHTGSIQALSMDEL-EGHEFDLIINATSS------------GI-SG 93 query 106 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS--V----G-AYGPIKDVY 158 : :: :::::::: : : :::::: :::::::: : : : : ::::::::: d1nyta1 94 D-IP-AIPSSLIH--P--G-IYCYDM---FYQKGKTP--F-LAWCEQRGSKRNADGLGML 140 query 159 KTSI-FRL--AEW------RNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 :::: :: : d1nyta1 141 VAQAA-HAFL--LWHGVLP----------------------------------------- 156 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 :::::::::::::: d1nyta1 157 -----------------------------------DVEPVIKQLQEELS-------- 170 HHsearch alignment (Probability: 0.04 E-value:0.17) query 7 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 66 ::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1nyta1 2 GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--SLDCAVTIT---------NRT 50 query 67 KGDAAELARRTGLNFRTVSIE 87 ::::::::::::::::::::: d1nyta1 51 VSRAEELAKLFAHTGSIQALS 71
Intermediate <-- 1.830 --> HitDALI alignment (Z-score: 10.6 Raw score:796.20) d1nyta1 1 --DGVGLLSDLERLSFI---------RPGLRILLIGAG-GASRGVLLPLLSLDCAVTITN 48 ::::::::::::::: :::::::::::: ::::::::::::::::::::: d1edza1 1 pcTPLAIVKILEFLKIYnnllpegnrLYGKKCIVINRSeIVGRPLAALLANDGATVYSVD 60 d1nyta1 49 RTV--sraeelaklfaHTGSIQ--aLSMDELEGH--EFDLIINATSSgiSGDIPaiPSSL 102 ::: :::::: ::::::::: ::::::::::: ::::: :::: d1edza1 61 VNNiqkftrgeslklnKHHVEDlgeYSEDLLKKCslDSDVVITGVPS--ENYKF--PTEY 116 d1nyta1 103 IHPGIYCYDMFYqkgkTPFL-AWCEqRGSKRNA-DGLGMLVAQAAHAFLLWHGVlpdvep 160 :::::::::::: :::: :::: ::::::: :::::::::::::::::::: d1edza1 117 IKEGAVCINFAC----TKNFsDDVK-EKASLYVpMTGKVTIAMLLRNMLRLVRN------ 165 d1nyta1 161 vikqlqeels 170 d1edza1 166 ----velske 171 FAST alignment (Normalized score: 8.29 Raw score:1413.00) d1nyta1 1 D---GVGLLSDLERLSFI----------RPGLRILLIGA-GGASRGVLLPLLSLDCAVTI 46 ::::::::::::: ::::::::::: :::::::::::::::::::: d1edza1 1 -PCTPLAIVKILEFLKI-YNNLLPEGNRLYGKKCIVINRSEIVGRPLAALLANDGATVYS 58 d1nyta1 47 TNRTVSRAEELAKLFAHTG-----------------SIQA---LSMDELEG--HEFDLII 84 ::: :::: :::::::: ::::::: d1edza1 59 VDV----------------NNIQKFTRGESLKLNKHHVEDLGEYSEDLLKKCSLDSDVVI 102 d1nyta1 85 NATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPF------LAWCEQRGSKRNAD--- 135 :::: :::: :::::::::::::::: ::::: ::::::: d1edza1 103 TGVP--SENY--KFPTEYIKEGAVCINF---------ACTKNFSDDVK-EKASLYV-PMT 147 d1nyta1 136 GLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS-------- 170 :::::::::::::::: d1edza1 148 GKVTIAMLLRNMLRLV-------------------RNVELSKE 171 TMalign alignment (TM-score: 0.65 Raw score:110.71) d1nyta1 1 --DGVGLLSDLERLSFIR--------P-GLRILLIGAG-GASRGVLLPLLSLDCAVTITN 48 :::::::::::::::: : :::::::::: ::::::::::::::::::::: d1edza1 1 PCTPLAIVKILEFLKIYNNLLPEGNRLYGKKCIVINRSEIVGRPLAALLANDGATVYSVD 60 d1nyta1 49 RTVSRAEELA--KLFAH-----TGSIQAL-SMD-ELEGH--EFDLIINATSSGISGDIPA 97 ::: :: :: ::: ::::::: ::: ::::: ::::::::::: : ::: d1edza1 61 VNN--IQ-KFTR--GESLKLNKHHVEDLGEYSEDLLKKCSLDSDVVITGVPS--E-NYK- 111 d1nyta1 98 IPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNA-DGLGMLVAQAAHAFLLWHGV-- 154 :::::::::::::::::: :::::::: ::::::: :::::::::::::::::::: d1edza1 112 FPTEYIKEGAVCINFACT---KNFSDDVK-EKASLYVPMTGKVTIAMLLRNMLRLVRNVE 167 d1nyta1 155 ----LPDVEPVIKQLQEELS 170 d1edza1 168 LSKE---------------- 171 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 3 VGLLSDLERLSF---------IRPGLRILLIGAGG-ASRGVLLPLLSLDCAVTITNRTVS 52 :::::::::::: :::::::::::::: :::::::::::::::::::::: d1edza1 5 LAIVKILEFLKIYNNLLPEGNRLYGKKCIVINRSEIVGRPLAALLANDGATVYSVDVN-- 62 d1nyta1 53 RAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDM 112 :: :::::::::::::::: :::::::::::::::::::: d1edza1 63 NI-------------------QKFTRGESLKLNKHHV---EDLGEYSEDLLKKCSLDSDV 100 d1nyta1 113 FYQKGKT 119 ::::::: d1edza1 101 VITGVPS 107