HHsearch alignment of GI: 254780237 and MMDB domain: 3iyd_A_1-48_181-246

>3iyd_A (A:1-48,A:181-246) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}
Probab=100.00  E-value=7.5e-34  Score=239.03  Aligned_cols=109  Identities=38%  Similarity=0.674  Sum_probs=101.1

Q ss_pred             CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH
Q ss_conf             52205751797420158636788815899996169756678889999987416983068899988714431466462444
Q gi|254780237|r    2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED   81 (340)
Q Consensus         2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED   81 (340)
                      |+++|.+|++|+.++   +++.+++||+|+++|||||||+|||||||||||                             
T Consensus         1 m~~~m~~~~~p~~~~---~~~~~~~~g~f~~ePLerG~g~TlGNaLRRvLL-----------------------------   48 (114)
T 3iyd_A            1 MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILL-----------------------------   48 (114)
T ss_dssp             -CCCSCCSCCCCEEE---CCCSSSSEECCEESCBCTTHHHHHHHTTTTSSS-----------------------------
T ss_pred             CCCHHHHHCCCCEEE---EECCCCCEEEEEEECCCCCCHHHHHHHHHHHHH-----------------------------
T ss_conf             960466623896778---722788678999966899617677889999998-----------------------------


Q ss_pred             HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCC
Q ss_conf             99999840114177727982799999944716996335138985998888089997789649999997468763203444
Q gi|254780237|r   82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH  161 (340)
Q Consensus        82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~  161 (340)
                                                                                                      
T Consensus        49 --------------------------------------------------------------------------------   48 (114)
T 3iyd_A           49 --------------------------------------------------------------------------------   48 (114)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             46557543021243111144223577641168877621899999938961777999999999999888762244443221
Q gi|254780237|r  162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV  241 (340)
Q Consensus       162 ~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~  241 (340)
                                         +||||.||++|||++++||||+|||||||||+|++|+++||+||++||.+|.++++.....
T Consensus        49 -------------------kkVnY~VE~~rv~~~~~~erLileI~TnGsI~P~dAl~~Aa~iL~~~f~~f~~~~~~~e~~  109 (114)
T 3iyd_A           49 -------------------ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPE  109 (114)
T ss_dssp             -------------------SCEEECCCBCCCSSCSCCBCCCEEEECCSSSCHHHHHHHHHHHHHHTTTTTTTCCCCCCCC
T ss_pred             -------------------EEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             -------------------8898889860334667544237998316750336337899999999999754002221102