HHsearch alignment for GI: 254780815 and conserved domain: pfam04280

>pfam04280 Tim44 Tim44-like domain. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane.
Probab=100.00  E-value=1.5e-39  Score=271.26  Aligned_cols=146  Identities=29%  Similarity=0.591  Sum_probs=143.0

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHH
Q ss_conf             45777766126767989999999999999999984276789997318999999998777644349820236620001245
Q gi|254780815|r   85 NKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLVGIDDMKI  164 (232)
Q Consensus        85 ~~~~~~i~~~~~~Fd~~~Fl~gAk~af~~I~~A~~~gD~~~L~~lls~~~~~~f~~~i~~r~~~~~~~~~~~v~i~~~~i  164 (232)
T Consensus         1 ~~~~~~i~~~dp~F~~~~Fl~~Ak~~f~~I~~A~~~~D~~~L~~~~s~~~~~~~~~~i~~r~~~g~~~~~~~v~i~~~~i   80 (146)
T pfam04280         1 ASALAAIKAADPSFDVEEFLEGAREAYEMIQEAWANGDLETLRELLTPEVYEEFAAEIAEREAQGLTNDATIVGIRDAEL   80 (146)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEE
T ss_conf             96899999878598989999999999999999998599889987648999999999999999769965408998745798


Q ss_pred             HHHCCCCCEEEEEEEEEEEEEEEEECCCCCEECCCCCCCEEEEEEEEEEECCCCCCCCEEEEEEEC
Q ss_conf             421134645699999988877766768996805765784899999999961898998668957632
Q gi|254780815|r  165 INASIEENTVYITIRIVGQFISASYDKDNLLISSDPEIFGKVIDIWTFVRNIPPSNPNWVLISTKL  230 (232)
Q Consensus       165 ~~~~~~~~~~~itV~F~~~~i~~~~d~~g~vveG~~~~~~~~~e~WtF~R~~~~~~p~W~L~~iq~  230 (232)
T Consensus        81 ~~~~~~~~~~~itV~f~~~qi~~~~d~~G~iieG~~~~~~~~~e~W~F~R~~~~~~~~W~L~~i~q  146 (146)
T pfam04280        81 LEAKMEGNTAVVTVRFVTQQISVTDDASGEVVEGDPDEPVEVTEVWTFERDLGSPDPNWRLVGIQQ  146 (146)
T ss_pred             EEEEECCCCEEEEEEEEEEEEEEEECCCCCEEECCCCCCEEEEEEEEEEECCCCCCCCEEEEEECC
T ss_conf             665973990799999999999999969997972898872798899999976899797989998529