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 <-- 2.003 --> Hit

SVM
scoreSVM
score

The query (542d3.pdb) is transitively linked to the hit (d1tqia1) 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 d1tqia1 Rio2 serine protein kinase N-​terminal domain"​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 <-- 2.003 --> Hit

DALI alignment (Z-score: 7.3   Raw score:284.40)

d1on2a1        1 ---------TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYL     51
                          :::::::::::::::::::::::::::::::::::::::::::::::::::
d1tqia1        1 mniaelygkMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVV     60

d1on2a1       52 IYEKY--rGLVL------------------     61
                 :::::   ::::                  
d1tqia1       61 QNRQKdyeGSTFtfiglslyslhrlvrsgk     90

FAST alignment (Normalized score: 8.51   Raw score:630.90)

d1on2a1        1 ---------TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYL     51
                          :::::::::::::::::::::::::::::::::::::::::::::::::::
d1tqia1        1 MNIAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVV     60

d1on2a1       52 IY-EKYRGLVL-----------------------     61
                 :: ::::                           
d1tqia1       61 QNRQKDY----EGSTFTFIGLSLYSLHRLVRSGK     90

TMalign alignment (TM-score: 0.76   Raw score:46.27)

d1on2a1        1 ---------TTPSMEMYIEQIYMLIEEKG-YARVSDIAEALAVHPSSVTKMVQKLDKDEY     50
                          :::::::::::::::: ::: ::::::::::::::::::::::::::::::
d1tqia1        1 MNIAELYGKMGKHSWRIMDAIFKNL-WDYEYVPLQLISSHARIGEEKARNILKYLSDLRV     59

d1on2a1       51 LIYE-KYR-GLVL------------------     61
                 :::: ::: ::::                  
d1tqia1       60 VQNRQKDYEGSTFTFIGLSLYSLHRLVRSGK     90

HHsearch alignment (Probability: 0.95   E-value:0.00)

d1on2a1        8 YIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE--KYRGLVL     61
                 :::::::::::::::::::::::::::::::::::::::::::::::  :::::::
d1tqia1       17 IMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNRQKDYEGSTF     72