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 <-- 1.647 --> Intermediate <-- 1.281 --> Hit

SVM
scoreSVM
score

The query (542d3.pdb) is transitively linked to the hit (d1biaa1) through the intermediate protein (d1gdta1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gdta1 gamma,​delta resolvase (C-​terminal domain)Homeodomain-​likeDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1biaa1 Biotin repressor,​ N-​terminal domain"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 1.647 --> Intermediate

FAST alignment (Normalized score: 4.60   Raw score:264.60)

query          1 PDYP------VLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
                           ::::::::: ::::::::::: ::::::::::::::              
d1gdta1        1 ----GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVINE--------------     41

query         54 TKISAKGFGKDRRLPITNRWREGH--     77
                                           
d1gdta1       42 ------------------------SN     43

TMalign alignment (TM-score: 0.39   Raw score:30.18)

query          1 --PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMVDTAEYKRRQYPPGTKIS     57
                   ::::::::::::: :::::::::::::::: ::::::: :: ::              
d1gdta1        1 GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVI-NE-SN--------------     43

query         58 AKGFGKDRRLPITNRWREGH     77
                                     
d1gdta1       44 --------------------     44

HHsearch alignment (Probability: 0.15   E-value:0.00)

query          7 DAILELYVDRDTGADAIVAA-GYDRELVVKTLR     38
                 ::::::: :::::::::::: ::::::::::::
d1gdta1        9 DAVLNMW-QQGLGASHISKTMNIARSTVYKVIN     40


Intermediate <-- 1.281 --> Hit

DALI alignment (Z-score: 3.4   Raw score:122.10)

d1gdta1        1 gRKRKiDRDAVLNMWQ--qGLGASHISKTMNIARSTVYKVINESN---------------     43
                  :::: ::::::::::   ::::::::::::::::::::::::::               
d1biaa1        1 -MKDNtVPLKLIALLAngeFHSGEQLGETLGMSRAAINKHIQTLRdwgvdvftvpgkgys     59

d1gdta1       44 ----     44
                     
d1biaa1       60 lpep     63

FAST alignment (Normalized score: 5.47   Raw score:284.50)

d1gdta1        1 GRKRKIDRDAVLNMWQ--QGLGASHISKTMNIARSTVYKVINESN---------------     43
                 ::::: ::::::::::  ::::::::::::::::::::::::                  
d1biaa1        1 MKDNT-VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQ---TLRDWGVDVFTVPGK     56

d1gdta1       44 -------     44
                        
d1biaa1       57 GYSLPEP     63

TMalign alignment (TM-score: 0.60   Raw score:25.89)

d1gdta1        1 -GRKRKIDRDAVLNMWQQ--GLGASHISKTMNIARSTVYKVINESN--------------     43
                    :::::::::::::::  ::::::::::::::::::::::::::              
d1biaa1        1 M--KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGY     58

d1gdta1       44 -----     44
                      
d1biaa1       59 SLPEP     63

HHsearch alignment (Probability: 0.88   E-value:0.00)

d1gdta1        9 DAVLNMWQQ--GLGASHISKTMNIARSTVYKVINE     41
                 :::::::::  ::::::::::::::::::::::::
d1biaa1        8 LKLIALLANGEFHSGEQLGETLGMSRAAINKHIQT     42