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