HHsearch alignment for GI: 254780470 and conserved domain: cd04456
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=97.50 E-value=0.00081 Score=43.36 Aligned_cols=61 Identities=25% Similarity=0.270 Sum_probs=52.0
Q ss_pred EEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEECCCE
Q ss_conf 89998158981799981667765333233544333445555444555554455568828999912511201647702996
Q gi|254780470|r 11 GIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDK 90 (110)
Q Consensus 11 G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~GDk 90 (110)
T Consensus 4 ~~V~~~lG~~r~~v~c--------------------------------------~DG~~rl~~ipGk~rk-rvWI~~gD~ 44 (78)
T cd04456 4 VRVLRMLGNNRHEVEC--------------------------------------ADGQRRLVSIPGKLRK-NIWIKRGDF 44 (78)
T ss_pred EEEEECCCCCEEEEEE--------------------------------------CCCCEEEEEECCCCEE-EEEEECCCE
T ss_conf 9999836997799991--------------------------------------8999999994063334-089836999
Q ss_pred EEEEECCC-CCCCCEEEEEEC
Q ss_conf 99997467-578435988429
Q gi|254780470|r 91 VKVAMNPY-DMTRARITYRFK 110 (110)
Q Consensus 91 V~Ve~SPY-DLtkGRItyR~K 110 (110)
T Consensus 45 VlV~~~e~~~d~K~dIi~ky~ 65 (78)
T cd04456 45 LIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred EEEEEHHHCCCCEEEEEEECC
T ss_conf 999881237984699999679