HHsearch alignment for GI: 254780450 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=98.48 E-value=6.1e-06 Score=59.81 Aligned_cols=101 Identities=26% Similarity=0.271 Sum_probs=57.5
Q ss_pred CCEEEEECCCCCEEEEHHHHHHHCCCCHHHHCCCCCCHHHHCCCHHHHHHHHHHHHH-CCCCEEEEEEEEEEEECCEEEE
Q ss_conf 961999929996897646798642999678045632188808820489999998620-0267148889999804897999
Q gi|254780450|r 170 PVGFMSADHQGKILYINATLAEWIGIDLTTFTSKSISIGDITAGEGLALIQAIRTEP-SHQKITTLDLDLRRIDNGHGIP 248 (803)
Q Consensus 170 ~~gi~~~D~~g~i~~~N~~~~~llG~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~e~~~~~~~~g~~~~ 248 (803)
T Consensus 2 ~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~ 78 (103)
T cd00130 2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKS--LLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKD-GSVIW 78 (103)
T ss_pred CEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCC-CCEEE
T ss_conf 62899997989899998899998798878916996--5424552116999999999997499852489999999-99999
Q ss_pred EEEEEEEEECCCCCEEEEEEEEEEH
Q ss_conf 9995567653888554799999860
Q gi|254780450|r 249 VKIVHHILASCDGKPGESRTVVVSR 273 (803)
Q Consensus 249 v~~~~~~~~~~~G~~~~~~~~~~Di 273 (803)
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 79 VLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEECCCCCEEEEEEEEECC
T ss_conf 9999999999998999999999829