Query         gi|254781218|ref|YP_003065631.1| hypothetical protein CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 205
No_of_seqs    204 out of 5029
Neff          6.4 
Searched_HMMs 39220
Date          Mon May 30 08:13:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781218.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09706 transcriptional repre  99.7 6.5E-17 1.6E-21  124.3  10.5   69   30-98      4-72  (135)
  2 PRK09706 transcriptional repre  99.7   3E-17 7.8E-22  126.3   8.2   72  110-181     2-73  (135)
  3 PHA01976 helix-turn-helix prot  99.7 4.8E-17 1.2E-21  125.1   8.4   63   31-93      2-64  (67)
  4 PHA01976 helix-turn-helix prot  99.6 2.5E-15 6.3E-20  114.5   8.3   63  113-175     2-64  (67)
  5 PRK09943 DNA-binding transcrip  99.6   1E-14 2.7E-19  110.7   8.1   70   27-96      3-72  (185)
  6 PRK09943 DNA-binding transcrip  99.5 6.9E-14 1.8E-18  105.6   8.6   67  112-178     6-72  (185)
  7 PRK08154 anaerobic benzoate ca  99.4 5.2E-12 1.3E-16   94.0   9.7  151   23-177    20-186 (304)
  8 TIGR03070 couple_hipB transcri  99.4 1.7E-12 4.2E-17   97.1   7.1   58   30-87      1-58  (58)
  9 pfam01381 HTH_3 Helix-turn-hel  99.4 1.7E-12 4.3E-17   97.1   7.0   55   36-90      1-55  (55)
 10 smart00530 HTH_XRE Helix-turn-  99.4   2E-12 5.2E-17   96.5   7.1   56   35-90      1-56  (56)
 11 smart00530 HTH_XRE Helix-turn-  99.3 8.8E-12 2.2E-16   92.6   7.0   56  117-172     1-56  (56)
 12 COG1476 Predicted transcriptio  99.3 1.3E-11 3.3E-16   91.6   7.7   61   34-94      4-64  (68)
 13 pfam01381 HTH_3 Helix-turn-hel  99.3 1.1E-11 2.7E-16   92.1   6.8   55  118-172     1-55  (55)
 14 PRK13890 conjugal transfer pro  99.3   2E-11 5.1E-16   90.4   8.1   66   32-97      6-71  (119)
 15 cd00093 HTH_XRE Helix-turn-hel  99.2 3.8E-11 9.7E-16   88.7   7.2   58   33-90      1-58  (58)
 16 COG1476 Predicted transcriptio  99.2 1.2E-10 3.1E-15   85.6   7.2   61  116-176     4-64  (68)
 17 TIGR03070 couple_hipB transcri  99.1 1.5E-10 3.9E-15   84.9   7.0   57  113-169     2-58  (58)
 18 PRK13890 conjugal transfer pro  99.1 2.6E-10 6.6E-15   83.5   8.1   62  114-175     6-67  (119)
 19 cd00093 HTH_XRE Helix-turn-hel  99.1 1.7E-10 4.2E-15   84.7   6.9   58  115-172     1-58  (58)
 20 PRK08154 anaerobic benzoate ca  99.1 7.6E-10 1.9E-14   80.7   8.8   72  112-183    27-98  (304)
 21 PRK09726 DNA-binding transcrip  99.1 5.1E-10 1.3E-14   81.7   7.0   64   25-88      6-69  (88)
 22 COG1813 Predicted transcriptio  99.0 2.2E-09 5.5E-14   77.8   7.7   64  114-177    80-143 (165)
 23 PRK06424 transcription factor;  99.0 2.8E-09 7.2E-14   77.1   8.2   57  113-169    84-140 (144)
 24 PRK08359 transcription factor;  98.9 4.9E-09 1.3E-13   75.6   7.6   56  114-169    84-139 (175)
 25 COG3620 Predicted transcriptio  98.9 7.9E-09   2E-13   74.4   8.2  101   34-145     8-118 (187)
 26 COG1813 Predicted transcriptio  98.9   7E-09 1.8E-13   74.7   6.5   74   24-97     72-145 (165)
 27 PRK09726 DNA-binding transcrip  98.8 1.1E-08 2.7E-13   73.5   6.8   65  107-171     6-70  (88)
 28 PRK06424 transcription factor;  98.8 1.8E-08 4.7E-13   72.1   7.0   67   21-87     74-140 (144)
 29 PRK08359 transcription factor;  98.8 2.3E-08 5.9E-13   71.5   6.6   66   27-92     79-144 (175)
 30 PRK04140 hypothetical protein;  98.7 4.9E-08 1.3E-12   69.4   7.2  136   33-173   127-279 (319)
 31 PRK04140 hypothetical protein;  98.7   7E-08 1.8E-12   68.5   7.0   56  114-169   126-181 (319)
 32 PRK13355 bifunctional HTH-doma  98.7 9.6E-08 2.5E-12   67.6   7.2   67   31-97      5-76  (518)
 33 PRK13355 bifunctional HTH-doma  98.5   4E-07   1E-11   63.8   7.9   67  113-179     5-76  (518)
 34 TIGR02607 antidote_HigA addict  98.5 4.7E-07 1.2E-11   63.4   6.2   55   38-92     14-68  (81)
 35 pfam07022 Phage_CI_repr Bacter  98.4   1E-06 2.7E-11   61.2   7.3   62  117-179     2-64  (65)
 36 COG2944 Predicted transcriptio  98.4 7.9E-07   2E-11   62.0   6.2   48  115-162    46-93  (104)
 37 COG1395 Predicted transcriptio  98.4 9.9E-07 2.5E-11   61.4   6.6   55   33-87    127-181 (313)
 38 KOG3398 consensus               98.4 6.1E-07 1.6E-11   62.7   5.5  108   46-172    23-132 (135)
 39 COG1395 Predicted transcriptio  98.4 1.2E-06 3.1E-11   60.8   6.5   63  114-176   126-192 (313)
 40 TIGR00270 TIGR00270 conserved   98.3   9E-07 2.3E-11   61.7   5.6   74   26-99     78-151 (169)
 41 COG3620 Predicted transcriptio  98.3 1.4E-06 3.5E-11   60.5   6.5   60  116-175     8-73  (187)
 42 TIGR02607 antidote_HigA addict  98.3 1.6E-06   4E-11   60.2   6.3   62  112-173     5-67  (81)
 43 KOG3398 consensus               98.3 1.2E-06   3E-11   60.9   5.2   77   11-89     55-131 (135)
 44 COG2944 Predicted transcriptio  98.3 1.4E-06 3.7E-11   60.4   5.5   43   33-75     46-88  (104)
 45 COG1709 Predicted transcriptio  98.3 7.6E-07 1.9E-11   62.1   3.7   75   17-93     14-89  (241)
 46 COG1709 Predicted transcriptio  98.2 1.9E-06 4.8E-11   59.7   4.7   53  113-165    27-80  (241)
 47 COG3093 VapI Plasmid maintenan  98.2 5.9E-06 1.5E-10   56.6   6.7   52   42-93     21-72  (104)
 48 PRK10072 putative transcriptio  98.2 5.9E-06 1.5E-10   56.6   6.4   54  117-171    37-90  (96)
 49 COG3093 VapI Plasmid maintenan  98.2   1E-05 2.6E-10   55.1   7.5   64  111-174     7-71  (104)
 50 COG1396 HipB Predicted transcr  98.1 2.1E-05 5.5E-10   53.1   8.3   65   32-96      2-67  (120)
 51 COG1426 Predicted transcriptio  98.1 1.5E-05 3.7E-10   54.2   6.7   64   30-93      2-71  (284)
 52 pfam07022 Phage_CI_repr Bacter  98.0 3.4E-05 8.6E-10   51.9   7.1   59   36-95      3-62  (65)
 53 TIGR00270 TIGR00270 conserved   97.9 1.4E-05 3.6E-10   54.3   4.9   71  106-176    76-146 (169)
 54 PRK10856 hypothetical protein;  97.9 4.9E-05 1.3E-09   50.9   7.6   64   30-93     13-82  (332)
 55 COG1396 HipB Predicted transcr  97.9 0.00011 2.8E-09   48.8   9.2   63  114-176     2-65  (120)
 56 TIGR02612 mob_myst_A mobile my  97.9 2.9E-05 7.5E-10   52.3   5.3   56   36-91     30-87  (150)
 57 PRK10072 putative transcriptio  97.9 4.4E-05 1.1E-09   51.2   6.1   49   35-84     37-85  (96)
 58 TIGR02612 mob_myst_A mobile my  97.8 1.6E-05   4E-10   54.0   3.6   78  117-199    29-108 (150)
 59 COG1426 Predicted transcriptio  97.8 9.3E-05 2.4E-09   49.2   7.5   65  113-177     3-73  (284)
 60 PRK10856 hypothetical protein;  97.7 0.00019 4.8E-09   47.3   7.3   67  110-176    11-83  (332)
 61 COG3655 Predicted transcriptio  97.6 0.00015 3.7E-09   48.0   5.9   61   33-93      4-65  (73)
 62 COG3655 Predicted transcriptio  97.5 0.00034 8.5E-09   45.8   6.1   62  114-175     3-65  (73)
 63 TIGR02885 spore_sigF RNA polym  97.4 0.00037 9.5E-09   45.5   5.4  123   17-148    67-221 (231)
 64 TIGR02684 dnstrm_HI1420 probab  97.3 0.00065 1.6E-08   44.0   6.2   59  110-170    31-89  (91)
 65 COG5499 Predicted transcriptio  97.3 0.00062 1.6E-08   44.1   5.8   57  116-173    63-119 (120)
 66 COG5499 Predicted transcriptio  97.2 0.00077   2E-08   43.5   5.7   73   18-91     44-119 (120)
 67 pfam08667 BetR BetR domain. Th  97.2  0.0026 6.6E-08   40.3   8.3   64  110-173     2-69  (146)
 68 COG4800 Predicted transcriptio  97.2  0.0019 4.7E-08   41.2   7.3   59   24-83      9-67  (170)
 69 COG4800 Predicted transcriptio  96.8   0.008   2E-07   37.3   7.6   54  111-165    14-67  (170)
 70 PRK05932 RNA polymerase factor  96.7  0.0025 6.3E-08   40.4   4.5   36  126-161   349-384 (461)
 71 COG2522 Predicted transcriptio  96.7  0.0075 1.9E-07   37.4   6.8   58   31-89      9-68  (119)
 72 pfam04552 Sigma54_DBD Sigma-54  96.7  0.0045 1.2E-07   38.8   5.5  136    6-157    13-157 (160)
 73 PHA00542 putative Cro-like pro  96.6  0.0065 1.6E-07   37.8   6.0   57   27-83     14-71  (82)
 74 PRK07408 RNA polymerase sigma   96.6    0.06 1.5E-06   31.9  11.0  137   21-165   104-251 (256)
 75 TIGR02684 dnstrm_HI1420 probab  96.5  0.0042 1.1E-07   39.0   4.4   54   32-87     35-88  (91)
 76 COG2522 Predicted transcriptio  96.3   0.013 3.3E-07   35.9   6.2   40  114-153    10-49  (119)
 77 PRK02866 cyanate hydratase; Va  96.3   0.097 2.5E-06   30.6  10.8   62   30-91      4-65  (147)
 78 PRK02866 cyanate hydratase; Va  96.2   0.038 9.6E-07   33.1   8.1   64  110-173     2-65  (147)
 79 PRK07122 RNA polymerase sigma   96.2   0.095 2.4E-06   30.6  10.1  131   17-149   113-253 (263)
 80 PRK12469 RNA polymerase factor  96.1  0.0062 1.6E-07   38.0   3.7   40  125-164   362-401 (475)
 81 COG1508 RpoN DNA-directed RNA   96.1   0.069 1.8E-06   31.5   8.9  102   45-159   331-441 (444)
 82 KOG3802 consensus               96.0   0.055 1.4E-06   32.1   8.2  126   26-170   205-336 (398)
 83 TIGR02846 spore_sigmaK RNA pol  96.0   0.003 7.7E-08   39.9   1.7   25   42-66    193-217 (228)
 84 pfam08667 BetR BetR domain. Th  96.0   0.055 1.4E-06   32.1   8.1   63   30-92      4-70  (146)
 85 COG1191 FliA DNA-directed RNA   95.9   0.084 2.1E-06   30.9   8.6   43  116-165   202-244 (247)
 86 pfam07900 DUF1670 Protein of u  95.8    0.02 5.1E-07   34.8   5.2   94   44-148   105-219 (220)
 87 TIGR02980 SigBFG RNA polymeras  95.8  0.0082 2.1E-07   37.2   3.2  118   15-148    58-218 (229)
 88 PRK05911 RNA polymerase sigma   95.8    0.12 3.1E-06   29.9   8.9  125   25-149   105-244 (257)
 89 smart00352 POU Found in Pit-Oc  95.7   0.022 5.6E-07   34.6   5.0   53   29-83      9-67  (75)
 90 PRK06288 RNA polymerase sigma   95.7    0.16   4E-06   29.3   9.3  125   25-149   109-247 (261)
 91 PHA00542 putative Cro-like pro  95.5   0.038 9.8E-07   33.0   5.6   49  117-165    22-71  (82)
 92 PRK08558 adenine phosphoribosy  95.5   0.075 1.9E-06   31.2   7.0   56   30-85      5-64  (238)
 93 PRK12427 flagellar biosynthesi  95.4    0.21 5.5E-06   28.4  11.8  113   26-149    95-220 (229)
 94 pfam00157 Pou Pou domain - N-t  95.4   0.021 5.4E-07   34.6   4.1   53   29-83      9-67  (75)
 95 COG5606 Uncharacterized conser  95.4   0.025 6.3E-07   34.2   4.4   61   28-88     25-86  (91)
 96 PRK03975 tfx putative transcri  95.2   0.034 8.7E-07   33.4   4.4   32   37-69     13-44  (139)
 97 PRK08583 RNA polymerase sigma   95.0     0.3 7.6E-06   27.6  10.2  127   20-149   106-244 (257)
