HHsearch alignment for GI: 254780413 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=98.44  E-value=3.7e-06  Score=63.09  Aligned_cols=99  Identities=18%  Similarity=0.257  Sum_probs=76.5

Q ss_pred             HCCHHEEECCCCEEEEEHHHHHHHHCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             22043078599838721568998848960320786443345645627789999988606984022348887638972899
Q gi|254780413|r  461 TSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLS  540 (820)
Q Consensus       461 ~~~gI~~~D~~G~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  540 (820)
T Consensus         1 ~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~g~~~~   78 (103)
T cd00130           1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPV--TLEVRLRRKDGSVIW   78 (103)
T ss_pred             CCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHEECCHHHHHHHHHHHHHHHCCCCC--EEEEEEECCCCCEEE
T ss_conf             962899997989899998899998798878916996542455211699999999999749985--248999999999999


Q ss_pred             EEEEEEECCCC----CEEEEEEEEH
Q ss_conf             99998871788----7399998651
Q gi|254780413|r  541 LRIIIKKLPFS----SCYSLTMHDI  561 (820)
Q Consensus       541 ~~~~~~~~~~~----~~~~~v~~Di  561 (820)
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          79 VLVSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEEEECCCCCEEEEEEEEECC
T ss_conf             9999999999998999999999829