HHsearch alignment for GI: 254780788 and conserved domain: cd04460

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=96.69  E-value=0.0083  Score=39.87  Aligned_cols=68  Identities=25%  Similarity=0.411  Sum_probs=56.9

Q ss_pred             CEEEEEEEECCCCEEEEEECCCEEEEEHHHC-----------------CCCCCCCCCCEEEEEEEEECCCC---CEEEEE
Q ss_conf             3899999840576389995793587447874-----------------88751152766999997611358---702898
Q gi|254780788|r  140 EIISGTVKRVEYGNVIVDLGNSDGVIRRDET-----------------ISRENLRPGDRVKSYIYDVRREQ---RGPQVL  199 (526)
Q Consensus       140 eiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~-----------------ip~E~~~~Gdrika~i~~V~~~~---rgpqi~  199 (526)
T Consensus         1 Ev~eG~Vs~Vt~fG~FV~L~~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~Ig   80 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG   80 (99)
T ss_pred             CEEEEEEEEEEECCEEEEECCCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEEE
T ss_conf             97999999588256699932810689936757843998124468985127869847999999999980620676764665


Q ss_pred             EECCCHHH
Q ss_conf             71598899
Q gi|254780788|r  200 LSRTHPQF  207 (526)
Q Consensus       200 lSRt~p~~  207 (526)
T Consensus        81 Ltmrqp~l   88 (99)
T cd04460          81 LTMRQPGL   88 (99)
T ss_pred             ECCCCCCC
T ss_conf             02247889