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 | d1pdnc_ | Paired protein (prd) | Homeodomain-like | 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 <-- 0.834 --> HitDALI alignment (Z-score: 4.0 Raw score:163.70) d1on2a1 1 -----------------tTPSMEMYIEQIYMLieekgyARVSDIAEALAVHPSSVTKMVQ 43 :::::::::::::: :::::::::::::::::::::: d1pdnc_ 1 qgrvnqlggvfingrplpNNIRLKIVEMAADG------IRPCVISRQLRVSHGCVSKILN 54 d1on2a1 44 KLDKDEY---------------------------------------------------li 52 ::::::: d1pdnc_ 55 RYQETGSirpgviggskpriatpeienrieeykrsspgmfsweirekliregvcdrstap 114 d1on2a1 53 yekyrglvl 61 d1pdnc_ 115 svsaisrlv 123 FAST alignment (Normalized score: 4.24 Raw score:367.60) d1on2a1 1 -----------------TTPSMEMYIEQIYMLIEEKG-YARVSDIAEALAVHPSSVTKMV 42 ::::::::::::: :::::::::::::::::::::: d1pdnc_ 1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAA-------DGIRPCVISRQLRVSHGCVSKIL 53 d1on2a1 43 QKLDKDEYLIYEKYRGLVL----------------------------------------- 61 :::::: d1pdnc_ 54 NRYQET-------------GSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIRE 100 d1on2a1 62 ----------------------- 62 d1pdnc_ 101 KLIREGVCDRSTAPSVSAISRLV 123 TMalign alignment (TM-score: 0.37 Raw score:22.67) d1on2a1 1 ------------------------------------------------------------ 1 d1pdnc_ 1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETG 60 d1on2a1 1 ----------T----TPS-MEMYIEQIYMLIEEKGYA--R-VSDIAEALA-VHPSSVTK- 40 : ::: ::::::: ::::: ::: : ::::::: : :::::::: d1pdnc_ 61 SIRPGVIGGSKPRIATPEIENRIEEY-KRSSP--GMFSWEIREKLIRE-GVCDRSTAPSV 116 d1on2a1 41 MVQKLDKDEYLIYEKYRGLVL 61 ::::: :: d1pdnc_ 117 -SAISR---LV---------- 123 HHsearch alignment (Probability: 0.96 E-value:0.00) d1on2a1 4 SMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRG 58 :::::::::: :::: : ::::::::::::::::::::::::::::::::::::: d1pdnc_ 18 PNNIRLKIVE-MAAD-G-IRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 69