HHsearch alignment for GI: 254780750 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, ß-strand 3, the loop C-terminal to ß-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and ß-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 ß-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 ß-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 ß-strand 2 and the loop C-terminal to that strand, all of which are greater than 90
Probab=92.37  E-value=0.17  Score=29.64  Aligned_cols=133  Identities=19%  Similarity=0.279  Sum_probs=85.5

Q ss_pred             EEEEEEECCCCCCCCCEEEEEECCCCCCHHHH-HHHHHHHHHHHHCCCCCCHHHCCCCCCCEEEEE-EECC-CCCCCCCC
Q ss_conf             44345635877776643999967784407899-999999999997198530353206822105676-5237-66113853
Q gi|254780750|r  635 IANDCDLSCPNDKNSGKLWLLTGPNMGGKSTF-LRQNALIVIMAQMGSYVPASYAHIGIVDKLFSR-VGSA-DNLASGRS  711 (920)
Q Consensus       635 VpNdi~l~~~~~~~~~~~~iiTGpNmgGKSt~-lRqval~vilAQiG~fVPA~~a~i~~~D~IftR-iGa~-D~l~~g~S  711 (920)
T Consensus        41 l~LD~AlG~GG~-P~GRi~EiYGpESsGKTTLal~~iA~~Qk~Gg~~afiDAEHAl----D~~YA~~LGv~~~~L~~sQP  115 (322)
T TIGR02012        41 LALDLALGVGGL-PKGRIIEIYGPESSGKTTLALHVIAEAQKAGGVAAFIDAEHAL----DPVYAKKLGVDIDNLLVSQP  115 (322)
T ss_pred             HHHHHHHCCCCC-CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECHHHC----CHHHHHHHCCCHHHHEEECC
T ss_conf             134355167989-8750799854898847899999999997439838998451303----77889983645247112088


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----------CHHHHHH--HHHHHHHHH---HHHCCCEEEEECCC
Q ss_conf             2899999999999958998569993258898----------8056799--999999999---97269849997487
Q gi|254780750|r  712 TFMVEMIETASILNQATNQSFVILDEIGRGT----------ATLDGLS--IAWATIEYL---HETNRCRGLLATHF  772 (920)
Q Consensus       712 TF~vEm~e~~~IL~~at~~SLVllDElGrGT----------st~DG~a--iA~aile~l---~~~~~~~~lfaTHy  772 (920)
T Consensus       116 d~GE~ALeI~~~L~rSgAvD~iVvDSVAAL~P~aEieGemgd~~~Gl~ARLMS~ALRKl~g~~~k~~t~~iFiNQ~  191 (322)
T TIGR02012       116 DTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSKSNTTLIFINQI  191 (322)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEHH
T ss_conf             8714699999998723761179973400138712317543544232578889999998887653205237640022