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