HHsearch alignment for GI: 254780545 and conserved domain: TIGR00362

>TIGR00362 DnaA chromosomal replication initiator protein DnaA; InterPro: IPR001957 The bacterial dnaA protein , , plays an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) .; GO: 0003677 DNA binding, 0003688 DNA replication origin binding, 0005524 ATP binding, 0006270 DNA replication initiation, 0006275 regulation of DNA replication.
Probab=95.49  E-value=0.22  Score=28.96  Aligned_cols=141  Identities=23%  Similarity=0.357  Sum_probs=91.7

Q ss_pred             HCC-CCCCEEECCCCCHHHHHHHHHHHCCC-----CCCEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCHHEEHHHHH
Q ss_conf             012-33311003787425888999974246-----997020585788644420332459999999987378012063235
Q gi|254780545|r  177 GGR-IPHGVLLVGPPGTGKTLLARAVAGEA-----NVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEID  250 (647)
Q Consensus       177 g~~-~p~g~ll~GppGtGKTlla~a~a~e~-----~~~f~~~~~s~~~~~~~g~g~~~vr~lf~~a~~~~p~iifiDeid  250 (647)
T Consensus       176 p~~p~~~p~~~~gg~glg~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-d~~l~dd~~  254 (493)
T TIGR00362       176 PGKPAYNPLFLYGGTGLGKTHLLHAIGNGVLELHPNAKVLYVTSENFLNDFVKALRDNKLDDFKKKYRSL-DFLLIDDIQ  254 (493)
T ss_pred             CCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHH
T ss_conf             7876656247744754215678777643444306773278850146789999875200168888876311-123111047


Q ss_pred             HHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCC---CCCHHHCCCCCCC--CEEEECHHHHHHHHH
Q ss_conf             64144557898862688988998998530323577829999629810---0883331656423--141000134788999
Q gi|254780545|r  251 AVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPD---VLDAALLRPGRFD--RQITVPNPDIVGREH  325 (647)
Q Consensus       251 a~~~~r~~~~~~~~~e~~~~ln~ll~~mdg~~~~~~v~vi~aTn~~~---~lD~al~RpgRfd--~~i~~~~P~~~~r~~  325 (647)
T Consensus       255 ~~~~~~~~-----~~~~~~~~~~l~------~~~~~-~~~~~d~~p~~~~~~~~~l~~--~~~~g~~~~~~~p~~~~~~~  320 (493)
T TIGR00362       255 FLAGKEKT-----QEEFFHTFNALH------EDGKQ-IVLTSDRSPKEIPGLEDRLKS--RFGWGLTADIEPPDLETRLA  320 (493)
T ss_pred             HHHCCCCH-----HHHHHHHHHHHH------HCCCE-EEEECCCCCCHHCHHHHHHHH--HHHCCCEEECCCCCHHHHHH
T ss_conf             64135203-----688888888774------06852-788516662010004677765--43014100024652357899


Q ss_pred             HHHHHHC
Q ss_conf             9999854
Q gi|254780545|r  326 ILMVHSR  332 (647)
Q Consensus       326 i~~~~~~  332 (647)
T Consensus       321 ~~~~~~~  327 (493)
T TIGR00362       321 ILKKKAE  327 (493)
T ss_pred             HHHHHHH
T ss_conf             9886544