Query         T0611 YP_960827.1, Marinobacter aquaeolei vt8, 227 residues
Match_columns 227
No_of_seqs    159 out of 8127
Neff          9.5 
Searched_HMMs 11830
Date          Mon Jul  5 09:14:57 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0611.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0611.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00440 TetR_N:  Bacterial reg  99.1 2.6E-11 2.2E-15  100.8   6.4   47    9-55      1-47  (47)
  2 PF08362 TetR_C_3:  YcdC-like p  98.2 2.5E-05 2.1E-09   56.0  13.5  139   57-198     2-141 (143)
  3 PF08359 TetR_C_4:  YsiA-like p  97.4  0.0011 9.4E-08   43.5  10.4  104   57-163     6-112 (133)
  4 PF02796 HTH_7:  Helix-turn-hel  94.1   0.021 1.8E-06   33.9   4.0   34   10-47     11-44  (45)
  5 PF08361 TetR_C_2:  MAATS-type   93.3    0.23 1.9E-05   26.2  11.0   89   76-164     2-98  (121)
  6 PF08360 TetR_C_5:  QacR-like p  93.2    0.11 9.6E-06   28.4   6.4   78   76-154    19-98  (131)
  7 PF00356 LacI:  Bacterial regul  92.8   0.031 2.6E-06   32.7   3.0   34   26-59      1-34  (46)
  8 PF01726 LexA_DNA_bind:  LexA D  92.2   0.097 8.2E-06   29.0   4.9   42    6-48      8-50  (65)
  9 PF06056 Terminase_5:  Putative  90.8    0.13 1.1E-05   28.1   4.4   33   10-46      3-35  (58)
 10 PF01022 HTH_5:  Bacterial regu  90.6    0.14 1.1E-05   27.9   4.3   38    4-48      2-39  (47)
 11 PF03811 Ins_element1:  Inserti  90.5    0.14 1.1E-05   27.9   4.2   35    5-47     52-86  (88)
 12 PF08279 HTH_11:  HTH domain;    90.0    0.14 1.2E-05   27.7   4.1   33   16-50      9-41  (55)
 13 PF04967 HTH_10:  HTH DNA bindi  90.0    0.15 1.3E-05   27.5   4.1   37    8-48      7-47  (53)
 14 PF01710 Transposase_14:  Trans  88.0     0.3 2.5E-05   25.3   4.5   40    3-51      5-44  (119)
 15 PF05225 HTH_psq:  helix-turn-h  86.5    0.32 2.7E-05   25.1   4.0   41    7-50      2-42  (45)
 16 PF10654 DUF2481:  Protein of u  86.4    0.58 4.9E-05   23.1   5.2   42   11-52     67-109 (126)
 17 PF11740 KfrA_N:  Plasmid repli  84.0    0.71   6E-05   22.5   4.8   40    5-46      2-42  (120)
 18 PF09339 HTH_IclR:  IclR helix-  83.9    0.23   2E-05   26.1   2.3   34   14-48      9-42  (52)
 19 PF10668 Phage_terminase:  Phag  83.6     0.5 4.2E-05   23.6   3.9   37   11-49     10-46  (60)
 20 PF00292 PAX:  'Paired box' dom  83.3    0.53 4.5E-05   23.4   3.9   35    1-43     18-52  (125)
 21 PF04218 CENP-B_N:  CENP-B N-te  81.3    0.86 7.3E-05   21.9   4.3   28   26-53     24-51  (53)
 22 PF01325 Fe_dep_repress:  Iron   81.2     0.9 7.6E-05   21.7   4.4   43    2-46      2-44  (60)
 23 PF00165 HTH_AraC:  Bacterial r  80.7    0.51 4.3E-05   23.6   3.0   30   19-48      3-32  (42)
 24 PF08220 HTH_DeoR:  DeoR-like h  79.5     1.1 9.2E-05   21.1   4.4   34   14-49      6-39  (57)
 25 PF08281 Sigma70_r4_2:  Sigma-7  79.3    0.45 3.8E-05   24.0   2.4   34   13-46     15-48  (54)
 26 PF12116 SpoIIID:  Stage III sp  78.7     1.2 9.9E-05   20.8   4.4   37    6-46      5-41  (82)
 27 PF00196 GerE:  Bacterial regul  78.5    0.49 4.2E-05   23.7   2.4   26   22-47     16-41  (58)
 28 PF01418 HTH_6:  Helix-turn-hel  76.1     1.8 0.00015   19.4   4.8   39    6-46     18-56  (107)
 29 PF01381 HTH_3:  Helix-turn-hel  76.1    0.54 4.6E-05   23.4   2.0   32   23-54      8-39  (55)
 30 PF04297 UPF0122:  Putative hel  75.8     1.5 0.00013   20.1   4.2   41   14-54     23-63  (101)
 31 PF04703 FaeA:  FaeA-like prote  75.1     1.3 0.00011   20.4   3.8   35    6-45      2-36  (62)
 32 PF04182 B-block_TFIIIC:  B-blo  73.1     1.3 0.00011   20.6   3.3   39   12-50      6-44  (75)
 33 PF05043 Mga:  Mga helix-turn-h  71.3     1.8 0.00015   19.5   3.7   33   21-53     27-59  (87)
 34 PF00046 Homeobox:  Homeobox do  70.1     1.6 0.00014   19.8   3.3   41   10-50     12-53  (57)
 35 PF02082 Rrf2:  Transcriptional  69.4     2.5 0.00022   18.3   5.1   44    3-46      3-47  (83)
 36 PF01978 TrmB:  Sugar-specific   69.1     1.2  0.0001   20.8   2.4   27   23-49     21-47  (68)
 37 PF05930 Phage_AlpA:  Prophage   68.0       1 8.5E-05   21.4   1.9   24   25-48      4-27  (51)
 38 PF00376 MerR:  MerR family reg  67.7     1.1 9.7E-05   20.9   2.1   20   26-45      1-20  (38)
 39 PF05732 RepL:  Firmicute plasm  65.8     2.7 0.00023   18.1   3.7   40    7-46     58-97  (165)
 40 PF03444 DUF293:  Domain of unk  63.3     3.3 0.00028   17.5   5.4   46    5-51      5-50  (78)
 41 PF02001 DUF134:  Protein of un  58.9     2.3 0.00019   18.7   2.3   27   21-47     54-80  (106)
 42 PF07022 Phage_CI_repr:  Bacter  58.7     1.9 0.00016   19.3   1.9   34   18-53      8-41  (66)
 43 PF01527 Transposase_8:  Transp  55.1    0.86 7.2E-05   21.9  -0.4   24   23-46     22-45  (76)
 44 PF02954 HTH_8:  Bacterial regu  54.5       3 0.00025   17.8   2.3   22   24-45     18-39  (42)
 45 PF06163 DUF977:  Bacterial pro  53.8     4.6 0.00039   16.4   5.0   40    5-46      9-48  (127)
 46 PF08280 HTH_Mga:  M protein tr  50.1     5.2 0.00044   16.0   4.3   37   15-53     12-48  (59)
 47 PF07750 GcrA:  GcrA cell cycle  49.8     3.5  0.0003   17.3   2.1   28   11-42      9-37  (162)
 48 PF00382 TFIIB:  Transcription   48.6     5.5 0.00047   15.8   3.2   21  123-143    15-35  (71)
 49 PF04036 DUF372:  Domain of unk  47.4     2.4  0.0002   18.5   0.9   17   31-47      4-20  (38)
 50 PF10078 DUF2316:  Uncharacteri  46.1       6 0.00051   15.5   5.6   44    5-48      4-47  (89)
 51 PF06971 Put_DNA-bind_N:  Putat  45.8     4.1 0.00035   16.7   1.9   37    9-45     13-49  (50)
 52 PF04545 Sigma70_r4:  Sigma-70,  44.9     1.2  0.0001   20.7  -0.9   25   21-45     17-41  (50)
 53 PF04552 Sigma54_DBD:  Sigma-54  44.5     1.9 0.00016   19.3   0.0   41    9-49     32-74  (160)
 54 PF01047 MarR:  MarR family;  I  44.2     6.4 0.00054   15.3   4.1   30   15-46     10-39  (59)
 55 PF06322 Phage_NinH:  Phage Nin  40.2       5 0.00042   16.1   1.6   29   26-54     18-46  (64)
 56 PF08667 BetR:  BetR domain;  I  39.3     7.5 0.00063   14.8   4.7   46    6-51      3-49  (147)
 57 PF03690 UPF0160:  Uncharacteri  39.2     7.5 0.00064   14.8   3.8   40   36-75     81-131 (318)
 58 PF00392 GntR:  Bacterial regul  39.1     7.6 0.00064   14.8   5.2   39    7-45      3-45  (64)
 59 PF08784 RPA_C:  Replication pr  35.3     8.6 0.00073   14.4   3.4   16  125-140    81-96  (102)
 60 PF04539 Sigma70_r3:  Sigma-70   35.2     8.6 0.00073   14.4   4.2   38    7-45      4-41  (78)
 61 PF01498 Transposase_5:  Transp  34.5     8.5 0.00072   14.4   2.1   21   25-45     14-39  (72)
 62 PF08535 KorB:  KorB domain;  I  33.3       8 0.00068   14.6   1.8   24   23-46      2-25  (93)
 63 PF06230 DUF1009:  Protein of u  31.3     9.9 0.00084   13.9   4.2   49    7-55     52-100 (214)
 64 PF07453 NUMOD1:  NUMOD1 domain  30.9      10 0.00085   13.9   2.5   20   25-44     17-36  (37)
 65 PF07498 Rho_N:  Rho terminatio  30.0     8.9 0.00075   14.2   1.5   30   26-59      9-38  (43)
 66 PF08006 DUF1700:  Protein of u  28.8      11 0.00091   13.6   4.1   37    1-37     17-53  (181)
 67 PF09862 DUF2089:  Protein of u  27.6      11 0.00096   13.5   3.4   18   26-43     51-68  (113)
 68 PF04963 Sigma54_CBD:  Sigma-54  24.5     8.5 0.00072   14.4   0.6   32    8-39     36-67  (195)
 69 PF08822 DUF1804:  Protein of u  24.4      13  0.0011   13.1  14.0   24   22-45     17-40  (165)
 70 PF03374 ANT:  Phage antirepres  24.3      13  0.0011   13.1   3.5   17  195-211    91-107 (111)
 71 PF07471 Phage_Nu1:  Phage DNA   23.7      13  0.0011   13.0   2.0   23   24-46      2-24  (164)
 72 PF04760 IF2_N:  Translation in  23.3      13  0.0011   12.9   2.0   23   23-45      2-24  (54)
 73 PF11849 DUF3369:  Domain of un  22.7      11 0.00089   13.7   0.8   37    7-43     22-61  (174)
 74 PF00126 HTH_1:  Bacterial regu  20.4      15  0.0013   12.5   4.3   34   15-52      8-41  (60)
 75 PF04269 DUF440:  Protein of un  20.3      15  0.0013   12.5   3.2   31    1-31      1-31  (103)

