HHsearch alignment for GI: 254780417 and conserved domain: pfam02559

>pfam02559 CarD_TRCF CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Probab=99.76  E-value=1.2e-18  Score=140.12  Aligned_cols=98  Identities=36%  Similarity=0.566  Sum_probs=84.8

Q ss_pred             HCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf             13899869748785099976789864873025302202488856998052012104543344102467898507866446
Q gi|254780417|r   13 GFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVK   92 (188)
Q Consensus        13 ~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~~~   92 (188)
T Consensus         1 ~~~~GD~VVh~~~Gvg~~~gi~~~~~~~~~~~y~~l~y~~~-~~l~vPv~~~~~i~-ry~~~~~~~-~~l~~L~~~----   73 (98)
T pfam02559         1 MLKVGDYVVHPDHGVGRFEGIETIEVGGEKREYYVLEYADG-DKLYVPVDQLDLIG-RYIGSEDEV-PVLDKLGGG----   73 (98)
T ss_pred             CCCCCCEEECCCCCCEEEEEEEEEEECCCCCEEEEEEECCC-CEEEEEHHHHHHHH-CCCCCCCCC-CHHHHCCCH----
T ss_conf             99999999777996489968899830891437999996599-88998778876750-376888875-322212856----


Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             6550389999999851689999999999998
Q gi|254780417|r   93 RTMWSRRAQEYDAKINSGDLIAIAEVVRDLH  123 (188)
Q Consensus        93 ~~~~~~R~~~~~~~lksgd~~~~a~vik~L~  123 (188)
T Consensus        74 --~W~~rk~----k~k~~~~~~a~ell~~~a   98 (98)
T pfam02559        74 --TWKKRKR----KIKSGDIDIAAELLRLLA   98 (98)
T ss_pred             --HHHHHHH----HHHHHHHHHHHHHHHHCC
T ss_conf             --5899999----999789999999999619