Query         gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 340
No_of_seqs    142 out of 1377
Neff          5.5 
Searched_HMMs 33803
Date          Mon May 23 23:39:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780237.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2a6h_A DNA-directed RNA polym 100.0       0       0  394.1  12.0  181   13-318     7-189 (190)
  2 >3iyd_A DNA-directed RNA polym 100.0 1.4E-45       0  315.4   2.2  128   53-180     1-132 (132)
  3 >1bdf_A RNA polymerase alpha s 100.0 8.4E-43       0  297.0  13.1  124   55-178     1-128 (128)
  4 >2a6h_A DNA-directed RNA polym 100.0 4.7E-42       0  292.1  10.5  123   55-178     1-125 (125)
  5 >3iyd_A DNA-directed RNA polym 100.0 7.5E-34 2.2E-38  239.0   4.5  109    2-241     1-109 (114)
  6 >1bdf_A RNA polymerase alpha s 100.0 9.2E-32 2.7E-36  225.5  10.9  107    2-235     1-107 (107)
  7 >1lb2_B DNA-directed RNA polym  99.9 2.3E-24 6.9E-29  177.5   7.9   81  251-331     3-83  (84)
  8 >1coo_A RNA polymerase alpha s  99.9 9.8E-25 2.9E-29  180.0   5.0   85  246-330    12-96  (98)
  9 >1z3e_B DNA-directed RNA polym  99.9 7.3E-22 2.2E-26  161.4   7.6   71  251-321     2-72  (73)
 10 >3gfk_B DNA-directed RNA polym  99.8 1.3E-21 3.9E-26  159.7   6.5   74  247-320     5-78  (79)
 11 >2pa8_D DNA-directed RNA polym  96.6  0.0052 1.5E-07   39.3   5.9   55  100-154    57-115 (118)
 12 >1wcn_A Transcription elongati  95.7   0.024 7.2E-07   35.0   5.5   51  264-314    14-64  (70)
 13 >1b22_A DNA repair protein RAD  95.5   0.015 4.5E-07   36.3   3.9   58  256-313    23-81  (114)
 14 >1twf_C B44.5, DNA-directed RN  95.2   0.088 2.6E-06   31.3   7.1  123   19-233     9-132 (190)
 15 >1twf_K B13.6, DNA-directed RN  95.1   0.088 2.6E-06   31.4   6.7   48  180-233    56-103 (120)
 16 >1twf_C B44.5, DNA-directed RN  94.9   0.062 1.8E-06   32.4   5.4   55  101-155    56-125 (128)
 17 >2pa8_L DNA-directed RNA polym  94.7     0.1   3E-06   31.0   6.2   48  180-233    38-85  (92)
 18 >1twf_C B44.5, DNA-directed RN  94.5   0.087 2.6E-06   31.4   5.4   16  176-191    41-56  (190)
 19 >1twf_K B13.6, DNA-directed RN  94.4    0.12 3.4E-06   30.6   5.9   54    6-65      7-63  (120)
 20 >3h0g_K DNA-directed RNA polym  94.2   0.077 2.3E-06   31.7   4.7   48  180-233    55-102 (123)
 21 >2pa8_L DNA-directed RNA polym  93.7   0.092 2.7E-06   31.2   4.3   41   20-65      5-45  (92)
 22 >1xpp_A TA1416, DNA-directed R  93.6    0.11 3.4E-06   30.6   4.6   31  200-231    62-92  (115)
 23 >3h0g_C DNA-directed RNA polym  93.6   0.071 2.1E-06   32.0   3.5   36  198-233    94-129 (165)
 24 >3h0g_C DNA-directed RNA polym  93.6   0.086 2.6E-06   31.4   4.0   55  101-155    62-128 (132)
 25 >3h0g_K DNA-directed RNA polym  92.8    0.14 4.1E-06   30.1   3.9   44    6-54      7-52  (123)
 26 >3h0g_C DNA-directed RNA polym  92.7     0.1   3E-06   30.9   3.2   38   19-60      8-45  (165)
 27 >1pzn_A RAD51, DNA repair and   92.0    0.27 7.9E-06   28.3   4.6   48  266-313    44-91  (95)
 28 >2aq4_A DNA repair protein REV  84.0    0.83 2.5E-05   25.1   2.8   48  258-307     2-53  (67)
 29 >1feu_A 50S ribosomal protein   82.9       1 3.1E-05   24.4   2.9   53   88-140    27-84  (113)
 30 >1jx4_A DNA polymerase IV (fam  80.6    0.95 2.8E-05   24.7   2.0   40  267-308     6-45  (55)
 31 >3c1y_A DNA integrity scanning  79.4     2.7 8.1E-05   21.7   4.1   44  269-313    24-67  (74)
 32 >1u9l_A Transcription elongati  79.1     4.6 0.00013   20.3   6.2   59  255-313     4-62  (70)
 33 >1t94_A Polymerase (DNA direct  78.0     2.6 7.7E-05   21.8   3.6   53  255-310     9-62  (70)
 34 >1z00_A DNA excision repair pr  76.5     3.9 0.00012   20.7   4.2   44  269-313    31-74  (89)
 35 >2zjr_S 50S ribosomal protein   72.7     1.6 4.6E-05   23.3   1.4   54   89-142    26-85  (146)
 36 >1kft_A UVRC, excinuclease ABC  71.8     3.5  0.0001   21.0   3.0   34  278-311    44-77  (78)
 37 >3bzc_A TEX; helix-turn-helix,  66.2     9.1 0.00027   18.3   4.9   50  285-335     5-59  (70)
 38 >2pa8_D DNA-directed RNA polym  59.6      12 0.00036   17.5   7.6   48  173-229    34-81  (92)
 39 >2cz9_A Probable galactokinase  53.2      15 0.00045   16.9   8.2  112  204-315     6-117 (165)
 40 >1pie_A Galactokinase; galacto  52.3      16 0.00047   16.8   4.5   64  259-322    71-134 (177)
 41 >3bqs_A Uncharacterized protei  52.1      16 0.00047   16.7   5.8   74  259-338     5-84  (93)
 42 >2ztd_A Holliday junction ATP-  46.0      20 0.00058   16.1   3.4   45  269-313    22-67  (75)
 43 >2kp7_A Crossover junction end  44.7      21 0.00061   16.0   3.0   43  268-316    42-84  (87)
 44 >1szp_A DNA repair protein RAD  44.0      21 0.00062   15.9   4.1   40  279-321     1-40  (56)
 45 >2kg5_A ARF-GAP, RHO-GAP domai  37.6      25 0.00074   15.5   2.5   40  260-300    33-74  (100)
 46 >1eu8_A Trehalose/maltose bind  35.9      28 0.00083   15.1   2.9   21  208-228    83-103 (107)
 47 >1ixr_A Holliday junction DNA   32.8      32 0.00093   14.8   4.6   45  269-313    85-130 (191)
 48 >2w9m_A Polymerase X; SAXS, DN  32.1      32 0.00096   14.7   2.8   36  280-315     2-38  (123)
 49 >3bz1_U Photosystem II 12 kDa   31.7      32 0.00094   14.8   2.3   39  267-313    44-82  (104)
 50 >3hil_A Ephrin type-A receptor  31.6      33 0.00097   14.7   3.2   39  260-299    30-70  (82)
 51 >2nrt_A Uvrabc system protein   30.8      21 0.00062   16.0   1.2   33  277-310    31-63  (64)
 52 >2gha_A Maltose ABC transporte  29.9      35   0.001   14.5   2.9   43  169-230    49-91  (98)
 53 >2gru_A 2-deoxy-scyllo-inosose  29.5      22 0.00064   15.9   1.1   19  299-317   111-129 (195)
 54 >1s5l_U Photosystem II 12 kDa   27.4      39  0.0012   14.2   2.6   39  267-313    27-65  (87)
 55 >1vdd_A Recombination protein   26.9      40  0.0012   14.2   4.3   38  290-338    12-49  (66)
 56 >3dm0_A Maltose-binding peripl  26.6      36  0.0011   14.5   1.8   19  207-225    66-84  (86)
 57 >1cuk_A RUVA protein; DNA repa  26.2      41  0.0012   14.1   4.2   45  269-313    21-66  (79)
 58 >2w9m_A Polymerase X; SAXS, DN  25.8      14 0.00042   17.1  -0.4   27  286-312    53-79  (118)
 59 >2fmp_A DNA polymerase beta; n  24.6      44  0.0013   13.9   3.6   32  286-317    53-84  (119)
 60 >2vqe_M 30S ribosomal protein   24.1      45  0.0013   13.8   3.4   48  289-339    16-63  (64)
 61 >3bq0_A POL IV, DBH, DNA polym  24.1      30 0.00088   15.0   1.0   27  270-296     8-34  (51)
 62 >2rkh_A Putative APHA-like tra  23.7      42  0.0013   14.0   1.7   21  205-225     2-22  (99)
 63 >3i0w_A 8-oxoguanine-DNA-glyco  23.6      45  0.0013   13.8   2.8   26  281-306    20-49  (58)
 64 >3bbo_O Ribosomal protein L16;  23.2      46  0.0014   13.7   1.9   26  199-224   100-125 (135)
 65 >1wuu_A Galactokinase; galacto  23.1      47  0.0014   13.7   5.0   80  259-338    66-155 (167)
 66 >3clh_A 3-dehydroquinate synth  23.0      34   0.001   14.6   1.1   13   38-50     68-80  (183)
 67 >2uyg_A 3-dehydroquinate dehyd  22.7      47  0.0014   13.7   2.2   23  299-321    22-44  (149)
 68 >2p6r_A Afuhel308 helicase; pr  22.6      48  0.0014   13.7   2.1   43  267-313     9-51  (68)
 69 >3i1n_M 50S ribosomal protein   22.5      48  0.0014   13.6   2.6   26  199-224    99-124 (136)
 70 >2duy_A Competence protein com  22.2      47  0.0014   13.7   1.7   20  289-308    52-71  (75)
 71 >3k17_A LIN0012 protein; prote  21.5      50  0.0015   13.5   2.3   79  260-338    38-131 (140)
 72 >1ujn_A Dehydroquinate synthas  21.3      38  0.0011   14.3   1.1   22  260-281   105-126 (188)
 73 >1gtd_A MTH169; synthetase, FG  21.2      49  0.0015   13.6   1.7   48  174-229    21-68  (85)
 74 >1qme_A Penicillin-binding pro  20.9      34   0.001   14.6   0.8   33  287-319     4-36  (71)
 75 >2abk_A Endonuclease III; DNA-  20.3      53  0.0016   13.4   2.4   52  256-307    50-104 (111)

No 1  
>>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:1-47,A:173-315)
Probab=100.00  E-value=0  Score=394.12  Aligned_cols=181  Identities=34%  Similarity=0.467  Sum_probs=162.6

Q ss_pred             CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             42015863678881589999616975667888999998741698306889998871443146646244499999840114
Q gi|254780237|r   13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI   92 (340)
Q Consensus        13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I   92 (340)
                      ..++. ..++.+++||+|+++||+||||+||||||||||||                                       
T Consensus         7 ~~~e~-~~~~~~~~yg~f~~~Ple~G~g~TiGN~lRR~LLs---------------------------------------   46 (190)
T 2a6h_A            7 KAPVF-TVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS---------------------------------------   46 (190)
T ss_dssp             SCCEE-EEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHH---------------------------------------
T ss_pred             CCCEE-EEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHH---------------------------------------
T ss_conf             89567-88756885689999568896175778899999885---------------------------------------


