HorA Server Transitive Detail

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


Query <-- 0.886 --> Intermediate <-- 2.026 --> Hit

SVM
score
SVM
score

The query (542d3.pdb) is transitively linked to the hit (d1in4a1) through the intermediate protein (d1on2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1on2a1 Manganese transport regulator MntR"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1in4a1 Holliday junction helicase RuvB"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 0.886 --> Intermediate
DALI 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 <-- 2.026 --> Hit
DALI alignment (Z-score: 7.7 Raw score:273.10) d1on2a1 1 --TTPSMEMYIEQIYMLIEekgYARVSDIAEALAVHPSSVT-KMVQKLDKDEYLIYEkYR 57 ::::::::::::::::: ::::::::::::::::::: ::::::::::::::: :: d1in4a1 1 egLDEFDRKILKTIIEIYR-ggPVGLNALAASLGVEADTLSeVYEPYLLQAGFLART-PR 58 d1on2a1 58 GLVL------------- 61 :::: d1in4a1 59 GRIVtekaykhlkyevp 75 FAST alignment (Normalized score: 8.84 Raw score:598.10) d1on2a1 1 --TTPSMEMYIEQIYMLIEEKG----YARVSDIAEALAVHPSSV-TKMVQKLDKDEYLIY 53 ::::::::::::::: :::::::::::::::::: ::::::::::::::: d1in4a1 1 EGLDEFDRKILKTIIEI-----YRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLAR 55 d1on2a1 54 EKYRGLVL-------------- 61 : ::::: d1in4a1 56 T-PRGRI-VTEKAYKHLKYEVP 75 TMalign alignment (TM-score: 0.75 Raw score:45.74) d1on2a1 1 --TTPSMEMYIEQIY-MLIEEKGYARVSDIAEALAVHPSSVTK-MVQKLDKDEYLIYEKY 56 ::::::::::::: :: :: ::::::::::::::::::::: :::::::::::::: : d1in4a1 1 EGLDEFDRKILKTIIEIY-RG-GPVGLNALAASLGVEADTLSEVYEPYLLQAGFLART-P 57 d1on2a1 57 RGLVL------------- 61 ::::: d1in4a1 58 RGRIVTEKAYKHLKYEVP 75 HHsearch alignment (Probability: 0.87 E-value:0.00) d1on2a1 5 MEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQ-KLDKDEYLIYEKYRGL 59 :::::::::: :::::::::::::::::::::::::::: :::::::::::::::: d1in4a1 7 DRKILKTIIE-IYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTPRGRI 61