HHsearch alignment for GI: 254780468 and conserved domain: cd00130

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.73  E-value=9.7e-07  Score=71.61  Aligned_cols=103  Identities=23%  Similarity=0.476  Sum_probs=91.4

Q ss_pred             CCCEEEEEECCCCEEEECHHHHHHHCCCHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEE
Q ss_conf             59389999879978999888997628997783389789886269768999999999996078973899999986999689
Q gi|254780468|r  414 SGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFH  493 (963)
Q Consensus       414 s~~~i~~~d~~~~~~~~n~~~~~~lG~~~~~l~~~~~~~~~~ihp~D~~~~~~~l~~~~~~~~~~~~~e~r~r~~dG~~~  493 (963)
T Consensus         1 ~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~g~~~   77 (103)
T cd00130           1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKS--LLDLIHPEDREELRERLENLLSG-GEPVTLEVRLRRKDGSVI   77 (103)
T ss_pred             CCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHEECCHHHHHHHHHHHHHHHC-CCCCEEEEEEECCCCCEE
T ss_conf             962899997989899998899998798878916996--54245521169999999999974-998524899999999999


Q ss_pred             EEEEEEEEEECCCCCEEEEEEEEEEC
Q ss_conf             99872267687999889999999853
Q gi|254780468|r  494 WMIIRIRPMSNSNGDILRYIGIANDI  519 (963)
Q Consensus       494 w~~~~~~~i~~~~g~~~~~~g~~~DI  519 (963)
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          78 WVLVSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEEEEECCCCCEEEEEEEEECC
T ss_conf             99999999999998999999999829