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 | d1fsea_ | Germination protein GerE | 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 <-- 1.990 --> HitDALI alignment (Z-score: 4.8 Raw score:185.60) d1on2a1 1 ----TTPSMEMYIEQIYMLieekgyARVSDIAEALAVHPSSVTKMVQKLDKDEyliyeky 56 ::::::::::::::: :::::::::::::::::::::::::::: d1fsea_ 1 skplLTKREREVFELLVQD------KTTKEIASELFISEKTVRNHISNAMQKL-----gv 49 d1on2a1 57 rGLVL------------- 61 :::: d1fsea_ 50 kGRSQavvellrmgelel 67 FAST alignment (Normalized score: 6.54 Raw score:418.30) d1on2a1 1 ----TTPSMEMYIEQIYMLIEEKG-YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK 55 ::::::::::::: ::::::::::::::::::::::::::: d1fsea_ 1 SKPLLTKREREVFELLV-------QDKTTKEIASELFISEKTVRNHISNAMQ-------- 45 d1on2a1 56 YRGLVL---------------------- 61 d1fsea_ 46 ------KLGVKGRSQAVVELLRMGELEL 67 TMalign alignment (TM-score: 0.58 Raw score:35.18) d1on2a1 1 ---TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYL-IYEKY 56 :: :::::::::::: : ::::::::::::::::::::::::::::::: ::: d1fsea_ 1 SKPLL--TKREREVFELLV--Q-DKTTKEIASELFISEKTVRNHISNAMQKLGVKGRS-- 53 d1on2a1 57 RGLVL----------- 61 ::: d1fsea_ 54 --QAVVELLRMGELEL 67 HHsearch alignment (Probability: 0.81 E-value:0.00) d1on2a1 12 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD 48 :::::::: ::::::::::::::::::::::::::: d1fsea_ 12 VFELLVQD--KTTKEIASELFISEKTVRNHISNAMQK 46