HHsearch alignment for GI: 254780332 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=97.80  E-value=0.0019  Score=45.63  Aligned_cols=214  Identities=22%  Similarity=0.370  Sum_probs=125.6

Q ss_pred             CCCCCCCCCHHHHHHH--HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH
Q ss_conf             3664432101377655--64167726776213100276999999999985101112333332124797589995852179
Q gi|254780332|r  198 RLAGVSTGIQTLDKQM--GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSE  275 (504)
Q Consensus       198 ~~~Gi~TG~~~LD~~~--gGl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEMs~~  275 (504)
T Consensus        32 ~v~~i~tGsl~LD~AlG~GG~P~GRi~EiYGpESsGKTTLal~~iA~~Qk---------------~Gg~~afiDAEHAlD   96 (322)
T TIGR02012        32 DVEVISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHVIAEAQK---------------AGGVAAFIDAEHALD   96 (322)
T ss_pred             CEEEECCCCHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH---------------CCCEEEEEECHHHCC
T ss_conf             10021253013435516798987507998548988478999999999974---------------398389984513037


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHC
Q ss_conf             99878999987410110001213768899899999998627807825899889999998864022444746776713532
Q gi|254780332|r  276 QLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLM  355 (504)
Q Consensus       276 el~~R~is~~s~I~~~~i~~g~l~~~e~~~i~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~~~gi~~vvIDYLqli  355 (504)
T Consensus        97 ~~----YA~~LGv~~~~-------------------------L~~sQ-Pd-~GE~ALeI~~~L~rSgAvD~iVvDSVAAL  145 (322)
T TIGR02012        97 PV----YAKKLGVDIDN-------------------------LLVSQ-PD-TGEQALEIAETLVRSGAVDIIVVDSVAAL  145 (322)
T ss_pred             HH----HHHHHCCCHHH-------------------------HEEEC-CC-CCHHHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf             78----89983645247-------------------------11208-88-71469999999872376117997340013


Q ss_pred             CCCCCCCCH-HHHHHH----HHHHHHHHH---HHHHCCCEEEEEECCCCC-------CCCCCCCCC------CCCCCCCC
Q ss_conf             566443211-378899----999999999---988279199977138220-------168999984------01014324
Q gi|254780332|r  356 TTSKKIEEN-RVLEIT----GITMALKAL---AKELNIPIIALSQLSRQV-------ENRDNKRPQ------LSDLRESG  414 (504)
Q Consensus       356 ~~~~~~~~~-r~~~i~----~is~~lK~l---A~e~~ipvi~lsQLnR~~-------e~r~~krP~------lsDLr~Sg  414 (504)
T Consensus       146 ~P~aEieGemgd~~~Gl~ARLMS~ALRKl~g~~~k~~t~~iFiNQ~R~KiGv~fG~peTTtGG~ALKFYas~Rldirr~~  225 (322)
T TIGR02012       146 VPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSKSNTTLIFINQIREKIGVMFGNPETTTGGRALKFYASVRLDIRRIG  225 (322)
T ss_pred             CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHCCCEECCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             87123175435442325788899999988876532052376400222232211178888776414233443344431146


Q ss_pred             HHHHHCCEEEEEECHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCC---EEEEEEEECCCCCEEEC
Q ss_conf             22331387889725566164423333222111000000112338838999974089972---59999974685402007
Q gi|254780332|r  415 SIEQDADVVLFVIRDEYYIRNKEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPT---GTVTLAFQAEFTRFSAL  490 (504)
Q Consensus       415 ~IEqdAD~v~~l~R~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~elivaKnR~G~~---g~~~~~f~~~~~~f~~~  490 (504)
T Consensus       226 ~~K~g~---------------------------------~~~~G~~~~vkv~KNKvApPF~~aefdi~yg~Gi~~~g~~  271 (322)
T TIGR02012       226 SVKEGE---------------------------------NEAVGNRVKVKVVKNKVAPPFREAEFDILYGEGISKLGEI  271 (322)
T ss_pred             HHHCCC---------------------------------HHHCCCEEEEEEEEECCCCCHHHHHEEEEECCCHHHHHHH
T ss_conf             541540---------------------------------0101433578987506798521300102211140233456