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