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 | d1ps9a3 | 2,4-dienoyl-CoA reductase, middle domain | Nucleotide-binding domain | Nucleotide-binding domain | α/β |
| Hit | d3lada2 | Dihydrolipoamide dehydrogenase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
Query <-- 1.613 --> IntermediateDALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 1.569 --> HitDALI alignment (Z-score: 6.6 Raw score:499.60) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpaVQKK-NLAVVGAGPAGLAFA 59 :::: ::::::::::::::: d3lada2 1 ----------------------papvdqdvivdstgaldfQNVPgKLGVIGAGVIGLELG 38 d1ps9a3 60 INAAARGHQVTLFDAHSEIGgqfNIAKqipgkeefYETLRYYRRMIEVTGVTLKLNHTVT 119 :::::::::::::::::::: :::: ::::::::::::::::::::::::: d3lada2 39 SVWARLGAEVTVLEAMDKFL---PAVD--------EQVAKEAQKILTKQGLKILLGARVT 87 d1ps9a3 120 AD-----------------QLQAFDETILASGipnralaqplidsgktvhliggcdvame 162 :: ::::::::::::: d3lada2 88 GTevknkqvtvkfvdaegeKSQAFDKLIVAVG---------------------------- 119 d1ps9a3 163 ldarraiaqgtrlalei 179 d3lada2 120 ----------------- 120 FAST alignment (Normalized score: 6.75 Raw score:984.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPIL----------------PAVQK- 43 ::::: d3lada2 1 --------------------------------------PAPVDQDVIVDSTGALDFQNVP 22 d1ps9a3 44 KNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEE-FYETLRYYR 102 :::::::::::::::::::::::::::::::::::::: ::::::::: d3lada2 23 GKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPA------------VDEQVAKEAQ 70 d1ps9a3 103 RMIEVTGVTLKLNHTVTAD-------------------QLQAFDETILASGIPNRALAQP 143 ::::::::::::::::: ::::::::::: d3lada2 71 KILTKQGLKILLGARVT--GTEVKNKQVTVKFVDAEGEKSQAFDKLIVA----------- 117 d1ps9a3 144 LIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI-- 179 d3lada2 118 ------------------------------------VG 119 TMalign alignment (TM-score: 0.40 Raw score:71.84) d1ps9a3 1 ------------------INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQ 42 ::: d3lada2 1 PAPVDQDVIVDSTGALDF---------------------------------------QNV 21 d1ps9a3 43 KKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFY-ETLRYY 101 ::::::::::::::::::::::::::::::::::::: : : :: :::::: d3lada2 22 PGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFL---P--A-------VDEQVAKEA 69 d1ps9a3 102 RRMIEVTGVTLKLNHTVTAD---------Q-------L-QAFDETILASGIPNRALAQPL 144 :::::::::::::::::::: : : ::::::::::: d3lada2 70 QKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVG---------- 119 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 d3lada2 120 ----------------------------------- 120 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 ::::::::::::::::::::::::::::::::::::::::::::: :::: d3lada2 16 LDFQNVPGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPA-----------VDEQ 64 d1ps9a3 97 TLRYYRRMIEVTGVTLKLNHTVTAD 121 ::::::::::::::::::::::::: d3lada2 65 VAKEAQKILTKQGLKILLGARVTGT 89