HHsearch alignment for GI: 254780695 and conserved domain: TIGR02544
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia. The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=99.97 E-value=4.4e-30 Score=219.18 Aligned_cols=179 Identities=27% Similarity=0.357 Sum_probs=162.5
Q ss_pred HHHHHHHHHHCCCCCE-EECCCCCHHHHHHHHHHHHHCCCCEEE------C--CCC--CEEEECHHHHHHHHHHHHHCCC
Q ss_conf 9999999984699824-503899989999999999977992999------1--899--7799518999999999997699
Q gi|254780695|r 34 MLFMAARFFVNSPHYD-NLYVKLEVSDVNRISVALSEANIDFRI------S--DNG--SSISVPSSMVGKARIHLAAQGL 102 (563)
Q Consensus 34 ~~~~~~~~~~~~p~y~-~L~~~l~~~d~~~i~~~L~~~gI~y~~------~--~~g--~~I~Vp~~~~~~~r~~La~~gl 102 (563)
T Consensus 5 ~~~~~l~llL~GC~~~~~Ly~gL~e~eANe~lA~L~~~gI~A~K~~~~~~~~~k~Gv~~~~~Ve~~~~~~A~~lL~~~GL 84 (203)
T TIGR02544 5 LLLLLLLLLLTGCKVDLELYSGLSEREANEMLALLMRHGIDAEKVQAVSEKSGKGGVLYTISVEESDFARAVELLRQNGL 84 (203)
T ss_pred HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHCCCCEEECHHHEECCCCCEEEEEEECCHHHHHHHHHHHHHCCC
T ss_conf 89999999971787405650478987899999999966983453122100378852588986187899999999986388
Q ss_pred CCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCC-CCCCCCCCCCEEEEEECCC
Q ss_conf 887766325653058884259999999999999999999996057631489999833666-5555555871599970687
Q gi|254780695|r 103 PSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMG-SFRKIGARPTASVMIRAIN 181 (563)
Q Consensus 103 p~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~-~f~~~~~~~sASV~l~~~~ 181 (563)
T Consensus 85 P~~~~~~~~~~Fp~-~gLvsSP~eEraR~~ya~eQ~Le~tLs~IdGV~~ArVhVvlP~~d~~~~~~~~P~sAsVfikY~~ 163 (203)
T TIGR02544 85 PRQSFVNLGELFPK-DGLVSSPTEERARLLYAIEQELEQTLSQIDGVISARVHVVLPENDNENGRPKKPSSASVFIKYRP 163 (203)
T ss_pred CCCCCCCHHHHCCC-CCEECCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCCCCEEEEEEEECC
T ss_conf 89532368875135-77034869999999999999999986017926866799972167887788988543889998668
Q ss_pred CCCH-H-HHHHHHHHHHHHHHCCCCCCEEEEECC
Q ss_conf 7898-8-999999999865401883526998289
Q gi|254780695|r 182 PSVY-K-SAEAIRHLVAAAVPNLDMGDVTVLDST 213 (563)
Q Consensus 182 ~l~~-~-qv~~I~~lVa~sV~gL~~e~VtVvD~~ 213 (563)
T Consensus 164 ~~~~~~h~~~~IK~Lv~~Si~gL~Yd~vSVvl~p 197 (203)
T TIGR02544 164 GLNLDAHLIPKIKRLVANSIPGLAYDNVSVVLVP 197 (203)
T ss_pred CCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf 9782003365268999860378871656899860