 98 PRK06986 fliA flagellar biosyn  94.9    0.16   4E-06   29.3   7.3  127   25-165    90-231 (234)
 99 pfam04814 HNF-1_N Hepatocyte n  94.9    0.11 2.8E-06   30.2   6.4   54  108-161   110-163 (177)
100 TIGR02980 SigBFG RNA polymeras  94.8   0.015 3.8E-07   35.6   1.7   31   36-66    188-218 (229)
101 PRK09526 lacI lac repressor; R  94.7   0.058 1.5E-06   32.0   4.5   48   41-88      2-52  (342)
102 PRK07670 RNA polymerase sigma   94.7    0.28 7.2E-06   27.7   8.1  117   32-149   107-236 (250)
103 COG3636 Predicted transcriptio  94.6    0.16 4.1E-06   29.2   6.7   56  112-169    37-92  (100)
104 PRK09492 treR trehalose repres  94.6    0.09 2.3E-06   30.8   5.4   48   42-89      2-52  (315)
105 PRK10014 DNA-binding transcrip  94.6   0.075 1.9E-06   31.3   5.0   48   41-88      3-53  (342)
106 COG2390 DeoR Transcriptional r  94.6   0.091 2.3E-06   30.7   5.3   71   23-93      5-88  (321)
107 TIGR01321 TrpR trp operon repr  94.5   0.071 1.8E-06   31.4   4.6   57   17-76     30-88  (95)
108 TIGR00721 tfx DNA-binding prot  94.5   0.027 6.9E-07   34.0   2.4   28   42-69     19-46  (142)
109 PRK10014 DNA-binding transcrip  94.4   0.091 2.3E-06   30.7   5.1   36  125-160     5-40  (342)
110 PRK09492 treR trehalose repres  94.3    0.12 3.1E-06   30.0   5.5   45  126-170     4-51  (315)
111 TIGR02395 rpoN_sigma RNA polym  94.2    0.02   5E-07   34.9   1.2  104   40-156   361-474 (477)
112 pfam01710 Transposase_14 Trans  94.1    0.34 8.8E-06   27.2   7.5   90   28-148     3-93  (120)
113 PRK09526 lacI lac repressor; R  94.0    0.13 3.3E-06   29.8   5.1   37  125-161     4-40  (342)
114 PRK08558 adenine phosphoribosy  94.0    0.31 7.9E-06   27.4   7.0   43  125-167    22-64  (238)
115 TIGR02885 spore_sigF RNA polym  94.0    0.02   5E-07   34.9   0.9   28   39-66    194-221 (231)
116 pfam05339 DUF739 Protein of un  93.9    0.24   6E-06   28.2   6.3   57  116-172     6-62  (69)
117 COG5606 Uncharacterized conser  93.9    0.11 2.8E-06   30.2   4.6   61  110-170    25-86  (91)
118 COG2973 TrpR Trp operon repres  93.9    0.29 7.3E-06   27.7   6.7   64   17-83     34-99  (103)
119 PRK11303 DNA-binding transcrip  93.6    0.17 4.4E-06   29.0   5.2   46   45-90      1-52  (330)
120 COG3636 Predicted transcriptio  93.5    0.46 1.2E-05   26.4   7.2   54   32-87     39-92  (100)
121 pfam00356 LacI Bacterial regul  93.5    0.19 4.8E-06   28.8   5.3   35  128-162     1-35  (46)
122 PRK05901 RNA polymerase sigma   93.5    0.61 1.6E-05   25.6   8.2  129   19-149   235-378 (398)
123 COG1191 FliA DNA-directed RNA   93.4    0.12 3.1E-06   30.0   4.1   15  127-141   127-141 (247)
124 smart00352 POU Found in Pit-Oc  93.1    0.15 3.9E-06   29.3   4.2   52  112-165    10-67  (75)
125 TIGR00673 cynS cyanate hydrata  93.1     0.7 1.8E-05   25.2   9.2  106   27-135     9-114 (156)
126 pfam00356 LacI Bacterial regul  93.1    0.26 6.7E-06   27.9   5.4   37   46-82      1-37  (46)
127 PRK07405 RNA polymerase sigma   93.0    0.73 1.9E-05   25.1   9.2  107   43-149    55-208 (318)
128 PRK10401 DNA-binding transcrip  92.8    0.28 7.2E-06   27.7   5.3   44   45-88      2-48  (346)
129 smart00354 HTH_LACI helix_turn  92.8    0.27   7E-06   27.8   5.2   27   46-72      2-28  (70)
130 KOG1168 consensus               92.8   0.065 1.6E-06   31.7   2.0  128   23-168   210-349 (385)
131 PRK05657 RNA polymerase sigma   92.8    0.78   2E-05   25.0  10.4  125   43-173   191-328 (328)
132 COG1356 tfx Transcriptional re  92.7   0.072 1.8E-06   31.4   2.1   47   41-88     20-69  (143)
133 smart00354 HTH_LACI helix_turn  92.7    0.32 8.2E-06   27.3   5.4   45  128-172     2-49  (70)
134 pfam04814 HNF-1_N Hepatocyte n  92.6     0.7 1.8E-05   25.2   7.1   67    5-71     84-155 (177)
135 PRK10727 DNA-binding transcrip  92.6    0.31 7.9E-06   27.5   5.2   44   45-88      2-48  (342)
136 PRK09210 RNA polymerase sigma   92.5    0.86 2.2E-05   24.7   8.6  130   18-149   205-349 (368)
137 pfam02376 CUT CUT domain. The   92.4     0.3 7.6E-06   27.6   4.9   40  109-148     3-43  (81)
138 PRK11041 DNA-binding transcrip  92.3    0.36 9.1E-06   27.1   5.3   46   44-89      9-57  (341)
139 PRK10703 DNA-binding transcrip  92.2    0.36 9.2E-06   27.0   5.2   44   46-89      3-49  (335)
140 PRK08099 nicotinamide-nucleoti  92.0    0.59 1.5E-05   25.7   6.1   55   35-89      6-61  (411)
141 PRK01381 Trp operon repressor;  91.9    0.38 9.8E-06   26.9   5.1   64   17-83     29-94  (99)
142 COG1609 PurR Transcriptional r  91.9    0.44 1.1E-05   26.5   5.3   43   45-87      1-46  (333)
143 cd04762 HTH_MerR-trunc Helix-T  91.8    0.19 4.8E-06   28.8   3.4   28  127-154     1-28  (49)
144 PRK10339 DNA-binding transcrip  91.7    0.51 1.3E-05   26.1   5.5   42   45-86      2-48  (327)
145 cd04780 HTH_MerR-like_sg5 Heli  91.6    0.15 3.9E-06   29.4   2.7   69   45-138     1-70  (95)
146 PRK10703 DNA-binding transcrip  91.4    0.54 1.4E-05   25.9   5.4   12   35-46     35-46  (335)
147 pfam08965 DUF1870 Domain of un  91.2     0.6 1.5E-05   25.7   5.5   47   35-81      4-52  (117)
148 COG1609 PurR Transcriptional r  91.2    0.53 1.3E-05   26.0   5.2   46  127-172     1-49  (333)
149 pfam00157 Pou Pou domain - N-t  91.2    0.35   9E-06   27.1   4.2   51  113-165    11-67  (75)
150 KOG3802 consensus               91.1    0.25 6.4E-06   28.0   3.5   59  110-173   207-271 (398)
151 PRK07500 rpoH2 RNA polymerase   91.1    0.22 5.7E-06   28.3   3.1  113   46-165   150-277 (289)
152 PRK05572 sporulation sigma fac  91.0     1.2 3.1E-05   23.8   9.9  121   22-149   108-240 (251)
153 cd04774 HTH_YfmP Helix-Turn-He  90.6     1.3 3.4E-05   23.5   8.2   70   45-140     1-71  (96)
154 pfam01371 Trp_repressor Trp re  90.6    0.55 1.4E-05   25.9   4.8   38   29-66     32-71  (88)
155 smart00342 HTH_ARAC helix_turn  90.5     1.2 3.1E-05   23.8   6.5   69   44-145     1-70  (84)
156 COG4197 Uncharacterized protei  90.4    0.31   8E-06   27.4   3.4   44  129-172    15-60  (96)
157 PRK10344 DNA-binding transcrip  90.2     1.2   3E-05   23.9   6.2   54  117-173    12-65  (90)
158 pfam08535 KorB KorB domain. Th  89.9    0.92 2.4E-05   24.5   5.5   44   43-87      2-59  (93)
159 PHA00675 hypothetical protein   89.5     0.6 1.5E-05   25.7   4.3   35  114-148    27-61  (78)
160 TIGR02846 spore_sigmaK RNA pol  89.5     0.2 5.2E-06   28.6   1.9   23  126-148   195-217 (228)
161 PRK10423 transcriptional repre  89.5     0.8   2E-05   24.9   4.9   42   48-89      2-46  (327)
162 COG3423 Nlp Predicted transcri  89.5     1.6   4E-05   23.1   6.4   56  117-175    12-67  (82)
163 cd01392 HTH_LacI Helix-turn-he  89.5    0.73 1.9E-05   25.1   4.7   34  131-164     2-35  (52)
164 PRK03975 tfx putative transcri  89.3    0.39   1E-05   26.8   3.2   28  123-150    16-43  (139)
165 pfam02001 DUF134 Protein of un  89.2    0.37 9.3E-06   27.0   3.0   38  121-165    47-84  (100)
166 PRK07598 RNA polymerase sigma   89.1     1.7 4.5E-05   22.8   9.7   23   70-92    177-202 (410)
167 cd04789 HTH_Cfa Helix-Turn-Hel  89.1     1.6 4.1E-05   23.1   6.1   27   45-71      2-29  (102)
168 PRK07921 RNA polymerase sigma   89.0     1.8 4.6E-05   22.7   8.2   22  127-148   279-300 (320)
169 PHA00675 hypothetical protein   89.0     0.7 1.8E-05   25.3   4.3   35   30-64     25-59  (78)
170 COG4197 Uncharacterized protei  89.0    0.45 1.1E-05   26.5   3.3   47   46-92     14-62  (96)
171 cd01110 HTH_SoxR Helix-Turn-He  88.9     1.6   4E-05   23.1   6.1   28   44-71      1-29  (139)
172 pfam04545 Sigma70_r4 Sigma-70,  88.9    0.54 1.4E-05   26.0   3.6   28   38-65     14-41  (50)
173 PRK12427 flagellar biosynthesi  88.9    0.62 1.6E-05   25.6   3.9   20  127-146   116-135 (229)
174 PRK08215 sporulation sigma fac  88.7     1.9 4.8E-05   22.6  10.4   30  120-149   219-248 (257)
175 pfam02001 DUF134 Protein of un  88.6    0.56 1.4E-05   25.9   3.5   27   40-66     48-74  (100)
176 COG4565 CitB Response regulato  88.4       2   5E-05   22.5   7.7   24  124-147   171-194 (224)
177 TIGR02392 rpoH_proteo alternat  88.3    0.82 2.1E-05   24.8   4.2  127   19-149   111-268 (279)
178 cd04781 HTH_MerR-like_sg6 Heli  88.2     1.6 4.1E-05   23.0   5.7   27   45-71      1-28  (120)
179 PRK10227 DNA-binding transcrip  88.1     2.1 5.3E-05   22.4   7.3   46   45-90      1-63  (135)
180 PRK09744 DNA-binding transcrip  88.0    0.86 2.2E-05   24.7   4.2   35  128-165    12-46  (75)
181 TIGR02835 spore_sigmaE RNA pol  87.9    0.29 7.4E-06   27.6   1.7   24  126-149   198-221 (234)
182 TIGR02850 spore_sigG RNA polym  87.9     0.9 2.3E-05   24.6   4.3   32  118-149   214-245 (254)
183 PRK09514 zntR zinc-responsive   87.8    0.87 2.2E-05   24.7   4.1   28   45-72      2-30  (140)
184 PRK08301 sporulation sigma fac  87.7    0.79   2E-05   24.9   3.8   26  124-149   201-226 (239)
185 TIGR02959 SigZ RNA polymerase   87.6    0.45 1.2E-05   26.4   2.6   30  121-150   111-141 (170)
186 PRK06596 RNA polymerase factor  87.6     2.2 5.6E-05   22.2   7.7  112   36-149   139-271 (284)
187 PRK12529 RNA polymerase sigma   87.5    0.79   2E-05   24.9   3.7   29  120-148   137-165 (178)
188 PRK06759 RNA polymerase factor  87.2    0.98 2.5E-05   24.4   4.1   33  117-149   113-145 (154)
189 PRK13752 putative transcriptio  87.0     2.4 6.1E-05   22.0   6.0   30   43-72      6-36  (144)
190 PRK05949 RNA polymerase sigma   86.9     2.4 6.2E-05   21.9  10.2  109   43-151    64-219 (327)
191 cd04782 HTH_BltR Helix-Turn-He  86.8     2.4 6.2E-05   21.9   6.2   28   45-72      1-29  (97)
192 pfam05269 Phage_CII Bacterioph  86.7    0.48 1.2E-05   26.3   2.3   44   43-88     22-65  (91)
193 cd00569 HTH_Hin_like Helix-tur  86.5     1.2 3.1E-05   23.8   4.2   25  122-146    17-41  (42)
194 COG1513 CynS Cyanate lyase [In  86.4     2.6 6.6E-05   21.8  10.1  103   29-134     6-108 (151)
195 TIGR02937 sigma70-ECF RNA poly  86.3       1 2.7E-05   24.2   3.8   32  117-148   121-152 (162)
196 PRK09863 putative frv operon r  86.0     2.7 6.9E-05   21.6   8.0   98   39-148    12-114 (585)
197 TIGR00721 tfx DNA-binding prot  85.7    0.66 1.7E-05   25.4   2.6   38  122-166    17-54  (142)
198 cd04764 HTH_MlrA-like_sg1 Heli  85.5     0.6 1.5E-05   25.7   2.3   66   45-137     1-67  (67)
