HHsearch alignment for GI: 254780456 and conserved domain: cd04462
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.56 E-value=0.016 Score=32.62 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=11.1
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEH
Q ss_conf 221369999985016999706884135400
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHL 399 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~ 399 (576)
T Consensus 2 GEVvDavVt~Vnk~G~Fa~~G-Pl~~fvS~ 30 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEVG-PLSIFISR 30 (88)
T ss_pred CCEEEEEEEEECCEEEEEEEC-CEEEEEEC
T ss_conf 957999999983478999804-75899991