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 | d1t1ra2 | 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 <-- 1.630 --> HitDALI alignment (Z-score: 4.6 Raw score:375.80) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkKNLAVVGA-GPAGLAFA 59 :::::::: :::::::: d1t1ra2 1 -------------------------------------------KQLTILGStGSIGCSTL 17 d1ps9a3 60 INAAARG--HQVT-LFDAHseiggqfniakqipgkeefyetLRYYRRMIEVTGVT-LKLN 115 ::::::: :::: ::::: :::::::::::::: :::: d1t1ra2 18 DVVRHNPehFRVVaLVAGK---------------------nVTRMVEQCLEFSPRyAVMD 56 d1ps9a3 116 -------------------------hTVTA-dqLQAFDETILASGIPN-RALAQPLIDSG 148 :::: ::::::::::::::: ::::::::::: d1t1ra2 57 deasakllktmlqqqgsrtevlsgqqAACDmaaLEDVDQVMAAIVGAAgLLPTLAAIRAG 116 d1ps9a3 149 KTVHLigGCDVameldarraiaqgtrlalei 179 ::::: :::: d1t1ra2 117 KTILL--ANKE-------------------- 125 FAST alignment (Normalized score: 3.58 Raw score:536.20) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVV-GAGPAGLAFA 59 :::::: :::::::::: d1t1ra2 1 -------------------------------------------KQLTILGSTGSIGCSTL 17 d1ps9a3 60 INAAARGHQ-------VTLFDAHSEIGGQFNIAKQIPGKEEFYE-TLRYYRRMIEVTGVT 111 ::::: :::::: :::::::::::::: d1t1ra2 18 DVVRH----NPEHFRVVALVAG----------------------KNVTRMVEQCLEFSP- 50 d1ps9a3 112 LKLNHTVTADQL----------------------------------------QAFDETIL 131 :::::::: d1t1ra2 51 ------------RYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMA 98 d1ps9a3 132 ASGIPN--RALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI---- 179 ::::: :::::::::::::::: d1t1ra2 99 AIVGA-AGLLPTLAAIRAGKTILL--------------------------ANKE 125 TMalign alignment (TM-score: 0.40 Raw score:72.16) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-AGPAGLAFA 59 ::::::: ::::::::: d1t1ra2 1 -------------------------------------------KQLTILGSTGSIGCSTL 17 d1ps9a3 60 INAAARG--HQV-TLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTL--KL 114 ::::::: ::: :::::::::: ::: ::: :::: :: d1t1ra2 18 DVVRHNPEHFRVVALVAGKNVTR---------------------MVE-QCL-EFSPRYAV 54 d1ps9a3 115 N-----------------------HT---VTADQL--QA-FDETILASGIPNRA-LAQPL 144 : :: :: :: :: :::::::::::::: ::::: d1t1ra2 55 MDDEASAKLLKTMLQQQGSRTEVLSGQQAAC--DMAALEDVDQVMAAIVGAAGLLPTLAA 112 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 :::::::::: ::: d1t1ra2 113 IRAGKTILLA--NKE-------------------- 125 HHsearch alignment (Probability: 0.10 E-value:0.01) d1ps9a3 44 KNLAVVGA-GPAGLAFAINAAAR--GHQVTLFDAHSEIGG 80 :::::::: :::::::::::::: ::::::::::::::: d1t1ra2 1 KQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTR 40