199 PRK04217 hypothetical protein;  85.5     1.1 2.7E-05   24.1   3.5   38  121-165    53-90  (110)
200 COG1974 LexA SOS-response tran  85.2     1.3 3.4E-05   23.5   4.0   48   39-87      7-54  (201)
201 cd04767 HTH_HspR-like_MBC Heli  85.1       3 7.6E-05   21.4   5.7   74   45-149     2-76  (120)
202 PRK12523 RNA polymerase sigma   84.7     1.3 3.4E-05   23.6   3.8   29  120-148   129-157 (172)
203 cd04766 HTH_HspR Helix-Turn-He  84.7     3.1 7.9E-05   21.3   6.0   69   45-139     2-71  (91)
204 KOG1168 consensus               84.6    0.55 1.4E-05   25.9   1.8   38  112-149   220-266 (385)
205 pfam01047 MarR MarR family. Th  84.5     1.3 3.3E-05   23.6   3.6   27   38-64     11-37  (59)
206 PRK00423 tfb transcription ini  84.5     3.2 8.1E-05   21.2   9.9  102   43-145   181-295 (310)
207 COG2842 Uncharacterized ATPase  84.2     2.7 6.9E-05   21.6   5.2   54   32-86      7-61  (297)
208 PRK12528 RNA polymerase sigma   84.1     2.1 5.3E-05   22.3   4.5   31  118-148   127-157 (167)
209 pfam02787 CPSase_L_D3 Carbamoy  83.9     1.4 3.6E-05   23.4   3.6   52  122-173    67-119 (122)
210 TIGR01764 excise DNA binding d  83.9       1 2.6E-05   24.3   2.9   31  127-157     2-32  (49)
211 PHA01083 hypothetical protein   83.7     2.4   6E-05   22.0   4.7   63   36-98      5-69  (153)
212 pfam05930 Phage_AlpA Prophage   83.6     1.5 3.8E-05   23.3   3.6   32  127-158     4-35  (51)
213 smart00419 HTH_CRP helix_turn_  83.4     1.1 2.9E-05   24.0   2.9   20   45-64      9-28  (48)
214 COG1342 Predicted DNA-binding   83.4     1.3 3.3E-05   23.6   3.2   38  121-165    44-81  (99)
215 TIGR02999 Sig-70_X6 RNA polyme  82.9     1.8 4.5E-05   22.8   3.8   32  116-147   151-183 (194)
216 pfam07037 DUF1323 Putative tra  82.5     1.1 2.8E-05   24.1   2.6   22   45-66      1-22  (122)
217 COG2512 Predicted membrane-ass  82.5     1.6 4.2E-05   23.0   3.5   33  116-148   199-232 (258)
218 PRK08311 putative RNA polymera  82.0       4  0.0001   20.6   5.4   99   59-168   120-221 (237)
219 PRK07773 replicative DNA helic  82.0     3.4 8.7E-05   21.0   5.0   53  111-166   709-761 (868)
220 cd04773 HTH_TioE_rpt2 Second H  81.9     1.8 4.7E-05   22.7   3.5   28   45-72      1-29  (108)
221 PRK12525 RNA polymerase sigma   81.8     2.1 5.3E-05   22.4   3.8   28  120-147   128-155 (168)
222 pfam00376 MerR MerR family reg  81.7     1.8 4.6E-05   22.7   3.5   27  128-154     1-27  (38)
223 PRK09954 hypothetical protein;  81.6     1.9 4.9E-05   22.6   3.5   28   36-63      9-36  (362)
224 cd04761 HTH_MerR-SF Helix-Turn  81.4     1.9 4.9E-05   22.6   3.5   28  127-154     1-28  (49)
225 smart00422 HTH_MERR helix_turn  81.4       2   5E-05   22.5   3.6   68   45-138     1-69  (70)
226 PRK07406 RNA polymerase sigma   81.2     4.3 0.00011   20.4   9.9  108   44-151   122-276 (385)
227 TIGR02405 trehalos_R_Ecol treh  81.0    0.71 1.8E-05   25.2   1.2   31   45-75      2-32  (311)
228 cd06571 Bac_DnaA_C C-terminal   80.9     4.3 0.00011   20.4   7.5   61   74-145     3-64  (90)
229 TIGR02997 Sig70-cyanoRpoD RNA   80.7     4.4 0.00011   20.3   7.4  141   37-178    55-266 (336)
230 TIGR02941 Sigma_B RNA polymera  80.6    0.75 1.9E-05   25.1   1.2  136   10-148    79-244 (256)
231 PRK03573 transcriptional regul  80.3     2.4 6.1E-05   21.9   3.7   29   36-64     37-66  (144)
232 KOG2252 consensus               80.3     2.8 7.1E-05   21.6   4.0  119   28-173   327-469 (558)
233 pfam08279 HTH_11 HTH domain. T  80.2     2.6 6.7E-05   21.7   3.9   20  127-146    16-35  (55)
234 cd04765 HTH_MlrA-like_sg2 Heli  80.2     4.6 0.00012   20.2   5.3   67   45-137     1-69  (99)
235 TIGR02147 Fsuc_second hypothet  80.1     1.5 3.9E-05   23.2   2.6   43   44-86     27-71  (281)
236 cd04768 HTH_BmrR-like Helix-Tu  80.1     2.4   6E-05   22.0   3.6   28   45-72      1-29  (96)
237 PRK11512 DNA-binding transcrip  79.7     2.8 7.2E-05   21.5   3.9   29   36-64     46-74  (144)
238 PRK10046 dpiA two-component re  79.6     4.8 0.00012   20.1   5.4   24  124-147   175-198 (225)
239 cd06171 Sigma70_r4 Sigma70, re  79.6     2.9 7.4E-05   21.5   3.9   27  120-146    20-46  (55)
240 cd00092 HTH_CRP helix_turn_hel  79.2     4.9 0.00013   20.0   5.1   23  125-147    24-46  (67)
241 cd04763 HTH_MlrA-like Helix-Tu  79.2     2.3 5.9E-05   22.1   3.3   64   46-136     2-67  (68)
242 COG0568 RpoD DNA-directed RNA   78.8     5.1 0.00013   19.9   6.8  103   43-149   204-322 (342)
243 cd01107 HTH_BmrR Helix-Turn-He  78.7     2.7 6.8E-05   21.7   3.5   29   45-73      1-30  (108)
244 PRK10430 DNA-binding transcrip  78.7     5.1 0.00013   19.9   5.3   32  116-147   165-199 (239)
245 smart00347 HTH_MARR helix_turn  78.5     3.2 8.3E-05   21.1   3.9   29   37-65     17-45  (101)
246 pfam07638 Sigma70_ECF ECF sigm  78.4     3.5 8.9E-05   20.9   4.0   29  118-146   143-171 (185)
247 cd04787 HTH_HMRTR_unk Helix-Tu  78.4     2.8 7.2E-05   21.5   3.6   28   45-72      1-29  (133)
248 COG3415 Transposase and inacti  78.1     5.3 0.00014   19.8   5.1   40   30-69      7-46  (138)
249 cd01108 HTH_CueR Helix-Turn-He  77.9       3 7.6E-05   21.4   3.6   28   45-72      1-29  (127)
250 cd04783 HTH_MerR1 Helix-Turn-H  77.8     2.9 7.5E-05   21.4   3.5   28   45-72      1-29  (126)
251 COG0789 SoxR Predicted transcr  77.8     2.9 7.4E-05   21.4   3.5   28   45-72      1-29  (124)
252 PRK11511 DNA-binding transcrip  77.7     5.5 0.00014   19.7   9.0   84   42-172    23-107 (127)
253 pfam04218 CENP-B_N CENP-B N-te  77.7     4.5 0.00011   20.3   4.4   35  116-150    11-46  (53)
254 cd04770 HTH_HMRTR Helix-Turn-H  77.6     2.8 7.2E-05   21.5   3.4   27   45-71      1-28  (123)
255 cd00592 HTH_MerR-like Helix-Tu  77.6     3.1 7.9E-05   21.3   3.6   67   45-138     1-68  (100)
256 COG1318 Predicted transcriptio  77.5     4.8 0.00012   20.1   4.5   31  122-152    57-87  (182)
257 PRK06930 positive control sigm  77.3     4.7 0.00012   20.2   4.4   43  120-169   124-166 (170)
258 PRK13413 mpi multiple promoter  77.2     3.1   8E-05   21.2   3.5   29  122-150   168-196 (200)
259 pfam05225 HTH_psq helix-turn-h  77.0     5.7 0.00015   19.6   4.9   39  113-152     4-42  (45)
260 PRK10572 DNA-binding transcrip  76.9     5.8 0.00015   19.6   9.6   33  124-156   197-229 (290)
261 pfam07471 Phage_Nu1 Phage DNA   76.8     2.6 6.7E-05   21.7   3.0   24   43-66      1-24  (164)
262 PRK09651 RNA polymerase sigma   76.8     3.6 9.2E-05   20.9   3.7   29  119-147   128-156 (172)
263 PRK11753 cAMP-regulatory prote  76.7     5.8 0.00015   19.6   5.3   23  126-148   168-190 (211)
264 PRK09646 RNA polymerase sigma   76.6     5.9 0.00015   19.6   6.1   42  120-168   152-193 (194)
265 cd01104 HTH_MlrA-CarA Helix-Tu  76.4     3.2 8.2E-05   21.2   3.4   65   45-136     1-67  (68)
266 TIGR02479 FliA_WhiG RNA polyme  76.2       6 0.00015   19.5   9.8  117   25-147    78-215 (227)
267 pfam02796 HTH_7 Helix-turn-hel  76.2     3.2 8.1E-05   21.2   3.3   28  122-149    17-44  (45)
268 pfam04967 HTH_10 HTH DNA bindi  76.2     2.8 7.2E-05   21.5   3.0   23  125-147    22-44  (53)
269 cd04785 HTH_CadR-PbrR-like Hel  76.1     3.5   9E-05   20.9   3.5   28   45-72      1-29  (126)
270 cd04769 HTH_MerR2 Helix-Turn-H  76.1     3.3 8.5E-05   21.1   3.4   66   45-137     1-67  (116)
271 TIGR00160 MGSA methylglyoxal s  75.7     1.6 4.1E-05   23.0   1.7   25   69-93     89-120 (143)
272 PRK12527 RNA polymerase sigma   75.6     3.6 9.3E-05   20.8   3.5   29  118-146   113-141 (159)
273 pfam01527 Transposase_8 Transp  75.5     5.6 0.00014   19.7   4.4   27  123-149    20-46  (75)
274 cd04772 HTH_TioE_rpt1 First He  75.2     3.9   1E-04   20.6   3.6   21   46-66      2-22  (99)
275 pfam02954 HTH_8 Bacterial regu  75.0     5.7 0.00015   19.6   4.4   31  116-146     8-38  (42)
276 PRK05803 sporulation sigma fac  74.6     4.8 0.00012   20.1   3.9   26  124-149   192-217 (228)
277 cd01282 HTH_MerR-like_sg3 Heli  74.6     4.2 0.00011   20.5   3.6   67   45-138     1-68  (112)
278 PRK07037 extracytoplasmic-func  74.6     6.3 0.00016   19.4   4.5   29  120-148   133-161 (183)
279 PRK11161 fumarate/nitrate redu  74.3     6.7 0.00017   19.2   5.1   24  125-148   183-206 (235)
280 cd01105 HTH_GlnR-like Helix-Tu  74.2     4.2 0.00011   20.5   3.5   67   45-137     2-69  (88)
281 TIGR02044 CueR Cu(I)-responsiv  74.2     6.8 0.00017   19.2   5.7   78   47-124     3-101 (127)
282 cd04786 HTH_MerR-like_sg7 Heli  74.1     4.4 0.00011   20.4   3.6   28   45-72      1-29  (131)
283 cd01109 HTH_YyaN Helix-Turn-He  73.8     3.9  0.0001   20.6   3.3   27   45-71      1-28  (113)
284 cd01106 HTH_TipAL-Mta Helix-Tu  73.4     4.6 0.00012   20.2   3.6   28   45-72      1-29  (103)
285 PRK11179 DNA-binding transcrip  73.4     5.2 0.00013   19.9   3.8   27   36-62     15-41  (153)
286 COG3311 AlpA Predicted transcr  73.3     4.3 0.00011   20.4   3.4   34  125-158    12-45  (70)
287 cd01279 HTH_HspR-like Helix-Tu  73.2     7.2 0.00018   19.0   5.0   71   45-141     2-73  (98)
288 PRK11169 leucine-responsive tr  72.9     5.4 0.00014   19.8   3.8   27   36-62     20-46  (164)
289 PRK09775 hypothetical protein;  72.7     5.2 0.00013   19.9   3.7   31   35-65      3-33  (443)
290 cd04784 HTH_CadR-PbrR Helix-Tu  72.5     4.9 0.00012   20.0   3.5   28   45-72      1-29  (127)
291 cd04775 HTH_Cfa-like Helix-Tur  71.9     5.3 0.00013   19.8   3.6   25   45-69      2-27  (102)
292 COG1522 Lrp Transcriptional re  71.7     5.9 0.00015   19.6   3.8   28   36-63     14-41  (154)
293 PRK13918 CRP/FNR family transc  71.4       4  0.0001   20.6   2.9   41  126-166   145-198 (201)
294 PRK13749 transcriptional regul  70.9     6.8 0.00017   19.2   4.0   48   43-90      2-66  (121)
295 PRK09391 fixK transcriptional   70.7     4.3 0.00011   20.4   2.9   24  124-147   171-194 (224)
296 TIGR02985 Sig70_bacteroi1 RNA   70.5     6.7 0.00017   19.2   3.8   27  120-146   129-155 (167)
297 smart00344 HTH_ASNC helix_turn  70.5     6.8 0.00017   19.2   3.9   27   36-62      9-35  (108)
298 pfam08281 Sigma70_r4_2 Sigma-7  70.2     8.3 0.00021   18.6   4.3   29  118-146    18-46  (54)
299 PRK13503 transcriptional activ  69.8     8.6 0.00022   18.5   8.5   41  117-157   176-218 (278)
