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 | d1u5tb2 | Vacuolar protein sorting-associated protein VPS36 | (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 <-- 1.286 --> HitDALI alignment (Z-score: 6.8 Raw score:249.80) d1on2a1 1 --TTPSMEMYIEQIYMLIeekgYARVSDIAEALA-------VHPSSVTKMVQKLDKDEYL 51 :::::::::::::::: :::::::::::: ::::::::::::::::::: d1u5tb2 1 ekFDVVKEKLVDLIGDNP----GSDLLRLTQILSsnnsksnWTLGILMEVLQNCVDEGDL 56 d1on2a1 52 IYEKY---RGLVL------ 61 ::::: ::::: d1u5tb2 57 LIDKQlsgIYYYKnsywps 75 FAST alignment (Normalized score: 6.86 Raw score:464.00) d1on2a1 1 --TTPSMEMYIEQIYMLIEEKG--YARVSDIAEAL--------AVHPSSVTKMVQKLDKD 48 :::::::::::::: :::::::::: ::::::::::::::::: d1u5tb2 1 EKFDVVKEKLVDLIGD------NPGSDLLRLTQI-LSSNNSKSNWTLGILMEVLQNCVDE 53 d1on2a1 49 EYLIYEKYRGLVL---------------- 61 :::::: d1u5tb2 54 GDLLID-------KQLSGIYYYKNSYWPS 75 TMalign alignment (TM-score: 0.61 Raw score:37.15) d1on2a1 1 TTPSMEMYIEQIYMLIEEKGY-A---RVS-DIAE----ALAVHPSSVTKMVQKLDKDEYL 51 :::::::::::::::: :: : ::: :: : :::::::::::::::::::::: d1u5tb2 1 -EKFDVVKEKLVDLIGD--NPGSDLLRLTQIL-SSNNSKSNWTLGILMEVLQNCVDEGDL 56 d1on2a1 52 IYE-K-Y-RGLVL------ 61 ::: : : ::::: d1u5tb2 57 LIDKQLSGIYYYKNSYWPS 75 HHsearch alignment (Probability: 0.01 E-value:0.63) d1on2a1 5 MEMYIEQIYMLIEEKGYARVSDIAEALAVHP-------SSVTKMVQKLDKDEYLIY 53 ::::::::::::::::::::::::::::::: :::::::::::::::::: d1u5tb2 3 FDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLI 58