Q ss_pred             EEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEEC
Q ss_conf             17772798279999994471699633513898599888808999778964999999746876320344446557543021
Q gi|254780237|r   93 NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT  172 (340)
Q Consensus        93 ~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~  172 (340)
                                                                                                      
T Consensus        47 --------------------------------------------------------------------------------   46 (190)
T 2a6h_A           47 --------------------------------------------------------------------------------   46 (190)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--HHHCCCC
Q ss_conf             24311114422357764116887762189999993896177799999999999988876224444322100--0000000
Q gi|254780237|r  173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--DINVKSL  250 (340)
Q Consensus       173 iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~--~~~~~~~  250 (340)
                           |||++|||.|+++|||+.++||||+|||||||||+|++|+++||++|++||.+|.++.........  ....+..
T Consensus        47 -----sPV~kVnY~Ve~~~v~~~~~~ekL~leI~TdGsItP~eAl~~Aa~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (190)
T 2a6h_A           47 -----SPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPP  121 (190)
T ss_dssp             -----TCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC-----------------
T ss_pred             -----CHHHHEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             -----611104457888521777766610599954886452335999999999888763353212223442111111221


Q ss_pred             HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             11233311122101105888989883983718887449888861889886449999999998083126
Q gi|254780237|r  251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG  318 (340)
Q Consensus       251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg  318 (340)
                      ..+..+.++|++|+||+|++||||+|||+|||||+++|++||++++|||+||++||+++|+++||+|.
T Consensus       122 ~~~~~~~~~IeeL~Ls~R~~n~Lk~a~I~ti~dL~~~s~~dL~~i~n~G~ksl~EI~~~L~~~gl~L~  189 (190)
T 2a6h_A          122 EQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK  189 (190)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             CHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             01354268599905878888678775894799988499999845999760559999999998599888


No 2  
>>3iyd_A 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} (A:49-180)
Probab=100.00  E-value=1.4e-45  Score=315.44  Aligned_cols=128  Identities=45%  Similarity=0.813  Sum_probs=123.8

Q ss_pred             CCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCE
Q ss_conf             16983068899988714431466462444999998401141777279827999999447169963351389859988880
Q gi|254780237|r   53 SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH  132 (340)
Q Consensus        53 ssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~  132 (340)
                      ||++|+|||+|||+||.|||++||||+|||++|+||||+|+|++.++++++++++++||++|||+||++|++++|+||||
T Consensus         1 Ssi~G~aIt~vkI~gv~HEfsti~GV~Edv~eIiLNLK~i~~k~~~~~~~~~~l~~~Gp~~VtA~di~~p~~ieivnpd~   80 (132)
T 3iyd_A            1 SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQH   80 (132)
T ss_dssp             SSCCCCEEEECCCSSCCSSSSCCTTBSSCTTHHHHGGGTCCEEESSCSCEECCBCEESSSCCCGGGBCCCTTEEESCTTC
T ss_pred             HCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCEEEEEEECCCCCEEECCCCCCCCEEEECCCE
T ss_conf             66984589999999954430238770452999998557550665268851799960686666822676788889926988


Q ss_pred             EEEEEC-CCCEEEEEEEEECCCCCEECCCCC---CCCCCCCEECCCCCHHEE
Q ss_conf             899977-896499999974687632034444---655754302124311114
Q gi|254780237|r  133 VICNLD-VDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPI  180 (340)
Q Consensus       133 ~IaTl~-~~~~l~iel~ie~G~GY~~~e~~~---~~~~~ig~i~iDa~FsPV  180 (340)
                      |||||+ +++.|+|+++|++||||++++.++   .+..++|+|++||+||||
T Consensus        81 ~Iatl~~~~~~l~~el~i~~G~GY~~~~~~~~~~~~~~~~g~i~iDa~fsPV  132 (132)
T 3iyd_A           81 VICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV  132 (132)
T ss_dssp             CCCCBCSTTCEECCCCEEECCSSCCCHHHHC-----CCSSSCSBCCCCCCSC
T ss_pred             EEEEECCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             8999757894799999998056602142244553334657733257766776


No 3  
>>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:51-178)
Probab=100.00  E-value=8.4e-43  Score=296.98  Aligned_cols=124  Identities=44%  Similarity=0.799  Sum_probs=119.4

Q ss_pred             CCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEE
Q ss_conf             98306889998871443146646244499999840114177727982799999944716996335138985998888089
Q gi|254780237|r   55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI  134 (340)
Q Consensus        55 i~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~I  134 (340)
                      ++|+|||+|||+|+.|||++||||+|||++|+||||+|+|++++++++.+++.++||++|||+||++|+++||+||||||
T Consensus         1 i~G~aI~~vkI~Gv~HEfs~i~GV~EDv~eIilNLK~i~~~~~~~~~~~~~l~~~gp~~VtA~di~~p~~veIvnpd~~I   80 (128)
T 1bdf_A            1 MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVI   80 (128)
T ss_dssp             CCCEEEEEEEETTCCSTTCCCTTBSSCHHHHHHHHHTCCEECSSCSEEEEEEEEESSEEEEGGGBCCCSSCEESCTTCEE
T ss_pred             CCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCCCCEEEEECCCCCCEEECCCCCCCCEEEECCCEEE
T ss_conf             97639999962787664320653667699999971765367427886069994388741895166688988992698789


Q ss_pred             EEEC-CCCEEEEEEEEECCCCCEECCCCC---CCCCCCCEECCCCCHH
Q ss_conf             9977-896499999974687632034444---6557543021243111
Q gi|254780237|r  135 CNLD-VDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS  178 (340)
Q Consensus       135 aTl~-~~~~l~iel~ie~G~GY~~~e~~~---~~~~~ig~i~iDa~Fs  178 (340)
                      |||+ +++.|+|+++|++||||+++++++   .+..++|+||+||+||
T Consensus        81 aTl~~~~~~l~~el~i~~GrGYv~ae~~~~~~~~~~~ig~i~iDa~fS  128 (128)
T 1bdf_A           81 CHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYS  128 (128)
T ss_dssp             EEECSTTCEEEEEEEEEECCSEECGGGTC-----CCCCSCCBCCEECC
T ss_pred             EEECCCCCEEEEEEEEECCCCEECCCCCCCCCCCCCCCCCEECCCCCC
T ss_conf             997578947999999974555130432334432246667250464566


No 4  
>>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:48-172)
Probab=100.00  E-value=4.7e-42  Score=292.11  Aligned_cols=123  Identities=40%  Similarity=0.673  Sum_probs=117.1

Q ss_pred             CCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC--CCEEEEEEEECCEEEEEEEEECCCCEEEECCCE
Q ss_conf             983068899988714431466462444999998401141777279--827999999447169963351389859988880
Q gi|254780237|r   55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH  132 (340)
Q Consensus        55 i~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~--~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~  132 (340)
                      ++|+|||+|||+|+.|||++||||+|||++|+||||+|+|+.+.+  ++.+++++++||++|||+||++|++++|+||||
T Consensus         1 l~G~AIt~vkI~Gv~hEf~~i~GV~EDv~eIilNLK~i~~~~~~~~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNp~~   80 (125)
T 2a6h_A            1 IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDL   80 (125)
T ss_dssp             CEEEEEEEEEESSCCSTTCBCTTBSSBHHHHHHHHHTCCEEECSTTCSBCCEEEEEESSCEEEGGGSCCCTTEEESCTTC
T ss_pred             CCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCEEEEECCCCCCEEEEEEECCCCEEEEECCCCCCCCEEEECCCE
T ss_conf             98538999999994343020898521699999853051899615886249999943898279802356888589976988


Q ss_pred             EEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHH
Q ss_conf             8999778964999999746876320344446557543021243111
Q gi|254780237|r  133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS  178 (340)
Q Consensus       133 ~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~Fs  178 (340)
                      |||||++++.|+|+++|++||||+++++++.. .++|+|++||+||
T Consensus        81 ~Iatl~~~~~l~~el~i~~GrGYv~a~~~~~~-~~~g~i~iDa~fS  125 (125)
T 2a6h_A           81 HIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVDAVFS  125 (125)
T ss_dssp             EEEEBCSSCEEEEEEEEEEEESEECHHHHCCC-SSTTCEECCEECC
T ss_pred             EEEEECCCCEEEEEEEEECCEEEEEECCCCCC-CCCCCCCCCCCCH
T ss_conf             89995568628899997058012220103674-5577654464430


No 5  
>>3iyd_A 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} (A:1-48,A:181-246)
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


No 6  
>>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:1-50,A:179-235)
Probab=99.97  E-value=9.2e-32  Score=225.51  Aligned_cols=107  Identities=40%  Similarity=0.697  Sum_probs=100.0

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~~~~~~~~~~~~~~~---~~~~~~~~~f~~~Ple~g~g~TlGNaLRRvLLs----------------------------   49 (107)
T 1bdf_A            1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRAILLS----------------------------   49 (107)
T ss_dssp             -CCCSSCSCCCCEEEE---EESSSSEEEEEEEEEETTHHHHHHHHHHHHHTT----------------------------
T ss_pred             CCHHHHHHCCCCEEEE---CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH----------------------------
T ss_conf             9605667218857786---257885789999578996353678899999886----------------------------


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        50 --------------------------------------------------------------------------------   49 (107)
T 1bdf_A           50 --------------------------------------------------------------------------------   49 (107)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             46557543021243111144223577641168877621899999938961777999999999999888762244
Q gi|254780237|r  162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE  235 (340)
Q Consensus       162 ~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~  235 (340)
                                      |||++|+|.|+++++|+.++||+|+|||||||||+|+||+.+||++|++||.+|.+++
T Consensus        50 ----------------sPV~~v~Y~Ve~~~~~~~~~~ekL~leI~TdGsI~P~eAl~~Aa~iL~~~~~~~~~~n  107 (107)
T 1bdf_A           50 ----------------SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR  107 (107)
T ss_dssp             ----------------SSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC---
T ss_pred             ----------------CCEEEEEECCEEECCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             ----------------4434235110420247898606999999979989999999999999999999875479


No 7  
>>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} (B:)
Probab=99.91  E-value=2.3e-24  Score=177.54  Aligned_cols=81  Identities=57%  Similarity=1.030  Sum_probs=77.7

Q ss_pred             HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             11233311122101105888989883983718887449888861889886449999999998083126768789867799
Q gi|254780237|r  251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE  330 (340)
Q Consensus       251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~  330 (340)
                      ..+..+.++|++|+||+|++|||+++||+|||||+++|++||++++|||+||++||+++|+++|++|||++++|+|..++
T Consensus         3 ~~~~~l~~~I~~L~Ls~R~~n~L~~agI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~lg~~~~~~~~~~~e   82 (84)
T 1lb2_B            3 EFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIA   82 (84)
T ss_dssp             --CCTTTSBGGGGCCCHHHHHHHHHTTCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHHHTTCCSSCCCSCC------
T ss_pred             CCCHHHCCCHHHHCCCHHHHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             53678629798707889999999891894699987289999974889878899999999998598789989998921223


Q ss_pred             H
Q ss_conf             9
Q gi|254780237|r  331 E  331 (340)
Q Consensus       331 ~  331 (340)
                      +
T Consensus        83 ~   83 (84)
T 1lb2_B           83 D   83 (84)
T ss_dssp             -
T ss_pred             C
T ss_conf             4