300 pfam08299 Bac_DnaA_C domain.    69.7     8.6 0.00022   18.5   7.2   61   74-145     4-65  (70)
301 PHA00361 cI Repressor           69.5     2.3 5.9E-05   22.0   1.3   19   78-96      1-19  (165)
302 cd04790 HTH_Cfa-like_unk Helix  69.0     6.5 0.00017   19.3   3.5   47   45-91      2-65  (172)
303 TIGR02417 fruct_sucro_rep D-fr  68.9       4  0.0001   20.6   2.4   48   46-93      1-54  (335)
304 COG2452 Predicted site-specifi  68.4     6.3 0.00016   19.4   3.3   23   44-66      1-23  (193)
305 TIGR02051 MerR Hg(II)-responsi  68.3     1.6   4E-05   23.1   0.2   21   48-68      3-24  (126)
306 cd06170 LuxR_C_like C-terminal  68.1     6.1 0.00015   19.5   3.2   23  124-146    13-35  (57)
307 pfam07750 GcrA GcrA cell cycle  67.8     5.3 0.00013   19.8   2.9   28   34-61      6-36  (162)
308 COG3413 Predicted DNA binding   67.3     5.8 0.00015   19.6   3.0   69   73-148   125-200 (215)
309 pfam09048 Cro Cro. Members of   67.1     8.4 0.00021   18.6   3.8   30   38-69      7-36  (58)
310 cd04776 HTH_GnyR Helix-Turn-He  67.0     7.5 0.00019   18.9   3.5   64   45-138     1-67  (118)
311 pfam10668 Phage_terminase Phag  66.7     4.2 0.00011   20.5   2.2   21  127-147    23-43  (60)
312 TIGR03001 Sig-70_gmx1 RNA poly  66.5     4.3 0.00011   20.4   2.2   29  121-149   177-205 (249)
313 pfam00196 GerE Bacterial regul  65.8     7.1 0.00018   19.0   3.2   23  124-146    16-38  (58)
314 PRK09637 RNA polymerase sigma   65.8       8  0.0002   18.7   3.4   42  118-166   114-155 (181)
315 PRK12516 RNA polymerase sigma   65.6     7.4 0.00019   18.9   3.3   44  118-168   127-170 (190)
316 PRK13182 racA polar chromosome  65.5     5.8 0.00015   19.6   2.7   23   45-67      1-23  (178)
317 PRK13919 putative RNA polymera  65.4      10 0.00027   18.0   4.6   28  120-147   146-173 (187)
318 cd01111 HTH_MerD Helix-Turn-He  65.3     7.5 0.00019   18.9   3.2   28   45-72      1-29  (107)
319 PRK11557 putative DNA-binding   65.0      11 0.00027   18.0   4.0   58   26-83     15-74  (282)
320 pfam01418 HTH_6 Helix-turn-hel  64.9     6.6 0.00017   19.2   2.9   56   29-84     18-75  (106)
321 cd04788 HTH_NolA-AlbR Helix-Tu  64.4     9.2 0.00023   18.4   3.5   28   45-72      1-29  (96)
322 PRK11922 RNA polymerase sigma   64.2     8.9 0.00023   18.4   3.4   29  120-148   159-187 (231)
323 PRK12541 RNA polymerase sigma   64.0     8.3 0.00021   18.6   3.2   28  119-146   121-148 (161)
324 PRK09392 ftrB transcriptional   63.9     7.2 0.00018   19.0   2.9   23  125-147   172-194 (236)
325 smart00421 HTH_LUXR helix_turn  63.9       8  0.0002   18.7   3.2   24  123-146    15-38  (58)
326 COG5484 Uncharacterized conser  63.4     6.5 0.00017   19.3   2.6   27   42-68     17-43  (279)
327 cd04777 HTH_MerR-like_sg1 Heli  63.4     7.3 0.00018   19.0   2.9   64   45-138     1-67  (107)
328 PRK12539 RNA polymerase sigma   63.0      11 0.00028   17.9   3.7   27  120-146   141-167 (184)
329 COG2826 Tra8 Transposase and i  62.5     8.2 0.00021   18.7   3.0   34   35-69     15-49  (318)
330 PRK12532 RNA polymerase sigma   62.3     9.4 0.00024   18.3   3.3   27  120-146   146-172 (195)
331 PRK12517 RNA polymerase sigma   61.7      11 0.00027   18.0   3.4   29  119-147   137-165 (188)
332 pfam09339 HTH_IclR IclR helix-  61.5     7.1 0.00018   19.0   2.5   26  123-148    15-40  (52)
333 smart00420 HTH_DEOR helix_turn  61.5      11 0.00027   18.0   3.4   28  118-145     6-33  (53)
334 PRK12526 RNA polymerase sigma   61.4      11 0.00027   17.9   3.4   28  120-147   163-190 (206)
335 pfam04760 IF2_N Translation in  60.9      13 0.00032   17.5   5.4   42  126-167     3-51  (52)
336 PRK12524 RNA polymerase sigma   60.8      11 0.00028   17.9   3.4   51  119-176   145-195 (196)
337 PRK12543 RNA polymerase sigma   60.3      12 0.00029   17.7   3.4   30  118-147   137-166 (190)
338 PRK10360 DNA-binding transcrip  60.3      11 0.00028   17.9   3.3   27  122-148   148-174 (196)
339 PRK12547 RNA polymerase sigma   60.2      11 0.00027   18.0   3.3   30  118-147   120-149 (164)
340 PRK09647 RNA polymerase sigma   59.7      11 0.00027   17.9   3.2   28  120-147   167-194 (222)
341 PRK09935 transcriptional regul  59.7      11 0.00028   17.9   3.3   33  116-148   152-186 (210)
342 TIGR01529 argR_whole arginine   59.3      13 0.00033   17.4   3.6   32   34-65      5-43  (155)
343 PRK12542 RNA polymerase sigma   59.2      11 0.00029   17.8   3.2   41  118-165   130-170 (185)
344 TIGR02233 Myxo_sigma_rel Myxoc  59.1     6.8 0.00017   19.2   2.1   32  120-151    34-65  (106)
345 PRK12536 RNA polymerase sigma   58.9      12 0.00029   17.7   3.3   28  120-147   136-163 (178)
346 PRK09644 RNA polymerase sigma   58.9      11 0.00027   18.0   3.1   29  118-146   116-144 (165)
347 PRK09047 RNA polymerase factor  58.5      11 0.00028   17.9   3.1   27  120-146   116-142 (161)
348 TIGR02047 CadR-PbrR Cd(II)/Pb(  58.3     5.4 0.00014   19.8   1.5   25   48-72      4-28  (127)
349 PRK12546 RNA polymerase sigma   58.2      12  0.0003   17.7   3.2   42  120-168   123-164 (188)
350 PRK12519 RNA polymerase sigma   57.9      13 0.00034   17.4   3.4   28  120-147   151-178 (194)
351 PRK09978 DNA-binding transcrip  57.9      14 0.00036   17.2   6.9   24   42-65    156-179 (274)
352 PRK11302 DNA-binding transcrip  57.9      14 0.00036   17.2   3.9   58   27-84     16-75  (284)
353 smart00418 HTH_ARSR helix_turn  57.8      13 0.00034   17.3   3.4   23  124-146     8-30  (66)
354 TIGR02329 propionate_PrpR prop  57.8      13 0.00032   17.5   3.3   36  113-148   622-657 (658)
355 cd04779 HTH_MerR-like_sg4 Heli  57.7      14 0.00036   17.2   3.5   27   46-72      2-29  (134)
356 PRK10403 transcriptional regul  57.6      12 0.00032   17.5   3.2   36  122-168   164-199 (215)
357 PHA01082 putative transcriptio  57.6     6.4 0.00016   19.3   1.7   40   42-81     28-68  (133)
358 PRK09958 DNA-binding transcrip  57.4      13 0.00033   17.4   3.3   27  122-148   154-180 (204)
359 PRK11924 RNA polymerase sigma   57.4      15 0.00037   17.1   4.4   30  118-147   133-162 (180)
360 COG3888 Predicted transcriptio  57.2      13 0.00033   17.5   3.2   28   36-63     10-39  (321)
361 pfam06056 Terminase_5 Putative  56.7      11 0.00028   17.9   2.8   29  124-152    11-39  (58)
362 PRK12544 RNA polymerase sigma   56.7      13 0.00034   17.3   3.3   28  120-147   159-186 (207)
363 PRK05602 RNA polymerase sigma   56.7      15 0.00038   17.0   3.9   29  119-147   137-165 (186)
364 PRK09645 RNA polymerase sigma   56.3      15 0.00039   17.0   3.8   47  118-168   124-170 (171)
365 COG1737 RpiR Transcriptional r  56.3      12  0.0003   17.7   2.9   57   29-85     20-78  (281)
366 COG3355 Predicted transcriptio  56.3      15 0.00039   17.0   3.6   23   41-63     39-61  (126)
367 PRK08295 RNA polymerase factor  56.2      15 0.00039   17.0   4.5   26  122-147   166-191 (209)
368 COG2197 CitB Response regulato  55.7      14 0.00036   17.2   3.2   27  122-148   159-185 (211)
369 PRK13502 transcriptional activ  55.6      16  0.0004   16.9   8.3   28  124-151   190-217 (282)
370 PRK12540 RNA polymerase sigma   55.6      14 0.00036   17.2   3.2   42  120-168   121-162 (181)
371 PRK12530 RNA polymerase sigma   55.5      15 0.00037   17.1   3.3   27  120-146   146-172 (191)
372 PRK10840 transcriptional regul  55.3      15 0.00037   17.1   3.3   47  122-168   161-211 (216)
373 PRK09483 response regulator; P  55.0      15 0.00038   17.0   3.3   51  122-172   159-214 (216)
374 PRK10783 mltD membrane-bound l  54.3      16 0.00042   16.8   7.7   54  123-176   348-431 (449)
375 COG1497 Predicted transcriptio  54.3      13 0.00034   17.3   3.0   26   40-65     21-46  (260)
376 pfam08220 HTH_DeoR DeoR-like h  53.9      17 0.00042   16.8   3.4   29  117-145     5-33  (57)
377 PRK12538 RNA polymerase sigma   53.9      17 0.00042   16.8   3.4   29  119-147   180-208 (233)
378 PRK12512 RNA polymerase sigma   53.8      16 0.00042   16.8   3.3   30  118-147   139-168 (184)
379 TIGR02899 spore_safA spore coa  53.5     8.1 0.00021   18.7   1.7   20   74-93      5-24  (44)
380 PRK11923 algU RNA polymerase s  53.4      17 0.00043   16.7   3.4   27  120-146   148-174 (193)
381 PRK12522 RNA polymerase sigma   53.4      16 0.00041   16.8   3.3   28  119-146   128-155 (173)
382 PRK09640 RNA polymerase sigma   53.0      17 0.00042   16.8   3.3   30  117-146   141-170 (188)
383 PRK12514 RNA polymerase sigma   53.0      16 0.00042   16.8   3.2   28  120-147   139-166 (179)
384 pfam11268 DUF3071 Protein of u  53.0      17 0.00044   16.7   3.5   28  120-147    62-89  (169)
385 PRK09638 RNA polymerase sigma   52.8      17 0.00044   16.7   4.1   29  119-147   136-164 (177)
386 pfam07278 DUF1441 Protein of u  52.8      17 0.00044   16.6   3.4   25   45-69      2-26  (152)
387 COG1595 RpoE DNA-directed RNA   52.7      17 0.00044   16.6   3.8   29  120-148   137-165 (182)
388 COG0856 Orotate phosphoribosyl  52.6      14 0.00035   17.3   2.8   55   30-93      2-62  (203)
389 PRK12537 RNA polymerase sigma   52.5      17 0.00045   16.6   4.0   28  120-147   145-172 (184)
390 PRK03902 manganese transport t  52.4      18 0.00045   16.6   9.9  121   22-172     3-127 (142)
391 smart00346 HTH_ICLR helix_turn  52.1      13 0.00032   17.5   2.5   24  124-147    18-41  (91)
392 PRK12535 RNA polymerase sigma   51.9      18 0.00045   16.6   3.3   28  120-147   142-169 (195)
393 PRK09649 RNA polymerase sigma   51.7      18 0.00045   16.6   3.2   28  120-147   140-167 (185)
394 cd00090 HTH_ARSR Arsenical Res  51.4      18 0.00046   16.5   3.9   28  118-146    13-40  (78)
395 TIGR00491 aIF-2 translation in  51.4     4.6 0.00012   20.2   0.2   47   32-84    415-461 (1145)
396 TIGR01817 nifA Nif-specific re  51.3      18 0.00047   16.5   3.6   30  116-145   533-562 (574)
397 PRK10371 DNA-binding transcrip  51.2      18 0.00047   16.5   9.1   42  114-155   193-236 (302)
398 PRK11337 DNA-binding transcrip  51.2      18 0.00047   16.5   4.6   59   27-85     29-89  (293)
399 PRK09641 RNA polymerase sigma   51.0      18 0.00047   16.5   4.1   27  120-146   146-172 (187)
