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