No 8  
>>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:)
Probab=99.90  E-value=9.8e-25  Score=179.98  Aligned_cols=85  Identities=54%  Similarity=0.963  Sum_probs=78.5

Q ss_pred             HCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             00000112333111221011058889898839837188874498888618898864499999999980831267687898
Q gi|254780237|r  246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP  325 (340)
Q Consensus       246 ~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~  325 (340)
                      .....+..+.+.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++|++|||++++|+
T Consensus        12 ~~~~~~~~~~l~~~I~~L~Ls~Rs~N~Lk~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~Ei~~~L~~~gl~lg~~~~~~~   91 (98)
T 1coo_A           12 KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP   91 (98)
T ss_dssp             ------CCHHHHSBGGGGTCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHTTCCTTCCCSSSS
T ss_pred             CCCCCCHHHHHHCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             33330034674094998268899998999939975999985899999867798787899999999982867688789999


Q ss_pred             HHHHH
Q ss_conf             67799
Q gi|254780237|r  326 PESIE  330 (340)
Q Consensus       326 ~~~~~  330 (340)
                      +..++
T Consensus        92 ~~~~~   96 (98)
T 1coo_A           92 PASIA   96 (98)
T ss_dssp             CSTTC
T ss_pred             CCCCC
T ss_conf             74555


No 9  
>>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:)
Probab=99.86  E-value=7.3e-22  Score=161.39  Aligned_cols=71  Identities=42%  Similarity=0.589  Sum_probs=67.7

Q ss_pred             HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             11233311122101105888989883983718887449888861889886449999999998083126768
Q gi|254780237|r  251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL  321 (340)
Q Consensus       251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l  321 (340)
                      +.++.+.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++|++|||+-
T Consensus         2 ~~~~~l~~~I~~L~Ls~R~~N~L~~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~l~~~~   72 (73)
T 1z3e_B            2 EKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD   72 (73)
T ss_dssp             -CHHHHTCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHHTTCCCC---
T ss_pred             CCHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             50566268898835889999999883894799998779999975889766059999999998599889999


No 10 
>>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:)
Probab=99.85  E-value=1.3e-21  Score=159.70  Aligned_cols=74  Identities=41%  Similarity=0.565  Sum_probs=69.6

Q ss_pred             CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             00001123331112210110588898988398371888744988886188988644999999999808312676
Q gi|254780237|r  247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN  320 (340)
Q Consensus       247 ~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~  320 (340)
                      .+..+....+.++|++|+||+|++|||+++||+|||||+++|++||++++|||+||++||+++|+++|++|||+
T Consensus         5 ~~~~~~~~~l~~~I~~L~Ls~R~~n~L~~~gI~tv~dL~~~s~~dLl~i~nlG~ksl~EI~~~L~~~gl~l~~~   78 (79)
T 3gfk_B            5 KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKD   78 (79)
T ss_dssp             CCCSSCCCGGGCBGGGSCCBHHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHHTTCCCC--
T ss_pred             CCCCHHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             31015679864949984688999999989189679999878999998578986736999999999859989999


No 11 
>>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D (D:36-153)
Probab=96.62  E-value=0.0052  Score=39.31  Aligned_cols=55  Identities=18%  Similarity=0.291  Sum_probs=50.6

Q ss_pred             CCEEEEEEEECCE---EEEEEEEEC-CCCEEEECCCEEEEEECCCCEEEEEEEEECCCC
Q ss_conf             8279999994471---699633513-898599888808999778964999999746876
Q gi|254780237|r  100 SHKRVTIFKRGPG---VVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG  154 (340)
Q Consensus       100 ~~~~~~l~~~Gp~---~vtA~Di~~-p~~veivNpd~~IaTl~~~~~l~iel~ie~G~G  154 (340)
                      .....+|++++|.   .|+++|+++ ++.+.-++++-.|+.|..+-.++++....+|.|
T Consensus        57 c~v~~~L~v~~~~~~~~VyS~dL~~~~~~v~pv~~~I~I~KL~~gQ~i~l~~~a~kGiG  115 (118)
T 2pa8_D           57 CYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYG  115 (118)
T ss_dssp             TEEEEEEEEECCSSCEEEEGGGCEESSTTCCBSCSCCEEEEECTTCEEEEEEEEEEECT
T ss_pred             EEEEEEEEEECCCCCCEEEHHHCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCC
T ss_conf             48999999884899847984452036997312148806999179956999999995820


No 12 
>>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B (A:)
Probab=95.70  E-value=0.024  Score=34.96  Aligned_cols=51  Identities=8%  Similarity=0.062  Sum_probs=46.7

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             110588898988398371888744988886188988644999999999808
Q gi|254780237|r  264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG  314 (340)
Q Consensus       264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g  314 (340)
                      .++....+-|..+||+|+.||...+.++|..++++|++..+.|.....+.|
T Consensus        14 Gig~~~a~~L~~aGi~TvedLa~a~~~eL~~i~Gi~~~~A~~ii~~Ar~~~   64 (70)
T 1wcn_A           14 GVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARNIC   64 (70)
T ss_dssp             TCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHCC
T ss_conf             989999999999699759999872999997651799999999999998655


No 13 
>>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:)
Probab=95.52  E-value=0.015  Score=36.29  Aligned_cols=58  Identities=5%  Similarity=0.041  Sum_probs=49.7

Q ss_pred             HHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             31112210-11058889898839837188874498888618898864499999999980
Q gi|254780237|r  256 LLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       256 L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ...++.++ +...+...-|+.+||+|++||...+.++|.++.+||.+....|.+....+
T Consensus        23 ~~~~l~~i~GVG~~~~~~L~~~Gi~Tv~~la~~~~~~L~~i~G~~~~~a~~i~~~ar~~   81 (114)
T 1b22_A           23 QPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKL   81 (114)
T ss_dssp             CCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH
T ss_pred             CCHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             24899976899989999999969853999985899999862063699999999999986


No 14 
>>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:1-40,C:169-318)
Probab=95.24  E-value=0.088  Score=31.35  Aligned_cols=123  Identities=17%  Similarity=0.184  Sum_probs=73.3

Q ss_pred             ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC-CCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEC
Q ss_conf             63678881589999616975667888999998741-69830688999887144314664624449999984011417772
Q gi|254780237|r   19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMS-SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS   97 (340)
Q Consensus        19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLs-si~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~   97 (340)
                      .+.+.++.+-+|.+.    |--..++|||||+||+ --.-+|..+.|..-..+==.++.++.++.....           
T Consensus         9 ~I~~~~~~~v~F~L~----~vd~s~ANalRRimiAEKWsPva~v~y~y~P~i~i~~~~~~~e~cp~~v~-----------   73 (190)
T 1twf_C            9 KIREASKDNVDFILS----NVDLAMANSLRRVMIAEKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEW-----------   73 (190)
T ss_dssp             CCSCCCSSEECCEEB----SSCHHHHHHHHHHHHHCGGCCEEEEEEEECSSTTSCCSCCCCSSCHHHHS-----------
T ss_pred             EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHCEECCCEEEEEEECCCCCCCCCCCCCCCCCHHHC-----------
T ss_conf             999767998999997----88838999999999972554530378752554333445333102423218-----------


Q ss_pred             CCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCH
Q ss_conf             79827999999447169963351389859988880899977896499999974687632034444655754302124311
Q gi|254780237|r   98 GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY  177 (340)
Q Consensus        98 ~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~F  177 (340)
                                   |                       |+..              +-+   .+.....            
T Consensus        74 -------------~-----------------------~s~~--------------~~~---~~~~~~~------------   88 (190)
T 1twf_C           74 -------------P-----------------------QSKN--------------CEY---EDPPNEG------------   88 (190)
T ss_dssp             -------------C-----------------------CCGG--------------GTT---SCCCCSS------------
T ss_pred             -------------C-----------------------CCCC--------------EEE---ECCCCCC------------
T ss_conf             -------------7-----------------------6542--------------358---6123335------------


Q ss_pred             HEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             11442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       178 sPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                                ...++...  -++.+|.|+|.|++.|++.+.+|.++|+.-+..|..
T Consensus        89 ----------~~i~v~~~--~d~FiF~VES~Gsl~p~~Iv~~Ai~vLk~Kl~~l~~  132 (190)
T 1twf_C           89 ----------DPFDYKAQ--ADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILL  132 (190)
T ss_dssp             ----------SCCCTTCC--CCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------CCEEEECC--CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ----------40576336--548999999458879999999999999999999999


No 15 
>>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (K:)
Probab=95.07  E-value=0.088  Score=31.36  Aligned_cols=48  Identities=19%  Similarity=0.314  Sum_probs=38.5

Q ss_pred             EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      |.-+.|.|..      .-..+..|-|.|+|+++|.+||..|++-|.+.+..|.+
T Consensus        56 V~fagY~ipH------Pl~~~~~lrIqT~~~~~p~eal~~a~~~l~~~~~~l~~  103 (120)
T 1twf_K           56 VLFAAYKVEH------PFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKT  103 (120)
T ss_dssp             EEEEEEECSC------TTSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCC------CCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3386641688------88880389999699999999999999999999999999


No 16 
>>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:41-168)
Probab=94.86  E-value=0.062  Score=32.36  Aligned_cols=55  Identities=16%  Similarity=0.178  Sum_probs=46.3

Q ss_pred             CEEEEEEE----ECCEEEEEEEEECCC-----------CEEEECCCEEEEEECCCCEEEEEEEEECCCCC
Q ss_conf             27999999----447169963351389-----------85998888089997789649999997468763
Q gi|254780237|r  101 HKRVTIFK----RGPGVVTAGDIQTVN-----------DIEVLNPDHVICNLDVDAVVRMELTVSKGHGY  155 (340)
Q Consensus       101 ~~~~~l~~----~Gp~~vtA~Di~~p~-----------~veivNpd~~IaTl~~~~~l~iel~ie~G~GY  155 (340)
                      +...+|++    .+|..|+++|+++..           .+.-++++-.|+.|..+-.++|++...+|.|=
T Consensus        56 tv~~~L~v~~~~~~~~~V~s~dL~~~~~~~~~~~~~~~~~~p~~~~I~I~KL~~gQ~I~l~~~a~kGiGk  125 (128)
T 1twf_C           56 SVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAK  125 (128)
T ss_dssp             EEEEEEEEECCSSSCEEEEGGGEEECSCCTTCSEEEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECTT
T ss_pred             CEEEEEEEECCCCCCCEEECHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCCC
T ss_conf             2689999624777763345000211144444677886654677897699995798479999999547234


No 17 
>>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L (L:)
Probab=94.75  E-value=0.1  Score=30.99  Aligned_cols=48  Identities=29%  Similarity=0.317  Sum_probs=39.0

Q ss_pred             EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      |.-+.|.|..      .-.++..|-|.|+|+++|.+||..|++-|.+.+..|.+
T Consensus        38 V~fagY~ipH------Pl~~~~~i~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~   85 (92)
T 2pa8_L           38 VSFASYYQPH------PLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYID   85 (92)
T ss_dssp             EEEEEEECSS------TTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             0698887777------88780599999689999899999999999999999999


No 18 
>>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:1-40,C:169-318)
Probab=94.47  E-value=0.087  Score=31.40  Aligned_cols=16  Identities=6%  Similarity=0.322  Sum_probs=8.8