400 KOG3647 consensus               50.8      19 0.00047   16.5   4.8  136   25-173    48-195 (338)
401 PRK10651 transcriptional regul  50.3      19 0.00048   16.4   3.3   25  123-147   167-191 (216)
402 PRK10219 DNA-binding transcrip  50.3      19 0.00048   16.4  11.0   81   32-145     7-90  (107)
403 PRK12545 RNA polymerase sigma   50.1      19 0.00049   16.4   3.2   30  118-147   147-176 (201)
404 pfam02042 RWP-RK RWP-RK domain  50.0      19 0.00049   16.4   4.5   33  118-150     7-39  (52)
405 PRK12515 RNA polymerase sigma   49.9      19 0.00049   16.4   3.7   48  120-171   141-188 (189)
406 PRK12511 RNA polymerase sigma   49.8      10 0.00025   18.1   1.7   26  121-146   122-147 (182)
407 TIGR02043 ZntR Zn(II)-responsi  49.7     7.7  0.0002   18.8   1.1   27   47-73      4-31  (132)
408 COG1654 BirA Biotin operon rep  49.6      19  0.0005   16.3   4.1   19   45-63     20-38  (79)
409 PRK12531 RNA polymerase sigma   49.3      20  0.0005   16.3   4.1   30  118-147   149-178 (194)
410 PRK09834 DNA-binding transcrip  49.1      15 0.00039   17.0   2.6   25   40-64     22-46  (264)
411 PRK09643 RNA polymerase sigma   48.9      20 0.00051   16.3   3.4   30  118-147   139-168 (197)
412 TIGR01369 CPSaseII_lrg carbamo  48.2     7.5 0.00019   18.9   0.9  117   58-174   416-557 (1089)
413 pfam00325 Crp Bacterial regula  48.1      16  0.0004   16.9   2.5   22  126-147     2-23  (32)
414 PRK11608 pspF phage shock prot  47.7      21 0.00053   16.2   4.5   94   55-148   208-321 (325)
415 PRK04182 cytidylate kinase; Pr  47.7      21 0.00053   16.2   4.1  113   19-137     7-124 (178)
416 smart00760 Bac_DnaA_C Bacteria  46.7      22 0.00055   16.1   6.5   53   74-137     4-56  (60)
417 PRK10163 DNA-binding transcrip  46.3      22 0.00056   16.0   3.0   25   41-65     37-61  (271)
418 PRK01905 DNA-binding protein F  46.1      22 0.00056   16.0   3.9   32  116-147    40-71  (77)
419 COG4189 Predicted transcriptio  46.0      22 0.00056   16.0   4.9   25  120-144    31-55  (308)
420 pfam00440 TetR_N Bacterial reg  45.8      22 0.00057   16.0   3.8   33  118-150     8-40  (47)
421 PRK11569 transcriptional repre  45.5      22 0.00057   16.0   2.9   24   41-64     40-63  (274)
422 pfam09572 RE_XamI XamI restric  44.7      23 0.00059   15.9   4.8   74   20-96      6-92  (251)
423 TIGR03454 partition_RepB plasm  44.6      23 0.00059   15.9   3.3   57  119-175   170-227 (325)
424 PRK10141 DNA-binding transcrip  44.1      24  0.0006   15.8   3.7   21  126-146    28-48  (106)
425 PRK09652 RNA polymerase sigma   43.9      24 0.00061   15.8   4.5   27  120-146   147-173 (192)
426 PRK06811 RNA polymerase factor  43.6      24 0.00061   15.8   4.1   27  120-146   138-164 (185)
427 PRK12534 RNA polymerase sigma   43.5      24 0.00062   15.8   4.1   29  118-146   145-173 (187)
428 PRK12518 RNA polymerase sigma   42.7      25 0.00063   15.7   4.1   29  119-147   129-157 (175)
429 pfam01022 HTH_5 Bacterial regu  42.6      25 0.00064   15.7   4.1   26  122-147    11-36  (47)
430 COG2963 Transposase and inacti  42.6      25 0.00064   15.7   3.3   40   25-64      5-45  (116)
431 PRK09642 RNA polymerase sigma   42.5      25 0.00064   15.7   3.2   27  120-146   116-142 (160)
432 pfam02540 NAD_synthase NAD syn  42.4      25 0.00064   15.6   7.6   32  116-147   199-230 (243)
433 TIGR01950 SoxR redox-sensitive  42.1      12 0.00032   17.5   1.2   25   45-69      2-27  (142)
434 PRK09393 ftrA transcriptional   42.0      26 0.00065   15.6  10.9   31  122-152   228-258 (320)
435 TIGR02702 SufR_cyano iron-sulf  41.7      25 0.00063   15.7   2.7   27   37-63      8-34  (215)
436 pfam06413 Neugrin Neugrin. Thi  40.9      27 0.00068   15.5   5.3   45   34-78     17-63  (225)
437 pfam04645 DUF603 Protein of un  40.0      27  0.0007   15.4   3.5   30   43-72     17-51  (181)
438 pfam04458 DUF505 Protein of un  39.9      27  0.0007   15.4   3.5   47   32-83    105-152 (591)
439 COG1321 TroR Mn-dependent tran  39.9      28  0.0007   15.4   4.4  115   23-167     6-122 (154)
440 smart00497 IENR1 Intron encode  39.6      20  0.0005   16.3   1.9   24  128-151    19-42  (53)
441 TIGR02812 fadR_gamma fatty aci  39.6      12 0.00031   17.6   0.9  116   48-191    34-163 (275)
442 PRK09648 RNA polymerase sigma   39.3      28 0.00072   15.4   3.3   27  120-146   147-173 (187)
443 PRK12513 RNA polymerase sigma   39.3      28 0.00072   15.4   4.6   28  120-147   149-176 (194)
444 PRK10365 transcriptional regul  38.8      29 0.00073   15.3   4.1   32  116-147   408-439 (441)
445 PRK09409 insertion element IS2  38.5      29 0.00074   15.3   3.5   26   41-66      8-33  (301)
446 TIGR02983 SigE-fam_strep RNA p  38.3      15 0.00039   17.0   1.2   59   88-146    81-149 (165)
447 TIGR02960 SigX5 RNA polymerase  38.3      29 0.00074   15.3   2.7   24  121-144   154-177 (329)
448 PRK10906 DNA-binding transcrip  37.8      30 0.00076   15.2   3.0   28   36-63     11-38  (252)
449 COG1510 Predicted transcriptio  37.6      22 0.00056   16.0   1.9   33   32-64     28-61  (177)
450 pfam04297 UPF0122 Putative hel  37.4      30 0.00077   15.2   2.6   22   42-63     31-52  (101)
451 PRK13509 transcriptional repre  37.4      30 0.00077   15.2   3.1   29   36-64     11-39  (251)
452 PRK09802 DNA-binding transcrip  37.0      31 0.00078   15.1   3.0   28   36-63     23-50  (269)
453 PRK12533 RNA polymerase sigma   36.7      31 0.00079   15.1   3.3   28  120-147   147-174 (217)
454 PRK11388 DNA-binding transcrip  36.3      31  0.0008   15.1   4.4   32  116-147   594-625 (639)
455 COG1414 IclR Transcriptional r  35.8      32 0.00081   15.0   3.6   22   43-64     18-39  (246)
456 cd07377 WHTH_GntR Winged helix  35.7      32 0.00082   15.0   3.3   17   46-62     27-43  (66)
457 PRK09639 RNA polymerase sigma   35.7      32 0.00082   15.0   4.9   24  124-147   125-148 (166)
458 PRK13501 transcriptional activ  35.5      32 0.00082   15.0   7.0   31  125-155   191-221 (290)
459 pfam07453 NUMOD1 NUMOD1 domain  35.5      24 0.00061   15.8   1.8   19  128-146    18-36  (37)
460 pfam05732 RepL Firmicute plasm  34.5      31 0.00079   15.1   2.3   46  127-178    76-126 (165)
461 PRK00430 fis DNA-binding prote  34.4      34 0.00086   14.9   3.9   61   75-146    31-91  (98)
462 COG0656 ARA1 Aldo/keto reducta  34.3      34 0.00086   14.9   3.2   59  129-187   175-238 (280)
463 PRK10923 glnG nitrogen regulat  34.1      34 0.00087   14.8   4.2   33  116-148   432-464 (469)
464 pfam02084 Bindin Bindin.        34.0      34 0.00086   14.9   2.4   52   62-127    90-141 (239)
465 PRK00118 putative DNA-binding   33.9      34 0.00087   14.8   2.8   23   41-63     30-52  (105)
466 PRK09480 slmA nucleoid occlusi  33.9      34 0.00087   14.8   2.6   30   41-70     27-56  (194)
467 PRK10681 DNA-binding transcrip  33.5      35 0.00089   14.8   4.3   30   34-63     11-40  (252)
468 KOG0774 consensus               33.3      17 0.00043   16.7   0.8   23  130-152   222-244 (334)
469 PRK09940 transcriptional regul  33.1      35  0.0009   14.7   8.7   37  114-150   135-174 (253)
470 PRK09415 RNA polymerase factor  32.9      36 0.00091   14.7   5.7   27  120-146   137-163 (177)
471 PRK05234 mgsA methylglyoxal sy  32.9      36 0.00091   14.7   2.8   45   54-98     62-128 (146)
472 PRK04280 arginine repressor; P  32.9      33 0.00085   14.9   2.2   29   36-64     10-44  (149)
473 COG1339 Transcriptional regula  32.7      36 0.00091   14.7   3.4   26   39-65     15-40  (214)
474 PRK13500 transcriptional activ  31.9      37 0.00094   14.6   7.0   42  114-155   208-251 (312)
475 PRK10402 DNA-binding transcrip  31.8      37 0.00095   14.6   2.8   39  127-165   157-208 (213)
476 TIGR00651 pta phosphate acetyl  31.5      38 0.00096   14.6   2.5   34   21-54     55-88  (322)
477 PRK09390 fixJ response regulat  31.5      38 0.00096   14.6   3.2   33  116-148   144-178 (202)
478 PRK12681 cysB transcriptional   31.4      38 0.00096   14.6   4.1   29   35-63      5-35  (324)
479 COG1725 Predicted transcriptio  31.0      38 0.00098   14.5   2.6   36   28-63     12-54  (125)
480 COG1349 GlpR Transcriptional r  30.8      39 0.00098   14.5   4.3   31   33-63      8-38  (253)
481 COG1124 DppF ABC-type dipeptid  30.7      39 0.00099   14.5   3.3   49   48-97    122-170 (252)
482 pfam01325 Fe_dep_repress Iron   30.1      40   0.001   14.4   3.7   22   43-64     19-40  (58)
483 PRK10434 srlR DNA-bindng trans  30.1      40   0.001   14.4   3.3   28   36-63     11-38  (256)
484 PRK05294 carB carbamoyl phosph  29.7      40   0.001   14.4   4.1  107   64-174   419-540 (1063)
485 PRK13980 NAD synthetase; Provi  29.5      40   0.001   14.4   7.6   71   75-146   167-238 (264)
486 pfam08822 DUF1804 Protein of u  29.4      41   0.001   14.4   4.7  118   29-160     4-127 (165)
487 COG3829 RocR Transcriptional r  29.4      41   0.001   14.4   4.1   34  116-149   523-556 (560)
488 cd00086 homeodomain Homeodomai  29.4      41   0.001   14.4   2.5   17  131-147    32-48  (59)
489 PRK11361 acetoacetate metaboli  29.4      41   0.001   14.4   4.1   31  117-147   421-451 (457)
490 cd04778 HTH_MerR-like_sg2 Heli  29.4      41   0.001   14.4   2.8   28   45-72      2-30  (219)
491 COG2378 Predicted transcriptio  29.3      41   0.001   14.3   3.3   34   31-64      9-42  (311)
492 PHA02519 plasmid partition pro  28.9      42  0.0011   14.3   5.4   64   23-86      8-97  (387)
493 COG1582 FlgEa Uncharacterized   28.8      28 0.00072   15.3   1.3   46    1-46     12-61  (67)
494 pfam05043 Mga Mga helix-turn-h  28.6      42  0.0011   14.3   3.7   46  116-169    20-65  (87)
495 TIGR01132 pgm phosphoglucomuta  28.5      32 0.00082   15.0   1.5   27   10-36    224-255 (553)
496 pfam00165 HTH_AraC Bacterial r  28.5      42  0.0011   14.3   2.8   36   42-77      6-42  (43)
497 cd01422 MGS Methylglyoxal synt  28.3      38 0.00098   14.5   1.9   18   70-87     87-104 (115)
498 PRK04435 hypothetical protein;  28.2      33 0.00085   14.9   1.6   28  119-146    26-53  (146)
499 pfam04936 DUF658 Protein of un  28.2      43  0.0011   14.2   2.7   27  128-154    16-42  (134)
500 pfam01316 Arg_repressor Argini  28.1      36 0.00093   14.7   1.7   18   46-63     21-43  (70)

