HHsearch alignment for GI: 254780314 and conserved domain: cd00342
>cd00342 gram_neg_porins Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus.
Probab=90.17 E-value=1.5 Score=23.36 Aligned_cols=187 Identities=20% Similarity=0.219 Sum_probs=100.1
Q ss_pred CCHHHHEEEHHH-----EEECCEEEE----CCCCCCCCCCE-----EEECCCCCC-CCCCEEEEEE-ECCCEEEEEEHHH
Q ss_conf 112520001100-----000122200----24444555510-----231122244-4332268998-2575451033032
Q gi|254780314|r 134 LSVEELSLSMKG-----ARLGYYKSW----SDEVNPVYSPT-----TLYNDARGL-DKMMSLSYRH-SFGLLKAGLSTDL 197 (351)
Q Consensus 134 l~ldeayLdi~G-----fRaG~FySW----WDEtddIgS~~-----TL~Nd~rg~-dk~~SirYqY-e~G~F~AGiSvDe 197 (351)
T Consensus 72 ~~~R~~~VGL~~~~~G~v~~Gr~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~R~~N~i~Y~sp~~~Gf~~~a~y~~ 151 (329)
T cd00342 72 LFGRQAYVGLSSDTYGTLTLGRQYTPLYDVLGTTDPFGGSGGGSAPGDGDNLAGTGRANNSVKYTSPFFGGLTFGAMYAF 151 (329)
T ss_pred CCCCEEEEEECCCCCEEEEEEECCCHHHHEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCEEEEEEEEC
T ss_conf 52536899862588308998603777764114325553355442301246645670660289997676577899999953
Q ss_pred CCCCCC-CCEEEEEEEEEEEECCEEEEEEEEEECCCC-------------CCEEEEEEEECCCCCCEEEEEEEEECCC--
Q ss_conf 146666-540347889634541268999852211466-------------5127988861367882024678873386--
Q gi|254780314|r 198 LQKDGL-KQVLGIGYMASYAIGKIRSTVTGGYDAGTN-------------NVAIRANISSPVSRAGTLDCGAVWASGD-- 261 (351)
Q Consensus 198 LE~dg~-~n~VGV~g~vsg~aGavS~qltGGyDtd~e-------------eGAIRAl~ta~iG~PGTlglAgVwASgp-- 261 (351)
T Consensus 152 g~~~~~~~~~~~~~~~~~Y~~g~~--~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~ga~Y~~g---~~~l~~~Y~~~~~~ 226 (329)
T cd00342 152 GNQAGSTSNGRGYGAGLSYENGPL--SLGAAYDQQRNGGGAAGGAAGATSQRAYGAGASYDFG---GLKLGAGYTNTRND 226 (329)
T ss_pred CCCCCCCCCCCEEEEEEEEECCCE--EEEEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEEEC---CEEEEEEEEEEECC
T ss_conf 667787777857999999952999--9999999850676444566776514899999999968---99999999998835
Q ss_pred C----CCCCCCCEEEEEEEEEEECEEEEECCCEEEECC--C--CCCCCCEEEEEEEEEEEEECCCEEEEEEEECCC
Q ss_conf 4----000112113664355631104786045254045--6--767852277877888885159127789873274
Q gi|254780314|r 262 N----SYYDKSKYSVFAGYKFDVAKSITISGGGQYFGD--I--NKTGKDGWSAGISAKYMISSGLEAQASVAFNDN 329 (351)
Q Consensus 262 N----aYY~~SEWaVAAeYaikaTDKl~ITPG~QY~gd--~--~~sg~DaWk~GlTvDYqItegL~tK~SVqY~D~ 329 (351)
T Consensus 227 ~~~~~~~~~~~~~~~ga~y~~~~--~--~~~~~~y~~~~~~~~~~~~~~~~~~~lG~~Y~lSKrT~lY~~~~~~~n 298 (329)
T cd00342 227 NGGGGGSAKFNGYELGATYQLTP--A--LRLGAAYYYTKDRNDGGGDGKANQVALGADYALSKRTDLYAEYGYQKN 298 (329)
T ss_pred CCCCCCCEEEEEEEEEEEEECCC--C--EEEEEEEEEEECCCCCCCCCCEEEEEEEEEEEECCCHHHHHHHHHEEC
T ss_conf 77778750268999999998078--7--389999999944567688897189999999971554898665054110