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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1lvla2 | Dihydrolipoamide dehydrogenase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1dxya1 | D-2-hydroxyisocaproate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.313 --> IntermediateDALI alignment (Z-score: 4.5 Raw score:353.40) query 1 -----------------GMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAfw 43 ::::::::::: ::::::::::::::::::::::: d1lvla2 1 mlplggpvisstealapKALPQHLVVVG------gGYIGLELGIAYRKLGAQVSVVEA-- 52 query 44 gLLLLrdpekasqedkslyeqafssltprEAEElplskmnlggigkkmllemmkeekapK 103 :::: :::: : d1lvla2 53 -RERI-----------------------lPTYD------------------------seL 64 query 104 LSDLLSGARKKEVKFYAX------------qLSVEImgfkkeelfpevqimdvkeyLKNA 151 :::::::::::::::::: ::::: :::: d1lvla2 65 TAPVAESLKKLGIALHLGhsvegyengcllaNDGKG------------------gqLRLE 106 query 152 leSDLQLFI-- 160 ::::::: d1lvla2 107 --ADRVLVAvg 115 FAST alignment (Normalized score: 4.50 Raw score:610.50) query 1 GMEN---------------------KKMNLLLFSGDYDK---ALASLIIANAAREMEIEV 36 ::::: :::::::::::::::::: d1lvla2 1 ----MLPLGGPVISSTEALAPKALPQHLVV---------VGGGYIGLELGIAYRKLGAQV 47 query 37 TIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMM 96 ::::: d1lvla2 48 SVVEA------------------------------------------------------- 52 query 97 KEEKAP-----------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVK 145 ::::::::::::::::: ::::: d1lvla2 53 ------RERILPTYDSELTAPVAESLKKLGIALH--------------------LGHSV- 85 query 146 EYLKNA-------------------LESDLQLFI---- 160 ::::::: d1lvla2 86 ------EGYENGCLLANDGKGGQLRLEADRVL--VAVG 115 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ------------------GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAF 42 :: :::::::: :::::::::::::::::::::::: d1lvla2 1 MLPLGGPVISSTEALAPKAL-PQHLVVVG------GGYIGLELGIAYRKLGAQVSVVEA- 52 query 43 WGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP 102 :::::: :::::: d1lvla2 53 -RERILP--------------------TYDSEL--------------------------- 64 query 103 KLSDLLSGARKKEVKFYA-X-------------QLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::::::: : :: : ::: : d1lvla2 65 -TAPVAESLKKLGIALHLGHSVEGYENGCLLANDG--K--------------GGQ--L-- 103 query 149 KNALESDLQLFI- 160 :: ::::::::: d1lvla2 104 RL-EADRVLVAVG 115 HHsearch alignment (Probability: 0.19 E-value:0.00) query 20 LASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPL 79 :::::::::::::::::::: ::::: d1lvla2 31 YIGLELGIAYRKLGAQVSVV-----------------------------------EARER 55 query 80 SKMNLGGIGKKMLLEMMKEEKA 101 :::::::::::::::::::::: d1lvla2 56 ILPTYDSELTAPVAESLKKLGI 77
Intermediate <-- 1.423 --> HitDALI alignment (Z-score: 3.5 Raw score:316.00) d1lvla2 1 mlplggpviSSTEALA--PKAL---------------------------pQHLVVVGGGY 31 ::::::: :::: :::::::::: d1dxya1 1 -----spaaIAEFALTdtLYLLrnmgkvqaqlqagdyekagtfigkelgqQTVGVMGTGH 55 d1lvla2 32 IGLELGIAYRKLGAQVSVVEAreRILPtydseltapvaESLKklGIALHlghsvegyeng 91 ::::::::::::::::::::: :::: :::: ::::: d1dxya1 56 IGQVAIKLFKGFGAKVIAYDP--YPMK-----------GDHP--DFDYV----------- 89 d1lvla2 92 cllandgkggqLRLE--ADRVLVAVG---------------------------------- 115 :::: ::::::::: d1dxya1 90 ---------slEDLFkqSDVIDLHVPgieqnthiineaafnlmkpgaivintarpnlidt 140 d1lvla2 116 ----------------------------------------------------------- 116 d1dxya1 141 qamlsnlksgklagvgidtyeyetedllnlakhgsfkdplwdellgmpnvvlsphiayy 199 FAST alignment (Normalized score: 3.25 Raw score:491.00) d1lvla2 1 MLPLGGPVI--------SSTEALAPKALP------------------------------- 21 :::::: d1dxya1 1 ---------SPAAIAEFALTDTL------YLLRNMGKVQAQLQAGDYEKAGTFIGKELGQ 45 d1lvla2 22 QHLVVVGGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKL------ 75 ::::::::::::::::::::::::::::::: d1dxya1 46 QTVGVMGTGHIGQVAIKLFKGFGAKVIAYDP-----------------------YPMKGD 82 d1lvla2 76 --GIALHLGHSVEGYENGCLLANDGKGGQLR-------LEADRVLVAVG----------- 115 :::: :::::::::: d1dxya1 83 HPDFDY-------------------------VSLEDLFKQSDVIDLHV-PGIEQNTHIIN 116 d1lvla2 116 ------------------------------------------------------------ 116 d1dxya1 117 EAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYETEDLLNLAKHGSF 176 d1lvla2 116 ----------------------- 116 d1dxya1 177 KDPLWDELLGMPNVVLSPHIAYY 199 TMalign alignment (TM-score: 0.51 Raw score:58.50) d1lvla2 1 ----MLPLGGPVISSTEALA--PK-A-------------------------LP-QHLVVV 27 ::::::: :: : :: :::::: d1dxya1 1 SPAA---------IAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVM 51 d1lvla2 28 GGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEG 87 :::::::::::::::::::::::::: :: : :: : :: :::: : : d1dxya1 52 GTGHIGQVAIKLFKGFGAKVIAYDPY-PM---------K--GD-H-PD-FDYV--S-L-- 91 d1lvla2 88 YENGCLLANDGKGGQLR-LEADRVLVAVG------------------------------- 115 : :: ::::::::::: d1dxya1 92 ------E--------DLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNL 137 d1lvla2 116 ------------------------------------------------------------ 116 d1dxya1 138 IDTQAMLSNLKSGKLAGVGIDTYEYETEDLLNLAKHGSFKDPLWDELLGMPNVVLSPHIA 197 d1lvla2 116 -- 116 d1dxya1 198 YY 199 HHsearch alignment (Probability: 0.90 E-value:0.00) d1lvla2 20 LPQHLVVVGGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSE---LTAPVA------- 69 :::::::::::::::::::::::::::::::::::::::::::: :::::: d1dxya1 44 GQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPDFDYVSLEDLFKQSDVIDL 103 d1lvla2 70 -ESLKKLGIALHLGHSVEGYENGCLLANDGKGG 101 :::::::::::::::::::::::::::::::: d1dxya1 104 HVPGIEQNTHIINEAAFNLMKPGAIVINTARPN 136