HHsearch alignment for GI: 254780436 and conserved domain: TIGR02552

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD; InterPro: IPR005415 The type III secretion system of Gram-negative bacteria 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. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Yersinia spp. secrete effector proteins called YopB and YopD that facilitate the spread of other translocated proteins through the type III needle and the host cell cytoplasm . Both are believed to act as pore translocases, forming apertures in the host cell membrane and allowing the bacterium easy access to its cytoplasm. YopD also acts as a negative regulator of the Yersinia low-calcium response, and in turn is controlled by a chaperone, SycD . This protein also regulates YopB secretion. SycD is located on the Yop pathogenicity island of Yersinia spp., and is speculated to prevent a premature interaction between YopB, YopD and the calcium-response LcrV protein . It has been speculated that a type III secretion mechanism also exists in Chlamydial species. With the sequencing of the Chlamydia trachomatis genome, several proteins similar to characterised type III proteins have emerged, including a SycD homologue . The Pseudomonas aeruginosa gene PcrH is also similar to the Yersinia chaperone, suggesting a comparable function. Proteins in this entry are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system ,. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role . In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent . ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array .; GO: 0006950 response to stress.
Probab=98.68  E-value=1.8e-08  Score=62.83  Aligned_cols=104  Identities=13%  Similarity=0.151  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHC
Q ss_conf             99999999999981998999999999998168998999999999997298522221111111111111111211000000
Q gi|254780436|r   35 VILLIEGCSSLFPSMGRRVNIDSLTAVIRAHPSDPEGYNVRGVVYGMNGDFEKALLDFQSALDLNPRYYKVYANRALIRY  114 (298)
Q Consensus        35 ~~~~~~~~~~~~~~~~~~~Ai~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  114 (298)
T Consensus        18 L~~~Y~~AY~~y~~G~Y~~A~~~F~~L~~~~~~~~~Y~~gLa~c~q~~~~Y~~A~~~Y~~a~~l~~~~P~p~~~~a~C~l   97 (137)
T TIGR02552        18 LEAIYALAYNLYQQGRYDEALKLFQLLAAYDPWNADYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYYHAAECYL   97 (137)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             99999999999853667999999999999743036899999999998616789999999997527686951269989998


Q ss_pred             CCCCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf             01122221111112222111-1111
Q gi|254780436|r  115 KMGDVPMAIRDYGTALKINP-DYDV  138 (298)
Q Consensus       115 ~~~~~~~a~~~~~~~~~~~~-~~~~  138 (298)
T Consensus        98 ~~g~~~~A~~aL~~a~~~~~~~~~~  122 (137)
T TIGR02552        98 ALGEPESALKALDLAIEIAGGENPE  122 (137)
T ss_pred             HHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             7289789999999999984889963