No 1  
>PF00440 TetR_N:  Bacterial regulatory proteins, tetR family;  InterPro: IPR001647   This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD , , . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1zk8_A 2oi8_A 2g7l_A 2opt_B 3b6a_F 3b6c_B 2hxo_A 2hxi_B 1z0x_B 1bjy_A ....
Probab=99.15  E-value=2.6e-11  Score=100.81  Aligned_cols=47  Identities=34%  Similarity=0.656  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
Q ss_conf             99999999987281036579999985778778999834489999999
Q T0611             9 ILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEI   55 (227)
Q Consensus         9 Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av   55 (227)
                      ||++|.++|.++||.++||++||+++|||++++|+||+||++|+.++
T Consensus         1 Il~aa~~l~~~~G~~~~t~~~ia~~agvs~~~iy~~F~~k~~L~~av   47 (47)
T PF00440_consen    1 ILDAAIELFAERGYEAVTIRDIAERAGVSRGSIYRHFPSKEDLLEAV   47 (47)
T ss_dssp             HHHHHHHHHHHS-GTTSSHHHHHHHHTSBHHHHHHHSSSHHHHHHHH
T ss_pred             CHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHCCCHHHHHHHC
T ss_conf             99999999998592218799999876479350256569999999669


No 2  
>PF08362 TetR_C_3:  YcdC-like protein, C-terminal region;  InterPro: IPR013573   This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (P75899 from SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.; GO: 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 1pb6_C.
Probab=98.23  E-value=2.5e-05  Score=55.96  Aligned_cols=139  Identities=14%  Similarity=0.119  Sum_probs=106.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998752217998778999999999999998778865444-441268899999999999999999999999986
Q T0611            57 QEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLWSYRFFHRDLE-YLLDSDPRLRQDYREFTNRCLAAINRIFAKLAD  135 (227)
Q Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~  135 (227)
                      ++..+.....+.......+|.+.+..|++..++...++|...+.+. ++....|.+............+....+|+.+++
T Consensus         2 ~~il~~Wl~~~~~~~~~~dP~~aL~~YIr~Kl~~sr~~P~~Srlfa~Eii~Gap~l~~~l~~~l~~~~~~~~~vI~~Wi~   81 (143)
T PF08362_consen    2 EDILEDWLAPLDDIDAEDDPAEALRAYIRAKLEMSRDHPEASRLFANEIIQGAPRLKDYLSEELKPWVDEKVAVIERWIA   81 (143)
T ss_dssp             HHHHHHHTHHHHT--TTS-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH---TTTHHHH---HHHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             77899999888756867999999999999999999889416399999998484666999999999999989999999998


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             598889938899999999999999988776553100220001089999999999998712189
Q T0611           136 AGIIQPQPEDLRSAMSLNVWLVITNWMAFLKTAHAAEEPASLSLTELKQGIYQVLTLEVPYLT  198 (227)
Q Consensus       136 ~G~l~~~~~~~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~p~lt  198 (227)
                      +|.+++.++.   .+..+||.++..+..|.............+..++.++...+..++...+.
T Consensus        82 ~G~i~~vdP~---hLlf~IWa~TQhYADf~~Qi~~~~g~~~~~~~~~~~a~~~v~~lvL~g~g  141 (143)
T PF08362_consen   82 QGKIAPVDPH---HLLFSIWATTQHYADFDAQIRALLGKDELDEDDFEQAAEFVTRLVLRGCG  141 (143)
T ss_dssp             -----S--HH---HHHHHHHHHHHHHHHTHHHHHHH----TTSHHHHHHHHHHHHHHHH----
T ss_pred             CCCCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             6998998999---99999999852063379999998598858888999999999999996168


No 3  
>PF08359 TetR_C_4:  YsiA-like protein, C-terminal region;  InterPro: IPR013570   This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YsiA (P94548 from SWISSPROT) from Bacillus subtilis, which is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YsiA and TetR share a multi-helical, interlocking structure.; PDB: 1vi0_B.
Probab=97.37  E-value=0.0011  Score=43.53  Aligned_cols=104  Identities=15%  Similarity=0.183  Sum_probs=73.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998752217998778999999999999998778865444-441268899999999999999999999999986
Q T0611            57 QEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLWSYRFFHRDLE-YLLDSDPRLRQDYREFTNRCLAAINRIFAKLAD  135 (227)
Q Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~  135 (227)
                      .+..+.+...+   .+..++.+.+...+..++.....++.+...+. +....++++.....+...++...+..+|.+|++
T Consensus         6 ~~~~~~~~~~~---~~~~~~~ekL~~~i~~hl~~~~~~~~~~~v~~~E~~~~~~~~~~~i~~~~~~y~~~i~~iI~eGq~   82 (133)
T PF08359_consen    6 NELLEELEEAL---ASEDSPREKLRALIRAHLRFLEENPDLAIVFQLELRQSNPELREEINELRREYFRLIEEIIEEGQE   82 (133)
T ss_dssp             --HHHHHHHHH---CC--SHHHHHHHHHHHHHHHH---HHHHHHHHCTTS-SSHHHHHHHHHHH---HHHH---------
T ss_pred             HHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999987---168999999999999999999809974874899887578999999999999999999999999998


Q ss_pred             CCCCCCCHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf             598889938--8999999999999999887
Q T0611           136 AGIIQPQPE--DLRSAMSLNVWLVITNWMA  163 (227)
Q Consensus       136 ~G~l~~~~~--~~~~~l~~~~~~~~~~w~~  163 (227)
                      .|.++++.+  .+...+..++..++..|+-
T Consensus        83 ~G~fr~dld~~~~~~~i~G~i~~~v~~w~~  112 (133)
T PF08359_consen   83 QGEFRPDLDPELAARMIFGTINGTVTQWVL  112 (133)
T ss_dssp             ---B-----HHHHHHHH---HHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             598889899999999999999999999986


No 4  
>PF02796 HTH_7:  Helix-turn-helix domain of resolvase;  InterPro: IPR006120   Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur:  Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment.    Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation.   Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=94.14  E-value=0.021  Score=33.91  Aligned_cols=34  Identities=21%  Similarity=0.437  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             99999999872810365799999857787789998344
Q T0611            10 LLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRN   47 (227)
Q Consensus        10 l~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~s   47 (227)
                      ++.+.+|.. .|   .|+.+||+..|||+.|||+|+..
T Consensus        11 ~~~i~~l~~-~G---~s~~~IAk~~gvsr~TvyR~l~~   44 (45)
T PF02796_consen   11 IEEIRELYA-QG---MSISEIAKRFGVSRSTVYRYLNK   44 (45)
T ss_dssp             HHHHHHHHH--------HHHHHHHCTS-HHHHHHHHCC
T ss_pred             HHHHHHHHH-CC---CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             999999999-79---99999999989199999999741


No 5  
>PF08361 TetR_C_2:  MAATS-type transcriptional repressor, C-terminal region;  InterPro: IPR013572    This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (Q6RV06 from SWISSPROT), AcrR (P34000 from SWISSPROT), ArpR (Q9KJC4 from SWISSPROT), TtgR (Q9AIU0 from SWISSPROT) and SmeT (Q8KLP4 from SWISSPROT). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins , , . ; GO: 0003677 DNA binding; PDB: 2w53_B 2uxu_A 2uxp_A 2uxi_B 2uxo_B 2uxh_A 2qop_A 3bcg_A.
Probab=93.35  E-value=0.23  Score=26.21  Aligned_cols=89  Identities=16%  Similarity=0.141  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHHHHHHHHHH---HHHHHHH---HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH--HHH
Q ss_conf             7789999999999999987---7886544---4441268899999999999999999999999986598889938--899
Q T0611            76 TLEDMTFYLESVFDGLWSY---RFFHRDL---EYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPE--DLR  147 (227)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~---~~~~~~l---~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~G~l~~~~~--~~~  147 (227)
                      |+..++..+...+......   +.++..+   ++.......+.++...........+...++.++++|.+.++.+  ...
T Consensus         2 PL~~Lr~~~~~~l~~l~~d~~~Rrv~~Il~~KcE~~~E~~~~~~r~~~~~~~~~~~i~~~l~~a~~~g~L~~~ld~~~AA   81 (121)
T PF08361_consen    2 PLERLRELLIYALRQLAEDERTRRVFEILFHKCEFVEEMAPVLERRREAQQEFYARIERLLRRAIARGQLPADLDPRLAA   81 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHS---BTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSC-TTB-HHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             68999999999999996079898999999997101024299999999999999999999999999869999998999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998877
Q T0611           148 SAMSLNVWLVITNWMAF  164 (227)
Q Consensus       148 ~~l~~~~~~~~~~w~~~  164 (227)
                      ..+...+..+...|+..
T Consensus        82 ~~l~a~~~GL~~~WL~~   98 (121)
T PF08361_consen   82 IMLHALLSGLLHNWLLD   98 (121)
T ss_dssp             HHHHHHH---HHHHHHS
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             99999999999998569


No 6  
>PF08360 TetR_C_5:  QacR-like protein, C-terminal region;  InterPro: IPR013571   This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump . The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites . The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 transcription factor activity, 0016481 negative regulation of transcription; PDB: 2hq5_E 1rkw_B 1qvt_B 1jum_B 2gby_B 2dtz_D 1rpw_D 1jtx_A 1jup_A 1jus_E ....
Probab=93.17  E-value=0.11  Score=28.45  Aligned_cols=78  Identities=10%  Similarity=0.090  Sum_probs=53.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             778999999999999998778--865444441268899999999999999999999999986598889938899999999
Q T0611            76 TLEDMTFYLESVFDGLWSYRF--FHRDLEYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLN  153 (227)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~G~l~~~~~~~~~~l~~~  153 (227)
                      ..+.+..+...++..+ ++|.  ...++..-...+|++..+...+..+....+..+|++|+++|.+++++......+..+
T Consensus        19 a~eKLyg~a~~~l~~~-~~pl~~a~~EF~~~~~~~~ev~e~l~~l~~~~~~~~~~Ii~eGI~~GeF~~~n~~~~~~il~s   97 (131)
T PF08360_consen   19 ATEKLYGMAEFVLYDI-QTPLLRAIEEFYSSQYKSPEVLERLNELRRKYLDFYRDIIEEGIQSGEFRIENVEELALILIS   97 (131)
T ss_dssp             HHHHHHHHHHHHHHSS-SGGGHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHHHH----------STHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHC-CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             8999999999999870-350689999998753499899999999999999999999999988698217889999999999


Q ss_pred             H
Q ss_conf             9
Q T0611           154 V  154 (227)
Q Consensus       154 ~  154 (227)
                      +
T Consensus        98 l   98 (131)
T PF08360_consen   98 L   98 (131)
T ss_dssp             H
T ss_pred             H
T ss_conf             9


