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 | d1ldda_ | Anaphase promoting complex (APC) | (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 <-- 1.153 --> HitDALI alignment (Z-score: 6.5 Raw score:239.20) d1on2a1 1 -tTPSMEMYIEQIYMLIEEKGYARVSDIAEALA-----------VHPSSVTKMVQKLDKD 48 ::::::::::::::::::::::::::::::: :::::::::::::::: d1ldda_ 1 kyELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKitvpkdwgynrITLQQLEGYLNTLADE 60 d1on2a1 49 EYLIYEKYRGLVL- 61 ::::::::::::: d1ldda_ 61 GRLKYIANGSYEIv 74 FAST alignment (Normalized score: 6.92 Raw score:465.10) d1on2a1 1 T--TPSMEMYIEQIYMLIEEKGYARVSDIAEAL------------AVHPSSVTKMVQKLD 46 ::::::::::::::::::::::::::::: ::::::::::::::: d1ldda_ 1 -KYELTLQRSLPFIEGMLTNLGAMKLHKIHSF-LKITVPKDWGYNRITLQQLEGYLNTLA 58 d1on2a1 47 KDEYLIYEKYRGLVL------- 61 ::::::::: d1ldda_ 59 DEGRLKYIA------NGSYEIV 74 TMalign alignment (TM-score: 0.64 Raw score:39.30) d1on2a1 1 --TTP--SMEMYIEQIYMLI-EEKGYARVSDIAE-A---------LA-VHPSSVTKMVQK 44 :: : ::: ::::::: : ::::::::::: : :: :::::::::::: d1ldda_ 1 KY-ELTLQ-RSL-PFIEGMLTN-LGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNT 56 d1on2a1 45 LDKDEYLIYEKYRGLVL- 61 ::::::::::::::::: d1ldda_ 57 LADEGRLKYIANGSYEIV 74 HHsearch alignment (Probability: 0.00 E-value:1.50) d1on2a1 7 MYIEQIYMLIEEKGYARVSDIAEALAVH-----------PSSVTKMVQKLDKDEYLIY 53 :::::::::::::::::::::::::::: ::::::::::::::::::: d1ldda_ 8 RSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKY 65