HHsearch alignment for GI: 254780468 and conserved domain: TIGR00229

>TIGR00229 sensory_box PAS domain S-box; InterPro: IPR000014 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs . In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand . Probably the most surprising identification of a PAS domain was that in EAG-like K^+-channels . ; GO: 0004871 signal transducer activity, 0007165 signal transduction.
Probab=99.18  E-value=8.5e-10  Score=96.23  Aligned_cols=125  Identities=26%  Similarity=0.422  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHCCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHC-CCCCEEEE
Q ss_conf             88899999832593899998799789998889976289977833897898862697689999999999960-78973899
Q gi|254780468|r  403 DGERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVG-YRRGRLQY  481 (963)
Q Consensus       403 ~~er~~~al~~s~~~i~~~d~~~~~~~~n~~~~~~lG~~~~~l~~~~~~~~~~ihp~D~~~~~~~l~~~~~-~~~~~~~~  481 (963)
T Consensus         3 ~e~~~~~~~e~~~~~~~~~d~~g~~~~~n~~~~~~~Gy~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (130)
T TIGR00229         3 SEERYRAIFESSPDAIIVVDLEGNILYVNPAFEELFGYSAEELLGRN--VLELIPEEDREELRERIERLLETGEREPVSE   80 (130)
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHHCCCHHHHCCCC--CCCCCCCCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             58999998622454268870576157503257776178758953875--1000276414689999987632675432012


Q ss_pred             EEEE--ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECHHHHHHHHHH
Q ss_conf             9999--86999689998722676879998899999998530577312321
Q gi|254780468|r  482 EFRV--RAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKSLEGI  529 (963)
Q Consensus       482 e~r~--r~~dG~~~w~~~~~~~i~~~~g~~~~~~g~~~DIt~~~~~~~~l  529 (963)
T Consensus        81 ~~~~~~~~~~G~~~~~~~~~~~~~~~~g~~~~~~~~~~d~t~~~~~~~~l  130 (130)
T TIGR00229        81 ERRVLGRRKDGSEIWVEVSVSPIRDSNGGVLGVLGIVRDITERKEAEEAL  130 (130)
T ss_pred             EEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEECHHHHHHHHHCC
T ss_conf             34666443789688998730100001377036776652114789988509