No 7  
>PF00356 LacI:  Bacterial regulatory proteins, lacI family;  InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR , . Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1l1m_B 2bjc_A 1lcc_A 1osl_A 2pe5_A 1lcd_A 1efa_A 1cjg_B 1lqc_A 1jwl_A ....
Probab=92.77  E-value=0.031  Score=32.71  Aligned_cols=34  Identities=15%  Similarity=0.102  Sum_probs=26.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             5799999857787789998344899999999999
Q T0611            26 TTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEY   59 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av~~~~   59 (227)
                      ||.|||+.+|||++|+-+++.++..+-.+.-+++
T Consensus         1 Ti~diA~~agvS~~TVSr~Ln~~~~vs~~tr~rI   34 (46)
T PF00356_consen    1 TIKDIAKAAGVSVATVSRVLNGPPRVSEETRERI   34 (46)
T ss_dssp             SHHHHHHHTTSSHHHHHHHHHTCTTSTHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             9999998989499999999758999989999999


No 8  
>PF01726 LexA_DNA_bind:  LexA DNA binding domain;  InterPro: IPR006199   This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif . This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=92.17  E-value=0.097  Score=28.98  Aligned_cols=42  Identities=19%  Similarity=0.305  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC-HHHHHHHHCCH
Q ss_conf             99999999999987281036579999985778-77899983448
Q T0611             6 RDKILLSSLELFNDKGERNITTNHIAAHLAIS-PGNLYYHFRNK   48 (227)
Q Consensus         6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs-~gtlY~~F~sK   48 (227)
                      -++||+.-.+-+.++||. -|+++|+++.|++ ++++++|-+.=
T Consensus         8 Q~~vL~~I~~~~~~~G~~-Pt~rEI~~~~gl~S~~tV~~~L~~L   50 (65)
T PF01726_consen    8 QQEVLDFIKDYIREHGYP-PTVREIAEALGLKSPSTVHKHLKAL   50 (65)
T ss_dssp             HHHHHHHHHHHHHH-------HHHHHHH----SHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCC-CCHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             999999999999983889-8899999881999809999999999


No 9  
>PF06056 Terminase_5:  Putative ATPase subunit of terminase (gpP-like);  InterPro: IPR010332   This family of proteins are annotated as ATPase subunits of phage terminase after . Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=90.84  E-value=0.13  Score=28.10  Aligned_cols=33  Identities=24%  Similarity=0.314  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999999987281036579999985778778999834
Q T0611            10 LLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        10 l~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      -..|..||.    .|.|..+||+.+|||..|||++..
T Consensus         3 r~~A~~Ly~----~G~~~~eIA~~Lgv~~~TV~~W~~   35 (58)
T PF06056_consen    3 RRQARELYL----QGYTPKEIAEELGVSRRTVYSWKK   35 (58)
T ss_pred             HHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             899999999----689999999998868889999999


No 10 
>PF01022 HTH_5:  Bacterial regulatory protein, arsR family;  InterPro: IPR001845   Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis.   The HTH motif is thought to be located in the central part of these proteins . The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C-terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) . It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA .   The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers . The dimer interface is formed by helix 5 and an N-terminal part . Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N-terminus, called the alpha3(N) site . The second metal-binding site is located in helix 5 (and C-terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites , . Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognized by multimeric arsR-type metalloregulators. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1uly_A 2cwe_A 1ku9_A 3gw2_A 2p4w_B 3f6v_A 3f6o_B 2oqg_D 2ia0_B 2zny_C ....
Probab=90.62  E-value=0.14  Score=27.89  Aligned_cols=38  Identities=32%  Similarity=0.338  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             779999999999998728103657999998577877899983448
Q T0611             4 KTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus         4 ~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      .||-+||..-.+       ...++.+|++..|+|++++++|.+.=
T Consensus         2 ~~R~~Il~~L~~-------~~~~~~eia~~l~~s~~tvs~HL~~L   39 (47)
T PF01022_consen    2 PTRLKILKLLSE-------GPLSVSEIAEELGISQSTVSRHLKKL   39 (47)
T ss_dssp             HHHHHHHHHHHH-------SCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-------CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             889999999986-------89679998836123565899999999


No 11 
>PF03811 Ins_element1:  Insertion element protein;  InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. This protein is absolutely required for transposition of insertion element 1.; GO: 0006313 transposition, DNA-mediated
Probab=90.47  E-value=0.14  Score=27.90  Aligned_cols=35  Identities=26%  Similarity=0.306  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             7999999999999872810365799999857787789998344
Q T0611             5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRN   47 (227)
Q Consensus         5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~s   47 (227)
                      ++++|++..        ..+.++++||+..|||..|++++.++
T Consensus        52 ~k~~i~~l~--------~~G~siR~iArvl~Is~~Tv~r~lK~   86 (88)
T PF03811_consen   52 VKQKILELM--------VEGMSIRDIARVLGISINTVLRWLKN   86 (88)
T ss_pred             HHHHHHHHH--------HCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             999999998--------76851999999868789999999862


No 12 
>PF08279 HTH_11:  HTH domain;  InterPro: IPR013196   Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 . The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions.   This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon . It is also found in other proteins including regulators of amino acid biosynthsis such as LysM , and regulators of carbohydrate metabolisms such as LicR and FrvR , .; PDB: 1j5y_A 2ewn_B 1hxd_B 1bia_A 1bib_A 2dbb_B 1i1g_B 2cg4_B.
Probab=90.05  E-value=0.14  Score=27.67  Aligned_cols=33  Identities=21%  Similarity=0.434  Sum_probs=26.7

Q ss_pred             HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf             99872810365799999857787789998344899
Q T0611            16 LFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD   50 (227)
Q Consensus        16 lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~   50 (227)
                      |+..+|+  +|.++||+.+|||+.|++++...=++
T Consensus         9 L~~~~~~--it~~eLA~~l~vS~~Ti~~~i~~L~~   41 (55)
T PF08279_consen    9 LLKNDGP--ITAKELAEELGVSRRTIRRDIKELEE   41 (55)
T ss_dssp             HHHCCTT--S-HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHHCCCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             9985999--88999999969799999999999998


No 13 
>PF04967 HTH_10:  HTH DNA binding domain;  InterPro: IPR007050   Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium halobium and described as a putative bacterio-opsin activator. 
Probab=89.96  E-value=0.15  Score=27.52  Aligned_cols=37  Identities=30%  Similarity=0.469  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHCCC----CCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             999999999987281----03657999998577877899983448
Q T0611             8 KILLSSLELFNDKGE----RNITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus         8 ~Il~aA~~lf~e~G~----~~~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      .+|.+|.    +.||    .++|+.+||+++|||++|+.+|-..=
T Consensus         7 e~L~~A~----~~GYfd~PR~~tl~elA~~lgis~~T~~~~LRra   47 (53)
T PF04967_consen    7 EVLRTAY----EMGYFDWPRRITLEELAEELGISKSTFSEHLRRA   47 (53)
T ss_pred             HHHHHHH----HCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9999999----8688779875889999989499999999999999


No 14 
>PF01710 Transposase_14:  Transposase;  InterPro: IPR002622   Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily .   More information about these proteins can be found at Protein of the Month: Transposase .
Probab=88.03  E-value=0.3  Score=25.31  Aligned_cols=40  Identities=13%  Similarity=0.382  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf             3779999999999998728103657999998577877899983448999
Q T0611             3 MKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDI   51 (227)
Q Consensus         3 ~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~L   51 (227)
                      ..=|++||++     .+.   |-|.+++|+.-|||+.|+|+... +.+.
T Consensus         5 ~DlR~kvi~~-----~~~---G~S~~eaA~~F~VS~~Tv~rW~k-~~~~   44 (119)
T PF01710_consen    5 IDLRQKVIAY-----VEQ---GMSIREAAKRFGVSRSTVYRWLK-RRET   44 (119)
T ss_pred             HHHHHHHHHH-----HHC---CCCHHHHHHHHCCCHHHHHHHHH-HHHC
T ss_conf             9999999999-----995---99999999996955999999998-6411


No 15 
>PF05225 HTH_psq:  helix-turn-helix, Psq domain;  InterPro: IPR007889   This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster . In pipsqueak this domain binds to GAGA sequence . The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex .; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2cob_A.
Probab=86.53  E-value=0.32  Score=25.08  Aligned_cols=41  Identities=12%  Similarity=0.259  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf             99999999999872810365799999857787789998344899
Q T0611             7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD   50 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~   50 (227)
                      +.-|+.|++.+...+   .|++..|+.-||++.||+++..++..
T Consensus         2 ee~l~~Ai~~v~~g~---~Si~~aA~~ygVp~sTL~~r~~g~~~   42 (45)
T PF05225_consen    2 EERLQEAIEAVKNGK---LSIRKAARKYGVPRSTLRRRLKGKPS   42 (45)
T ss_dssp             HHHHHHHHHHHH--------HHHHHHH----HHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHCCC---CCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf             699999999999099---57999999989398999999927877


No 16 
>PF10654 DUF2481:  Protein of unknown function (DUF2481) 
Probab=86.37  E-value=0.58  Score=23.13  Aligned_cols=42  Identities=21%  Similarity=0.283  Sum_probs=29.5

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC-CHHHHH
Q ss_conf             999999987281036579999985778778999834-489999
Q T0611            11 LSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR-NKSDII   52 (227)
Q Consensus        11 ~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~-sKe~Ll   52 (227)
                      ++.+.-|...-+.|+|-.+||+--|||++++|.|.. +|++-.
T Consensus        67 ei~i~Ef~~lR~AGvt~~~IAd~F~Isks~v~Nf~qrNk~ey~  109 (126)
T PF10654_consen   67 EITIREFAELRHAGVTWYAIADHFNISKSTVFNFTQRNKEEYR  109 (126)
T ss_pred             CCCHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1219999999964887899999828739999999998099999


No 17 
>PF11740 KfrA_N:  Plasmid replication region DNA-binding N-term
Probab=84.01  E-value=0.71  Score=22.50  Aligned_cols=40  Identities=15%  Similarity=0.176  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHHHHHC
Q ss_conf             7999999999999872810365799999857-78778999834
Q T0611             5 TRDKILLSSLELFNDKGERNITTNHIAAHLA-ISPGNLYYHFR   46 (227)
Q Consensus         5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aG-vs~gtlY~~F~   46 (227)
                      |+++|.+||-.|+.+..  ..|++.|=+++| .|+.+|-.|.+
T Consensus         2 t~e~V~~Aa~~L~~~G~--~PTv~~VR~~lG~GS~~ti~~~lk   42 (120)
T PF11740_consen    2 TYEDVAAAADALLAAGK--RPTVDAVRERLGTGSMSTISKHLK   42 (120)
T ss_pred             CHHHHHHHHHHHHHCCC--CCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             69999999999987489--998999999987958899999999