No 1  
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.72  E-value=6.5e-17  Score=124.32  Aligned_cols=69  Identities=17%  Similarity=0.256  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCC
Q ss_conf             999999999999859988999998489999999887799888999999999982899999614532210
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDR   98 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~   98 (205)
                      +-||+||+.+|+.+||||.+||+.+|||+++||+||+|...|+.+.|.+||++|+||++|||.|+.-..
T Consensus         4 ~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~G~~d~~   72 (135)
T PRK09706          4 ETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLFGDEDKQ   72 (135)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCC
T ss_conf             309999999999859999999999698899999998289888999999999998909999848887789


No 2  
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.71  E-value=3e-17  Score=126.34  Aligned_cols=72  Identities=28%  Similarity=0.445  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCH
Q ss_conf             467779999999997298389999997799999999741488999899999999828999995247210254
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVIVP  181 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~  181 (205)
                      +...+|.||+.+|+.+||||.+||+.+|+++++|++||+|.+.|+.+.+.+||++|||+++|||+|++...|
T Consensus         2 ~~~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~G~~d~~~   73 (135)
T PRK09706          2 KNETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLFGDEDKQP   73 (135)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCC
T ss_conf             713099999999998599999999996988999999982898889999999999989099998488877899


No 3  
>PHA01976 helix-turn-helix protein
Probab=99.70  E-value=4.8e-17  Score=125.10  Aligned_cols=63  Identities=17%  Similarity=0.276  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             999999999998599889999984899999998877998889999999999828999996145
Q gi|254781218|r   31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        31 ~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      .+|.||+.+|+.+||||+|||+++||++++|++||+|.+.|+++.|+.||++|+||+|||++.
T Consensus         2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~LlGr   64 (67)
T PHA01976          2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR   64 (67)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
T ss_conf             789999999998699999999994998999999987898999899999999979789999267


