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 | d1q1ra2 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1c1da1 | Phenylalanine dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.466 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.730 --> HitDALI alignment (Z-score: 5.2 Raw score:391.60) d1q1ra2 1 rplpvasgavgkannfrylrtlEDAECIRRQ-------lIADNRLVVIGGGYIGLEVAAT 53 ::::::::: ::::::::::::::::::::: d1c1da1 1 ---------------safttavGVFEAMKATvahrglgsLDGLTVLVQGLGAVGGSLASL 45 d1q1ra2 54 AIKANMHVTLLDTAARVlervtappvsafyEHLHREAGVDIRtgTQVCgfemstdqqkvt 113 ::::::::::::::::: :::::::::::: :::: d1c1da1 46 AAEAGAQLLVADTDTER-------------VAHAVALGHTAV--ALED------------ 78 d1q1ra2 114 avlcedgTRLPADLVIAGIG---------------------------------------- 133 ::::::::::::: d1c1da1 79 ------vLSTPCDVFAPCAMggvittevartldcsvvagaannviadeaasdilhargil 132 d1q1ra2 134 ------------------------------------------------------------ 134 d1c1da1 133 yapdfvanaggaihlvgrevlgwsesvvheravaigdtlnqvfeisdndgvtpdeaartl 192 d1q1ra2 134 --------- 134 d1c1da1 193 agrrareas 201 FAST alignment (Normalized score: 5.15 Raw score:842.30) d1q1ra2 1 RPLPVASGAVGKANNFRYLR-----TLEDAECIRRQL---------IADNRLVVIGGGYI 46 :::::::::: :::::::::::::: d1c1da1 1 --------------------SAFTTAVGVFEAMKA--TVAHRGLGSLDGLTVLVQGLGAV 38 d1q1ra2 47 GLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMS 106 :::::::::::::::::::: :::::::::::::::: d1c1da1 39 GGSLASLAAEAGAQLLVADT-------------DTERVAHAVALGHTAV----------- 74 d1q1ra2 107 TDQQKVTAVLCEDG-----TRLPADLVIAGIG---------------------------- 133 ::::::::::: d1c1da1 75 --------------ALEDVLSTPCDVFAPC--AMGGVITTEVARTLDCSVVAGAANNVIA 118 d1q1ra2 134 ------------------------------------------------------------ 134 d1c1da1 119 DEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEIS 178 d1q1ra2 134 ----------------------- 134 d1c1da1 179 DNDGVTPDEAARTLAGRRAREAS 201 TMalign alignment (TM-score: 0.48 Raw score:64.27) d1q1ra2 1 ---RPLPVASGAVGKANNFRYLRTLEDAECIRR-Q------LIADNRLVVIGGGYIGLEV 50 :::::::::::: : ::::::::::::::::::: d1c1da1 1 SAF------------------TTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSL 42 d1q1ra2 51 AATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQ 110 ::::::::::::::: ::: : :::::::::::::: :::: d1c1da1 43 ASLAAEAGAQLLVAD-TDT----------E--RVAHAVALGHTAVA-LEDV--------- 79 d1q1ra2 111 KVTAVLCEDGTRLPADLVIAGIG------------------------------------- 133 :: ::::::::::: d1c1da1 80 ----LS------TPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHAR 129 d1q1ra2 134 ------------------------------------------------------------ 134 d1c1da1 130 GILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAA 189 d1q1ra2 134 ------------ 134 d1c1da1 190 RTLAGRRAREAS 201 HHsearch alignment (Probability: 0.95 E-value:0.00) d1q1ra2 34 ADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVD 93 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1c1da1 26 DGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCD 85 d1q1ra2 94 IRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIA 130 :::::::::: :::::::::::::::: d1c1da1 86 VFAPCAMGGV-----------ITTEVARTLDCSVVAG 111