No 18 
>PF09339 HTH_IclR:  IclR helix-turn-helix domain;  InterPro: IPR005471   The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium.    These proteins have a Helix-Turn-Helix motif at the N-terminus that is similar to that of other DNA-binding proteins .; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2ia2_C 2g7u_D 2o0y_D 1mkm_B.
Probab=83.89  E-value=0.23  Score=26.12  Aligned_cols=34  Identities=18%  Similarity=0.212  Sum_probs=26.5

Q ss_pred             HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             99998728103657999998577877899983448
Q T0611            14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus        14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      ++.|.+++-. .|+.+||++.|++++|+|++..+=
T Consensus         9 L~~l~~~~~~-~t~~eia~~~gl~~st~~r~l~~L   42 (52)
T PF09339_consen    9 LEALARAPRP-LTLSEIARALGLPKSTVHRLLQTL   42 (52)
T ss_dssp             HHTHCTTBSS-EEHHHHHHHTT--HHHHHHHHHHH
T ss_pred             HHHHHHCCCC-CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9999878999-899999999891999999999999


No 19 
>PF10668 Phage_terminase:  Phage terminase small subunit
Probab=83.62  E-value=0.5  Score=23.63  Aligned_cols=37  Identities=16%  Similarity=0.431  Sum_probs=30.4

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf             999999987281036579999985778778999834489
Q T0611            11 LSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKS   49 (227)
Q Consensus        11 ~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe   49 (227)
                      +-|++++.++| ...+..+||+++|||..+|- .+++++
T Consensus        10 dkA~e~y~~~~-g~~~~k~IAe~lgvs~~tIr-~WKs~d   46 (60)
T PF10668_consen   10 DKAFEIYKESN-GKIKLKDIAEKLGVSESTIR-KWKSRD   46 (60)
T ss_pred             HHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHH-HHHHHC
T ss_conf             99999999818-98419999999797999987-341022


No 20 
>PF00292 PAX:  'Paired box' domain;  InterPro: IPR001523   The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see ) , . Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0007275 multicellular organismal development, 0005634 nucleus; PDB: 6pax_A 1pdn_C 1k78_E 1mdm_A 2k27_A.
Probab=83.26  E-value=0.53  Score=23.44  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9737799999999999987281036579999985778778999
Q T0611             1 MTMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYY   43 (227)
Q Consensus         1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~   43 (227)
                      ++..+|++|++.+.        .+++..+||+..+||+|.+..
T Consensus        18 lp~~~R~rIv~l~~--------~G~r~~~Isr~l~VS~gcVsK   52 (125)
T PF00292_consen   18 LPNELRQRIVELAH--------EGVRPCDISRQLRVSHGCVSK   52 (125)
T ss_dssp             S-HHHHHHHHHHHH------------HHHHHHHHT-----HHH
T ss_pred             CCHHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHH
T ss_conf             88999999999976--------258774899876514769999


No 21 
>PF04218 CENP-B_N:  CENP-B N-terminal DNA-binding domain;  InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .; GO: 0003677 DNA binding, 0000775 chromosome, pericentric region; PDB: 2elh_A 1hlv_A 1bw6_A.
Probab=81.27  E-value=0.86  Score=21.86  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=26.4

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf             5799999857787789998344899999
Q T0611            26 TTNHIAAHLAISPGNLYYHFRNKSDIIY   53 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~   53 (227)
                      |..+||+..||++.|++.--++|+.++.
T Consensus        24 s~~~iAr~fgi~~sTi~~i~k~k~~i~~   51 (53)
T PF04218_consen   24 SQREIAREFGISRSTISRILKNKEKILE   51 (53)
T ss_dssp             -HHHHHHHHT--CCHHHHHCCTHHHHCC
T ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             8999998919988899999983999985


No 22 
>PF01325 Fe_dep_repress:  Iron dependent repressor, N-terminal DNA binding domain;  InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group . In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N-terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation .; GO: 0003700 transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2h09_A 1ddn_A 1bi3_B 1g3t_A 1f5t_C 2qqb_A 2qq9_A 1bi0_A 1bi2_B 1c0w_C ....
Probab=81.20  E-value=0.9  Score=21.73  Aligned_cols=43  Identities=21%  Similarity=0.301  Sum_probs=33.3

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             737799999999999987281036579999985778778999834
Q T0611             2 TMKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         2 ~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      --.+.|.-|.+=..+-.  .-..++..+||+++|||++|+..-.+
T Consensus         2 ls~~~e~YL~~I~~l~~--~~~~v~~~~IA~~L~vs~~TVs~ml~   44 (60)
T PF01325_consen    2 LSESEEDYLKAIYELSE--EGGPVSTSDIAERLGVSPPTVSEMLK   44 (60)
T ss_dssp             CSSHHHHHHHHHHHHHH--H-S--BHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             88069999999999980--69972199999997899078999999


No 23 
>PF00165 HTH_AraC:  Bacterial regulatory helix-turn-helix proteins, AraC family;  InterPro: IPR000005   Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins ,  is related to the arabinose operon regulatory protein AraC , . Except for celD , all of these proteins seem to be positive transcriptional factors.   Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerization .   The known structure of MarA (P27246 from SWISSPROT) shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1xs9_A 1bl0_A 1d5y_A 1wpk_A 2k9s_A 1zgw_A 1u8b_A.
Probab=80.70  E-value=0.51  Score=23.55  Aligned_cols=30  Identities=23%  Similarity=0.360  Sum_probs=25.1

Q ss_pred             HCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             728103657999998577877899983448
Q T0611            19 DKGERNITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus        19 e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      ++=-...|+.+||.++|+|+..+++.|+..
T Consensus         3 ~~~~~~~~i~~iA~~~g~s~~~~~r~Fk~~   32 (42)
T PF00165_consen    3 EHLSEPISIEDIAEELGYSPSYFSRLFKKE   32 (42)
T ss_dssp             TTTCSS--HHHHHHHTTSSHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             756898979999999798999999999999


No 24 
>PF08220 HTH_DeoR:  DeoR-like helix-turn-helix domain;  InterPro: IPR001034   The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively.   DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=79.50  E-value=1.1  Score=21.11  Aligned_cols=34  Identities=18%  Similarity=0.396  Sum_probs=27.7

Q ss_pred             HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf             999987281036579999985778778999834489
Q T0611            14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKS   49 (227)
Q Consensus        14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe   49 (227)
                      ++++.++|+  +|+.++|+..|||..|+.+++..-+
T Consensus         6 l~~l~~~~~--~s~~ela~~~~VS~~TiRRDl~~L~   39 (57)
T PF08220_consen    6 LELLKQHGK--VSVKELAEEFGVSEMTIRRDLNELE   39 (57)
T ss_pred             HHHHHHCCC--EEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999698--9799999998949889999899999


No 25 
>PF08281 Sigma70_r4_2:  Sigma-70, region 4;  InterPro: IPR013249   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2h27_D 1or7_A 2o8x_B.
Probab=79.29  E-value=0.45  Score=23.98  Aligned_cols=34  Identities=21%  Similarity=0.189  Sum_probs=28.8

Q ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999987281036579999985778778999834
Q T0611            13 SLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        13 A~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      -..+|.-+=+++.|..+||+..|+|.++++.+..
T Consensus        15 ~r~i~~l~~~~g~s~~eIA~~l~is~~tv~~~l~   48 (54)
T PF08281_consen   15 QREIFLLRYFEGLSYKEIAEILGISESTVKSRLS   48 (54)
T ss_dssp             HHHHHHHHHT----HHHHHHHCTS----HHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999695899999998919999999999


No 26 
>PF12116 SpoIIID:  Stage III sporulation protein D
Probab=78.71  E-value=1.2  Score=20.85  Aligned_cols=37  Identities=11%  Similarity=0.181  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999999999987281036579999985778778999834
Q T0611             6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      .+|.++.|-=....    ..|++..|+.-||||+|++.-+.
T Consensus         5 eeR~~~ia~yIi~~----~aTVR~tAk~FGVSKSTVHkDvT   41 (82)
T PF12116_consen    5 EERVLEIANYIIEN----KATVRQTAKVFGVSKSTVHKDVT   41 (82)
T ss_pred             HHHHHHHHHHHHHC----CHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999974----51699999997852999989999


No 27 
>PF00196 GerE:  Bacterial regulatory proteins, luxR family;  InterPro: IPR000792   This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.   The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers , , .   LuxR-type HTH proteins can be activated by one of four different mechanisms:   1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase , . Some proteins that belong to this category are:  Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes)   2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria : V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene)   3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE . B. subtilis gerE (transcription activator and repressor for the regulation of spore formation)   4) Multiple ligand-binding regulators, exemplified by malT . E. coli malT (activates maltose operon; MalT binds ATP and maltotriose) ; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1fse_B 2jpc_A 1x3u_A 1yio_A 1zn2_A 1p4w_A 3clo_B 1l3l_C 1h0m_B 2q0o_A ....
Probab=78.46  E-value=0.49  Score=23.69  Aligned_cols=26  Identities=27%  Similarity=0.387  Sum_probs=22.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             10365799999857787789998344
Q T0611            22 ERNITTNHIAAHLAISPGNLYYHFRN   47 (227)
Q Consensus        22 ~~~~t~~~IA~~aGvs~gtlY~~F~s   47 (227)
                      ..|.|..+||+.+|+|..|+.+|-.+
T Consensus        16 ~~G~~~~eIA~~l~is~~TV~~~~~~   41 (58)
T PF00196_consen   16 AQGLSNKEIAERLGISEKTVKSHRRR   41 (58)
T ss_dssp             CTT--HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHCCCCHHHHHHHCCCHHHHHHHHHH
T ss_conf             97398378998835452479999999


No 28 
>PF01418 HTH_6:  Helix-turn-helix domain, rpiR family;  InterPro: IPR000281 This domain contains a helix-turn-helix motif . Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2o3f_C.
Probab=76.11  E-value=1.8  Score=19.43  Aligned_cols=39  Identities=18%  Similarity=0.199  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999999999987281036579999985778778999834
Q T0611             6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      -.+|.+.=++-..+  +...|+.+||+.+|||+.|+.+.-+
T Consensus        18 e~~Ia~yil~~~~~--~~~~si~~lA~~~~vS~atv~Rf~k   56 (107)
T PF01418_consen   18 EKKIADYILNNPDK--IANMSISELAKAAGVSPATVVRFCK   56 (107)
T ss_dssp             HHHHHHHHHH-HHH--HTT--HHHHHHHTT--HHHHHHHHH
T ss_pred             HHHHHHHHHHCHHH--HHHCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999929999--9775499999997989889999999


