HHsearch alignment for GI: 254780916 and conserved domain: TIGR02639

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461 Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=97.43  E-value=0.0001  Score=52.93  Aligned_cols=122  Identities=16%  Similarity=0.259  Sum_probs=75.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHH----HHHHCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             211111111222222222222222234432048873277743679999----9984267543321012346554210024
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR----FIHESGKRAFFPFFIVNCGMIDQDKIEK  209 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~----~iH~~s~r~~~~fi~v~c~~~~~~~~e~  209 (482)
T Consensus       202 A~~GkiDPLIGRE~EleRtiQvLCRR~KNN-P-l~VGEPGVGKTAI~EGLA~~I~~~~-------------kvPe~Lkn~  266 (774)
T TIGR02639       202 AKNGKIDPLIGREDELERTIQVLCRRKKNN-P-LLVGEPGVGKTAIVEGLAQRIAEGQ-------------KVPEVLKNA  266 (774)
T ss_pred             HHCCCCCCCCCCHHHHHHHHHHHCCCCCCC-C-CEECCCCCCHHHHHHHHHHHHHCCC-------------CCCHHHCCC
T ss_conf             860887873456688742333203456788-7-2044888644899999999864156-------------467002478


Q ss_pred             HHH---------C--CCCCCCCCCCCCCCCCCCCCCC-EEEECCCCHH---------HHHHHHHHHH-HHHHHHCCCCCC
Q ss_conf             331---------1--2555532211100123446671-4751664200---------1889998888-776420011235
Q gi|254780916|r  210 FLF---------G--DVDLQTKNSAQFLGKFIEANGG-TIVLEEPDAL---------PLAVQGRIYN-FIETGKIEFFDS  267 (482)
Q Consensus       210 ~lF---------G--~~~~~~~~~~~~~g~~~~a~~G-tl~l~ei~~L---------~~~~Q~~Ll~-~l~~~~~~~~g~  267 (482)
T Consensus       267 ~IY~LDmG~LLAGTKYRGDFE~RLK~V~~Ei~~~~~anILFIDEIHTIVGAGATSGGsmDA-SNLLKPaL~~G~i-----  340 (774)
T TIGR02639       267 KIYSLDMGTLLAGTKYRGDFEERLKAVVSEIEKEPNANILFIDEIHTIVGAGATSGGSMDA-SNLLKPALASGKI-----  340 (774)
T ss_pred             CEEEECHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCCCHHHHH-HHHHHHHHHCCCE-----
T ss_conf             3454043456410245424789999999998528999546641101033178787515524-4321125307877-----


Q ss_pred             CCCCCCCCEEEEECCCC
Q ss_conf             53212343156521433
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~  284 (482)
T Consensus       341 --------RCIGsTTy~  349 (774)
T TIGR02639       341 --------RCIGSTTYE  349 (774)
T ss_pred             --------EEECCCCHH
T ss_conf             --------862265248