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 <-- 1.524 --> Hit

SVM
score
SVM
score

The query (542d3.pdb) is transitively linked to the hit (d1j5ya1) 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 d1j5ya1 Putative transcriptional regulator TM1602,​ 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 <-- 1.524 --> Hit
DALI alignment (Z-score: 3.9 Raw score:135.00) d1gdta1 1 gRKRKI--DRDAVLNMWQQG---LGASHISKTMNIARSTVYKVINESN------------ 43 ::::: :::::::::::: ::::::::::::::::::::::::: d1j5ya1 1 -MKTVRqeRLKSIVRILERSkepVSGAQLAEELSVSRQVIVQDIAYLRslgynivatprg 59 d1gdta1 44 ------ 44 d1j5ya1 60 yvlagg 65 FAST alignment (Normalized score: 5.04 Raw score:266.40) d1gdta1 1 GRKRKI-------DRDAVLNMWQ---QGLGASHISKTMNIARSTVYKVINESN------- 43 :::::::::: ::::::::::::::::::::::: d1j5ya1 1 ------MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDI----AYLRSLG 50 d1gdta1 44 --------------- 44 d1j5ya1 51 YNIVATPRGYVLAGG 65 TMalign alignment (TM-score: 0.67 Raw score:28.96) d1gdta1 1 GRKR-KI--DRDAVLNMWQ--Q--GLGASHISKTMNIARSTVYKVINESN---------- 43 :: :: :::::::: : : :::::::::::::::::::::::::: d1j5ya1 1 --MKTVRQERLKSIVRI-LERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATP 57 d1gdta1 44 -------- 44 d1j5ya1 58 RGYVLAGG 65 HHsearch alignment (Probability: 0.91 E-value:0.00) d1gdta1 9 DAVLNMW-Q-Q-GLGASHISKTMNIARSTVYKVINE 41 ::::::: : : :::::::::::::::::::::::: d1j5ya1 10 KSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAY 45