No 29 
>PF01381 HTH_3:  Helix-turn-helix;  InterPro: IPR001387   This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2ef8_B 3f6w_A 3eus_A 1x57_A 1utx_A 2gzu_A 1rio_A 1lli_A 1lmb_3 3bdn_B ....
Probab=76.11  E-value=0.54  Score=23.37  Aligned_cols=32  Identities=22%  Similarity=0.252  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf             03657999998577877899983448999999
Q T0611            23 RNITTNHIAAHLAISPGNLYYHFRNKSDIIYE   54 (227)
Q Consensus        23 ~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a   54 (227)
                      .+.|..++|+.+|+|+++++.+..++...=..
T Consensus         8 ~gls~~~la~~~gis~~~i~~~e~g~~~~~~~   39 (55)
T PF01381_consen    8 RGLSQEELARRLGISRSTISRIENGKRNPSIE   39 (55)
T ss_dssp             TT--HHHHHHHHTS-HHHHHHHHTTSSGSBHH
T ss_pred             CCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHH
T ss_conf             69999999886498787888997699899999


No 30 
>PF04297 UPF0122:  Putative helix-turn-helix protein, YlxM / p13 like;  InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway .; PDB: 1s7o_B 1xsv_A.
Probab=75.81  E-value=1.5  Score=20.06  Aligned_cols=41  Identities=20%  Similarity=0.256  Sum_probs=32.8

Q ss_pred             HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf             99998728103657999998577877899983448999999
Q T0611            14 LELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYE   54 (227)
Q Consensus        14 ~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a   54 (227)
                      .+.|...=....|+.+||+..|||+.++|-..+.=+..+..
T Consensus        23 ~~~l~lyy~eDlSlsEIAe~~~iSRqaVyD~ikr~~~~L~~   63 (101)
T PF04297_consen   23 KEYLELYYNEDLSLSEIAEELGISRQAVYDNIKRAEKKLEE   63 (101)
T ss_dssp             HHHHHHHCTS---HHHHHHHCT--HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999998879989999989698899999999999999999


No 31 
>PF04703 FaeA:  FaeA-like protein;  InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=75.07  E-value=1.3  Score=20.43  Aligned_cols=35  Identities=26%  Similarity=0.223  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999999998728103657999998577877899983
Q T0611             6 RDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus         6 R~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      +++||+.=.++     ....|+++||+.+|+|.-+..+|-
T Consensus         2 ke~Il~~i~~~-----~~p~~t~eiA~~~gls~~qaR~~L   36 (62)
T PF04703_consen    2 KEKILEYIKRQ-----NGPCSTREIAEALGLSIYQARYYL   36 (62)
T ss_dssp             HHCHHHHHHHH--------B-HHHHHHHHTS-HHHHHHHH
T ss_pred             CHHHHHHHHHC-----CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             28899999962-----799889999999698899999999


No 32 
>PF04182 B-block_TFIIIC:  B-block binding subunit of TFIIIC;  InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding .
Probab=73.10  E-value=1.3  Score=20.57  Aligned_cols=39  Identities=18%  Similarity=0.308  Sum_probs=34.1

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf             999999872810365799999857787789998344899
Q T0611            12 SSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSD   50 (227)
Q Consensus        12 aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~   50 (227)
                      ..++..+..++.|.+-.++++..|+.+.+++|+.+.=++
T Consensus         6 ~lLe~Ia~~r~~Gi~q~dL~k~~~~D~r~~~~~~k~L~~   44 (75)
T PF04182_consen    6 CLLERIARSRYNGITQSDLWKLFGQDPRSVFYRVKKLED   44 (75)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             999999967768820537799858992256899999977


No 33 
>PF05043 Mga:  Mga helix-turn-helix domain;  InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions . The family also contains VirR like proteins which match only at the C terminus of the alignment.
Probab=71.28  E-value=1.8  Score=19.47  Aligned_cols=33  Identities=15%  Similarity=0.379  Sum_probs=27.0

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf             810365799999857787789998344899999
Q T0611            21 GERNITTNHIAAHLAISPGNLYYHFRNKSDIIY   53 (227)
Q Consensus        21 G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~   53 (227)
                      --+.+|+.++|+...||++|+++..+.=...+.
T Consensus        27 ~~~~~~~~~la~~l~vS~sTi~~~lk~i~~~L~   59 (87)
T PF05043_consen   27 NNEYVSIEDLAEELYVSRSTIYRDLKKINQILK   59 (87)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             489968999999979899999999999999999


No 34 
>PF00046 Homeobox:  Homeobox domain not present here.;  InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates , , . Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies . The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA . The first helix helps to stabilise the structure.   The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1ftz_A 1jgg_B 1hdd_D 1p7i_D 3hdd_B 2hot_A 1du0_B 2hdd_A 1enh_A 1ztr_A ....
Probab=70.10  E-value=1.6  Score=19.77  Aligned_cols=41  Identities=20%  Similarity=0.225  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHCCC-CCCCHHHHHHHHCCCHHHHHHHHCCHHH
Q ss_conf             9999999987281-0365799999857787789998344899
Q T0611            10 LLSSLELFNDKGE-RNITTNHIAAHLAISPGNLYYHFRNKSD   50 (227)
Q Consensus        10 l~aA~~lf~e~G~-~~~t~~~IA~~aGvs~gtlY~~F~sKe~   50 (227)
                      +..--+.|....| ..-.+..||...|++...|..+|.++..
T Consensus        12 ~~~Le~~f~~~~~P~~~~~~~La~~~~l~~~~V~~WF~nrR~   53 (57)
T PF00046_consen   12 LEILEEYFEKNPYPSEEEIEELAKELGLSEKQVKNWFQNRRA   53 (57)
T ss_dssp             HHHHHHHHHHSSSCCHHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999998757565005565423343200455124998788


No 35 
>PF02082 Rrf2:  Transcriptional regulator;  InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 1xd7_A 1ylf_A.
Probab=69.39  E-value=2.5  Score=18.33  Aligned_cols=44  Identities=20%  Similarity=0.301  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             3779999999999998728103-6579999985778778999834
Q T0611             3 MKTRDKILLSSLELFNDKGERN-ITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         3 ~~TR~~Il~aA~~lf~e~G~~~-~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      .+++-..---++-.+..+.-.. +|+++||++.|+|+..+...+.
T Consensus         3 ls~~~~~ai~~L~~La~~~~~~~~t~~~IA~~~~i~~~~v~kil~   47 (83)
T PF02082_consen    3 LSKRFDYAIRILIYLARQPDGKPVTSKEIAERLGISPSYVRKILQ   47 (83)
T ss_dssp             --HHHHHHHHHHHHHHCSTTCC---HHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             882788999999999809999849899999888909999999999


No 36 
>PF01978 TrmB:  Sugar-specific transcriptional regulator TrmB;  InterPro: IPR002831   TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively . Other members of this family are annotated as either transcriptional regulators or hypothetical proteins.  ; PDB: 2d1h_A 1sfx_A.
Probab=69.10  E-value=1.2  Score=20.80  Aligned_cols=27  Identities=26%  Similarity=0.364  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf             036579999985778778999834489
Q T0611            23 RNITTNHIAAHLAISPGNLYYHFRNKS   49 (227)
Q Consensus        23 ~~~t~~~IA~~aGvs~gtlY~~F~sKe   49 (227)
                      .+.|.++||+..|+|+.++|++..+=+
T Consensus        21 ~~~t~~eia~~~~i~~~~v~~~l~~L~   47 (68)
T PF01978_consen   21 GGATASEIAEKLGISRSTVYRILKRLE   47 (68)
T ss_dssp             S-EEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             995999999998909999999999999


No 37 
>PF05930 Phage_AlpA:  Prophage CP4-57 regulatory protein (AlpA);  InterPro: IPR010260   This family consists of several short bacterial and phage proteins, which are related to the Escherichia coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light . Several of the sequences in this family are thought to be DNA-binding proteins.; PDB: 1z4h_A.
Probab=68.05  E-value=1  Score=21.37  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=20.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             657999998577877899983448
Q T0611            25 ITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus        25 ~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      +++.++++..|+|+.|+|.+-+..
T Consensus         4 l~~~ev~~~lgvs~~t~y~~~~~g   27 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTLYRLIKDG   27 (51)
T ss_dssp             E-HHHHHHH-----HHHHHHHH--
T ss_pred             ECHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             249999999894999999997758


No 38 
>PF00376 MerR:  MerR family regulatory protein;  InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA , , , , , . Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1r8d_B 1jbg_A 3hh0_C 3d6z_A 3d71_A 3d6y_A 1r8e_A 1exi_A 1exj_A 1q06_A ....
Probab=67.71  E-value=1.1  Score=20.93  Aligned_cols=20  Identities=30%  Similarity=0.290  Sum_probs=17.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHH
Q ss_conf             57999998577877899983
Q T0611            26 TTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~~F   45 (227)
                      ||.++|+.+|||..+|-+|=
T Consensus         1 ti~e~a~~~gvs~~tlR~ye   20 (38)
T PF00376_consen    1 TIGEVAKLLGVSVRTLRYYE   20 (38)
T ss_dssp             EHHHHHHHCT--HHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             98999999896999999999


No 39 
>PF05732 RepL:  Firmicute plasmid replication protein (RepL);  InterPro: IPR008813 This family consists of Firmicute RepL proteins which are involved in plasmid replication.; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=65.77  E-value=2.7  Score=18.08  Aligned_cols=40  Identities=23%  Similarity=0.243  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999999999987281036579999985778778999834
Q T0611             7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      -+||-.-++-....+.--.|-++||++.|+|++|++.-|+
T Consensus        58 ~~Vl~~ll~~~d~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK   97 (165)
T PF05732_consen   58 FRVLMFLLENMDSDNAVVATQKEIAEELGISKPTVSRTIK   97 (165)
T ss_pred             HHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999984377983987899999997988889999999


No 40 
>PF03444 DUF293:  Domain of unknown function;  InterPro: IPR005104 This domain is always found N-terminal to a pair of cystathionine-beta-synthase (CBS) domains IPR000644 from INTERPRO. This region may be distantly related to the HrcA proteins of prokaryotes.
Probab=63.25  E-value=3.3  Score=17.50  Aligned_cols=46  Identities=22%  Similarity=0.417  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf             79999999999998728103657999998577877899983448999
Q T0611             5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDI   51 (227)
Q Consensus         5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~L   51 (227)
                      ...+||.+-.+++.+.| .-+.-+.||+.+++|.+|+.+--.+=++|
T Consensus         5 rq~~IL~~lv~~Y~~~~-~PVgSk~ia~~l~~s~aTIRN~M~~Le~l   50 (78)
T PF03444_consen    5 RQREILKALVELYIETG-EPVGSKTIAEELDRSPATIRNEMADLEEL   50 (78)
T ss_pred             HHHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             99999999999999739-97766999998688908899999999987


No 41 
>PF02001 DUF134:  Protein of unknown function  DUF134;  InterPro: IPR002852   The bacterial and archaeal proteins in this family have no known function.
Probab=58.95  E-value=2.3  Score=18.70  Aligned_cols=27  Identities=11%  Similarity=0.208  Sum_probs=17.0