Q ss_pred             CHHEEEEEEEEEEEEC
Q ss_conf             1111442235776411
Q gi|254780237|r  176 LYSPIKKVSYTVESAR  191 (340)
Q Consensus       176 ~FsPV~~Vny~Ve~~r  191 (340)
                      =|+||--|.|.-.+-.
T Consensus        41 KWsPva~v~y~y~P~i   56 (190)
T 1twf_C           41 KWGPAAAIEFEYDPWN   56 (190)
T ss_dssp             GGCCEEEEEEEECSST
T ss_pred             EECCCEEEEEEECCCC
T ss_conf             5545303787525543


No 19 
>>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (K:)
Probab=94.40  E-value=0.12  Score=30.59  Aligned_cols=54  Identities=19%  Similarity=0.297  Sum_probs=38.4

Q ss_pred             HHHCCCCC---CCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             57517974---2015863678881589999616975667888999998741698306889998
Q gi|254780237|r    6 WQELIKPN---NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI   65 (340)
Q Consensus         6 ~~~~~~P~---~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI   65 (340)
                      +.-|+.|.   ++++. +.+.++++++|.+    .|..|||||+||-.||.. |+.-..+-+|
T Consensus         7 ~e~~~l~~~e~ki~i~-~~~~~~n~~~f~i----~~EDHTLgNlLr~~Ll~~-p~V~fagY~i   63 (120)
T 1twf_K            7 FELFLLGEGESKLKID-PDTKAPNAVVITF----EKEDHTLGNLIRAELLND-RKVLFAAYKV   63 (120)
T ss_dssp             GGGTSCCTTCCSCCEE-ECSSSTTEEEEEE----ESCCHHHHHHHHHHHTTC-TTEEEEEEEC
T ss_pred             HHHCCCCCCCCCEEEE-ECCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCEEEEECC
T ss_conf             1200058998515998-5588885699999----289704899999999439-9833866416


No 20 
>>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (K:)
Probab=94.22  E-value=0.077  Score=31.73  Aligned_cols=48  Identities=13%  Similarity=0.093  Sum_probs=39.5

Q ss_pred             EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      |.-+.|.|..      ....+..|-|.|+|+++|.+||..|++-|.+.+..|.+
T Consensus        55 V~fagY~ipH------Pl~~~~~lrIqT~~~~~p~~al~~A~~~l~~~~~~l~~  102 (123)
T 3h0g_K           55 VLFAGYKVPH------PLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKV  102 (123)
T ss_dssp             CSCBCCBCSC------TTSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2498876789------98782079999699999999999999999999999999


No 21 
>>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L (L:)
Probab=93.71  E-value=0.092  Score=31.24  Aligned_cols=41  Identities=24%  Similarity=0.267  Sum_probs=32.2

Q ss_pred             CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             3678881589999616975667888999998741698306889998
Q gi|254780237|r   20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI   65 (340)
Q Consensus        20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI   65 (340)
                      +.+.+++++.|.+    .|..|||||+||-.|+.. |++-..+-+|
T Consensus         5 i~~~~~n~~~~~i----~~EdHTlgN~Lr~~L~~~-~~V~fagY~i   45 (92)
T 2pa8_L            5 ILKSESNYLELEI----EGEDHTLGNLIAGTLRRI-SGVSFASYYQ   45 (92)
T ss_dssp             EEEEETTEEEEEE----ETCCHHHHHHHHHHHHTS-TTEEEEEEEC
T ss_pred             EEECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCEEEEEEEC
T ss_conf             9607997899999----289944999999998359-9806988877


No 22 
>>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} (A:)
Probab=93.60  E-value=0.11  Score=30.63  Aligned_cols=31  Identities=10%  Similarity=0.120  Sum_probs=14.1

Q ss_pred             EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999993896177799999999999988876
Q gi|254780237|r  200 KLSMTIDTDGSITGEDSVALASRILQDQLGMF  231 (340)
Q Consensus       200 kL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f  231 (340)
                      +..|-|.|+|+ +|.+||..|++-|++.+..|
T Consensus        62 ~~~lrIqT~~~-~p~~al~~A~~~l~~~~~~l   92 (115)
T 1xpp_A           62 NPQIYVRVKSG-KPQSAIKRAVRKLSKLYEDL   92 (115)
T ss_dssp             CCEEEEEESSS-CHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCC-CHHHHHHHHHHHHHHHHHHH
T ss_conf             71899981899-97999999999999999999


No 23 
>>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:1-38,C:171-297)
Probab=93.59  E-value=0.071  Score=31.96  Aligned_cols=36  Identities=25%  Similarity=0.471  Sum_probs=32.4

Q ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             218999999389617779999999999998887622
Q gi|254780237|r  198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       198 ~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      .++.+|.|+|+|++.|++.+.+|.++|+.-+..|.+
T Consensus        94 ~d~FiF~VES~Gsl~p~~Iv~~Al~iLk~K~~~l~~  129 (165)
T 3h0g_C           94 PRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVR  129 (165)
T ss_dssp             CCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             878999999505659999999999999999999998


No 24 
>>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:39-170)
Probab=93.59  E-value=0.086  Score=31.42  Aligned_cols=55  Identities=15%  Similarity=0.214  Sum_probs=45.9

Q ss_pred             CEEEEEEE----ECCEEEEEEEEECCC-CE-------EEECCCEEEEEECCCCEEEEEEEEECCCCC
Q ss_conf             27999999----447169963351389-85-------998888089997789649999997468763
Q gi|254780237|r  101 HKRVTIFK----RGPGVVTAGDIQTVN-DI-------EVLNPDHVICNLDVDAVVRMELTVSKGHGY  155 (340)
Q Consensus       101 ~~~~~l~~----~Gp~~vtA~Di~~p~-~v-------eivNpd~~IaTl~~~~~l~iel~ie~G~GY  155 (340)
                      +...+|++    .|+..|+++|+++.+ +.       +-++++-.|+.|..+-.++|++...+|.|=
T Consensus        62 tv~f~L~v~~~~~~~~~V~S~dL~~~~~~~~~~~~~~~p~~~~I~I~KL~~gQ~i~l~~~a~kGiGk  128 (132)
T 3h0g_C           62 SVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKGIAK  128 (132)
T ss_dssp             SCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCCSTTSCCSEEEEECSSCCEEEEEEEEEECGG
T ss_pred             EEEEEEEEEECCCCCEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEECCCC
T ss_conf             6898887893577745774041662786340586443555788458970577359999999978411


No 25 
>>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (K:)
Probab=92.76  E-value=0.14  Score=30.11  Aligned_cols=44  Identities=20%  Similarity=0.289  Sum_probs=32.7

Q ss_pred             HHHCCCC--CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf             5751797--420158636788815899996169756678889999987416
Q gi|254780237|r    6 WQELIKP--NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS   54 (340)
Q Consensus         6 ~~~~~~P--~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLss   54 (340)
                      ...|..|  .++++.. .+.+++.+.|.+    .|..|||||+||-.||..
T Consensus         7 ~e~~~l~~~~km~i~~-~~~~~n~~~~~i----~~EDHTLgNlLr~~Ll~~   52 (123)
T 3h0g_K            7 YELIELMGLPKVTYEL-DSKSPNAAVVTL----EKEDHTLANMLANQLLSD   52 (123)
T ss_dssp             GGTSSCSSCCSCCEEE-CSSSTTEEEEEE----ESCCSSHHHHHHHTGGGS
T ss_pred             CCEECCCCCCEEEEEE-CCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC
T ss_conf             1131148986079873-477884699999----489856999999999549


No 26 
>>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:1-38,C:171-297)
Probab=92.68  E-value=0.1  Score=30.94  Aligned_cols=38  Identities=18%  Similarity=0.274  Sum_probs=29.9

Q ss_pred             ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             636788815899996169756678889999987416983068
Q gi|254780237|r   19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI   60 (340)
Q Consensus        19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ai   60 (340)
                      .+.+.++.+-+|.+.    |--..++|||||+|++=.|-+++
T Consensus         8 ~i~e~~~~~i~F~l~----~vd~s~ANalRRimiaWsPV~~a   45 (165)
T 3h0g_C            8 TIRNISKNSVDFVLT----NTSLAVANSLRRVVLAWSPTSAV   45 (165)
T ss_dssp             CCCCBCSSEEEEEEC----SCCHHHHHHHHHHHHSSCCBCCC
T ss_pred             EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHECCCEEE
T ss_conf             999856988999997----89837888999999876332025


No 27 
>>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95)
Probab=92.00  E-value=0.27  Score=28.25  Aligned_cols=48  Identities=8%  Similarity=0.094  Sum_probs=42.4

Q ss_pred             CHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             058889898839837188874498888618898864499999999980
Q gi|254780237|r  266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       266 SvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      .......|-.+++.|+.++..-+.+||.+++++|.+..+.|.+.+.+.
T Consensus        44 G~~~a~~L~~~~~~s~e~i~~As~e~L~~i~Gig~~~A~~I~~~~~~~   91 (95)
T 1pzn_A           44 GPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKA   91 (95)
T ss_dssp             CHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             999999999859971999982899999975498999999999999873


No 28 
>>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* (A:240-306)
Probab=84.01  E-value=0.83  Score=25.05  Aligned_cols=48  Identities=23%  Similarity=0.263  Sum_probs=34.1

Q ss_pred             CCHHHC-CCCHHHHHHHHHC--CCCCHHHHHHC-CHHHHHCCCCCCHHHHHHHH
Q ss_conf             112210-1105888989883--98371888744-98888618898864499999
Q gi|254780237|r  258 KKVEEL-ELSVRSTNCLRGE--NIVYMGDLIQR-TEADMLRMANFGRKSLVEIK  307 (340)
Q Consensus       258 ~~IeeL-eLSvRs~NcLk~a--~I~tigdLv~~-s~~dLl~ikNfG~KSl~EI~  307 (340)
                      .+|.++ ..--|+..-|++.  ||+|++||.++ +.+.|.  +-||.|.-..+-
T Consensus         2 Lpi~~i~GVG~~t~~kL~~~~~Gi~ti~dL~~~~~~~~L~--~~~G~k~G~~l~   53 (67)
T 2aq4_A            2 FKLDDLPGVGHSTLSRLESTFDSPHSLNDLRKRYTLDALK--ASVGSKLGMKIH   53 (67)
T ss_dssp             CCGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHHCCHHHHH--HHHCSSHHHHHH
T ss_pred             CCCCCHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH--HHHCCHHHHHHH
T ss_conf             5423012027899999998774357699999887777888--750228999999


No 29 
>>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} (A:94-206)
Probab=82.86  E-value=1  Score=24.40  Aligned_cols=53  Identities=17%  Similarity=0.213  Sum_probs=41.0

