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 | d1hw1a1 | Fatty acid responsive transcription factor FadR, N-terminal domain | "Winged helix" DNA-binding domain | 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 <-- 1.001 --> HitDALI alignment (Z-score: 5.4 Raw score:207.10) d1on2a1 1 tTPSMEMYIEQIYMLIEEKGY------aRVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE 54 :::::::::::::::::::: :::::::::::::::::::::::::::::::: d1hw1a1 1 aQSPAGFAEEYIIESIWNNRFppgtilpAERELSELIGVTRTTLREVLQRLARDGWLTIQ 60 d1on2a1 55 KYRGLVL------- 61 ::::::: d1hw1a1 61 HGKPTKVnnfwets 74 FAST alignment (Normalized score: 7.38 Raw score:495.60) d1on2a1 1 TT--PSMEMYIEQIYMLIEEKGY----------ARVSDIAEALAVHPSSVTKMVQKLDKD 48 ::::::::::::::: ::::::::::::::::::::::::::: d1hw1a1 1 --AQSPAGFAEEYIIESIW----NNRFPPGTILPAERELSELIGVTRTTLREVLQRLARD 54 d1on2a1 49 EYLIYEKYRGLVL-------- 61 :::::::::::: d1hw1a1 55 GWLTIQHGKPTK-VNNFWETS 74 TMalign alignment (TM-score: 0.67 Raw score:40.90) d1on2a1 1 -----TTPS-MEMYI-EQ---IYM--LIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD 48 :: ::::: :: ::: : ::::::::::::::::::::::::::::: d1hw1a1 1 AQSPA--GFAEEYIIESIWNNRFPPG--T--ILPAERELSELIGVTRTTLREVLQRLARD 54 d1on2a1 49 EYLIYE-KYRGLVL------- 61 :::::: :: :::: d1hw1a1 55 GWLTIQHGK-PTKVNNFWETS 74 HHsearch alignment (Probability: 0.98 E-value:0.00) d1on2a1 6 EMYIE-QIYMLIE-EKGYA-RVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLV 60 ::::: ::::::: ::::: :::::::::::::::::::::::::::::::::::::: d1hw1a1 9 EEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTK 66