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             810365799999857787789998344
Q T0611            21 GERNITTNHIAAHLAISPGNLYYHFRN   47 (227)
Q Consensus        21 G~~~~t~~~IA~~aGvs~gtlY~~F~s   47 (227)
                      -|.+.|-.+=|..+|||++|+.+-..+
T Consensus        54 D~egl~QeeAA~~MgVSR~Tf~ril~~   80 (106)
T PF02001_consen   54 DYEGLTQEEAAEQMGVSRQTFQRILKS   80 (106)
T ss_pred             HHHCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf             881798999999849779999999999


No 42 
>PF07022 Phage_CI_repr:  Bacteriophage CI repressor helix-turn-helix domain;  InterPro: IPR010744   This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic .; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 2fjr_A 3bd1_B.
Probab=58.75  E-value=1.9  Score=19.29  Aligned_cols=34  Identities=21%  Similarity=0.404  Sum_probs=24.8

Q ss_pred             HHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf             872810365799999857787789998344899999
Q T0611            18 NDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIY   53 (227)
Q Consensus        18 ~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~   53 (227)
                      ...|+.  |-.++|+.+|||++++.+.+..+..+=.
T Consensus         8 ~~~g~~--~~~elA~~LgIs~stvs~~~~~r~~~P~   41 (66)
T PF07022_consen    8 EAYGIK--TDKELAEKLGISQSTVSHTWKKRNSIPF   41 (66)
T ss_dssp             HH------SCHHHHCCTT--HHHHH-HHHH-----H
T ss_pred             HHHCCC--CHHHHHHHHCCCHHHHHHHHHHCCCCCH
T ss_conf             996899--6999999919988885567641688989


No 43 
>PF01527 Transposase_8:  Transposase;  InterPro: IPR002514   Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 .   More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2rn7_A 2jn6_A.
Probab=55.08  E-value=0.86  Score=21.88  Aligned_cols=24  Identities=29%  Similarity=0.497  Sum_probs=19.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             036579999985778778999834
Q T0611            23 RNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        23 ~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      .+.|+.+||.+.|||.++||+.-.
T Consensus        22 ~g~s~~~va~~~gI~~~tl~~W~~   45 (76)
T PF01527_consen   22 EGRSVSEVAREYGISPSTLYRWVR   45 (76)
T ss_dssp             H-HHHHHHCCC----HHHHHHHHH
T ss_pred             CCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             799799999970533026669999


No 44 
>PF02954 HTH_8:  Bacterial regulatory protein, Fis family;  InterPro: IPR002197   The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences ,. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli . Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion.    In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor .    The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution ,. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as 'feelers' suitable for DNA or protein (invertase) recognition . Other proteins belonging to this subfamily include: Escherichia coli: atoC, hydG, ntrC, fhlA, tyrR,  Rhizobium spp.: ntrC, nifA, dctD  ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ojl_E 1fip_A 1etw_B 4fis_B 1fia_A 1etq_D 3fis_A 1f36_A 1ety_B 1etx_A ....
Probab=54.48  E-value=3  Score=17.83  Aligned_cols=22  Identities=27%  Similarity=0.300  Sum_probs=18.3

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             3657999998577877899983
Q T0611            24 NITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus        24 ~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      +-++...|+.+|||+.+||+--
T Consensus        18 ~gn~~~aA~~Lgi~r~tL~~kl   39 (42)
T PF02954_consen   18 GGNISKAARLLGISRSTLYRKL   39 (42)
T ss_dssp             TT-HHHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9989999999798999999999


No 45 
>PF06163 DUF977:  Bacterial protein of unknown function (DUF977);  InterPro: IPR010382   This family consists of several hypothetical bacterial proteins of unknown function.
Probab=53.77  E-value=4.6  Score=16.38  Aligned_cols=40  Identities=23%  Similarity=0.298  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             799999999999987281036579999985778778999834
Q T0611             5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus         5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      -|+.|..-=+++..++|.  .|++++.+.-|+|+-|+-.||.
T Consensus         9 eR~ei~~rIVElVR~~GR--iTi~ql~~~TG~sR~T~k~~lr   48 (127)
T PF06163_consen    9 EREEIKARIVELVREHGR--ITIRQLVKMTGASRNTAKKYLR   48 (127)
T ss_pred             HHHHHHHHHHHHHHHHCH--HHHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999999999998163--0299999997867999999999


No 46 
>PF08280 HTH_Mga:  M protein trans-acting positive regulator (MGA) HTH domain;  InterPro: IPR013199   Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions .
Probab=50.14  E-value=5.2  Score=15.98  Aligned_cols=37  Identities=19%  Similarity=0.205  Sum_probs=27.9

Q ss_pred             HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHH
Q ss_conf             999872810365799999857787789998344899999
Q T0611            15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIY   53 (227)
Q Consensus        15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~   53 (227)
                      .++.+  -...|+.+||+..|+|..++-++...=.+.+.
T Consensus        12 ~~L~~--~~~~t~~ela~~l~~S~~ti~~~I~~l~~~f~   48 (59)
T PF08280_consen   12 ELLLK--NGWITLKELAKKLGLSERTIRNDINELNEEFP   48 (59)
T ss_pred             HHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             99997--79797999999979889999999999999863


No 47 
>PF07750 GcrA:  GcrA cell cycle regulator;  InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes . More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery .
Probab=49.80  E-value=3.5  Score=17.26  Aligned_cols=28  Identities=18%  Similarity=0.316  Sum_probs=20.5

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHH
Q ss_conf             9999999872810365799999857-7877899
Q T0611            11 LSSLELFNDKGERNITTNHIAAHLA-ISPGNLY   42 (227)
Q Consensus        11 ~aA~~lf~e~G~~~~t~~~IA~~aG-vs~gtlY   42 (227)
                      +...+|+.    +|.|-.+||+++| ||+.++-
T Consensus         9 e~Lk~lw~----eGlSasqIA~~LGgvsRNAVi   37 (162)
T PF07750_consen    9 ERLKKLWA----EGLSASQIAKQLGGVSRNAVI   37 (162)
T ss_pred             HHHHHHHH----CCCCHHHHHHHHCCCCHHHHH
T ss_conf             99999998----588899999997552066677


No 48 
>PF00382 TFIIB:  Transcription factor TFIIB repeat;  InterPro: IPR013150   Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles , and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E.   Cyclin homologues have been found in various viruses, including herpesvirus saimiri and Kaposi's sarcoma-associated herpesvirus. These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus .   In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognized by RNA polymerase II , . TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB .   This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex , .; GO: 0003700 transcription factor activity, 0005515 protein binding, 0006350 transcription, 0005634 nucleus; PDB: 1c9b_M 2phg_A 1vol_A 1tfb_A 1ais_B 1d3u_B.
Probab=48.61  E-value=5.5  Score=15.81  Aligned_cols=21  Identities=14%  Similarity=0.491  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCH
Q ss_conf             999999999998659888993
Q T0611           123 LAAINRIFAKLADAGIIQPQP  143 (227)
Q Consensus       123 ~~~~~~~l~~~i~~G~l~~~~  143 (227)
                      .+....+++.+.+.|.+++-.
T Consensus        15 ~~~A~~i~~~~~~~~~~~Gr~   35 (71)
T PF00382_consen   15 IETAKEIYKKAVEKGLLKGRS   35 (71)
T ss_dssp             HHHHHHHHHHHHHCTT-----
T ss_pred             HHHHHHHHHHHHHCCCCCCCC
T ss_conf             999999999998768757998


No 49 
>PF04036 DUF372:  Domain of unknown function (DUF372);  InterPro: IPR007179   This is a group of proteins of unknown function. It is found N-terminal to another domain of unknown function, DUF381 (IPR007181 from INTERPRO).; PDB: 2i52_B 2ogf_B 2iec_D.
Probab=47.36  E-value=2.4  Score=18.53  Aligned_cols=17  Identities=29%  Similarity=0.428  Sum_probs=13.8

Q ss_pred             HHHHCCCHHHHHHHHCC
Q ss_conf             99857787789998344
Q T0611            31 AAHLAISPGNLYYHFRN   47 (227)
Q Consensus        31 A~~aGvs~gtlY~~F~s   47 (227)
                      .=++||+-|+|||-|-+
T Consensus         4 ~FEaGIklGalyHQf~G   20 (38)
T PF04036_consen    4 VFEAGIKLGALYHQFVG   20 (38)
T ss_dssp             HHH-------HHHHH--
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             76500257578886517


No 50 
>PF10078 DUF2316:  Uncharacterized protein conserved in bacteria (DUF2316)
Probab=46.12  E-value=6  Score=15.54  Aligned_cols=44  Identities=18%  Similarity=0.188  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCH
Q ss_conf             79999999999998728103657999998577877899983448
Q T0611             5 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNK   48 (227)
Q Consensus         5 TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sK   48 (227)
                      |++++-.++.+|=+..-..+.|..+||+.+|+|..-+=+-+.=|
T Consensus         4 n~~e~~~T~~ELqanf~l~~Ls~~~ia~dL~~s~~~ve~vL~l~   47 (89)
T PF10078_consen    4 NKEERKATRKELQANFELSGLSIEQIAKDLGTSPEKVEQVLNLK   47 (89)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             89999976999999999849999999999689999999898604


No 51 
>PF06971 Put_DNA-bind_N:  Putative DNA-binding protein N-terminus;  InterPro: IPR009718   This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria . They modulate transcription in response to changes in cellular NADH/NAD^(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0016564 transcription repressor activity, 0006980 redox signal response, 0016481 negative regulation of transcription, 0005737 cytoplasm; PDB: 1xcb_F 2dt5_A 2vt3_A 2vt2_B.
Probab=45.81  E-value=4.1  Score=16.75  Aligned_cols=37  Identities=22%  Similarity=0.468  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999998728103657999998577877899983
Q T0611             9 ILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus         9 Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      +---.++.+.+.|...+|-.+||+.+||+...+-.=|
T Consensus        13 ~Y~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKDl   49 (50)
T PF06971_consen   13 LYLRYLKQLQEEGVERISSKELAEALGITPSQVRKDL   49 (50)
T ss_dssp             HHHHHHHHHHH----B--TTTHHHCCSS-HHHHHHHH
T ss_pred             HHHHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHCCC
T ss_conf             9999999999859945879999999797999961225


No 52 
>PF04545 Sigma70_r4:  Sigma-70, region 4;  InterPro: IPR007630   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .  Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif . Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2p7v_B 1tlh_B 1tty_A 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F 2a69_F ....
Probab=44.85  E-value=1.2  Score=20.73  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=21.3

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8103657999998577877899983
Q T0611            21 GERNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus        21 G~~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      =|++.|..+||+..|+|.+++....
T Consensus        17 ~~~~~t~~eIa~~lg~s~~~V~~~~   41 (50)
T PF04545_consen   17 YFEGLTLEEIAERLGISESTVRQRL   41 (50)
T ss_dssp             HTST-CTCCCHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             8499999999989797999998999


