HHsearch alignment for GI: 254780421 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=95.41  E-value=0.16  Score=27.87  Aligned_cols=96  Identities=17%  Similarity=0.125  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             99999999999984138766699999997312552069999999999995110057789999998731268957899999
Q gi|254780421|r   51 NIVGENFAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLAPLAVRYAAT  130 (218)
Q Consensus        51 ~~as~~y~~al~~~~~~~~~~A~~~l~~l~~~~~~~ya~lA~l~lA~~~~~~g~~~~A~~~l~~i~~~~~~~~~~~~lA~  130 (218)
T Consensus        16 ~~L~~~Y~~AY~~y~~G~Y~~A~~~F~~L~~~~~~~~~--Y~~gLa~c~q~~~~Y~~A~~~Y~~a~~l~-~~~P---~p~   89 (137)
T TIGR02552        16 EQLEAIYALAYNLYQQGRYDEALKLFQLLAAYDPWNAD--YWLGLAACCQMLKEYEEAIDAYALAAALD-PDDP---RPY   89 (137)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHH--HHHHHHHHHHHHHCHHHHHHHHHHHHHCC-CCCC---CCH
T ss_conf             89999999999998536679999999999997430368--99999999998616789999999997527-6869---512


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             9999963026998999999753
Q gi|254780421|r  131 LQAASILVDTSSYEEISKILQK  152 (218)
Q Consensus       131 l~la~~~~~~~~~d~a~~~l~~  152 (218)
T Consensus        90 ~~~a~C~l~~g~~~~A~~aL~~  111 (137)
T TIGR02552        90 YHAAECYLALGEPESALKALDL  111 (137)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHH
T ss_conf             6998999872897899999999