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 | d1leha1 | Leucine dehydrogenase | 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 <-- 1.611 --> HitDALI alignment (Z-score: 9.6 Raw score:829.10) d1nyta1 1 ---------------DGVGLLSDLErLSFI-------RPGLRILLIGAGGASRGVLLPLL 38 :::::::::: :::: ::::::::::::::::::::::: d1leha1 1 gispafgssgnpspvTAYGVYRGMK-AAAKeafgsdsLEGLAVSVQGLGNVAKALCKKLN 59 d1nyta1 39 SLDCAVTITNRTVSRAEELAKLFAhtgsIQALSMDELEGHEFDLIINATSSGisgdipaI 98 :::::::::::::::::::::::: :::::::::::::::::::::::: : d1leha1 60 TEGAKLVVTDVNKAAVSAAVAEEG----ADAVAPNAIYGVTCDIFAPCALGA--vlndfT 113 d1nyta1 99 PSSLIhpgIYCY-DMFYqkgktpfLAWCEQRGSkRNADG-LGMLvAQAAHAFLL-WHGV- 154 ::::: :::: :::: ::::::::: ::::: :::: ::::::::: :::: d1leha1 114 IPQLK--aKVIAgSADNqlkdprhGKYLHELGI-VYAPDyVINA-GGVINVADElYGYNr 169 d1nyta1 155 --LPDV-------------------epvikqLQEELS----------------------- 170 :::: :::::: d1leha1 170 trAMKRvdgiydsiekifaiskrdgvpsyvaADRMAEeriakvakarsqflqdqrnilng 229 d1nyta1 171 - 171 d1leha1 230 r 230 FAST alignment (Normalized score: 7.98 Raw score:1578.00) d1nyta1 1 D----------------GVGLLSDLERLSFI----------RPGLRILLIGAGGASRGVL 34 :::::::::: ::::::::::::::::::: d1leha1 1 -GISPAFGSSGNPSPVTAYGVYRGMKA----AAKEAFGSDSLEGLAVSVQGLGNVAKALC 55 d1nyta1 35 LPLLSLDCAVTITNRTVSRAEELAKLFAHTG-SIQALSMDELEGHEFDLIINATSSGISG 93 :::::::::::::::::::::::::: ::::::::::::::::::::::: d1leha1 56 KKLNTEGAKLVVTDVNKAAVSAAVAE-----EGADAVAPNAIYGVTCDIFAPCAL----- 105 d1nyta1 94 DIPAIPSSLIHPG--------------IYCYDMFYQKGK------TPFLAWCEQRGSKRN 133 ::::::: ::::::::::: ::: d1leha1 106 -------------GAVLNDFTIPQLKAKVIAGSA-----DNQLKDPRHGKYLHELG-IVY 146 d1nyta1 134 ADGLG-MLVAQAAHAFLLWHGVL-----------PDVEPVIKQLQEELS----------- 170 :::: :::::::::::::: ::::::::::::: d1leha1 147 APDY-VINAGGVINVADELY---GYNRTRAMKRVDGIYDSIEKIFAI--SKRDGVPSYVA 200 d1nyta1 171 ------------------------------ 171 d1leha1 201 ADRMAEERIAKVAKARSQFLQDQRNILNGR 230 TMalign alignment (TM-score: 0.66 Raw score:112.50) d1nyta1 1 ---------------DGVGLLSDLERL-S-F---I-RPGLRILLIGAGGASRGVLLPLLS 39 :::::::::::: : : : :::::::::::::::::::::::: d1leha1 1 GISPAFGSSGNPSPVTAYGVYRGMKAAAKEAFGSDSLEGLAVSVQGLGNVAKALCKKLNT 60 d1nyta1 40 LDCAVTITNRTVSRAEELAKLF-AHTGSIQALSMDELEGHEFDLIINATSSGISGDIP-A 97 ::::::::: : : ::::::: :::: :::::::::::::::::::::::: ::: : d1leha1 61 EGAKLVVTD-V--N-KAAVSAAVAEEG-ADAVAPNAIYGVTCDIFAPCALGA---VLNDF 112 d1nyta1 98 IPSSLIHPGIYCYDMFYQKGKTPFL-AW-CEQRGSKRNADG-LGMLVAQAAHAFL--LWH 152 ::::::: ::::::::: ::::: :: :::::::::::: ::::::::::::: ::: d1leha1 113 TIPQLKA--KVIAGSADN--QLKDPRHGKYLHELGIVYAPDYVINAGGVINVADELYGYN 168 d1nyta1 153 -GV--LP-DVE-PVI--KQ--------------LQE-ELS-------------------- 170 :: :: ::: :: :: ::: ::: d1leha1 169 RTRAMKRVDGIY-DSIEKIFAISKRDGVPSYVAADRMAEERIAKVAKARSQFLQDQRNIL 227 d1nyta1 171 --- 171 d1leha1 228 NGR 230 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 2 GVGLLSDLE----R-L-SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAE 55 ::::::::: : : ::::::::::::::::::::::::::::::::::::::::::: d1leha1 17 AYGVYRGMKAAAKEAFGSDSLEGLAVSVQGLGNVAKALCKKLNTEGAKLVVTDVNKAAVS 76 d1nyta1 56 ELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQ 115 ::::::: ::::::::::::::::::::: :::::::::::::: :::::::::: d1leha1 77 AAVAEEG----ADAVAPNAIYGVTCDIFAPCA---LGAVLNDFTIPQLK-AKVIAGSADN 128 d1nyta1 116 KGKTPFL-AWCEQRGSKRNADGLGMLVAQA--AHAFLLWHGVL 155 ::::::: ::::::::: : ::::::::: ::::::::::: d1leha1 129 QLKDPRHGKYLHELGIV-Y--APDYVINAGGVINVADELYGYN 168