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, 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=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