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