HHsearch alignment for GI: 255764460 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=100.00  E-value=0  Score=793.45  Aligned_cols=321  Identities=69%  Similarity=1.098  Sum_probs=315.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             69999999999986761887379703665533465501477278999723897268807999706872378999999875
Q gi|255764460|r   11 DKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQ   90 (363)
Q Consensus        11 ~k~~~l~~~~~~i~k~~g~~~~~~lg~~~~~~~~~~~i~TG~~~lD~~Lg~GG~p~Gri~ei~G~~~sGKTtlal~~~a~   90 (363)
T Consensus         1 ~k~~al~~A~~~iek~FGkG~im~Lg~~~~--~~v~~i~tGsl~LD~AlG~GG~P~GRi~EiYGpESsGKTTLal~~iA~   78 (322)
T TIGR02012         1 DKQKALEAALAQIEKQFGKGSIMKLGEKSV--EDVEVISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHVIAE   78 (322)
T ss_pred             CHHHHHHHHHHHHHHHCCCCEEEECCCCCC--CCEEEECCCCHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             946889999999865208821451255444--310021253013435516798987507998548988478999999999


Q ss_pred             HHHCCCEEEEEECCCCCCHHHHHHHCCCHHHEEEEECCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             20089879999738855668899819883344897258489999999999744897689981433322026554345553
Q gi|255764460|r   91 SQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGES  170 (363)
Q Consensus        91 ~qk~g~~~~~iD~E~~~~~~~a~~~Gvd~~~l~~~~~~~~E~~~~i~~~li~~~~~~liViDSi~al~p~~Eie~~~~d~  170 (363)
T Consensus        79 ~Qk~Gg~~afiDAEHAlD~~YA~~LGv~~~~L~~sQPd~GE~ALeI~~~L~rSgAvD~iVvDSVAAL~P~aEieGemgd~  158 (322)
T TIGR02012        79 AQKAGGVAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDS  158 (322)
T ss_pred             HHHCCCEEEEEECHHHCCHHHHHHHCCCHHHHEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCC
T ss_conf             97439838998451303778899836452471120888714699999998723761179973400138712317543544


Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCC-EEEEEE
Q ss_conf             0224788876776777764201781899986341145665466512565531111112489750455344577-247679
Q gi|255764460|r  171 LPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKD-SITGNQ  249 (363)
Q Consensus       171 ~~g~~ar~ms~~lrkl~~~~~k~~~~~i~iNQ~r~~ig~m~g~p~~~~GG~al~~~aS~rl~i~k~~~ik~~~-~~iG~~  249 (363)
T Consensus       159 ~~Gl~ARLMS~ALRKl~g~~~k~~t~~iFiNQ~R~KiGv~fG~peTTtGG~ALKFYas~Rldirr~~~~K~g~~~~~G~~  238 (322)
T TIGR02012       159 HVGLQARLMSQALRKLTGALSKSNTTLIFINQIREKIGVMFGNPETTTGGRALKFYASVRLDIRRIGSVKEGENEAVGNR  238 (322)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHCCCE
T ss_conf             23257888999999888765320523764002222322111788887764142334433444311465415400101433


Q ss_pred             EEEEEEECCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHCCCCEECCCEEEECCEEECCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99877405778985158999861874231115999997328623027447888945030389999998667999999999
Q gi|255764460|r  250 TRVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGRENSKIFLRENIEIAENIES  329 (363)
Q Consensus       250 v~~kv~Knk~~~P~~~a~~~i~fg~GI~~~~~lldla~~~giI~k~Gawy~~~~e~~gqGk~~~~~~l~enp~l~~~i~~  329 (363)
T Consensus       239 ~~vkv~KNKvApPF~~aefdi~yg~Gi~~~g~~id~~~~~~ii~k~Gsw~sY~~~~lGQG~e~~~~~l~~~~~~~~~i~~  318 (322)
T TIGR02012       239 VKVKVVKNKVAPPFREAEFDILYGEGISKLGEIIDLAVELDIIKKSGSWYSYGDEKLGQGRENVKEFLKENPELAEEIEK  318 (322)
T ss_pred             EEEEEEEECCCCCHHHHHEEEEECCCHHHHHHHHHHHHHCCHHHCCCCEEEECCCCCCCCHHHHHHHHHHCHHHHHHHHH
T ss_conf             57898750679852130010221114023345676444201122047513116752322379999998516899999999


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|255764460|r  330 LLRQ  333 (363)
Q Consensus       330 ~ire  333 (363)
T Consensus       319 ~~~~  322 (322)
T TIGR02012       319 KVRE  322 (322)
T ss_pred             HHCC
T ss_conf             8519