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 | d1l3la1 | Quorum-sensing transcription factor TraR, C-terminal domain | 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 <-- 1.340 --> HitDALI alignment (Z-score: 4.9 Raw score:182.60) d1on2a1 1 ----TTPSMEMYIEQIYMLieekgyARVSDIAEALAVHPSSVTKMVQKLDKDEyliyeky 56 ::::::::::::::: :::::::::::::::::::::::::::: d1l3la1 1 daawLDPKEATYLRWIAVG------KTMEEIADVEGVKYNSVRVKLREAMKRF-----dv 49 d1on2a1 57 rGLVL----------- 61 :::: d1l3la1 50 rSKAHltalairrkli 65 FAST alignment (Normalized score: 6.17 Raw score:388.70) d1on2a1 1 ----TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY 56 ::::::::::::: :::::::::::::::::::::::::::: d1l3la1 1 DAAWLDPKEATYLRWIA------VGKTMEEIADVEGVKYNSVRVKLREAMK--------- 45 d1on2a1 57 RGLVL-------------------- 61 d1l3la1 46 -----RFDVRSKAHLTALAIRRKLI 65 TMalign alignment (TM-score: 0.56 Raw score:34.16) d1on2a1 1 ---TTPSMEMYIEQIYML-IEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY 56 :: ::::::::: : : : ::::::::::::::::::::::::::::::::: d1l3la1 1 DAAWL--DPKEATYLR-WIA--V-GKTMEEIADVEGVKYNSVRVKLREAMKRFDVRS--- 51 d1on2a1 57 RGLV--L--------- 61 :: : d1l3la1 52 --KAHLTALAIRRKLI 65 HHsearch alignment (Probability: 0.80 E-value:0.00) d1on2a1 11 QIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD 48 ::::::::: ::::::::::::::::::::::::::: d1l3la1 11 TYLRWIAVG--KTMEEIADVEGVKYNSVRVKLREAMKR 46