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 | d1hq1a_ | Signal sequence binding protein Ffh | Signal peptide-binding domain | Signal peptide-binding domain | 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 <-- 0.857 --> HitDALI alignment (Z-score: 2.9 Raw score:141.40) d1on2a1 1 -------------TTPSMEMYIEQIYMLieEKGY---------aRVSDIAEALAVHPSSV 38 ::::::::::::::: :::: :::::::::::::::: d1hq1a_ 1 gfdlndfleqlrqDDKVLVRMEAIINSM--TMKErakpeiikgsRKRRIAAGSGMQVQDV 58 d1on2a1 39 TKMVQKLDKDEyliyekyrglvl 61 ::::::::::: d1hq1a_ 59 NRLLKQFDDMQ-----rmmkkmk 76 FAST alignment (Normalized score: 4.60 Raw score:313.30) d1on2a1 1 ----------------TTPSMEMYIEQIYMLIEEKGYA---------------RVSDIAE 29 ::::::::::: ::::::: d1hq1a_ 1 GFDLNDFLEQLRQDDKVLVRMEAIINS-----------MTMKERAKPEIIKGSRKRRIAA 49 d1on2a1 30 ALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVL--------- 61 :::::::::::::::::: d1hq1a_ 50 GSGMQVQDVNRLLKQFDD--------------MQRMMKKMK 76 TMalign alignment (TM-score: 0.52 Raw score:31.48) d1on2a1 1 ---------TTP-----S--MEM-YIEQIYMLIE-----EKGYA---RVSDIAEALAVHP 35 ::: : ::: : ::: :::: :: ::::::::::::: d1hq1a_ 1 GFDLNDFLEQLRQDDKVLVRMEAII-NSM-TMKERAKPE---IIKGSRKRRIAAGSGMQV 55 d1on2a1 36 SSVTKMVQKLDKDEY------LIYEKYRGLVL 61 ::::::::::::::: d1hq1a_ 56 QDVNRLLKQFDDMQRMMKKMK----------- 76 HHsearch alignment (Probability: 0.04 E-value:0.03) d1on2a1 22 ARVSDIAEALAVHPSSVTKMVQKLDK 47 :::::::::::::::::::::::::: d1hq1a_ 42 SRKRRIAAGSGMQVQDVNRLLKQFDD 67