HHsearch alignment for GI: 254780270 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=97.53  E-value=0.0002  Score=52.27  Aligned_cols=163  Identities=23%  Similarity=0.391  Sum_probs=112.2

Q ss_pred             HHHHCCCCCEEEEEECHHHHHHHC----CCCHHH-----HHHHHCCCCCCCCEEEEECCCCCCCCCEEEEEECC-----C
Q ss_conf             998327887399993315542311----771155-----66554060016813320103523644279999348-----6
Q gi|254780270|r  426 SLKRAKRSNPLLLLDEIDKMGSDL----RGDPSA-----ALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTAN-----T  491 (820)
Q Consensus       426 ~l~~~~~~npv~~ldeidk~~~~~----~gdp~~-----allevldp~qn~~f~d~y~~~~~dls~v~fi~tan-----~  491 (820)
T Consensus       262 A~~~vE-~~GiiFIDEIDKIa~~~~e~S~~DvSrEGVQRDlLPiVEG---S~V~TKyG~Vk--TdHiLFIAaGAF~lAKP  335 (463)
T TIGR00390       262 AIDRVE-QSGIIFIDEIDKIAKKGKESSGADVSREGVQRDLLPIVEG---STVNTKYGSVK--TDHILFIAAGAFHLAKP  335 (463)
T ss_pred             HHHHHH-HCCCEEEECCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC---CEEEEECCEEE--CCHHHHHHHHHHCCCCC
T ss_conf             999998-4782898530354216888678887655651011420226---66431001042--21578767523202777


Q ss_pred             CC-CCHHHCCCEEE-EEECCCCHHHHHHHHHH---HHHHH---HHHHHCCCCCCCCCCHHHHHHHHHC-C-----CCCCH
Q ss_conf             55-44131172479-98258786899989998---60898---9986257813132289999999731-7-----74102
Q gi|254780270|r  492 LN-IPLPLMDRMEI-IRIAGYTEEEKLQIAKN---HLVKK---VLTEHALKQEECCISDGVLLDIIRL-F-----THEAG  557 (820)
Q Consensus       492 ~~-i~~~l~drme~-i~~~~y~~~ek~~i~~~---~l~p~---~~~~~~~~~~~~~~~~~~i~~ii~~-Y-----t~EaG  557 (820)
T Consensus       336 SDLIPE-LQGRfPirVEL~~Lt~~d~~rIL~~p~~Sl~kQY~ALl~~eGv---~i~F~d~AI~~iAe~ay~~N~~teniG  411 (463)
T TIGR00390       336 SDLIPE-LQGRFPIRVELEALTVDDFERILTEPKNSLIKQYQALLKVEGV---NIEFSDEAIKKIAELAYNVNQKTENIG  411 (463)
T ss_pred             CCCCCH-HHCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC---CEEECHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             666631-1066737787676329999996208343689999998876276---403355689999999998164423346


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHHHHCCC
Q ss_conf             34788879999898765421178520127967867530520
Q gi|254780270|r  558 VRSFERALMKIARKAVTKIVKNSDTTVSINENNLQDYLGVP  598 (820)
Q Consensus       558 vR~l~r~i~~i~r~~~~~~~~~~~~~~~i~~~~l~~~lg~~  598 (820)
T Consensus       412 ARRLHTv~E~lledisFea~D~~~~~~~I~~~YV~~kL~~~  452 (463)
T TIGR00390       412 ARRLHTVLERLLEDISFEAPDVSGQKVTITADYVEKKLGDL  452 (463)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCCEEEECHHHHHHHHHHH
T ss_conf             50466899999987512666863432450789999998788