No 53 
>PF04552 Sigma54_DBD:  Sigma-54, DNA binding domain;  InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins .; PDB: 2o9l_A 2ahq_A 2o8k_A.
Probab=44.47  E-value=1.9  Score=19.30  Aligned_cols=41  Identities=20%  Similarity=0.260  Sum_probs=30.4

Q ss_pred             HHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHCCHH
Q ss_conf             9999999998--7281036579999985778778999834489
Q T0611             9 ILLSSLELFN--DKGERNITTNHIAAHLAISPGNLYYHFRNKS   49 (227)
Q Consensus         9 Il~aA~~lf~--e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe   49 (227)
                      |++-=.+-|.  .....-.||.+||+++|++.+|+-+--.+|.
T Consensus        32 Iv~~Q~~Ff~~g~~~l~Pltl~~vA~~lglheSTVSRav~~Ky   74 (160)
T PF04552_consen   32 IVERQEDFFLEGPKALKPLTLKDVAEELGLHESTVSRAVSNKY   74 (160)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCE
T ss_conf             9999999985585357685499999983988305779874853


No 54 
>PF01047 MarR:  MarR family;  InterPro: IPR000835   The marR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the marR/slyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli marR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds , , .   The crystal structures of marR, mexR and slyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerization. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerization, as most marR-like transcription regulators form dimers , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3bj6_A 2fbi_A 3e6m_E 3cjn_A 3cdh_A 2fxa_B 2fa5_B 1lnw_B 3ech_A 1jgs_A ....
Probab=44.21  E-value=6.4  Score=15.34  Aligned_cols=30  Identities=17%  Similarity=0.321  Sum_probs=22.1

Q ss_pred             HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99987281036579999985778778999834
Q T0611            15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      ..+.+.|  +.|+.+||+.+|++++++.....
T Consensus        10 ~~l~~~~--~~t~~~la~~l~~~~~~vs~~i~   39 (59)
T PF01047_consen   10 RILYENP--GMTQSELAERLGISKSTVSRIIK   39 (59)
T ss_dssp             HHHHHSS--SEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHCC--CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999879--98999999998868738999999


No 55 
>PF06322 Phage_NinH:  Phage NinH protein;  InterPro: IPR010454   This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=40.20  E-value=5  Score=16.14  Aligned_cols=29  Identities=14%  Similarity=0.039  Sum_probs=22.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf             57999998577877899983448999999
Q T0611            26 TTNHIAAHLAISPGNLYYHFRNKSDIIYE   54 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~a   54 (227)
                      .|.++|..++++++|+-.|-.+|++=-.+
T Consensus        18 N~teVaR~L~c~R~TVrkY~~D~~g~~Ha   46 (64)
T PF06322_consen   18 NQTEVARMLNCYRATVRKYARDKEGKKHA   46 (64)
T ss_pred             CHHHHHHHHCCHHHHHHHHHCCCCCCEEE
T ss_conf             68988788510188799772255662478


No 56 
>PF08667 BetR:  BetR domain;  InterPro: IPR013975    This entry includes an N-terminal helix-turn-helix domain. 
Probab=39.34  E-value=7.5  Score=14.82  Aligned_cols=46  Identities=22%  Similarity=0.211  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHCCCCC-CCHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf             9999999999998728103-657999998577877899983448999
Q T0611             6 RDKILLSSLELFNDKGERN-ITTNHIAAHLAISPGNLYYHFRNKSDI   51 (227)
Q Consensus         6 R~~Il~aA~~lf~e~G~~~-~t~~~IA~~aGvs~gtlY~~F~sKe~L   51 (227)
                      .+.|.+--.+++..+|+.. =...+|++-+|+|+++.|+-..+|-..
T Consensus         3 ~~~~~~rvr~ll~~~GI~kr~~~~~La~iL~Is~saa~RKL~G~~~f   49 (147)
T PF08667_consen    3 DQAIAERVRELLDRHGIPKRQHNTELADILGISKSAASRKLNGKSPF   49 (147)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf             48999999999997499820138999998788999985873799997


No 57 
>PF03690 UPF0160:  Uncharacterised protein family (UPF0160);  InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=39.18  E-value=7.5  Score=14.80  Aligned_cols=40  Identities=18%  Similarity=0.203  Sum_probs=22.4

Q ss_pred             CCHHHHHHHHCCH-----------HHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             7877899983448-----------999999999999999998752217998
Q T0611            36 ISPGNLYYHFRNK-----------SDIIYEIFQEYEKLVDYYLDIPEDRPI   75 (227)
Q Consensus        36 vs~gtlY~~F~sK-----------e~Ll~av~~~~~~~~~~~~~~~~~~~~   75 (227)
                      -|-|.||.||+.+           ++.+..+...+...+.+.++..+++..
T Consensus        81 SSAGLVykhfG~~ii~~~~~~~~~~~~~~~l~~k~y~~fi~~iDaiDNGv~  131 (318)
T PF03690_consen   81 SSAGLVYKHFGREIIANILGLPVDEEDVDLLYDKVYKSFIEPIDAIDNGVS  131 (318)
T ss_pred             ECHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             013369999879999987434798799999999999887432152017965


No 58 
>PF00392 GntR:  Bacterial regulatory proteins, gntR family;  InterPro: IPR000524   Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon . Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined . In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies . This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2ra5_A 3by6_D 2ek5_C 2du9_A 1v4r_A 3bwg_A 3eet_B 1h9t_B 1hw2_B 1hw1_B ....
Probab=39.07  E-value=7.6  Score=14.79  Aligned_cols=39  Identities=5%  Similarity=0.039  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHCCC---CCC-CHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999999987281---036-57999998577877899983
Q T0611             7 DKILLSSLELFNDKGE---RNI-TTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~---~~~-t~~~IA~~aGvs~gtlY~~F   45 (227)
                      ++|.+.=.+.+....+   +.. |.+++|++.|||+.++..-+
T Consensus         3 ~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~Al   45 (64)
T PF00392_consen    3 EQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREAL   45 (64)
T ss_dssp             HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999984999999993689999988687989999999


No 59 
>PF08784 RPA_C:  Replication protein A C terminal;  InterPro: IPR014892   This protein corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1quq_A 2pqa_C 2pi2_C 1l1o_B 1z1d_A 2z6k_B 1dpu_A.
Probab=35.31  E-value=8.6  Score=14.37  Aligned_cols=16  Identities=25%  Similarity=0.598  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHCCCCC
Q ss_conf             9999999998659888
Q T0611           125 AINRIFAKLADAGIIQ  140 (227)
Q Consensus       125 ~~~~~l~~~i~~G~l~  140 (227)
                      .+...++.+.+.|.|-
T Consensus        81 ~v~~a~~~L~~eG~IY   96 (102)
T PF08784_consen   81 EVRKAIDELSDEGLIY   96 (102)
T ss_dssp             HHHHHHHHHHH---EE
T ss_pred             HHHHHHHHHHHCCEEE
T ss_conf             9999999998598472


No 60 
>PF04539 Sigma70_r3:  Sigma-70 region 3;  InterPro: IPR007624   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .  Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 1tty_A 1rp3_G 1sc5_A 1l0o_C 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F ....
Probab=35.23  E-value=8.6  Score=14.36  Aligned_cols=38  Identities=29%  Similarity=0.284  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999999998728103657999998577877899983
Q T0611             7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      .+|-.|..+|..+.|-. -|..+||+.+|+|..-++...
T Consensus         4 ~ki~~a~~~L~~~lgR~-Pt~eEIA~~lgis~~~v~~~~   41 (78)
T PF04539_consen    4 NKIKKAKRELEQELGRE-PTEEEIAEELGISEEEVRELL   41 (78)
T ss_dssp             HHHHHHHHHHHHC------BHHHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999995889-899999999788899999999


No 61 
>PF01498 Transposase_5:  Transposase;  InterPro: IPR002492   Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in . Tc3 is a member of the Tc1/mariner family of transposable elements.   More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration, 0005634 nucleus; PDB: 3f2k_B 1u78_A.
Probab=34.47  E-value=8.5  Score=14.40  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=13.4

Q ss_pred             CCHHHHHHHH-----CCCHHHHHHHH
Q ss_conf             6579999985-----77877899983
Q T0611            25 ITTNHIAAHL-----AISPGNLYYHF   45 (227)
Q Consensus        25 ~t~~~IA~~a-----Gvs~gtlY~~F   45 (227)
                      .|..+|+.++     +||+.|+.+.+
T Consensus        14 ~T~~~l~~~l~~~~~~vS~~Tv~R~L   39 (72)
T PF01498_consen   14 ITLRELARELQEEGISVSKSTVRRRL   39 (72)
T ss_dssp             --HHHHHHHT---T--S-HHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             24999999998658997999999999


No 62 
>PF08535 KorB:  KorB domain;  InterPro: IPR013741   This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon . This domain includes the DNA-binding HTH motif . ; PDB: 1r71_B.
Probab=33.34  E-value=8  Score=14.59  Aligned_cols=24  Identities=29%  Similarity=0.308  Sum_probs=19.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             036579999985778778999834
Q T0611            23 RNITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        23 ~~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      .|.|-.+||+++|-|+..+-+|-.
T Consensus         2 ~G~tq~eIA~~lGks~s~Vs~~L~   25 (93)
T PF08535_consen    2 FGLTQEEIAKRLGKSRSWVSNHLR   25 (93)
T ss_dssp             -------HHHH----HHHHHHHHG
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             899999999998879999999999


No 63 
>PF06230 DUF1009:  Protein of unknown function (DUF1009);  InterPro: IPR010415   This is a family of uncharacterised bacterial proteins.
Probab=31.27  E-value=9.9  Score=13.91  Aligned_cols=49  Identities=18%  Similarity=0.203  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
Q ss_conf             9999999999987281036579999985778778999834489999999
Q T0611             7 DKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDIIYEI   55 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av   55 (227)
                      +.||.+-.+.|.++||.=++-.+++...=...|.+...=+|+++.-...
T Consensus        52 d~lL~ai~~~~E~~G~~vv~a~~~~p~ll~~~G~lt~~~P~~~~~~Di~  100 (214)
T PF06230_consen   52 DALLRAIIDEFEEEGFEVVGAHEILPELLAPEGVLTGRKPSKEERADIA  100 (214)
T ss_pred             HHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCCCHHHHHHHH
T ss_conf             9999999999997799997178953874689876679996988999999