No 4  
>PHA01976 helix-turn-helix protein
Probab=99.61  E-value=2.5e-15  Score=114.53  Aligned_cols=63  Identities=19%  Similarity=0.398  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             779999999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG  175 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G  175 (205)
                      .+|.||+++|+.+||||.|||+.+||++++|++||+|++.|+++.|.+||.+||||+|||+..
T Consensus         2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~LlGr   64 (67)
T PHA01976          2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR   64 (67)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
T ss_conf             789999999998699999999994998999999987898999899999999979789999267


No 5  
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.57  E-value=1e-14  Score=110.69  Aligned_cols=70  Identities=20%  Similarity=0.196  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf             9999999999999998599889999984899999998877998889999999999828999996145322
Q gi|254781218|r   27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVI   96 (205)
Q Consensus        27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~   96 (205)
                      +..-.||.|||.+|+++|||+++||++.|+|.++||++|||...||+.+|.+||++|+|++.+||..+..
T Consensus         3 d~~~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~~~~~   72 (185)
T PRK09943          3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK   72 (185)
T ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf             4032488999999998599899999887969999999987999999999999999849999998277455


No 6  
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.51  E-value=6.9e-14  Score=105.61  Aligned_cols=67  Identities=31%  Similarity=0.430  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf             7779999999997298389999997799999999741488999899999999828999995247210
Q gi|254781218|r  112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEV  178 (205)
Q Consensus       112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~  178 (205)
                      .+||.|||.+|+.+|||+.+||+..|+|++++|++|+|+..|++.+|.+||++|||++.+||.+.+.
T Consensus         6 ~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~~~~~   72 (185)
T PRK09943          6 LAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK   72 (185)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf             2488999999998599899999887969999999987999999999999999849999998277455


No 7  
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.37  E-value=5.2e-12  Score=94.03  Aligned_cols=151  Identities=19%  Similarity=0.214  Sum_probs=110.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC-
Q ss_conf             6689999999999999999859988999998489999999887799888999999999982899999614532210000-
Q gi|254781218|r   23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYE-  101 (205)
Q Consensus        23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~-  101 (205)
                      .+.-.|...+|.|+|.+|+.+|||+++||+..|||..++.++|.|..+|||-.|.++|.+|+|++.+|+.......+.- 
T Consensus        20 ~~~~~~l~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~~~~~~~~~~~   99 (304)
T PRK08154         20 AEEDPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLGDEDTSSPDWP   99 (304)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHHH
T ss_conf             43366999999999999997599899999872998999998825888851999999999959989998178888881289


Q ss_pred             CCCCH-HHHHHHHHHHHHHHHHHHCC----C-------CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCC
Q ss_conf             23213-45546777999999999729----8-------38999999779999999974148-899989999999982899
Q gi|254781218|r  102 DVTNK-KRLDPYAIGARLKSIRKDKG----M-------SQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       102 ~~~~~-~~~d~~~iG~rLk~lR~~~g----l-------sq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs  168 (205)
                      .+.+. ...+    ...++++|...+    .       ..--|--+.|.-++|+.+..... ..|-++.=..|.+..|++
T Consensus       100 ~~~~~l~~~~----~~~~~~~~~~l~~~~~~~~~~~~~~rIaLIGlmGaGKSTvGr~LA~~Lg~pFvDlD~~IEk~aG~s  175 (304)
T PRK08154        100 LIRELLEQAT----PAQLARARDALSGMLGTGGGAARRPRIALIGLRGAGKSTLGRMLAARLGVPFVELNREIEREAGLS  175 (304)
T ss_pred             HHHHHHHCCC----HHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCEEECHHHHHHHHCCC
T ss_conf             9999985189----999999999987630237666777847988999998889999999995989778779999992999


Q ss_pred             HHHHHC--CCC
Q ss_conf             999524--721
Q gi|254781218|r  169 LDWIYF--GDE  177 (205)
Q Consensus       169 ~d~L~~--G~e  177 (205)
                      +..+|.  |++
T Consensus       176 I~eIFa~~GE~  186 (304)
T PRK08154        176 VSEIFALYGQE  186 (304)
T ss_pred             HHHHHHHHCHH
T ss_conf             99999986889


No 8  
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=99.37  E-value=1.7e-12  Score=97.08  Aligned_cols=58  Identities=21%  Similarity=0.189  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             9999999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      ++||..||..|+.+||||.+||+.+|+|+++|+++|+|..+|+++.+.+||++|++++
T Consensus         1 ~~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~~~~l~~l~~i~~aLGi~l   58 (58)
T TIGR03070         1 KQIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKPTVRLDKVLRVLEALGLEL   58 (58)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             9588999999999499899999881998999999978999888999999999808989


No 9  
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.36  E-value=1.7e-12  Score=97.06  Aligned_cols=55  Identities=24%  Similarity=0.290  Sum_probs=46.0

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             9999998599889999984899999998877998889999999999828999996
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI   90 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L   90 (205)
                      ||.+|+.+|+||++||+.+|+++++|++||+|...|+++.+.+||++|+|+++||
T Consensus         1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l   55 (55)
T pfam01381         1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL   55 (55)
T ss_pred             CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             9898978299899999998969999999987999999999999999978979879


No 10 
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.36  E-value=2e-12  Score=96.52  Aligned_cols=56  Identities=27%  Similarity=0.332  Sum_probs=44.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             99999998599889999984899999998877998889999999999828999996
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI   90 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L   90 (205)
                      |||.+|+.+||||++||+.+|+++++|++||+|...|+++.+.+||++|+|+++||
T Consensus         1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~~~~~~l   56 (56)
T smart00530        1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL   56 (56)
T ss_pred             CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             98999977299999999998959999999997998999999999999988889879


No 11 
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.29  E-value=8.8e-12  Score=92.61  Aligned_cols=56  Identities=36%  Similarity=0.602  Sum_probs=54.7

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             99999997298389999997799999999741488999899999999828999995
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      ||+++|+.+||||.+||+.+|++++++++||+|.+.|+.+.+.+||++||++++||
T Consensus         1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~~~~~~l   56 (56)
T smart00530        1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL   56 (56)
T ss_pred             CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             98999977299999999998959999999997998999999999999988889879


No 12 
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.28  E-value=1.3e-11  Score=91.60  Aligned_cols=61  Identities=21%  Similarity=0.291  Sum_probs=51.7

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             9999999985998899999848999999988779988899999999998289999961453
Q gi|254781218|r   34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGE   94 (205)
Q Consensus        34 ~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge   94 (205)
                      .|+|.+|...|+||++||+.+|||+++|..||+|+..||+....+||..|+++++.+|.-+
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~~~   64 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE   64 (68)
T ss_pred             HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             5999999982858999999919579999999917988309999999999399799998652


