HHsearch alignment for GI: 254780903 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=99.42  E-value=2.7e-12  Score=106.71  Aligned_cols=125  Identities=16%  Similarity=0.304  Sum_probs=107.1

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHH-HHHHH-CCCCEE
Q ss_conf             9999999999722597459897689789997889977299943305898899976081205899999-99972-489848
Q gi|254780903|r  251 LEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIA-RSVTG-KHVKQL  328 (766)
Q Consensus       251 ~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a-~~~~~-~~~~~~  328 (766)
T Consensus         1 ~~~e~~~~~~~e~~~~~~~~~d~~g~~~~~n~~~~~~~Gy~~~e~~g~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (130)
T TIGR00229         1 RESEERYRAIFESSPDAIIVVDLEGNILYVNPAFEELFGYSAEELLGR-N-VLELIPEEDREELRERIERLLETGEREPV   78 (130)
T ss_pred             CCHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHHCCCHHHHCCC-C-CCCCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             915899999862245426887057615750325777617875895387-5-10002764146899999876326754320


Q ss_pred             EEEEEE--ECCCCCEEEEEEEEEEEEECCCE-EEEEEEEECCCHHHHHHHHH
Q ss_conf             999998--86989889988999999837960-69999984461799999999
Q gi|254780903|r  329 DQIFHM--RHASGADIWIQVRAQMMRTISGG-MNIIGIAMDLTEKYHLEKRY  377 (766)
Q Consensus       329 ~~e~Ri--~~~DG~~~Wi~~r~~~i~d~~G~-~~~iGi~~DITErK~ae~~l  377 (766)
T Consensus        79 ~~~~~~~~~~~~G~~~~~~~~~~~~~~~~g~~~~~~~~~~d~t~~~~~~~~l  130 (130)
T TIGR00229        79 SEERRVLGRRKDGSEIWVEVSVSPIRDSNGGVLGVLGIVRDITERKEAEEAL  130 (130)
T ss_pred             EEEEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEECHHHHHHHHHCC
T ss_conf             1234666443789688998730100001377036776652114789988509