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 | d2cmda1 | 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 <-- 1.814 --> HitDALI alignment (Z-score: 5.1 Raw score:430.20) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkKNLAVVGA-GPAGLAFA 59 :::::::: :::::::: d2cmda1 1 -------------------------------------------MKVAVLGAaGGIGQALA 17 d1ps9a3 60 INAAARG---HQVTLFDAHSEIggqfniakqipgkeefyetlryYRRMIEV----tGVTL 112 ::::::: :::::::::::: ::::::: :::: d2cmda1 18 LLLKTQLpsgSELSLYDIAPVT--------------------pgVAVDLSHiptavKIKG 57 d1ps9a3 113 KLNHTVTadqLQAFDETILASGI----------------PNRA-LAQPLID--SGKTVHL 153 ::::::: ::::::::::::: :::: ::::::: ::::::: d2cmda1 58 FSGEDAT-paLEGADVVLISAGVrrkpgmdrsdlfnvnaGIVKnLVQQVAKtcPKACIGI 116 d1ps9a3 154 IggCDVAM-----eldarraiaqgtrlalei 179 : ::::: d2cmda1 117 I--TNPVNttvaiaaevlkkagvydknklfg 145 FAST alignment (Normalized score: 4.47 Raw score:721.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVV-GAGPAGLAFA 59 :::::: :::::::::: d2cmda1 1 -------------------------------------------MKVAVLGAAGGIGQALA 17 d1ps9a3 60 INAAA---RGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRY-YRRMIEV-------T 108 ::::: :::::::::::: ::::::: : d2cmda1 18 LLLKTQLPSGSELSLYDIAP------------------------VTPGVAVDLSHIPTAV 53 d1ps9a3 109 GVTLKLNHTVT---ADQL-QAFDETILASGIPNRA------------------LAQPLID 146 :::::: :::: ::::::::::: ::::::: d2cmda1 54 KIKGFS-----GEDATPALEGADVVLISAG-----VRRKPGMDRSDLFNVNAGIVKNLVQ 103 d1ps9a3 147 ------SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI--------------------- 179 ::::::: d2cmda1 104 QVAKTCPKACIGI--------------------------ITNPVNTTVAIAAEVLKKAGV 137 d1ps9a3 180 -------- 180 d2cmda1 138 YDKNKLFG 145 TMalign alignment (TM-score: 0.41 Raw score:72.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-AGPAGLAFA 59 ::::::: ::::::::: d2cmda1 1 -------------------------------------------MKVAVLGAAGGIGQALA 17 d1ps9a3 60 INAAARG---HQVTLFDAHSEI--GGQFNIAKQIPGKEEFYETLRYYRRMIEV-T-GVTL 112 ::::::: :::::::::::: : ::::::: : :::: d2cmda1 18 LLLKTQLPSGSELSLYDIAPVTPG--------------------V-AVDLSHIPTAVKIK 56 d1ps9a3 113 KLNHTVTADQL-Q-AFDETILASGI--------------P--NR-ALAQPLID--SGKTV 151 ::::::: :: : ::::::::::: : :: :::::::: ::::: d2cmda1 57 GFSGEDA--TPALEGADVVLISAGVRRKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACI 114 d1ps9a3 152 HLIGGCDVA------------------------MELDARRAIAQGTRLALEI 179 ::: :::: d2cmda1 115 GII--TNPVNTTVAIAAEVLKKAGVYDKNKLFG------------------- 145 HHsearch alignment (Probability: 0.94 E-value:0.00) d1ps9a3 44 KNLAVVGA-GPAGLAFAINAAARGHQ---VTLFDAHSEIGGQFNIAKQIPGKEEFYETLR 99 :::::::: ::::::::::::::::: :::::::::::: ::: d2cmda1 1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPG----------------VAV 44 d1ps9a3 100 YYRRMIEVTGVTLKLNHTVTADQLQAFDETILASGIPNRALAQ 142 :::::::::::::::::: ::::::::::::::::: :::::: d2cmda1 45 DLSHIPTAVKIKGFSGED-ATPALEGADVVLISAGV-RRKPGM 85