No 64 
>PF07453 NUMOD1:  NUMOD1 domain;  InterPro: IPR010896   This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases . 
Probab=30.87  E-value=10  Score=13.87  Aligned_cols=20  Identities=20%  Similarity=0.107  Sum_probs=16.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHH
Q ss_conf             65799999857787789998
Q T0611            25 ITTNHIAAHLAISPGNLYYH   44 (227)
Q Consensus        25 ~t~~~IA~~aGvs~gtlY~~   44 (227)
                      -|+++-|+.+|+|+++|-+|
T Consensus        17 ~Si~eAa~~l~~~~~tI~~~   36 (37)
T PF07453_consen   17 SSIREAARALNISHSTISKY   36 (37)
T ss_pred             CCHHHHHHHHCCCHHHHHHH
T ss_conf             48999999809987789875


No 65 
>PF07498 Rho_N:  Rho termination factor, N-terminal domain;  InterPro: IPR011112   The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers . This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0003715 transcription termination factor activity, 0006353 transcription termination; PDB: 1pvo_F 1xpo_C 2a8v_B 1pv4_D 1a62_A 1a8v_A 1xpr_C 1xpu_D 1a63_A 2ht1_B ....
Probab=29.95  E-value=8.9  Score=14.25  Aligned_cols=30  Identities=27%  Similarity=0.442  Sum_probs=20.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             5799999857787789998344899999999999
Q T0611            26 TTNHIAAHLAISPGNLYYHFRNKSDIIYEIFQEY   59 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~~F~sKe~Ll~av~~~~   59 (227)
                      -+++||++.||+    .+.=-.|++|+.++++..
T Consensus         9 eL~~iA~elgI~----~~s~mrK~eLI~~Il~~q   38 (43)
T PF07498_consen    9 ELREIAKELGIE----NYSKMRKQELIFAILKAQ   38 (43)
T ss_dssp             HHHH------------SGTTS-HHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCC----CCCCCCHHHHHHHHHHHH
T ss_conf             999999995998----856478999999999999


No 66 
>PF08006 DUF1700:  Protein of unknown function (DUF1700);  InterPro: IPR012963   This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=28.85  E-value=11  Score=13.63  Aligned_cols=37  Identities=27%  Similarity=0.394  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             9737799999999999987281036579999985778
Q T0611             1 MTMKTRDKILLSSLELFNDKGERNITTNHIAAHLAIS   37 (227)
Q Consensus         1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs   37 (227)
                      |+-+.|+.|++--.+-|.+.|-+|-|=++|.+++|=.
T Consensus        17 Lp~~e~~dil~~Y~eyf~e~~~~G~sEeeii~~LG~P   53 (181)
T PF08006_consen   17 LPEEEREDILEYYEEYFDEGGEEGKSEEEIIAELGSP   53 (181)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCH
T ss_conf             9999999999999999998756899999999782999


No 67 
>PF09862 DUF2089:  Protein of unknown function(DUF2089)
Probab=27.62  E-value=11  Score=13.48  Aligned_cols=18  Identities=22%  Similarity=0.205  Sum_probs=7.2

Q ss_pred             CHHHHHHHHCCCHHHHHH
Q ss_conf             579999985778778999
Q T0611            26 TTNHIAAHLAISPGNLYY   43 (227)
Q Consensus        26 t~~~IA~~aGvs~gtlY~   43 (227)
                      ++.++|+..|||-.|+-+
T Consensus        51 nlKe~ak~lgiSYpTvR~   68 (113)
T PF09862_consen   51 NLKEVAKELGISYPTVRN   68 (113)
T ss_pred             CHHHHHHHHCCCHHHHHH
T ss_conf             899999997888289999


No 68 
>PF04963 Sigma54_CBD:  Sigma-54 factor, core binding domain;  InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme . The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation; PDB: 2k9l_A 2k9m_A.
Probab=24.54  E-value=8.5  Score=14.41  Aligned_cols=32  Identities=22%  Similarity=0.267  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf             99999999998728103657999998577877
Q T0611             8 KILLSSLELFNDKGERNITTNHIAAHLAISPG   39 (227)
Q Consensus         8 ~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~g   39 (227)
                      .|...=+....++||=..++.+||+..|++..
T Consensus        36 ~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~   67 (195)
T PF04963_consen   36 EIAEYIIDNLDDDGYLRESLEEIAEELGVSEE   67 (195)
T ss_dssp             HHHHHHCCCBTT---BSS-HHHHHHHCTS-HH
T ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHH
T ss_conf             99999998279999889999999978198999


No 69 
>PF08822 DUF1804:  Protein of unknown function (DUF1804);  InterPro: IPR014926   This entry consists of a bacterial protein which is uncharacterised. 
Probab=24.37  E-value=13  Score=13.06  Aligned_cols=24  Identities=13%  Similarity=0.029  Sum_probs=21.0

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             103657999998577877899983
Q T0611            22 ERNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus        22 ~~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      |++.|+..+|..+|||-+|.-++=
T Consensus        17 ~~~~~Le~aA~~~gVs~~TArrWK   40 (165)
T PF08822_consen   17 FDRLSLEEAAKKAGVSYGTARRWK   40 (165)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             768989999989299888899999


No 70 
>PF03374 ANT:  Phage antirepressor protein KilAC domain;  InterPro: IPR005039  Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=24.32  E-value=13  Score=13.05  Aligned_cols=17  Identities=24%  Similarity=0.255  Sum_probs=11.0

Q ss_pred             HCCCHHHHHHHHHHHHH
Q ss_conf             21898899999999998
Q T0611           195 PYLTPEYRERVLALREK  211 (227)
Q Consensus       195 p~lt~~~~~~l~~l~~~  211 (227)
                      +..|++|+..+..+...
T Consensus        91 ~~vT~kG~~~i~~~l~~  107 (111)
T PF03374_consen   91 TRVTPKGQEWIAEKLKK  107 (111)
T ss_pred             EEEEHHHHHHHHHHHHH
T ss_conf             89901579999999985


No 71 
>PF07471 Phage_Nu1:  Phage DNA packaging protein Nu1;  InterPro: IPR010906   Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA .; PDB: 1j9i_B.
Probab=23.75  E-value=13  Score=12.98  Aligned_cols=23  Identities=17%  Similarity=0.270  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             36579999985778778999834
Q T0611            24 NITTNHIAAHLAISPGNLYYHFR   46 (227)
Q Consensus        24 ~~t~~~IA~~aGvs~gtlY~~F~   46 (227)
                      .++-.++|+..|||+.||..+-.
T Consensus         2 ~vnk~~lA~~~gVS~~ti~~W~~   24 (164)
T PF07471_consen    2 EVNKKQLAEILGVSERTITKWQR   24 (164)
T ss_dssp             EEEHHHHHHH----HHHHHHHTT
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             66899999997989999999998


No 72 
>PF04760 IF2_N:  Translation initiation factor IF-2, N-terminal region;  InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms . Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1nd9_A.
Probab=23.35  E-value=13  Score=12.92  Aligned_cols=23  Identities=17%  Similarity=0.317  Sum_probs=17.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             03657999998577877899983
Q T0611            23 RNITTNHIAAHLAISPGNLYYHF   45 (227)
Q Consensus        23 ~~~t~~~IA~~aGvs~gtlY~~F   45 (227)
                      ..+|+.++|+++|++...|-...
T Consensus         2 ~~~rV~elAk~l~~~~~~ii~~L   24 (54)
T PF04760_consen    2 EKIRVYELAKELGVSSKEIIKKL   24 (54)
T ss_dssp             -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred             CCEEHHHHHHHHCCCHHHHHHHH
T ss_conf             95369999999892999999999


No 73 
>PF11849 DUF3369:  Domain of unknown function (DUF3369)
Probab=22.70  E-value=11  Score=13.69  Aligned_cols=37  Identities=24%  Similarity=0.416  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHCCCCCC---CHHHHHHHHCCCHHHHHH
Q ss_conf             9999999999987281036---579999985778778999
Q T0611             7 DKILLSSLELFNDKGERNI---TTNHIAAHLAISPGNLYY   43 (227)
Q Consensus         7 ~~Il~aA~~lf~e~G~~~~---t~~~IA~~aGvs~gtlY~   43 (227)
                      ++||+++..+|..+..+..   -+..|+.-.|++...+|-
T Consensus        22 e~Ii~as~~l~~~~sl~~fa~gVL~Ql~~Ll~~~~~~l~~   61 (174)
T PF11849_consen   22 EKIIDASANLFQLQSLQEFASGVLTQLASLLNLPSSGLYC   61 (174)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             9999988988633789999999999999995899870898


No 74 
>PF00126 HTH_1:  Bacterial regulatory helix-turn-helix protein, lysR family;  InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI , , , , . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ixc_B 1iz1_Q 2esn_D 1o7l_B 1b9n_A 1b9m_B 3fzv_B.
Probab=20.37  E-value=15  Score=12.50  Aligned_cols=34  Identities=15%  Similarity=0.255  Sum_probs=22.5

Q ss_pred             HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHCCHHHHH
Q ss_conf             99987281036579999985778778999834489999
Q T0611            15 ELFNDKGERNITTNHIAAHLAISPGNLYYHFRNKSDII   52 (227)
Q Consensus        15 ~lf~e~G~~~~t~~~IA~~aGvs~gtlY~~F~sKe~Ll   52 (227)
                      ..+.+.|    |+..-|+.+|+|.+++.++-+.-|+-+
T Consensus         8 ~~l~~~g----s~~~AA~~l~~s~~~vs~~i~~LE~~l   41 (60)
T PF00126_consen    8 VALAETG----SFSRAAEQLGISQSAVSRRIKRLEEEL   41 (60)
T ss_dssp             HHHHHHS-----HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHC----CHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             9999979----999999870899538999999999982


No 75 
>PF04269 DUF440:  Protein of unknown function, DUF440;  InterPro: IPR007376   This entry represents hypothetical proteins such as HI1450 (DUF440), which is believed to act as a putative dsDNA mimic. HI1450 is an acidic protein with a core structure consisting of alpha(2)-beta(4), where the alpha-helices are packed against the side of an anti-parallel 4-stranded beta meander. As such, it has some similarity to the dsDNA mimics uracil-DNA glycosylase inhibitor and nuclease A inhibitor (NuiA), including the distribution of surface charges and the position of the hydrophobic cavity . DNA mimics act to inhibit or regulate dsDNA-binding proteins. ; PDB: 1nnv_A.
Probab=20.27  E-value=15  Score=12.49  Aligned_cols=31  Identities=19%  Similarity=0.359  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf             9737799999999999987281036579999
Q T0611             1 MTMKTRDKILLSSLELFNDKGERNITTNHIA   31 (227)
Q Consensus         1 ~~~~TR~~Il~aA~~lf~e~G~~~~t~~~IA   31 (227)
                      |-+.|-+.+++.|-++|.|.--++..-.+|.
T Consensus         1 ~~~~t~de~id~AYDiFLE~A~dNL~paDi~   31 (103)
T PF04269_consen    1 MNLITEDEAIDQAYDIFLELAPDNLEPADII   31 (103)
T ss_dssp             -----HHHHHHHHHHHHHHH----S-HHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             9858888999999999998625319999999


Done!