Q ss_pred             HHCCCEEEECCC-CCEEEEEEEEC---CEEEEEEEEECCCCEEEE-CCCEEEEEECCC
Q ss_conf             401141777279-82799999944---716996335138985998-888089997789
Q gi|254780237|r   88 NIKGINLKMSGD-SHKRVTIFKRG---PGVVTAGDIQTVNDIEVL-NPDHVICNLDVD  140 (340)
Q Consensus        88 NLK~I~~k~~~~-~~~~~~l~~~G---p~~vtA~Di~~p~~veiv-Npd~~IaTl~~~  140 (340)
                      .+..|.++.... -|..+.+++.|   -..++.+||.+|.+++++ +++..|||+...
T Consensus        27 ~~~~i~v~~~p~~iP~~i~VDvs~l~~Gd~i~v~Di~lp~gv~~~~d~~~vV~sv~~~   84 (113)
T 1feu_A           27 IHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPP   84 (113)
T ss_dssp             CCSEEEEEECGGGCCSCEEEECTTCCTTEEEEGGGSCCCTTCEESSCTTCEEEEEECS
T ss_pred             EEEEEEEEEEHHCCCCEEEEECCCCCCCCEEEEEEECCCCCCEECCCCCCEEEEEECC
T ss_conf             8637889710322982799975127689869998332899948905899669999689


No 30 
>>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} (A:183-237)
Probab=80.56  E-value=0.95  Score=24.67  Aligned_cols=40  Identities=10%  Similarity=0.024  Sum_probs=30.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             588898988398371888744988886188988644999999
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      -++.--|++.||+|++||.+.+++.|.  +.||++.-..+-+
T Consensus         6 ~~t~~kL~~~GI~ti~dl~~~~~~~L~--~~~G~~~g~~l~~   45 (55)
T 1jx4_A            6 NITAEKLKKLGINKLVDTLSIEFDKLK--GXIGEAKAKYLIS   45 (55)
T ss_dssp             HHHHHHHHTTTCCBGGGGGSSCHHHHH--HHHCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHCCCCCHHHHH--HHHCCHHHHHHHH
T ss_conf             679999998489682312137999999--8968077899999


No 31 
>>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377)
Probab=79.36  E-value=2.7  Score=21.71  Aligned_cols=44  Identities=9%  Similarity=0.162  Sum_probs=36.3

Q ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             889898839837188874498888618898864499999999980
Q gi|254780237|r  269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ...-|-+. ..++.++.+-+.++|..++++|++..+.|.+.+..-
T Consensus        24 ~a~~L~~~-fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~~   67 (74)
T 3c1y_A           24 IGYNVVRM-FKTLDQISKASVEDLKKVEGIGEKRARAISESISSL   67 (74)
T ss_dssp             HHHHHHHH-HCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             99999998-538999985799888544784699999999999998


No 32 
>>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} (A:)
Probab=79.07  E-value=4.6  Score=20.26  Aligned_cols=59  Identities=10%  Similarity=0.138  Sum_probs=51.1

Q ss_pred             HHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             33111221011058889898839837188874498888618898864499999999980
Q gi|254780237|r  255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       255 ~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ....-++.|+..--....|-..|..++.++.--+-++|+.|.+|...-.+|+.+.=+.+
T Consensus         4 ~~~lF~e~LdvDe~iA~lLV~EGFtslEEiAyvp~~El~~IegfDee~a~eL~~RAk~~   62 (70)
T 1u9l_A            4 AIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA   62 (70)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             89999998387499999999846587999865899999760044799999999999999


No 33 
>>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} (A:271-340)
Probab=77.99  E-value=2.6  Score=21.83  Aligned_cols=53  Identities=13%  Similarity=0.086  Sum_probs=39.6

Q ss_pred             HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             331112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r  255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL  310 (340)
Q Consensus       255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L  310 (340)
                      +-.++|.++ ..--++.--|++.||+|++||.+.+.+-+.+   +|.++-..+.+.+
T Consensus         9 l~~lpi~~i~GIG~~~~~~L~~~gI~ti~dl~~~~~~~~~~---~~~~~g~~l~~~a   62 (70)
T 1t94_A            9 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLL---FSETSWHYFLHIS   62 (70)
T ss_dssp             HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHHTHHHHHHH---SCHHHHHHHHHHH
T ss_pred             HHHCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH---HHHHHHHHHHHHH
T ss_conf             97397140257631100454541358699999867778888---5111245656652


No 34 
>>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:)
Probab=76.47  E-value=3.9  Score=20.70  Aligned_cols=44  Identities=16%  Similarity=0.184  Sum_probs=36.8

Q ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             889898839837188874498888618898864499999999980
Q gi|254780237|r  269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ....|-+. ..++.++..-+.++|.+++++|.+...+|.+.+..-
T Consensus        31 ~a~~L~~~-F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~~~~   74 (89)
T 1z00_A           31 DSQTLLTT-FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             HHHHHHHH-TCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHHHCH
T ss_conf             99999999-099478766547510000332799999999998183


No 35 
>>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (S:92-237)
Probab=72.70  E-value=1.6  Score=23.27  Aligned_cols=54  Identities=11%  Similarity=0.207  Sum_probs=42.2

Q ss_pred             HCCCEEEE-C-CCCCEEEEEEEEC---CEEEEEEEEECCCCEEEE-CCCEEEEEECCCCE
Q ss_conf             01141777-2-7982799999944---716996335138985998-88808999778964
Q gi|254780237|r   89 IKGINLKM-S-GDSHKRVTIFKRG---PGVVTAGDIQTVNDIEVL-NPDHVICNLDVDAV  142 (340)
Q Consensus        89 LK~I~~k~-~-~~~~~~~~l~~~G---p~~vtA~Di~~p~~veiv-Npd~~IaTl~~~~~  142 (340)
                      +..|.++. . .+-|..+.+++.|   -..++++||.+|.+++++ +++..||++.....
T Consensus        26 ~~~i~V~~l~P~~IPe~I~VDVs~L~iGdsi~v~Dl~lp~gv~~~~d~d~vVvsV~~p~~   85 (146)
T 2zjr_S           26 VHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRL   85 (146)
T ss_dssp             CSEEEEECCCTTCCCSCCEEECTTCCSSCEEETTTSCCSTTCCCCSCTTCEEEEEECCC-
T ss_pred             HHHHHHHCCCHHHCCHHHCCCCCCCCCCCCEEEEEEECCCCEEEECCCCCEEEEEECCCC
T ss_conf             243665423843575230236434658984588777269984981489847999967874


No 36 
>>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:)
Probab=71.81  E-value=3.5  Score=21.01  Aligned_cols=34  Identities=9%  Similarity=0.040  Sum_probs=31.8

Q ss_pred             CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             8371888744988886188988644999999999
Q gi|254780237|r  278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG  311 (340)
Q Consensus       278 I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~  311 (340)
                      ..++.++.+-+.+||.++.++|.+..+.|.+.|.
T Consensus        44 Fgs~~~i~~As~eeL~~v~gIG~~~A~~I~~~l~   77 (78)
T 1kft_A           44 MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             CCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             0998999857899997389989999999999976


No 37 
>>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568)
Probab=66.22  E-value=9.1  Score=18.30  Aligned_cols=50  Identities=14%  Similarity=0.085  Sum_probs=39.7

Q ss_pred             HHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-----CCCCCCCCCCHHHHHHHHHH
Q ss_conf             7449888861889886449999999998083-----12676878986779999987
Q gi|254780237|r  285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGL-----FLGMNLPDWPPESIEELAKK  335 (340)
Q Consensus       285 v~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl-----~lg~~l~~~~~~~~~~~~~~  335 (340)
                      =.-+.++|.+++++|.+....|.+.....|.     .|. .++++++..++.++.-
T Consensus         5 N~A~~~~L~~lpgig~~~A~~Ii~~R~~~G~f~s~~dL~-~v~gl~~~~~~~l~~~   59 (70)
T 3bzc_A            5 NTASAALLARISGLNSTLAQNIVAHRDANGAFRTRDELK-KVSRLGEKTFEQAAGF   59 (70)
T ss_dssp             TTCCHHHHHTSTTCCHHHHHHHHHHHHHHCCCSSGGGGG-GSTTCCHHHHHHHGGG
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHH-HCCCCCHHHHHHCCEE
T ss_conf             875488886606978899999999999669957799998-5678881289871808


No 38 
>>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D (D:1-35,D:154-168,D:224-265)
Probab=59.56  E-value=12  Score=17.53  Aligned_cols=48  Identities=19%  Similarity=0.236  Sum_probs=33.5

Q ss_pred             CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             243111144223577641168877621899999938961777999999999999888
Q gi|254780237|r  173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG  229 (340)
Q Consensus       173 iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~  229 (340)
                      +-|-|-||.-..-  +..       -++-++||+.-||..|+-.|-+|.+-+..-+.
T Consensus        34 LYakfipvsl~~i--~~~-------~~kyILeiESVGSLkPeRILiEA~KSilrKie   81 (92)
T 2pa8_D           34 LYAKFIPVSLSVV--RYY-------PDKYILEIESVGSLKPERILLEAGKSIIRKIE   81 (92)
T ss_dssp             HSGGGCCEEEEEE--EEE-------EEEEEEEEEECSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCCCCCEEE--ECC-------CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             7132266652001--002-------37899999975762999999999999999999


No 39 
>>2cz9_A Probable galactokinase; structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.50A {Pyrococcus horikoshii} PDB: 2dei_A* 2dej_A* 1s4e_A* (A:179-343)
Probab=53.19  E-value=15  Score=16.86  Aligned_cols=112  Identities=11%  Similarity=0.018  Sum_probs=70.5

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHH
Q ss_conf             99938961777999999999999888762244443221000000000112333111221011058889898839837188
Q gi|254780237|r  204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD  283 (340)
Q Consensus       204 EI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigd  283 (340)
                      =++|+-.-+-.++.......-.+....+................-..........-+.+-.++..+..+|++.++..+|.
T Consensus         6 i~dsgv~~~t~~~~~~~r~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~al~~~d~~~lg~   85 (165)
T 2cz9_A            6 VFYTGVRRELASSEYAERKHIAEESLKILGKGSSKEVREGELSKLPPLHRKFFGYIVRENARVLEVRDALKEGNVEEVGK   85 (165)
T ss_dssp             EEECSCC----CHHHHHHHHHHHHHHHHHTCSCGGGCCGGGGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             EEECCCEECCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             97324200112102566789999999762432146777877752678999999999986067899998762141778888


Q ss_pred             HHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             87449888861889886449999999998083
Q gi|254780237|r  284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGL  315 (340)
Q Consensus       284 Lv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl  315 (340)
                      |+..+...|...-+..--.++.+.+.-.+.|.
T Consensus        86 lm~~~~~~l~~~~~vs~p~ld~l~~~a~~~Ga  117 (165)
T 2cz9_A           86 ILTTAHWDLAKNYEVSCKELDFFVERALKLGA  117 (165)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC
T ss_conf             99999999987506687899999999997699


No 40 
>>1pie_A Galactokinase; galactose, galactosemia, transferase; HET: GLA; 2.10A {Lactococcus lactis} (A:233-409)
Probab=52.35  E-value=16  Score=16.77  Aligned_cols=64  Identities=14%  Similarity=0.144  Sum_probs=52.9

Q ss_pred             CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             1221011058889898839837188874498888618898864499999999980831267687
Q gi|254780237|r  259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP  322 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~  322 (340)
                      -+.+-....++..+|+..++..+|.|+..+...|...-+..-..++-+.+...+.+=.+|-++.
T Consensus        71 ~~~e~~rv~~a~~al~~~d~~~lG~lm~~sh~~l~~~~~vS~peld~lv~~a~~~~Ga~GaKlt  134 (177)
T 1pie_A           71 AVYENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARMT  134 (177)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHHSTTEEEEEEC
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             5068899999998753277888999999999999997579979999999999984895798970


