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 <-- 1.021 --> Hit

SVM
scoreSVM
score

The query (542d3.pdb) is transitively linked to the hit (d1or7a1) 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 d1or7a1 SigmaE factor (RpoE)Sigma3 and sigma4 domains of RNA polymerase sigma factorsDNA/​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 <-- 1.021 --> Hit

DALI alignment (Z-score: 4.3   Raw score:147.00)

d1gdta1        1 ---------------grkrkiDRDAVLNMWQ-QGLGASHISKTMNIARSTVYKVINESN-     43
                                      :::::::::: ::::::::::::::::::::::::::: 
d1or7a1        1 nlmlseelrqivfrtieslpeDLRMAITLRElDGLSYEEIAAIMDCPVGTVRSRIFRARe     60

d1gdta1       44 --------     44
                         
d1or7a1       61 aidnkvqp     68

FAST alignment (Normalized score: 5.86   Raw score:317.10)

d1gdta1        1 GRKRKI---------------------DRDAVLNMW-QQGLGASHISKTMNIARSTVYKV     38
                                            ::::::::: :::::::::::::::::::::::
d1or7a1        1 ------NLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSR     54

d1gdta1       39 INESN------------     43
                 ::               
d1or7a1       55 IF---RAREAIDNKVQP     68

TMalign alignment (TM-score: 0.72   Raw score:30.83)

d1gdta1        1 -------------------GRKRKIDRDAVLNMWQ-QGLGASHISKTMNIARSTVYKVIN     40
                                        :::::::::::: ::::::::::::::::::::::::
d1or7a1        1 NLMLSEELRQIVFRTIESL----PEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIF     56

d1gdta1       41 E--S--N-----     43
                 :  :  :     
d1or7a1       57 RAREAIDNKVQP     68

HHsearch alignment (Probability: 0.81   E-value:0.00)

d1gdta1        7 DRDAVLNMWQQGLGASHISKTMNIARSTVYKVIN     40
                 ::::::::::::::::::::::::::::::::::
d1or7a1       23 LRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIF     56