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