No 41 
>>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:)
Probab=52.07  E-value=16  Score=16.74  Aligned_cols=74  Identities=15%  Similarity=0.108  Sum_probs=47.9

Q ss_pred             CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHH---HCCCCC--CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             12210-11058889898839837188874498888---618898--8644999999999808312676878986779999
Q gi|254780237|r  259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADM---LRMANF--GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL  332 (340)
Q Consensus       259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dL---l~ikNf--G~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~  332 (340)
                      ++.+| ++...+..-|.+.||+|+.||......++   ++-.+.  ....|--+.-++.      |.....|+++.-++|
T Consensus         5 ~l~~LPNiG~~~e~~L~~iGI~tv~~L~~~ga~~~~~~l~~~~~~~~~~~Lyal~~Ai~------g~~w~~l~~~~K~~L   78 (93)
T 3bqs_A            5 NLSELPNIGKVLEQDLIKAGIKTPVELKDVGSKEAFLRIWENDSSVCMSELYALEGAVQ------GIRWHGLDEAKKIEL   78 (93)
T ss_dssp             CGGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHTTCTTCCHHHHHHHHHHHH------TSCGGGSCHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHC------CCCHHHCCHHHHHHH
T ss_conf             78568999999999999839998999987799999999998589997999999999995------998677999999999


Q ss_pred             HHHHHC
Q ss_conf             987750
Q gi|254780237|r  333 AKKYED  338 (340)
Q Consensus       333 ~~~~~~  338 (340)
                      ...++.
T Consensus        79 ~~~~~~   84 (93)
T 3bqs_A           79 KKFHQS   84 (93)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
T ss_conf             999999


No 42 
>>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154)
Probab=46.02  E-value=20  Score=16.14  Aligned_cols=45  Identities=11%  Similarity=0.161  Sum_probs=32.1

Q ss_pred             HHHHHHHCCCCCHHHHHHC-CHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8898988398371888744-98888618898864499999999980
Q gi|254780237|r  269 STNCLRGENIVYMGDLIQR-TEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv~~-s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      +.++|..-+...+.+.+.- ...-|.++|+.|+|..+-|.--|+..
T Consensus        22 Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtA~rii~ELk~k   67 (75)
T 2ztd_A           22 AMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDK   67 (75)
T ss_dssp             HHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTT
T ss_pred             HHHHHCCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf             6232215776777788853688998508883568899999998411


No 43 
>>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:)
Probab=44.67  E-value=21  Score=16.01  Aligned_cols=43  Identities=12%  Similarity=0.088  Sum_probs=30.5

Q ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             8889898839837188874498888618898864499999999980831
Q gi|254780237|r  268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF  316 (340)
Q Consensus       268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~  316 (340)
                      ||.+.|++-..      --.+..|+..++++|.+...-|.+.|+..-..
T Consensus        42 kA~~slk~~p~------pi~s~~~l~~lpgiG~~ia~kI~e~l~tg~~e   84 (87)
T 2kp7_A           42 KALRSLQRYPL------PLRSGKEAKILQHFGDRLCRMLDEKLKQHLAS   84 (87)
T ss_dssp             HHHHHHHHCCS------CCCSHHHHHTCTTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCC------CCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999997898------87889998738998789999999999999987


No 44 
>>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81)
Probab=44.02  E-value=21  Score=15.95  Aligned_cols=40  Identities=8%  Similarity=0.120  Sum_probs=33.7

Q ss_pred             CCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             3718887449888861889886449999999998083126768
Q gi|254780237|r  279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL  321 (340)
Q Consensus       279 ~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l  321 (340)
                      +||..+..-+..+|..+++++.--.+-|.+.-.++   ++|..
T Consensus         1 ~Tve~ia~at~k~L~~ikGisE~ka~KIi~aA~kl---~~~gF   40 (56)
T 1szp_A            1 HTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARL---VPMGF   40 (56)
T ss_dssp             CSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHHH---SCCSC
T ss_pred             CCHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHH---HCCCC
T ss_conf             63999973899999876399999999999999987---44799


No 45 
>>2kg5_A ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-containing protein 3; SAM domain, helix bundle, cell membrane, cell projection, cytoplasm; NMR {Homo sapiens} (A:)
Probab=37.56  E-value=25  Score=15.47  Aligned_cols=40  Identities=10%  Similarity=0.219  Sum_probs=31.4

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCCH
Q ss_conf             221011058889898839837188874498888618--89886
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFGR  300 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG~  300 (340)
                      ++.++|+. -..++.+.+|..+..|...+.+||..+  .++|-
T Consensus        33 L~~igl~~-Y~~~F~~~~i~g~~~L~~l~~~dL~~lgI~~~gh   74 (100)
T 2kg5_A           33 LATVHLEQ-YADTFRRHGLATAGAARGLGHEELKQLGISATGH   74 (100)
T ss_dssp             HGGGTCGG-GHHHHHHTTCCBHHHHTTCCHHHHHHHTCCCHHH
T ss_pred             HHHCCCHH-HHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHH
T ss_conf             99884499-9999998699848999877899998749998899


No 46 
>>1eu8_A Trehalose/maltose binding protein; protein-carbohydrate complex, MBP 2 fold, ABC transporter fold, thermophilic protein; HET: TRE; 1.90A {Thermococcus litoralis} (A:175-230,A:359-409)
Probab=35.94  E-value=28  Score=15.14  Aligned_cols=21  Identities=14%  Similarity=0.338  Sum_probs=12.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q ss_conf             896177799999999999988
Q gi|254780237|r  208 DGSITGEDSVALASRILQDQL  228 (340)
Q Consensus       208 nGsi~P~eAl~~Aa~iL~~~l  228 (340)
                      .|..+|++||..|++-+...+
T Consensus        83 ~G~~tpeeAl~~a~~~i~~il  103 (107)
T 1eu8_A           83 AGKISPQEALDKAQKEAEELV  103 (107)
T ss_dssp             HTSSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHH
T ss_conf             599999999999999999999


No 47 
>>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:)
Probab=32.79  E-value=32  Score=14.82  Aligned_cols=45  Identities=13%  Similarity=0.069  Sum_probs=30.1

Q ss_pred             HHHHHHHCCCCCHH-HHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             88989883983718-8874498888618898864499999999980
Q gi|254780237|r  269 STNCLRGENIVYMG-DLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tig-dLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      +..-|..-+...+- .+.+.+.+.|.++|+.|+|..+.|...|+..
T Consensus        85 Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~eLk~k  130 (191)
T 1ixr_A           85 ALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGK  130 (191)
T ss_dssp             HHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTT
T ss_pred             HHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999855999999999982899985138884568899999999864


No 48 
>>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:119-241)
Probab=32.11  E-value=32  Score=14.75  Aligned_cols=36  Identities=19%  Similarity=0.192  Sum_probs=26.1

Q ss_pred             CHHHHHHCCH-HHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             7188874498-88861889886449999999998083
Q gi|254780237|r  280 YMGDLIQRTE-ADMLRMANFGRKSLVEIKGVLGTMGL  315 (340)
Q Consensus       280 tigdLv~~s~-~dLl~ikNfG~KSl~EI~~~L~~~gl  315 (340)
                      |+.||-..-+ ..+..+|+||.|+-+-|...|+.+.-
T Consensus         2 tleeL~~a~~~~~i~~l~gfG~K~~~~il~gl~~~~~   38 (123)
T 2w9m_A            2 SLERLREAAESGELAGLKGFGAKSAATILENVVFLFE   38 (123)
T ss_dssp             SHHHHHHHHHHTTTTTSTTCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             8999999876088012110138899999987878887


No 49 
>>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* (U:)
Probab=31.65  E-value=32  Score=14.79  Aligned_cols=39  Identities=8%  Similarity=0.128  Sum_probs=29.8

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             58889898839837188874498888618898864499999999980
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ..|.+.++...+..+        +||++++++|.+.++.|+..+...
T Consensus        44 ~~A~~Iv~~gpf~s~--------~dL~~v~gi~~~~~~~i~~~l~v~   82 (104)
T 3bz1_U           44 TLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLEHF   82 (104)
T ss_dssp             HHHHHHHHSCCCSSG--------GGGGGCTTCCHHHHHHHHHHGGGE
T ss_pred             HHHHHHHHCCCCCCH--------HHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             999999970897879--------999617998999999999876145


No 50 
>>3hil_A Ephrin type-A receptor 1; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.00A {Homo sapiens} PDB: 3kka_A (A:)
Probab=31.64  E-value=33  Score=14.70  Aligned_cols=39  Identities=18%  Similarity=0.261  Sum_probs=30.1

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCC
Q ss_conf             221011058889898839837188874498888618--8988
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFG  299 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG  299 (340)
                      ++.++|+ .-..++++.+|..+..|...++++|.++  +++|
T Consensus        30 L~~~gl~-~y~~~F~~~~i~g~~~L~~l~~~dL~~lGI~~~g   70 (82)
T 3hil_A           30 LESIRMK-RYILHFHSAGLDTMECVLELTAEDLTQMGITLPG   70 (82)
T ss_dssp             HHHTTCG-GGHHHHHHTTCCSGGGGTTCCHHHHHHTTCCCHH
T ss_pred             HHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHH
T ss_conf             9988769-8899999969786798733889999886989889


No 51 
>>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220)
Probab=30.79  E-value=21  Score=15.96  Aligned_cols=33  Identities=6%  Similarity=0.122  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             9837188874498888618898864499999999
Q gi|254780237|r  277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL  310 (340)
Q Consensus       277 ~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L  310 (340)
                      ...++..+.+-|.+||.+++++|++. +.|.+.|
T Consensus        31 ~F~s~~~i~~As~eeL~~v~gig~~A-~~I~~~f   63 (64)
T 2nrt_A           31 HFGSLENIRSASLEEIARVIGSTEIA-RRVLDIL   63 (64)
T ss_dssp             HHCSHHHHHTSCHHHHHHHHTCHHHH-HHHHHHC
T ss_pred             HCCCHHHHHCCCHHHHHHCCCCHHHH-HHHHHHH
T ss_conf             86899999709999998687929999-9999970


No 52 
>>2gha_A Maltose ABC transporter, periplasmic maltose- binding protein; periplasmic binding protein, MBP, maltotriose, sugar binding protein; HET: MLR; 1.60A {Thermotoga maritima MSB8} PDB: 2ghb_A 2fnc_A* (A:155-206,A:337-382)
Probab=29.94  E-value=35  Score=14.52  Aligned_cols=43  Identities=16%  Similarity=0.341  Sum_probs=28.6

Q ss_pred             CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             30212431111442235776411688776218999999389617779999999999998887
Q gi|254780237|r  169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM  230 (340)
Q Consensus       169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~  230 (340)
                      |.+|.-.+..|....-                   ..-.+|-.+|++||..|.+.+..+...
T Consensus        49 g~~pM~~VW~p~~~Al-------------------~~i~~gk~~p~~al~~AV~~Ik~~I~~   91 (98)
T 2gha_A           49 GILDMAAVWAAMNDAL-------------------NLVVNGKATVEEALKNAVERIKAQIQG   91 (98)
T ss_dssp             TSSCGGGTHHHHHHHH-------------------HHHHTTSSCHHHHHHHHHHHHHHHHC-
T ss_pred             CCCCHHHHHHHHHHHH-------------------HHHHCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             2678899999999999-------------------999859899999999999999999737


