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 | d1uxja1 | Malate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.832 --> HitDALI alignment (Z-score: 5.4 Raw score:445.30) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqKKNLAVVGAGPAGLAFAI 60 :::::::::::::::::: d1uxja1 1 ------------------------------------------RKKISIIGAGFVGSTTAH 18 d1ps9a3 61 NAAARG-HQVTLFDAHSEIggqfniakqipgkeefyetlryYRRMIEV--------tGVT 111 :::::: :::::::::::: ::::::: ::: d1uxja1 19 WLAAKElGDIVLLDIVEGV-------------------pqgKALDLYEaspiegfdvRVT 59 d1ps9a3 112 LKlnHTVTadqlQAFDETILASGI-------PNRA-LAQPLID--SGKTVHLIggCDVAM 161 :: :::: :::::::::::: :::: ::::::: :::::::: ::::: d1uxja1 60 GT--NNYA--dtANSDVIVVTSGAplikvnaDITRaCISQAAPlsPNAVIIMV--NNPLD 113 d1ps9a3 162 --eldarraiaqgtrlalei 179 d1uxja1 114 amtylaaevsgfpkervigq 133 FAST alignment (Normalized score: 5.13 Raw score:791.10) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 :::::::::::::::::: d1uxja1 1 ------------------------------------------RKKISIIGAGFVGSTTAH 18 d1ps9a3 61 NAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRY--YRRMIEV---------- 107 :::::: :::::::::: ::::::: d1uxja1 19 WLAAKELGDIVLLDIVE------------------------GVPQGKALDLYEASPIEGF 54 d1ps9a3 108 -TGVTLKLNHTVTADQL-------QAFDETILASGIPN-----------RALAQPLID-- 146 ::::: ::::::::::: ::::::::: d1uxja1 55 DVRVTG-----------TNNYADTANSDVIVVTSG---APLIKVNADITRACISQAAPLS 100 d1ps9a3 147 SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI------------------------- 179 :::::::: d1uxja1 101 PNAVIIMV-------------------------NNPLDAMTYLAAEVSGFPKERVIGQ 133 TMalign alignment (TM-score: 0.41 Raw score:73.98) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 :::::::::::::::::: d1uxja1 1 ------------------------------------------RKKISIIGAGFVGSTTAH 18 d1ps9a3 61 NAAARGH-QVTLFDAHSEIG-GQFNIAKQIPGKEEFYETLRYYRRMIEVT------GVTL 112 ::::::: :::::::::::: :: :::::::: :::: d1uxja1 19 WLAAKELGDIVLLDIVEGVPQ------------------GK-ALDLYEASPIEGFDVRVT 59 d1ps9a3 113 KLNHTVTADQ-LQAFDETILASGI-----P--NRA-LAQP-LI--DSGKTVHLIGGCDVA 160 :: ::: : ::::::::::::: : ::: :::: :: :::::::: :::: d1uxja1 60 GT-NNY---ADTANSDVIVVTSGAPLIKVNADITRACISQAAPLS-PNAVIIMV--NNPL 112 d1ps9a3 161 --------------------MELDARRAIAQGTRLALEI 179 : d1uxja1 113 DAMTYLAAEVSGFPKERVIG--------------Q---- 133 HHsearch alignment (Probability: 0.97 E-value:0.00) d1ps9a3 43 KKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYR 102 ::::::::::::::::::::::::::::::::::::: ::: :::::: d1uxja1 1 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGV--------PQG------KALDLY 46 d1ps9a3 103 RMIEVTGVTLKLNHTVTADQLQAFDETILASGIPNRA 139 ::::::::::::::::::::::::::::::::::::: d1uxja1 47 EASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPLIK 83