HHsearch alignment for GI: 254780725 and conserved domain: TIGR02012

>TIGR02012 tigrfam_recA protein RecA; InterPro: IPR001553 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response . In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs . RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage . RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved , , among eubacterial species. It is also found in the chloroplast of plants . RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, -strand 3, the loop C-terminal to -strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and -strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation [Lusetti and Cox, Annu. Rev. Biochem. 2002. 71:71-100.]. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between -strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at -strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at -strand 2 and the loop C-terminal to that strand, all of which are greater than 90
Probab=95.16  E-value=0.12  Score=29.25  Aligned_cols=46  Identities=20%  Similarity=0.190  Sum_probs=36.8

Q ss_pred             CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             345675379997469887756899999999996269949999787989
Q gi|254780725|r  156 GKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPY  203 (427)
Q Consensus       156 ~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~  203 (427)
T Consensus        50 GG~P~GRi~EiYGp-ESsGKTTLal~~i-A~~Qk~Gg~~afiDAEHAl   95 (322)
T TIGR02012        50 GGLPKGRIIEIYGP-ESSGKTTLALHVI-AEAQKAGGVAAFIDAEHAL   95 (322)
T ss_pred             CCCCCCEEEEEECC-CCCCHHHHHHHHH-HHHHHCCCEEEEEECHHHC
T ss_conf             98987507998548-9884789999999-9997439838998451303