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 <-- 0.715 --> Intermediate <-- 1.338 --> Hit

SVM
scoreSVM
score

The query (542d3.pdb) is transitively linked to the hit (d1fjla_) through the intermediate protein (d1ri7a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ri7a1 Putative transcriptional regulator PH1519"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1fjla_ Paired proteinHomeodomain-​likeDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 0.715 --> Intermediate

DALI alignment (Z-score: 3.0   Raw score:159.80)

query          1 pDYPVLDAILELYVDRD-TGADAIVAA-gYDRELVVKTLRMVDTAEykrrqyppgtkisa     58
                  :::::::::::::::: :::::::::  :::::::::::::::::              
d1ri7a1        1 -LDEIDKKIIKILQNDGkAPLREISKItgLAESTIHERIRKLRESG-----------vik     48

query         59 KGFGkdrrlpitnrwregh     77
                 ::::               
d1ri7a1       49 KFTA-------iidpealg     60

FAST alignment (Normalized score: 4.52   Raw score:307.00)

query          1 PDYPVLDAILELYVDR-DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISA     58
                  ::::::::::::::: ::::::::: :::::::::::::::::                
d1ri7a1        1 -LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRE----------------     43

query         59 KGFGKDRRLPITNRWREGH-----------------     77
                                                     
d1ri7a1       44 -------------------SGVIKKFTAIIDPEALG     60

TMalign alignment (TM-score: 0.42   Raw score:32.51)

query          1 PDYPVLDAILELYVDRD--TGADAIVAAGYDR-ELVVKTLRM-VDTAE--YKRRQYPPGT     54
                 :: :::::::::: :::  ::::::::::::: ::::::::: : :::    :       
d1ri7a1        1 LD-EIDKKIIKIL-QNDGKAPLREISKITGLAESTIHERIRKLR-ESGVI--K-------     48

query         55 KISAKGFGKDRR--------LPITNRWREGH     77
                       ::  ::                   
d1ri7a1       49 ------KF--TAIIDPEALG-----------     60

HHsearch alignment (Probability: 0.05   E-value:0.06)

query          4 PVLDAILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTA     43
                 ::::::::::::::  ::::::::: :::::::::::::::::
d1ri7a1        2 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES     44


Intermediate <-- 1.338 --> Hit

DALI alignment (Z-score: 3.8   Raw score:168.10)

d1ri7a1        1 ---------lDEIDKKIIKILQNDGKA---PLREISKITGLAESTIHERIRKLRESGvik     48
                           :::::::::::::::::   :::::::::::::::::::::::::::   
d1fjla_        1 kqrrsrttfsASQLDELERAFERTQYPdiyTREELAQRTNLTEARIQVWFQNRRARL---     57

d1ri7a1       49 kftaiidpealg     60
                             
d1fjla_       58 ----rkqhtsvs     65

FAST alignment (Normalized score: 5.95   Raw score:371.60)

d1ri7a1        1 ---------LDEIDKKIIKILQNDGKA---PLREISKITGLAESTIHERIRKLRESGVIK     48
                          ::::::::::::::::::   :::::::::::::::::::::::::     
d1fjla_        1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRA-----     55

d1ri7a1       49 KFTAIIDPEALG----------     60
                                       
d1fjla_       56 ------------RLRKQHTSVS     65

TMalign alignment (TM-score: 0.54   Raw score:32.29)

d1ri7a1        1 --------LD-E-IDKKIIKILQNDG--KA--PLREISKITGLAESTIHERIRKLRESGV     46
                          : : :::::::::: ::  ::  ::::::::::::::::::::::::::::
d1fjla_        1 KQRRSRTT-FSASQLDELERAFE-RTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR     58

d1ri7a1       47 -IK-----KFTAIIDPEALG     60
                   :                 
d1fjla_       59 K-QHTSVS------------     65

HHsearch alignment (Probability: 0.14   E-value:0.02)

d1ri7a1        5 DKKIIKIL-QNDGKAP---LREISKITGLAESTIHERI     38
                 :::::::: :::::::   :::::::::::::::::::
d1fjla_       13 QLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWF     50