HHsearch alignment for GI: 254781033 and conserved domain: pfam05843
>pfam05843 Suf Suppressor of forked protein (Suf). This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and an important role of the GU-rich sequence for this regulation to occur.
Probab=93.37 E-value=0.61 Score=25.35 Aligned_cols=144 Identities=16% Similarity=0.096 Sum_probs=88.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99999999995257456999999999502310357899999999999966998999999987543133527999999999
Q gi|254781033|r 190 VTEAVVQQYVLAKEWSRAITFLNQKKKNAKEWNRNRAILLIARSLENADKGDMIASYHDAIESLKLCDNSIMASICAAKS 269 (492)
Q Consensus 190 a~~~L~~l~~~~gdw~~A~~~l~~~~~~~~~~~~~~a~l~~~~a~~~~~~~~~~~A~~~~~~a~~~~p~~~~a~~~~a~~ 269 (492)
T Consensus 3 ~yi~~m~~~rR~eGi~~aR~vF~~aRk~~~~t~---~vyva~Al~E~~~~~d~~~a~kIFelGlK~f~~~~~y~~~Yld~ 79 (275)
T pfam05843 3 VYIQYMRAMRRAEGIKAARKVFKKARKKGRITY---HVYVASALMEYYCSKDPKTAFKIFELGLKLFPEDGEFVLKYLDF 79 (275)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCH---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 899999999984262889999999860789855---99999999999873780799999999987658978999999999
Q ss_pred HHHCCCHHHHHHHHHHHHHHCC-CHH---HHHHHHHHC--CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 9973994789999999998328-989---999999850--789589999999999826898368999999999
Q gi|254781033|r 270 LISQNKKRKAEVILEKIWKVNP-HPE---IANIYTHLL--SENTVGKLKRALRLEEINKESVESLVIVSKIAL 336 (492)
Q Consensus 270 l~~~g~~~~A~~~le~a~~~~p-~p~---La~a~~~~~--~~~~~~al~~~~~l~~~~P~~~e~~~~LA~~~~ 336 (492)
T Consensus 80 Li~~nd~~n~R~lFE~~~~~l~~~~e~~~i~~~~~~fEs~~gdL~~i~klE~R~~e~fPed~~l~~f~dRYs~ 152 (275)
T pfam05843 80 LISLNDDTNARVLFETVVTKLTPEPEAKPLWKKFIKYESKYGDLSSILKLEKRMFELFPEDPPLELFSDRYSF 152 (275)
T ss_pred HHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
T ss_conf 9871775018999999985048737779999999999885086999999999999867897279999998625