HHsearch alignment for GI: 254780766 and conserved domain: TIGR00606

>TIGR00606 rad50 rad50; InterPro: IPR004584 Rad50 is involved in recombination, recombinational repair, and/or non-homologous end joining. It is a component of an exonuclease complex with MRE11 homologs. The Saccharomyces cerevisiae Rad50/MRE11 complex possesses single-stranded endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides an ATP-dependent control of MRE11 by unwinding and repositioning DNA ends into the MRE11 active site. This family is distantly related to the SbcC family of bacterial proteins. When the N- and C-terminal globular regions of Rad50 from Pyrococcus furiosus P58301 from SWISSPROT are co-expressed in Escherichia coli, they spontaneously associate to form a stable complex that possesses ATP-binding and weak ATP-hydrolysing activities. The structure formed is known as the Rad50 catalytic domain (Rad50cd1). In the presence of ATP, two Rad50cd1 molecules interact via their ATP-binding and highly conserved 'signature' motifs to form a dimer. As ATP is buried deep within this dimer interface, the two Rad50cd1 molecules may have to completely disengage after ATP hydrolysis to allow the release of ADP before binding of a new ATP molecule. ATP binding is also accompanied by a 30 rotation of two distinct domains within each Rad50cd1 part of the dimer. This rotation and dimerisation creates a positively charged surface which, potentially, could provide a DNA-binding site capable of accommodating two DNA molecules. The Mre11-docking site within Rad50 has been mapped to two 40-residue heptad-repeat sequences that lie adjacent to the N- and C-terminal ATPase segments. A distinct region within this domain forms a conserved hydrophobic patch that is believed to be the actual Mre11-binding site and lies immediately adjacent to the putative DNA-binding site of Rad50. As Rad50 dimerises in the presence of ATP and forms a stoichiometric complex with Mre11 (one Mre11 subunit binding to one Rad50 subunit), it is possible that the MR complex forms a closely coordinated DNA-binding unit that has the potential to act on two DNA molecules simultaneously. Within this unit, ATP-dependent control of nuclease action might be achieved via Rad50 unwinding or repositioning DNA ends into the active-site of Mre11 . ; GO: 0005524 ATP binding, 0006281 DNA repair, 0030870 Mre11 complex.
Probab=97.01  E-value=0.0029  Score=40.51  Aligned_cols=83  Identities=25%  Similarity=0.356  Sum_probs=66.0

Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHCCCHHHHHHHHHHHHHC----------------CCCEEEE
Q ss_conf             312205899999999999999999870899789980122015989999999997417----------------9809998
Q gi|254780766|r  285 AHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI----------------GSQIFMT  348 (375)
Q Consensus       285 ~~~S~Gqqk~~~l~l~La~~~~~~~~~~~~pilLiDdi~s~LD~~~~~~ll~~l~~~----------------~~Qv~iT  348 (375)
T Consensus      1207 GRCSAGQK~LASL~IRlALAE~F~---~~C~~iALDEPTTNLD~~~~E~lA~~L~~II~~R~GfdenGkl~~R~~Ql~VI 1283 (1328)
T TIGR00606      1207 GRCSAGQKVLASLLIRLALAEVFC---LNCGIIALDEPTTNLDREKVESLAIVLVEIIKERSGFDENGKLRQRDFQLLVI 1283 (1328)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHC---CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEE
T ss_conf             665545799999999999987640---24442440588765664468899999999985305755366512562158887


Q ss_pred             ECCHHHHHHHH--C-CEEEEEECCC
Q ss_conf             06967854321--2-6007997289
Q gi|254780766|r  349 GTDKSVFDSLN--E-TAKFMRISNH  370 (375)
Q Consensus       349 t~~~~~~~~~~--~-~~~~~~i~~g  370 (375)
T Consensus      1284 THDE~~V~~l~~S~~~E~~Y~~~K~ 1308 (1328)
T TIGR00606      1284 THDEDLVELLGRSEYVEKIYRLKKD 1308 (1328)
T ss_pred             ECCHHHHHHHHHCCCCCEEEEECCC
T ss_conf             3557899862100242201454157