No 53 
>>2gru_A 2-deoxy-scyllo-inosose synthase; aminoglycoside, 2-deoxystreptamine, dehydroquinate synthase, lyase; HET: NAD EXO CAK; 2.15A {Bacillus circulans} PDB: 2d2x_A* (A:174-368)
Probab=29.47  E-value=22  Score=15.89  Aligned_cols=19  Identities=11%  Similarity=0.125  Sum_probs=8.3

Q ss_pred             CHHHHHHHHHHHHHHCCCC
Q ss_conf             8644999999999808312
Q gi|254780237|r  299 GRKSLVEIKGVLGTMGLFL  317 (340)
Q Consensus       299 G~KSl~EI~~~L~~~gl~l  317 (340)
                      .+..++++.+.|..+|+..
T Consensus       111 ~~~~~~~~~~~l~~~glp~  129 (195)
T 2gru_A          111 PEHDVSAHYWLLNKIGALQ  129 (195)
T ss_dssp             CHHHHHHHHHHHHHTTTTT
T ss_pred             CHHHHHHHHHHHHHCCCCC
T ss_conf             8999999999999759966


No 54 
>>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134)
Probab=27.35  E-value=39  Score=14.23  Aligned_cols=39  Identities=8%  Similarity=0.127  Sum_probs=25.3

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             58889898839837188874498888618898864499999999980
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ..+.+.++.-.+.        |-+||.+++++|.+.++.|+..|...
T Consensus        27 ~~A~~Iv~~g~f~--------s~~dL~~v~gi~~~~~~~i~~~l~v~   65 (87)
T 1s5l_U           27 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHF   65 (87)
T ss_dssp             HHHHHHHHTCCCS--------SGGGGGGCTTCCHHHHHHHHHHHTTE
T ss_pred             HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             9999999827848--------79999617757999999999865353


No 55 
>>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66)
Probab=26.92  E-value=40  Score=14.18  Aligned_cols=38  Identities=29%  Similarity=0.361  Sum_probs=27.1

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHC
Q ss_conf             8886188988644999999999808312676878986779999987750
Q gi|254780237|r  290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED  338 (340)
Q Consensus       290 ~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~~  338 (340)
                      +.|.++|+.|+||.+-+.-.           +-.||++.+.++.+-+.+
T Consensus        12 ~~l~~LPGIG~KsA~Rla~~-----------lL~~~~~~~~~l~~~l~~   49 (66)
T 1vdd_A           12 RELSRLPGIGPKSAQRLAFH-----------LFEQPREDIERLASALLE   49 (66)
T ss_dssp             HHHHTSTTCCHHHHHHHHHH-----------HSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHH-----------HHCCCHHHHHHHHHHHHH
T ss_conf             99967899889999999999-----------972999999999999999


No 56 
>>3dm0_A Maltose-binding periplasmic protein fused with RACK1; MBP RACK1A, receptor for activiated protein C-kinase 1, beta-propeller WD40 repeat; HET: GLC; 2.40A {Escherichia coli} (A:158-205,A:334-371)
Probab=26.61  E-value=36  Score=14.48  Aligned_cols=19  Identities=21%  Similarity=0.169  Sum_probs=13.3

Q ss_pred             ECCCCCHHHHHHHHHHHHH
Q ss_conf             3896177799999999999
Q gi|254780237|r  207 TDGSITGEDSVALASRILQ  225 (340)
Q Consensus       207 TnGsi~P~eAl~~Aa~iL~  225 (340)
                      ++|.-+|++||..|++.+.
T Consensus        66 ~~gkq~~~~AL~~A~~~I~   84 (86)
T 3dm0_A           66 ASGRQTVDAALAAAQTNAA   84 (86)
T ss_dssp             HHTSSCHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCCCCCCCCCC
T ss_conf             7530033211121222223


No 57 
>>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144)
Probab=26.23  E-value=41  Score=14.10  Aligned_cols=45  Identities=9%  Similarity=0.186  Sum_probs=29.3

Q ss_pred             HHHHHHHCCCCCHHHHH-HCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             88989883983718887-4498888618898864499999999980
Q gi|254780237|r  269 STNCLRGENIVYMGDLI-QRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv-~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ++++|..-....+.+.+ +-....|.++|+.|+|..+-|.--|+..
T Consensus        21 Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtAerii~eLk~K   66 (79)
T 1cuk_A           21 ALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDR   66 (79)
T ss_dssp             HHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             9999757999999999992899998419998899999999999988


No 58 
>>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118)
Probab=25.79  E-value=14  Score=17.07  Aligned_cols=27  Identities=7%  Similarity=0.182  Sum_probs=17.2

Q ss_pred             HCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             449888861889886449999999998
Q gi|254780237|r  286 QRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      ..+.+++.++++.|++..+-|.+.+..
T Consensus        53 ~~~~~~l~~lpGIG~~~a~kI~E~l~t   79 (118)
T 2w9m_A           53 ELLAREFTGIPKVGKGIAAELSDFARS   79 (118)
T ss_dssp             ------CCSSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             754988625999878999999999984


No 59 
>>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119)
Probab=24.55  E-value=44  Score=13.90  Aligned_cols=32  Identities=22%  Similarity=0.220  Sum_probs=24.2

Q ss_pred             HCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             44988886188988644999999999808312
Q gi|254780237|r  286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFL  317 (340)
Q Consensus       286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~l  317 (340)
                      -.+.+++.+++++|.+..+-|.+.|..--+..
T Consensus        53 i~s~~~~~~lpgiG~~ia~~I~e~l~tG~~~~   84 (119)
T 2fmp_A           53 IKSGAEAKKLPGVGTKIAEKIDEFLATGKLRK   84 (119)
T ss_dssp             CCCHHHHHTSTTCCHHHHHHHHHHHHHSSCHH
T ss_pred             CCCHHHHHCCCCCCHHHHHHHHHHHHCCCHHH
T ss_conf             47899984799964899999999996486589


No 60 
>>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64)
Probab=24.14  E-value=45  Score=13.85  Aligned_cols=48  Identities=15%  Similarity=0.233  Sum_probs=39.4

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             888861889886449999999998083126768789867799999877503
Q gi|254780237|r  289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK  339 (340)
Q Consensus       289 ~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~~~  339 (340)
                      .-.|..+.+.|++...+|   +...|++-.+++.++..++++.+.+-+++.
T Consensus        16 ~~aLt~I~GIG~~~A~~I---c~~lgi~~~~k~~~Lt~~qi~~i~~~i~~~   63 (64)
T 2vqe_M           16 DVALTYIYGIGKARAKEA---LEKTGINPATRVKDLTEAEVVRLREYVENT   63 (64)
T ss_dssp             HHHHTTSSSCCSHHHHHH---TTTTTCCTTSBGGGCCHHHHHHHHHHHHTT
T ss_pred             EEEEEEEECCCHHHHHHH---HHHCCCCCCCCCCCCCHHHHHHHHHHHHCC
T ss_conf             887330658189999999---998299833221513599999999987316


No 61 
>>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} (A:185-235)
Probab=24.10  E-value=30  Score=14.97  Aligned_cols=27  Identities=11%  Similarity=0.263  Sum_probs=21.9

Q ss_pred             HHHHHHCCCCCHHHHHHCCHHHHHCCC
Q ss_conf             898988398371888744988886188
Q gi|254780237|r  270 TNCLRGENIVYMGDLIQRTEADMLRMA  296 (340)
Q Consensus       270 ~NcLk~a~I~tigdLv~~s~~dLl~ik  296 (340)
                      .--|+..||+.+.|.++.+-++|.++-
T Consensus         8 ~~kL~~lGInkL~Dil~~~f~klk~ii   34 (51)
T 3bq0_A            8 ARRLNELGIQKLRDILSKNYNELEKIT   34 (51)
T ss_dssp             HHHHTTTTCCBGGGGGGSCHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             455453278747888764266788760


No 62 
>>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, structural genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum ms-1} (A:1-99)
Probab=23.69  E-value=42  Score=13.99  Aligned_cols=21  Identities=19%  Similarity=0.159  Sum_probs=16.8

Q ss_pred             EEECCCCCHHHHHHHHHHHHH
Q ss_conf             993896177799999999999
Q gi|254780237|r  205 IDTDGSITGEDSVALASRILQ  225 (340)
Q Consensus       205 I~TnGsi~P~eAl~~Aa~iL~  225 (340)
                      .++|-|.+|+||+..+|-=++
T Consensus         2 ~~~DNtL~PkEAvRL~aLG~i   22 (99)
T 2rkh_A            2 XFADNTLTPKEAVRLCALGTI   22 (99)
T ss_dssp             -----CCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHH
T ss_conf             887899891779999999998


No 63 
>>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236)
Probab=23.64  E-value=45  Score=13.79  Aligned_cols=26  Identities=8%  Similarity=0.148  Sum_probs=18.9

Q ss_pred             HHHHHHCCHHH----HHCCCCCCHHHHHHH
Q ss_conf             18887449888----861889886449999
Q gi|254780237|r  281 MGDLIQRTEAD----MLRMANFGRKSLVEI  306 (340)
Q Consensus       281 igdLv~~s~~d----Ll~ikNfG~KSl~EI  306 (340)
                      +..|-.++.++    |+++|+.|+|+.+=|
T Consensus        20 l~~L~~l~~eea~~~L~~i~GIGpwTAdci   49 (58)
T 3i0w_A           20 LEYIKSLNDNECHEELKKFMGVGPQVADCI   49 (58)
T ss_dssp             HHHHHHSCHHHHHHHHTTSTTCCHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHCCCCHHHHHHHH
T ss_conf             899731354467899982688129999999


No 64 
>>3bbo_O Ribosomal protein L16; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (O:)
Probab=23.17  E-value=46  Score=13.73  Aligned_cols=26  Identities=15%  Similarity=0.198  Sum_probs=22.9

Q ss_pred             CEEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             18999999389617779999999999
Q gi|254780237|r  199 DKLSMTIDTDGSITGEDSVALASRIL  224 (340)
Q Consensus       199 dkL~lEI~TnGsi~P~eAl~~Aa~iL  224 (340)
                      -+.+|||+++---..++||..|+..|
T Consensus       100 G~iifEi~~~~~~~a~~al~~a~~KL  125 (135)
T 3bbo_O          100 GRILYEISGVAENIARRAVAIAASKM  125 (135)
T ss_dssp             TCEEEEECSSCTTHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             91899965999999999999998728


No 65 
>>1wuu_A Galactokinase; galactosemia, GHMP superfamily, transferase; HET: GLA ANP; 2.50A {Homo sapiens} (A:223-389)
Probab=23.07  E-value=47  Score=13.72  Aligned_cols=80  Identities=10%  Similarity=0.129  Sum_probs=61.3

Q ss_pred             CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC--C--------CHHH
Q ss_conf             12210110588898988398371888744988886188988644999999999808312676878--9--------8677
Q gi|254780237|r  259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--W--------PPES  328 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~--~--------~~~~  328 (340)
                      -+.+-+...++..+|++.+...+|.|+..+..-|..+-+..-..++.+.+...+.+=.+|-++.+  |        +++.
T Consensus        66 ~~~e~~rv~~a~~al~~~d~~~lg~lm~~s~~~L~~~~~vs~peld~lv~~a~~~~Ga~GaKltGaG~GGcviaLv~~~~  145 (167)
T 1wuu_A           66 VVGEIRRTAQAAAALRRGDYRAFGRLXVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRXTGGGFGGCTVTLLEASA  145 (167)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHTSTTEEEEEECSSCSEEEEEEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECHHH
T ss_conf             52345678899987752899999999999999999853799789999999998618972888804777718999977268


