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 <-- 0.978 --> Hit

SVM
scoreSVM
score

The query (542d3.pdb) is transitively linked to the hit (d1dpua_) 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 d1dpua_ C-​terminal domain of RPA32​(​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 <-- 0.978 --> Hit

DALI alignment (Z-score: 2.7   Raw score:110.80)

d1gdta1        1 grkrkiDRDAVLNMWQQ-----GLGASHISKTMN-IARSTVYKVINESN-----------     43
                       :::::::::::     :::::::::::: ::::::::::::::           
d1dpua_        1 angltvAQNQVLNLIKAcprpeGLNFQDLKNQLKhMSVSSIKQAVDFLSneghiystvdd     60

d1gdta1       44 ---------     44
                          
d1dpua_       61 dhfkstdae     69

FAST alignment (Normalized score: 4.47   Raw score:243.70)

d1gdta1        1 GRKRKI------DRDAVLNMWQQ------GLGASHISKT-MNIARSTVYKVINESN----     43
                             ::::::::::       :::::::::: ::::::::::::        
d1dpua_        1 ------ANGLTVAQNQVLNLIK-ACPRPEGLNFQDLKNQLKHMSVSSIKQAV----DFLS     49

d1gdta1       44 --------------------     44
                                     
d1dpua_       50 NEGHIYSTVDDDHFKSTDAE     69

TMalign alignment (TM-score: 0.55   Raw score:23.77)

d1gdta1        1 ----GRKRKIDRDAVLN-MWQ-Q----GLGASHISKTMN-IARSTVYKVINES-N-----     43
                         ::::::::: : : :    :::::::::::: ::::::::::::: :     
d1dpua_        1 ANGL----TVAQNQVLNLI-KACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY     55

d1gdta1       44 --------------     44
                               
d1dpua_       56 STVDDDHFKSTDAE     69

HHsearch alignment (Probability: 0.47   E-value:0.00)

d1gdta1       15 WQQGLGASHISKTM-NIARSTVYKVINE     41
                 :::::::::::::: :::::::::::::
d1dpua_       20 RPEGLNFQDLKNQLKHMSVSSIKQAVDF     47