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