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999987750
Q gi|254780237|r  329 IEELAKKYED  338 (340)
Q Consensus       329 ~~~~~~~~~~  338 (340)
                      +++..+.+++
T Consensus       146 ~~~v~~~~~~  155 (167)
T 1wuu_A          146 APHAXRHIQE  155 (167)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 66 
>>3clh_A 3-dehydroquinate synthase; shikimate pathway, aromatic amino acid biosynthesis, DHQS, amino-acid biosynthesis, cytoplasm, lyase, NAD; HET: NAD; 2.40A {Helicobacter pylori} (A:161-343)
Probab=23.03  E-value=34  Score=14.63  Aligned_cols=13  Identities=31%  Similarity=0.787  Sum_probs=5.0

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             5667888999998
Q gi|254780237|r   38 GFAHTLGNALRRV   50 (340)
Q Consensus        38 G~g~TlGNaLRRv   50 (340)
                      +||||+|+|+-+.
T Consensus        68 n~gHt~~HalE~~   80 (183)
T 3clh_A           68 NYGHTFGHAIEKE   80 (183)
T ss_dssp             TTTHHHHHHHHHH
T ss_pred             HCCHHHHHHHHHH
T ss_conf             0122687654554


No 67 
>>2uyg_A 3-dehydroquinate dehydratase; typeii 3-dehydroquinase, lyase; 2.2A {Thermus thermophilus} (A:)
Probab=22.69  E-value=47  Score=13.67  Aligned_cols=23  Identities=30%  Similarity=0.570  Sum_probs=10.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             86449999999998083126768
Q gi|254780237|r  299 GRKSLVEIKGVLGTMGLFLGMNL  321 (340)
Q Consensus       299 G~KSl~EI~~~L~~~gl~lg~~l  321 (340)
                      |+.++++|.+.+++..-.+|..+
T Consensus        22 G~~tl~~i~~~~~~~a~~~g~~v   44 (149)
T 2uyg_A           22 GRTTLEELEALCEAWGAELGLGV   44 (149)
T ss_dssp             CSCCHHHHHHHHHHHHHHTTCCE
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             75699999999999999739705


No 68 
>>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} (A:635-702)
Probab=22.59  E-value=48  Score=13.66  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=30.9

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             58889898839837188874498888618898864499999999980
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      +|+. -|=+|||+|+.||..-. +.|.  .-+|+|-.+.|.+.+...
T Consensus         9 ~RAR-~Ly~aGiks~~dla~ap-~~l~--~~iG~k~A~~I~~~a~~~   51 (68)
T 2p6r_A            9 VRAR-KLYNAGIRNAEDIVRHR-EKVA--SLIGRGIAERVVEGISVK   51 (68)
T ss_dssp             HHHH-HHHTTTCCSHHHHHHTH-HHHH--HHHCHHHHHHHHHHHHHH
T ss_pred             HHHH-HHHHCCCCCHHHHHCCC-HHHH--HHHCCCHHHHHHHHHHHH
T ss_conf             9999-99987999999997498-8789--776346389999998787


No 69 
>>3i1n_M 50S ribosomal protein L16; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_K 1p86_K 1vs8_M 2aw4_M 2awb_M 1vs6_M 2i2v_M 2j28_M 2i2t_M* 2qao_M* 2qba_M* 2qbc_M* 2qbe_M 2qbg_M 2qbi_M* 2qbk_M* 2qov_M 2qox_M 2qoz_M* 2qp1_M* ... (M:)
Probab=22.52  E-value=48  Score=13.65  Aligned_cols=26  Identities=19%  Similarity=0.178  Sum_probs=22.7

Q ss_pred             CEEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             18999999389617779999999999
Q gi|254780237|r  199 DKLSMTIDTDGSITGEDSVALASRIL  224 (340)
Q Consensus       199 dkL~lEI~TnGsi~P~eAl~~Aa~iL  224 (340)
                      .+.++||+++---.-.+||..|+..|
T Consensus        99 G~iifei~~~~~~~a~~al~~a~~KL  124 (136)
T 3i1n_M           99 GKVLYEMDGVPEELAREAFKLAAAKL  124 (136)
T ss_dssp             TCEEEEECSSCHHHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             94899966989999999999998718


No 70 
>>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:)
Probab=22.20  E-value=47  Score=13.72  Aligned_cols=20  Identities=20%  Similarity=0.469  Sum_probs=10.3

Q ss_pred             HHHHHCCCCCCHHHHHHHHH
Q ss_conf             88886188988644999999
Q gi|254780237|r  289 EADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       289 ~~dLl~ikNfG~KSl~EI~~  308 (340)
                      -+||++++++|.+.++.|+.
T Consensus        52 ~~dL~~v~gl~~~~~~~l~~   71 (75)
T 2duy_A           52 VEDLLKVKGIGPATLERLRP   71 (75)
T ss_dssp             GGGGGGSTTCCHHHHHHHGG
T ss_pred             HHHHHHCCCCCHHHHHHHHH
T ss_conf             99996188989999999986


No 71 
>>3k17_A LIN0012 protein; protein structure initiative II(PSI II), NYSGXRC, structural genomics, NEW YORK SGX research center for structural genomics; HET: PGE; 2.10A {Listeria innocua} (A:211-350)
Probab=21.48  E-value=50  Score=13.51  Aligned_cols=79  Identities=11%  Similarity=0.086  Sum_probs=54.2

Q ss_pred             HHHCC-CCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCC-----CCCHHHHHHHHHHHHHHCCCCCCCCCC--------C-
Q ss_conf             22101-10588898988398371888744988886188-----988644999999999808312676878--------9-
Q gi|254780237|r  260 VEELE-LSVRSTNCLRGENIVYMGDLIQRTEADMLRMA-----NFGRKSLVEIKGVLGTMGLFLGMNLPD--------W-  324 (340)
Q Consensus       260 IeeLe-LSvRs~NcLk~a~I~tigdLv~~s~~dLl~ik-----NfG~KSl~EI~~~L~~~gl~lg~~l~~--------~-  324 (340)
                      +++++ +...+..+|.+.++..+|.|+..+..-|..+-     +.....++.+.+.....|.--.+-=.+        . 
T Consensus        38 ~~~~~~~~~~~~~al~~~d~~~~g~l~~~~~~~l~~l~~~~~~~is~~~l~~l~~~a~~~g~gaki~GAGgGG~v~al~~  117 (140)
T 3k17_A           38 LTRNNEIXKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENXGGAGKSSGSGGGDCGIAFSK  117 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCSCHHHHHHHHHHHHTTSEEEECTTCSSSEEEEEES
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEC
T ss_conf             99986668999987741699999999999999999754303876588999999999986793899803364018999987


Q ss_pred             CHHHHHHHHHHHHC
Q ss_conf             86779999987750
Q gi|254780237|r  325 PPESIEELAKKYED  338 (340)
Q Consensus       325 ~~~~~~~~~~~~~~  338 (340)
                      ++...+.+.+.+++
T Consensus       118 ~~~~~~~i~~~~~~  131 (140)
T 3k17_A          118 TKELAEKLVNEWEK  131 (140)
T ss_dssp             SHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             88999999999998


No 72 
>>1ujn_A Dehydroquinate synthase; riken structural genomics/proteomics initiative, RSGI, structural genomics, lyase; 1.80A {Thermus thermophilus HB8} (A:161-348)
Probab=21.27  E-value=38  Score=14.29  Aligned_cols=22  Identities=9%  Similarity=-0.177  Sum_probs=15.7

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCH
Q ss_conf             2210110588898988398371
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYM  281 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~ti  281 (340)
                      .-..+...|..++|++.++-+.
T Consensus       105 ~g~~~~~~~i~~~l~~~glp~~  126 (188)
T 1ujn_A          105 LGGEDLLPPVRRLLLWLSPPPL  126 (188)
T ss_dssp             TTCCCCHHHHHHHHHHHCCCCC
T ss_pred             HCCCHHHHHHHHHHHHCCCCCC
T ss_conf             3896169999999996599999


No 73 
>>1gtd_A MTH169; synthetase, FGAM synthetase, purine synthesis pathway, PSI, protein structure initiative, NESG; 2.56A {Methanobacterium thermoautotrophicum} (A:)
Probab=21.19  E-value=49  Score=13.57  Aligned_cols=48  Identities=17%  Similarity=0.132  Sum_probs=33.7

Q ss_pred             CCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             43111144223577641168877621899999938961777999999999999888
Q gi|254780237|r  174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG  229 (340)
Q Consensus       174 Da~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~  229 (340)
                      .|+..-..+..|.|++.|+|.       .+++|-++ -++.+|..++..+..+.|.
T Consensus        21 ~aI~~aL~~lG~~V~~VRvGK-------~iel~i~~-~~~e~a~~~v~~~c~~lLa   68 (85)
T 1gtd_A           21 ATIERALALLGYEVEDTDTTD-------VITFTXDE-DSLEAVEREVEDXCQRLLC   68 (85)
T ss_dssp             HHHHHHHHHHTCCCEEEEEEE-------EEEEEECC-SCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHCCCCCCEEEEEE-------EEEEEECC-CCHHHHHHHHHHHHHHHCC
T ss_conf             999999986598630478766-------99999778-9989999999999998639


No 74 
>>1qme_A Penicillin-binding protein 2X; peptidoglycan synthesis, resistance, cell WALL, transmembrane; 2.4A {Streptococcus pneumoniae} (A:579-649)
Probab=20.88  E-value=34  Score=14.62  Aligned_cols=33  Identities=9%  Similarity=-0.103  Sum_probs=25.1

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             498888618898864499999999980831267
Q gi|254780237|r  287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM  319 (340)
Q Consensus       287 ~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~  319 (340)
                      .+..+...++||-..+.++.++.|+..||....
T Consensus         4 s~~~~~v~vP~~~g~~~~~A~~~l~~~gl~~~~   36 (71)
T 1qme_A            4 VSQQSPYPMPSVKDISPGDLAEELRRNLVQPIV   36 (71)
T ss_dssp             ---BCCCBCCCCTTCCHHHHHHHHHTTTCEEEE
T ss_pred             HCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf             134665218867899999999999977993398


No 75 
>>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133)
Probab=20.32  E-value=53  Score=13.36  Aligned_cols=52  Identities=13%  Similarity=0.197  Sum_probs=32.1

Q ss_pred             HHCCHHHCCCC-HHHHHHHHHCCC--CCHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf             31112210110-588898988398--37188874498888618898864499999
Q gi|254780237|r  256 LLKKVEELELS-VRSTNCLRGENI--VYMGDLIQRTEADMLRMANFGRKSLVEIK  307 (340)
Q Consensus       256 L~~~IeeLeLS-vRs~NcLk~a~I--~tigdLv~~s~~dLl~ikNfG~KSl~EI~  307 (340)
                      +...|..+.++ .|+.++..-+..  .--+.=.....++|+++|+.|.|+.+-+-
T Consensus        50 ~~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~vl  104 (111)
T 2abk_A           50 VKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVL  104 (111)
T ss_dssp             HHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             7777674115677888999999999986041136779999989860635999999


Done!