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=99.17  E-value=1.6e-10  Score=87.83  Aligned_cols=157  Identities=20%  Similarity=0.227  Sum_probs=84.1

Q ss_pred             EEEEEEEECCCCHH--HE---EEECCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHCCC------CCEEE
Q ss_conf             89999992232545--53---673279879998689986444899999972886666787368874898------32058
Q gi|254780766|r    6 KIKFLNISEFRNYA--SL---RLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGS------PSFFS   74 (375)
Q Consensus         6 ~i~~l~i~nFR~~~--~~---~i~f~~~~n~i~G~NG~GKT~iLEAI~~l~~gksfR~~~~~~li~~~~------~~~~~   74 (375)
T Consensus         2 ~~~~l~I~GvRS~G~ED~D~~~I~F~SP~T~l~GPNG~GKTT~IE~L~y~~TG~~P~~~K~NtFvH~~~VA~~T~V~A~~   81 (1328)
T TIGR00606         2 KFLKLSILGVRSVGIEDKDKQIIDFLSPLTLLVGPNGAGKTTIIEALKYVTTGDFPPGKKGNTFVHDPKVARETDVRAQV   81 (1328)
T ss_pred             CCCCEEEEEEEECCCCCCCCCEEEEECCCCEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCEEEE
T ss_conf             43201443322026454444233211660101277887525898754332048898888886000372221105320588


Q ss_pred             E--EEEECCCCCCEEEEEEEECCCCCC--------CCCCCCCCCCCCCCC-------CCC-------CCCCCCEEECCHH
Q ss_conf             9--888628532002667530024663--------332112577433321-------012-------3334520210011
Q gi|254780766|r   75 T--FARVEGMEGLADISIKLETRDDRS--------VRCLQINDVVIRVVD-------ELN-------KHLRISWLVPSMD  130 (375)
Q Consensus        75 ~--~~~~~~~~~~~~~~~~~~~~~~~~--------~k~~~~n~~~~~~~~-------~l~-------~~l~~v~~~p~~~  130 (375)
T Consensus        82 ~L~F~DV~G~~~~~~R~lv~t-~~~K~~~~~~~~~~~~~~~~G~~~~LSSK~~~~~~~l~~~LGV~~aVl~~VIFCHQED  160 (1328)
T TIGR00606        82 RLEFRDVKGEEVAVVRSLVVT-QKTKKAELKELEGVIIRYKDGEKVSLSSKVAEIDRELLKHLGVSKAVLKYVIFCHQED  160 (1328)
T ss_pred             EEEEEEECCCEEEEEEEEEEE-CCCHHHHHHHHCCEEEECCCCCEEEHHHHHHHHHHHHHHHCCCCHHHHCCCEEEEECC
T ss_conf             998886176078877644550-5506777662262367637885530155677887999975486345651530321047


Q ss_pred             --HCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             --001268723412101000135846778887777666
Q gi|254780766|r  131 --RIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLM  166 (375)
Q Consensus       131 --~li~~~p~~RR~flD~~i~~~~~~y~~~l~~y~K~L  166 (375)
T Consensus       161 S~WPLSE~K~LK~~F-D-~IF~~-T~y~KA~e~l~~v~  195 (1328)
T TIGR00606       161 SNWPLSEGKALKKKF-D-EIFSL-TRYVKALERLRKVR  195 (1328)
T ss_pred             CCCCCCCCHHHHHHH-H-HHHHH-HHHHHHHHHHHHHH
T ss_conf             898988756777777-7-89988-88999999999999