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: 542d3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
---|---|---|---|---|---|
Intermediate | d1gdta1 | gamma,delta resolvase (C-terminal domain) | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α |
Hit | d1qbja_ | Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 | (Winged helix( DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
Query <-- 1.647 --> IntermediateFAST alignment (Normalized score: 4.60 Raw score:264.60) query 1 PDYP------VLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG 53 ::::::::: ::::::::::: :::::::::::::: d1gdta1 1 ----GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVINE-------------- 41 query 54 TKISAKGFGKDRRLPITNRWREGH-- 77 d1gdta1 42 ------------------------SN 43 TMalign alignment (TM-score: 0.39 Raw score:30.18) query 1 --PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMVDTAEYKRRQYPPGTKIS 57 ::::::::::::: :::::::::::::::: ::::::: :: :: d1gdta1 1 GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVI-NE-SN-------------- 43 query 58 AKGFGKDRRLPITNRWREGH 77 d1gdta1 44 -------------------- 44 HHsearch alignment (Probability: 0.15 E-value:0.00) query 7 DAILELYVDRDTGADAIVAA-GYDRELVVKTLR 38 ::::::: :::::::::::: :::::::::::: d1gdta1 9 DAVLNMW-QQGLGASHISKTMNIARSTVYKVIN 40
Intermediate <-- 1.005 --> HitDALI alignment (Z-score: 3.5 Raw score:129.10) d1gdta1 1 grKRKI-DRDAVLNMWQQG-----LGASHISKTMNIARSTVYKVINESN----------- 43 :::: :::::::::::: ::::::::::::::::::::::::: d1qbja_ 1 --SIYQdQEQRILKFLEELgegkaTTAHDLSGKLGTPKKEINRVLYSLAkkgklqkeagt 58 d1gdta1 44 ------- 44 d1qbja_ 59 pplwkia 65 FAST alignment (Normalized score: 4.93 Raw score:260.90) d1gdta1 1 GRKRKI-----DRDAVLNMWQ-----QGLGASHISKTMNIARSTVYKVINESN------- 43 :::::::::: :::::::::::::::::::::::: d1qbja_ 1 ------SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLY---SLAKKGK 51 d1gdta1 44 -------------- 44 d1qbja_ 52 LQKEAGTPPLWKIA 65 TMalign alignment (TM-score: 0.61 Raw score:26.38) d1gdta1 1 GRKR--KIDRDAVL--N--M-WQ-QGLGASHISKTMNIARSTVYKVINESN--------- 43 :: :: ::::: : : : ::::::::::::::::::::::::::: d1qbja_ 1 --SIYQDQ-EQRILKFLEELG-EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA 56 d1gdta1 44 --------- 44 d1qbja_ 57 GTPPLWKIA 65 HHsearch alignment (Probability: 0.44 E-value:0.00) d1gdta1 12 LNMWQQGL----GASHISKTMNIARSTVYKVIN 40 :::::::: ::::::::::::::::::::: d1qbja_ 12 KFLEELGEGKATTAHDLSGKLGTPKKEINRVLY 44