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=97.11 E-value=0.0023 Score=37.68 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=15.8
Q ss_pred CCEEEEEEEEEECCCCEEEECCCEEEEEEEEC
Q ss_conf 33024678875314717774483157886420
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLSGVDGLLHVTDI 229 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~l 229 (576)
T Consensus 2 GEVvDavVt~Vnk~G~Fa~~GPl~~fvS~~~i 33 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEVGPLSIFISRHLI 33 (88)
T ss_pred CCEEEEEEEEECCEEEEEEECCEEEEEECCCC
T ss_conf 95799999998347899980475899991118