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 | d1on2a1 | Manganese transport regulator MntR | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
| Hit | d1je8a_ | Nitrate/nitrite response regulator (NarL) | C-terminal effector domain of the bipartite response regulators | DNA/RNA-binding 3-helical bundle | All α |
Query <-- 0.886 --> IntermediateDALI alignment (Z-score: 1.6 Raw score:124.40) query 1 pDYPVLDAILELYVDRD-----TGADAIVAA-GYDRElvvKTLRMVDtaeykrrqyppgt 54 :::::::::::::::: ::::::::: ::::: ::::::: d1on2a1 1 -TTPSMEMYIEQIYMLIeekgyARVSDIAEAlAVHPSsvtKMVQKLD------------- 46 query 55 kisakgfgkdrrlpitnrwregh 77 d1on2a1 47 --------kdeyliyekyrglvl 61 FAST alignment (Normalized score: 4.60 Raw score:315.00) query 1 PDYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGT 54 :::::::::::::: :::::::::: ::::::::::::::::: d1on2a1 1 -TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDK------------ 47 query 55 KISAKGFGKDRRLPITNRWREGH-------------- 77 d1on2a1 48 -----------------------DEYLIYEKYRGLVL 61 TMalign alignment (TM-score: 0.41 Raw score:31.75) query 1 -PDYPVL-DAILELYVDR-D-----TGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYP 51 :: : ::::::: :: : ::::::::: :::::::::::::::::: d1on2a1 1 T-TP--SMEMYIEQI-YMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDE------- 49 query 52 PGTKISAKGFGKDRRLPITN-RW---RE--GH 77 : :: : : : d1on2a1 50 ---------Y----LI---YE-KYRG-LVL-- 61 HHsearch alignment (Probability: 0.04 E-value:0.09) query 4 PVLDAILELYVDRD-TGADAIVAA-GYDRELVVKTLRMVDTAEY 45 :::::::::::::: ::::::::: ::::::::::::::::::: d1on2a1 7 MYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEY 50
Intermediate <-- 2.085 --> HitDALI alignment (Z-score: 5.4 Raw score:198.50) d1on2a1 1 -----TTPSMEMYIEQIYMLieekgyARVSDIAEALAVHPSSVTKMVQKLDKDEYLIyek 55 ::::::::::::::: ::::::::::::::::::::::::::::::: d1je8a_ 1 rdvnqLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLK--- 51 d1on2a1 56 yrGLVL----------- 61 :::: d1je8a_ 52 --SRVEaavwvhqerif 66 FAST alignment (Normalized score: 6.78 Raw score:430.00) d1on2a1 1 -----TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK 55 ::::::::::::: :::::::::::::::::::::::::::: d1je8a_ 1 RDVNQLTPRERDILKLIA------QGLPNKMIARRLDITESTVKVHVKHMLK-------- 46 d1on2a1 56 YRGLVL-------------------- 61 d1je8a_ 47 ------KMKLKSRVEAAVWVHQERIF 66 TMalign alignment (TM-score: 0.65 Raw score:39.60) d1on2a1 1 -----TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD-EYLIYE 54 :::::::::::::: : ::::::::::::::::::::::::::: :::: d1je8a_ 1 RDVNQLTPRERDILKLIAQ-G-----LPNKMIARRLDITESTVKVHVKHMLKKMKLKS-- 52 d1on2a1 55 KYRGLV-L---------- 61 :: : d1je8a_ 53 ----RVEAAVWVHQERIF 66 HHsearch alignment (Probability: 0.78 E-value:0.00) d1on2a1 12 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD 48 :::::::: ::::::::::::::::::::::::::: d1je8a_ 13 ILKLIAQG--LPNKMIARRLDITESTVKVHVKHMLKK 47