HHsearch alignment for GI: 254780877 and conserved domain: COG3604

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms].
Probab=96.07  E-value=0.012  Score=40.51  Aligned_cols=116  Identities=28%  Similarity=0.512  Sum_probs=68.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHCC--CCCCCEEEECCCCCCHHHHHHHHHHHHHCC----------CCCHHHCCCEEEEEEHH
Q ss_conf             853333357899999996336--777866895288740777999999987348----------99844457437887313
Q gi|254780877|r  176 KLDPVIGRDDEMRRAIQVLSR--RTKNNPVLIGDPGVGKTAIIEGLASRIING----------DIPESLKGKRLMALDMG  243 (853)
Q Consensus       176 kLDPVIGRe~EI~~~~~iL~r--~~k~n~~lvGe~GvGKtaive~la~~i~~~----------~vp~~l~~~~i~~ld~~  243 (853)
T Consensus       221 ~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGHeKG  300 (550)
T COG3604         221 EVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGHEKG  300 (550)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHCCCCC
T ss_conf             44562306999999999999872689807984588853899999998737555798666312225378888887453322


Q ss_pred             HHHC-CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHCCCCCCCCCCCH-HHHHHHHHCCCCEEEEE
Q ss_conf             5421-745420245458999999860799769996362773026665543358-88876531246604899
Q gi|254780877|r  244 ALIA-GAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDA-SNLLKPSLARGELHCIG  312 (853)
Q Consensus       244 ~l~a-g~~~rg~~e~r~~~i~~~~~~~~~~~ilfide~h~~~gaG~~~g~~Da-an~LKP~LarG~l~~Ig  312 (853)
T Consensus       301 AFTGA~~~r~GrFE-----------lAdGG-TLFLDEIGel--------PL~lQaKLL-RvLQegEieRvG  350 (550)
T COG3604         301 AFTGAINTRRGRFE-----------LADGG-TLFLDEIGEL--------PLALQAKLL-RVLQEGEIERVG  350 (550)
T ss_pred             CCCCCHHCCCCCEE-----------ECCCC-EEECHHHCCC--------CHHHHHHHH-HHHHHCCEEECC
T ss_conf             33351014676356-----------55797-5760220367--------877889999-998636525347