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