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 | d1vi2a1 | Putative shikimate dehydrogenase YdiB | 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 <-- 1.558 --> HitDALI alignment (Z-score: 5.2 Raw score:451.50) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGAGPAGLAFAI 60 ::::::::::::::::::: d1vi2a1 1 -------------------------dgtghiraikesgfdiKGKTMVLLGAGGASTAIGA 35 d1ps9a3 61 NAAARGH-QVTLFDAHSEIggqfniakqipgkeefyetlryyRRMIEVTG------VTLK 113 ::::::: ::::::::::: :::::::: :::: d1vi2a1 36 QGAIEGLkEIKLFNRRDEF-------------------fdkaLAFAQRVNentdcvVTVT 76 d1ps9a3 114 LNHT-vtaDQLQ-AFDETILASGIP------NRAL-aQPLIdSGKTVHLIggcDVAMEL- 163 :::: :::: :::::::::::: :::: :::: :::::::: :::::: d1vi2a1 77 DLADqqafAEALaSADILTNGTKVGmkplenESLVndISLLhPGLLVTEC---VYNPHMt 133 d1ps9a3 164 ---------------------------------darraiaqgtrlalei 179 d1vi2a1 134 kllqqaqqagcktidgygmllwqgaeqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.32 Raw score:779.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAV----------------QKK 44 ::: d1vi2a1 1 -----------------------------------------DGTGHIRAIKESGFDIKGK 19 d1ps9a3 45 NLAVVGAGPAGLAFAINAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEF----YETLR 99 :::::::::::::::::::::: :::::::: ::::: d1vi2a1 20 TMVLLGAGGASTAIGAQGAIEGLKEIKLFNR--------------------RDEFFDKAL 59 d1ps9a3 100 YYRRM-IEV--TGVTLKLNHTVT-------ADQLQ-AFDETILASGIPN----------- 137 ::::: ::: :::::: ::::: :::::::: d1vi2a1 60 AFAQRVNENTDCVVTVT------DLADQQAFAEALASADILTNG-----TKVGMKPLENE 108 d1ps9a3 138 ------------------------RALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGT 173 ::::::::::::::: d1vi2a1 109 SLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTI--------------------- 147 d1ps9a3 174 RLALEI----------------------------------- 179 d1vi2a1 148 ------DGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.45 Raw score:80.75) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACH--ETKM--PIL---PAVQK-KNLAVVGAG 52 ::: : : : :::: ::::::::: d1vi2a1 1 -------------------------DGT--GHI---RAI--KESG-FDIKGKTMVLLGAG 27 d1ps9a3 53 PAGLAFAINAAARGHQ-VTLFDAH---SEIGGQFNIAKQIPGKEEFYETLRYYRRMIE-V 107 :::::::::::::::: ::::::: :::: :: :::::: : d1vi2a1 28 GASTAIGAQGAIEGLKEIKLFNRRDEFFDKA------------------LA-FAQRVNEN 68 d1ps9a3 108 T-GVTLKLNHTVT--ADQLQ-AFDETILASGIP------NRALAQPLIDSG-KTVHLIGG 156 : ::::::::::: ::::: :::::::::::: :::::::::::: :::::: d1vi2a1 69 TDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTEC-- 126 d1ps9a3 157 CDVAM------------------ELDARRA-IAQG-TR--LAL----------------- 177 :::: : ::: :: : d1vi2a1 127 -VYNPHMTKLLQQAQQAGCKTID------GY-GMLLWQGA--EQFTLWTGKDFPLEYVKQ 176 d1ps9a3 178 ------EI 179 d1vi2a1 177 VMGFGA-- 182 HHsearch alignment (Probability: 0.96 E-value:0.00) d1ps9a3 38 LPAVQKKNLAVVGAGPAGLAFAINAAARGH-QVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 :::::::::::::::::::::::::::::: ::::::::::: ::: d1vi2a1 13 GFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEF---------------FDK 57 d1ps9a3 97 TLRYYRRMIEVTGVTLKLNHTVT----ADQLQAFDETILAS--GIPN 137 ::::::::::::::::::::::: :::::::::::::: :::: d1vi2a1 58 ALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKP 104