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 | d1r0ka2 | 1-deoxy-D-xylulose-5-phosphate reductoisomerase | 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 <-- 1.521 --> HitDALI alignment (Z-score: 5.1 Raw score:420.00) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGA-GPAGLAFA 59 :::::::::: :::::::: d1r0ka2 1 -----------------------------------------QPRTVTVLGAtGSIGHSTL 19 d1ps9a3 60 INAAAR--GHQV-TLFDAHSEiggqfniakqipgkeefyetlryyrrmIEVTGV-TLKLN 115 :::::: :::: :::::::: :::::: ::::: d1r0ka2 20 DLIERNldRYQViALTANRNV---------------------kdladaAKRTNAkRAVIA 58 d1ps9a3 116 -----------------------hTVTAdqLQAFDETILASGIPN-RALAQPLIDSGKTV 151 :::: ::::::::::::::: :::::::::::::: d1r0ka2 59 dpslyndlkealagssveaaagadALVEaaMMGADWTMAAIIGCAgLKATLAAIRKGKTV 118 d1ps9a3 152 HLigGCDVameldarRAIAQGTRLALE-------------i 179 :: :::: :::::::::::: d1r0ka2 119 AL--ANKE-------DMRTPIGHTLAWpkrmetpaesldft 150 FAST alignment (Normalized score: 4.81 Raw score:788.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-AGPAGLAFA 59 ::::::::: ::::::::: d1r0ka2 1 -----------------------------------------QPRTVTVLGATGSIGHSTL 19 d1ps9a3 60 INAAA--RGHQ-VTLFDAHSEIGGQFNIAKQIPGKEEF--YETLRYYRRMIEVTG---VT 111 ::::: :::: :::::: :::::::::: :: d1r0ka2 20 DLIERNLDRYQVIALTAN--------------------RNVKDLADAAKR-----TNAKR 54 d1ps9a3 112 LKLNHTVTADQL---------------------------------QAFDETILASGIPN- 137 :: :::::::::::::: d1r0ka2 55 AV----------IADPSLYNDLKEALAGSSVEAAAGADALVEAAMMGADWTMAAIIGCAG 104 d1ps9a3 138 RALAQPLIDSGKTVHLIGGCDVAMELDAR----RAIAQGTRLALEI-------------- 179 :::::::::::::::: :::::::::: d1r0ka2 105 LKATLAAIRKGKTVAL-------------ANKEDMRTPIGHTL---AWPKRMETPAESLD 148 d1ps9a3 180 -- 180 d1r0ka2 149 FT 150 TMalign alignment (TM-score: 0.44 Raw score:78.49) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-AGPAGLAFA 59 ::::::::: ::::::::: d1r0ka2 1 -----------------------------------------QPRTVTVLGATGSIGHSTL 19 d1ps9a3 60 INAAAR-G-HQV-TLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVT-LKLN 115 :::::: : ::: :::::::::: ::: ::::::: :::: d1r0ka2 20 DLIERNLDRYQVIALTANRNVKD---------------------LAD-AAKRTNAKRAVI 57 d1ps9a3 116 ---------------------H-T--VTADQL--QAFDETILASGIPNRA-LAQPLIDSG 148 : : :: :: :::::::::::::::: ::::::::: d1r0ka2 58 ADPSLYNDLKEALAGSSVEAAAGADALV--EAAMMGADWTMAAIIGCAGLKATLAAIRKG 115 d1ps9a3 149 KTVHLIGGCDVAMELDARRAIAQGTRLAL---EI---------- 179 :::::: :: : :: ::::::::: :: d1r0ka2 116 KTVALA--NK-E-----DM-RTPIGHTLAWPKRMETPAESLDFT 150 HHsearch alignment (Probability: 0.16 E-value:0.01) d1ps9a3 42 QKKNLAVVGA-GPAGLAFAINAAAR--GHQVTLFDAHSEIGGQFNIAKQI-PGKEE--FY 95 :::::::::: :::::::::::::: ::::::::::::::::::::::: ::::: :: d1r0ka2 1 QPRTVTVLGATGSIGHSTLDLIERNLDRYQVIALTANRNVKDLADAAKRTNAKRAVIADP 60 d1ps9a3 96 ETLRYYRRMIEVTGVTLKLNHTVTAD-QLQAFDETILAS-GIPNRALAQPLIDSGKTVHL 153 :::::::::::::::::::::::::: :::::::::::: :::::::::::::::::::: d1r0ka2 61 SLYNDLKEALAGSSVEAAAGADALVEAAMMGADWTMAAIIGCAGLKATLAAIRKGKTVAL 120