HHsearch alignment for GI: 254780955 and conserved domain: pfam04386

>pfam04386 SspB Stringent starvation protein B. Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of
Probab=100.00  E-value=1.6e-42  Score=297.14  Aligned_cols=120  Identities=44%  Similarity=0.757  Sum_probs=114.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEE
Q ss_conf             49899999999999999999999708999874699998458888775989996397537998431121807645479999
Q gi|254780955|r   30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVG  109 (204)
Q Consensus        30 i~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~  109 (204)
T Consensus         1 ~~y~~~~~~~lRav~~w~L~~~~~~g-ld~~~~pyI~~~t~~~gV~vP~~l~~~~~~~mlnV~~~a~~~L~v~~d~~sf~   79 (152)
T pfam04386         1 ITYDSLRPYALRAVYRWVLTDVAKEG-LDNDHTPYITFDTTAPGVQVPDELVERYPQIMLNVLQHAFWDLEVGNDGFSFN   79 (152)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEEECCCCCCCCHHHHHCCCCEEEEECHHHHHCEEECCCEEEEE
T ss_conf             97788899999999999998765348-89998379999908999187899984399479995477760516627889999


Q ss_pred             EEECCEEEEEEEEHHHHEEEECCCCCEEEEECCCCCCCCCC
Q ss_conf             98498766899844242023067753035603467665433
Q gi|254780955|r  110 LSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHIEEK  150 (204)
Q Consensus       110 LsF~g~~e~L~IPf~AIt~F~DPSV~FgLqF~~~~~~~~~~  150 (204)
T Consensus        80 ~rF~G~~~~i~iP~~Ai~~i~~~e~g~Gl~F~~~~~~~~~~  120 (152)
T pfam04386        80 LRFGGVPERLYVPFAAILAFYDPENGFGLQFEPEEADEDEE  120 (152)
T ss_pred             EEECCEEEEEEEEHHHEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             99899307999744771466666678652058988777777