HHsearch alignment for GI: 255764476 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=98.67 E-value=3.8e-07 Score=66.87 Aligned_cols=111 Identities=17% Similarity=0.233 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCCCCHHHHHCCCCCCC-CHH----HHHHHHHHCC-CC-CEEE
Q ss_conf 999999998516800589815992898525789873677877566101585338-967----8999986125-78-7034
Q gi|255764476|r 191 HISVFKVLFDSLDFLVWHRDQAGDILWANISYKKNTETEGIVFQKAIGESRKLF-KEE----IKKRMISSSA-LE-KNFC 263 (792)
Q Consensus 191 ~~~~lr~llda~P~~vw~~D~dGri~~vN~A~~~~~e~~~~~~~~~i~~~~~ll-~~~----~~~~~~~~~~-~~-~~~~ 263 (792)
T Consensus 3 ~e~~~~~~~e~~~~~~~~~d~~g~~~~~n~~~~~~~---Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (130)
T TIGR00229 3 SEERYRAIFESSPDAIIVVDLEGNILYVNPAFEELF---GYSAEELLGRNVLELIPEEDREELRERIERLLETGEREPVS 79 (130)
T ss_pred HHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHH---CCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCE
T ss_conf 589999986224542688705761575032577761---78758953875100027641468999998763267543201
Q ss_pred EEEE---EEECCEEEEEEEEEEECC--C----CEEEEEEEHHHHHHHHHH
Q ss_conf 5788---865690789999976328--9----529998304589998878
Q gi|255764476|r 264 ETVS---TLEHGNNKSYKIVRVLNS--F----GEAGIAIDVSKEITVNDQ 304 (792)
Q Consensus 264 ~~~~---~~~~G~rr~~~v~~~~~~--~----G~~Gia~DITErk~ae~a 304 (792)
T Consensus 80 ~~~~~~~~~~~G~~~~~~~~~~~~~~~~g~~~~~~~~~~d~t~~~~~~~~ 129 (130)
T TIGR00229 80 EERRVLGRRKDGSEIWVEVSVSPIRDSNGGVLGVLGIVRDITERKEAEEA 129 (130)
T ss_pred EEEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEECHHHHHHHHHC
T ss_conf 23466644378968899873010000137703677665211478998850