HHsearch alignment for GI: 254780903 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=97.52  E-value=0.00085  Score=45.33  Aligned_cols=84  Identities=12%  Similarity=0.231  Sum_probs=55.4

Q ss_pred             HHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCC--CCCCCEEEEEEECCCE--EEE
Q ss_conf             445515883499699701789888399978942897178816520137899985211--2456405899916962--874
Q gi|254780903|r  391 TSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDP--ERSQDMSKEIKLADSR--WLQ  466 (766)
Q Consensus       391 ~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~e~~~~dg~--~~~  466 (766)
T Consensus         1 ~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   80 (103)
T cd00130           1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL   80 (103)
T ss_pred             CCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEE
T ss_conf             96289999798989999889999879887891699654245521169999999999974998524899999999999999


Q ss_pred             ECCEECCC
Q ss_conf             22324569
Q gi|254780903|r  467 INEWCTHD  474 (766)
Q Consensus       467 i~~~~~~d  474 (766)
T Consensus        81 ~~~~~~~~   88 (103)
T cd00130          81 VSLTPIRD   88 (103)
T ss_pred             EEEEEEEC
T ss_conf             99999999