HHsearch alignment for GI: 254780567 and conserved domain: TIGR00390

>TIGR00390 hslU heat shock protein HslVU, ATPase subunit HslU; InterPro: IPR004491 This family of proteins represent HslU, a bacterial clpX homolog, which is an ATPase and chaperone belonging to the AAA Clp/Hsp100 family and a component of the eubacterial proteasome. ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins. They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, ClpXP) complex in other eubacteria. Genes homologous to eubacterial HslV, IPR001353 from INTERPRO, (ClpQ,) and HslU (ClpY, ClpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa. They are expressed as precursors, with a propeptide that is removed to produce the active protease. The protease is probably located in the kinetoplast (mitochondrion). Phylogenetic analysis shows that HslV and HslU from trypanosomatids form a single clad with other eubacterial homologs . ; GO: 0005515 protein binding, 0005524 ATP binding, 0009377 HslUV protease activity, 0016887 ATPase activity, 0005737 cytoplasm, 0009376 HslUV protease complex.
Probab=96.53  E-value=0.0042  Score=38.98  Aligned_cols=197  Identities=13%  Similarity=0.167  Sum_probs=98.1

Q ss_pred             CCCCCEEECCCHH---HHHHHHHHHHCC-----------CCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHH-
Q ss_conf             8845416536189---999999851016-----------7884999878777868899999986276201356764445-
Q gi|254780567|r   38 ISRDDLLVHSAIE---QAVRLIDSWPSW-----------PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDS-  102 (246)
Q Consensus        38 ~~~dnFiv~~~N~---~A~~~i~~~~~~-----------~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~~~~~~~~~~~-  102 (246)
T Consensus         8 ~~LD~yIiGQ~~AKk~VAiALrNRyrR~~L~~~L~~EV~PKN-ILMiGpTGVGKTEIARRlAKL~~aPFiKVEAtKfTEV   86 (463)
T TIGR00390         8 AELDKYIIGQDEAKKAVAIALRNRYRRSQLEEELKDEVTPKN-ILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV   86 (463)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EEEECCCCCCHHHHHHHHHHHHCCCCEEEEEEEEEEC
T ss_conf             751442206366788999998866776128711135658743-0432788985447999999984489146664100110


Q ss_pred             -----------HHH--HHHHHHHHHHHHCCCC-----CCHHHHH-HHHHHHCC----CCCEEEEECCCCCCH---HHHHH
Q ss_conf             -----------466--6666533433210037-----6103354-55543112----342156403543200---22345
Q gi|254780567|r  103 -----------ILI--DTRKPVLLEDIDLLDF-----NDTQLFH-IINSIHQY----DSSLLMTARTFPVSW---GVCLP  156 (246)
Q Consensus       103 -----------~~~--~~~~~i~iddi~~~~~-----~ee~lf~-l~n~~~~~----~~~iilts~~~p~~~---~~~l~  156 (246)
T Consensus        87 GYVGrdVeSmvRDL~~~aV~lV~~e~~~~~r~~aee~~~erI~~~L~pp~~n~sGvknPfe~f~~~~ePN~~~e~~~~~~  166 (463)
T TIGR00390        87 GYVGRDVESMVRDLVDTAVKLVKEEKIEKVRDRAEEAAEERIVDKLLPPAKNQSGVKNPFEMFWGSEEPNEKDEEESSRE  166 (463)
T ss_pred             CEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHEECCCCCCHHHHHHHHHH
T ss_conf             21424100367878999999999988998899999999889998728889887766672230005668740246899999


Q ss_pred             HHHHHHHH--CCEEEECCCCHHHHHHHHHHHH--HHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf             66788521--2224507889789999999986--6628979889999999406679899999999999999984778788
Q gi|254780567|r  157 DLCSRLKA--ATVVKISLPDDDFLEKVIVKMF--ADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITR  232 (246)
Q Consensus       157 DL~SRl~~--g~~~~I~~pdde~~~~il~k~~--~~r~i~l~~~v~~yl~~r~~Rs~~~l~~~l~~Ld~~sl~~kr~ITi  232 (246)
T Consensus       167 ~~~~klr~r~ahqlalGeLDd~~iei~v~~~~pf~~~e~~~pp~~e~~~--------~~l~~~l~~l~~-~~kkkr~l~i  237 (463)
T TIGR00390       167 ALRKKLRERMAHQLALGELDDKEIEIEVSAKSPFSGIEILAPPGMEEMT--------MNLQSLLQNLGP-DKKKKRKLKI  237 (463)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCEEEEECCCCCCHHHHH--------HHHHHHHHHHCC-CCCEECCCCH
T ss_conf             9999999987766303664671589986137871267505888556776--------789999862045-3200011456


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             999999986741
Q gi|254780567|r  233 SLAAEVLKETQQ  244 (246)
Q Consensus       233 ~lvk~vL~~~~~  244 (246)
T Consensus       238 k~A~~~L~~Ee~  249 (463)
T TIGR00390       238 KEAKKALIAEEA  249 (463)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999899988