No 13 
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.27  E-value=1.1e-11  Score=92.10  Aligned_cols=55  Identities=33%  Similarity=0.550  Sum_probs=53.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             9999997298389999997799999999741488999899999999828999995
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      ||++|+.+||||.+||+.+|++++++++||+|.+.|+.+.+.+||++||++++||
T Consensus         1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l   55 (55)
T pfam01381         1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL   55 (55)
T ss_pred             CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             9898978299899999998969999999987999999999999999978979879


No 14 
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.27  E-value=2e-11  Score=90.42  Aligned_cols=66  Identities=14%  Similarity=0.154  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             999999999985998899999848999999988779988899999999998289999961453221
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID   97 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~   97 (205)
                      +=.+|+.+|.++|+||.+||++.|+|.+++|.+|+|+.+||+++|..||++++|++.+|+...+.|
T Consensus         6 fftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle~~dld   71 (119)
T PRK13890          6 FFTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLESTDLD   71 (119)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCC
T ss_conf             588799999985997999998829889999999779989879999999999879779987623589


No 15 
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=99.22  E-value=3.8e-11  Score=88.68  Aligned_cols=58  Identities=29%  Similarity=0.377  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             9999999998599889999984899999998877998889999999999828999996
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI   90 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L   90 (205)
                      |.+|+.+|+.+|+||.+||+.+|+++++|++||+|...|+++.+.+||+.|+|+++|+
T Consensus         1 g~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~~p~~~~l~~la~~~~~~~~~l   58 (58)
T cd00093           1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL   58 (58)
T ss_pred             CHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             9899999997599999995714999999999987998999999999999938989879


No 16 
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.15  E-value=1.2e-10  Score=85.58  Aligned_cols=61  Identities=31%  Similarity=0.498  Sum_probs=58.8

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             9999999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD  176 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~  176 (205)
                      .|++.+|...||||.+||+.+|++++||..||+|+..|++....+||+.|+++++.+|+-+
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~~~   64 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE   64 (68)
T ss_pred             HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             5999999982858999999919579999999917988309999999999399799998652


No 17 
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=99.13  E-value=1.5e-10  Score=84.93  Aligned_cols=57  Identities=21%  Similarity=0.378  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      .+|..||+.|+.+||||.+||+..|+++++++++|+|+..|+++.+.+|+.+||+++
T Consensus         2 ~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~~~~l~~l~~i~~aLGi~l   58 (58)
T TIGR03070         2 QIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKPTVRLDKVLRVLEALGLEL   58 (58)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             588999999999499899999881998999999978999888999999999808989


No 18 
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.13  E-value=2.6e-10  Score=83.54  Aligned_cols=62  Identities=19%  Similarity=0.267  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             79999999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG  175 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G  175 (205)
                      +...++.+|+++|||+.|||+..|+|.+.+|++|+|+..|++.++.+||++|+|++.+|+--
T Consensus         6 fftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle~   67 (119)
T PRK13890          6 FFTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLES   67 (119)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf             58879999998599799999882988999999977998987999999999987977998762


No 19 
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=99.12  E-value=1.7e-10  Score=84.72  Aligned_cols=58  Identities=36%  Similarity=0.606  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             9999999997298389999997799999999741488999899999999828999995
Q gi|254781218|r  115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      |.+|+.+|+.+|+||.+||+.+|++++++++||+|...|+.+.+.+||++||++++||
T Consensus         1 g~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~~p~~~~l~~la~~~~~~~~~l   58 (58)
T cd00093           1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL   58 (58)
T ss_pred             CHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf             9899999997599999995714999999999987998999999999999938989879


No 20 
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.08  E-value=7.6e-10  Score=80.65  Aligned_cols=72  Identities=21%  Similarity=0.317  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHH
Q ss_conf             777999999999729838999999779999999974148899989999999982899999524721025456
Q gi|254781218|r  112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVIVPKS  183 (205)
Q Consensus       112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~~~  183 (205)
                      ..+|.|+|.+|..+|||++++|+..|+|..++.+.|.|...|++..|.+||.+|+|++.+|+.......|+.
T Consensus        27 ~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~~~~~~~~~~   98 (304)
T PRK08154         27 AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLGDEDTSSPDW   98 (304)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHH
T ss_conf             999999999999759989999987299899999882588885199999999995998999817888888128


No 21 
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=99.06  E-value=5.1e-10  Score=81.70  Aligned_cols=64  Identities=20%  Similarity=0.192  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             8999999999999999985998899999848999999988779988899999999998289999
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD   88 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d   88 (205)
                      +....+.+|..||..|+.+||||.++|+.+|+.+++||++|+|-..+++++|.+|+.+|++.+.
T Consensus         6 ki~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~   69 (88)
T PRK09726          6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT   69 (88)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf             0289999999999999985987999999819749999999759987869999999996787688


No 22 
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.98  E-value=2.2e-09  Score=77.84  Aligned_cols=64  Identities=27%  Similarity=0.385  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf             7999999999729838999999779999999974148899989999999982899999524721
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDE  177 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e  177 (205)
                      +|.+|+..|+.+||||++||+.+++..+.+.+||+|+..|+.+.+.+|.++||+.+.|..-+++
T Consensus        80 Y~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~  143 (165)
T COG1813          80 YGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEE  143 (165)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCC
T ss_conf             9999999999828889999999654699999998413675588999999985855220035554


No 23 
>PRK06424 transcription factor; Provisional
Probab=98.98  E-value=2.8e-09  Score=77.13  Aligned_cols=57  Identities=25%  Similarity=0.390  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      .+|.+||.+|+.+||||.|||..++...+.|.++|+|...|+.+.+.+|-++|||++
T Consensus        84 Dy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L  140 (144)
T PRK06424         84 DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL  140 (144)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf             799999999998499999999996544999999983898999899999999849676


No 24 
>PRK08359 transcription factor; Validated
Probab=98.92  E-value=4.9e-09  Score=75.63  Aligned_cols=56  Identities=25%  Similarity=0.401  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             79999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      +|.+|+.+|+.+||||+|||..++...+.|.++|+|...|+.+.+.+|-++|||++
T Consensus        84 Y~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL  139 (175)
T PRK08359         84 YAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKL  139 (175)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEE
T ss_conf             99999999998599999999997222999999983887999899999999849068


No 25 
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.90  E-value=7.9e-09  Score=74.36  Aligned_cols=101  Identities=21%  Similarity=0.289  Sum_probs=74.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC------CCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf             999999998599889999984899999998877998889999999999828------99999614532210000232134
Q gi|254781218|r   34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE------ISFDWIYDGEVIDRRYEDVTNKK  107 (205)
Q Consensus        34 ~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~------vs~d~Ll~ge~~~~~~~~~~~~~  107 (205)
                      +-||..|+..|+||++||..+|+||+.|.++|.|...|.+.++.+|-++|.      +..+-++.......+.+|-    
T Consensus         8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~spvv~v~pdDs----   83 (187)
T COG3620           8 EDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHSPVVSVSPDDS----   83 (187)
T ss_pred             HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEHHHHCCCCEEEECCHHH----
T ss_conf             9999999875977899998708648889998638879308999999999998546667576653587058772466----


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHH---HC-CCHHHHHH
Q ss_conf             5546777999999999729838999999---77-99999999
Q gi|254781218|r  108 RLDPYAIGARLKSIRKDKGMSQIEFGKL---LG-MPNSTLSN  145 (205)
Q Consensus       108 ~~d~~~iG~rLk~lR~~~glsq~elA~~---lg-is~~tis~  145 (205)
                            + ...-.++..+|+||--+-+.   +| |+...+.+
T Consensus        84 ------i-~~vv~lM~~~g~SQlPVi~~~k~VGsItE~~iv~  118 (187)
T COG3620          84 ------I-SDVVNLMRDKGISQLPVIEEDKVVGSITENDIVR  118 (187)
T ss_pred             ------H-HHHHHHHHHCCCCCCCEEECCEEEEEECHHHHHH
T ss_conf             ------9-9999999975975275410886453314989999


No 26 
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.85  E-value=7e-09  Score=74.67  Aligned_cols=74  Identities=23%  Similarity=0.281  Sum_probs=68.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             68999999999999999985998899999848999999988779988899999999998289999961453221
Q gi|254781218|r   24 EIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID   97 (205)
Q Consensus        24 ~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~   97 (205)
                      +..+.-.+.|++|+..|+++||+|++||++++++.+.|.+||+|...|+++.+-+|.+.|+|.+.|...++...
T Consensus        72 ~~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~  145 (165)
T COG1813          72 ELPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEG  145 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCCCC
T ss_conf             17888877999999999982888999999965469999999841367558899999998585522003555446


No 27 
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=98.83  E-value=1.1e-08  Score=73.55  Aligned_cols=65  Identities=25%  Similarity=0.380  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf             45546777999999999729838999999779999999974148899989999999982899999
Q gi|254781218|r  107 KRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW  171 (205)
Q Consensus       107 ~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~  171 (205)
                      ++.+|..+|..||.+|+.+|+||.++|+.+|+.+++||++|++-..+++++|++|..+||+.+.-
T Consensus         6 ki~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~i   70 (88)
T PRK09726          6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL   70 (88)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf             02899999999999999859879999998197499999997599878699999999967876887


No 28 
>PRK06424 transcription factor; Provisional
Probab=98.79  E-value=1.8e-08  Score=72.09  Aligned_cols=67  Identities=18%  Similarity=0.169  Sum_probs=61.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             1566899999999999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        21 ~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      +.-+..+.-.+.|.+||..|+.+||||++||.+++...+.|.++|+|...|++++..+|-++|+|++
T Consensus        74 ~~~~~~elveDy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L  140 (144)
T PRK06424         74 ASDEDLDIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL  140 (144)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf             3034566887799999999998499999999996544999999983898999899999999849676


No 29 
>PRK08359 transcription factor; Validated
Probab=98.76  E-value=2.3e-08  Score=71.46  Aligned_cols=66  Identities=12%  Similarity=0.121  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             999999999999999859988999998489999999887799888999999999982899999614
Q gi|254781218|r   27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD   92 (205)
Q Consensus        27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~   92 (205)
                      +.-.+.|++||..|+.+||||++||.++++..+.|.++|+|...|++++.-+|-++|+|++-.-..
T Consensus        79 ElveDY~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL~E~~e  144 (175)
T PRK08359         79 DIVEDYAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKLIERVE  144 (175)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEEEEECC
T ss_conf             777569999999999859999999999722299999998388799989999999984906885146


No 30 
>PRK04140 hypothetical protein; Provisional
Probab=98.71  E-value=4.9e-08  Score=69.45  Aligned_cols=136  Identities=16%  Similarity=0.193  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH---HHCCCCCCCCCCCCCCHHHH
Q ss_conf             999999999859988999998489999999887799888999999999982899999---61453221000023213455
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW---IYDGEVIDRRYEDVTNKKRL  109 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~---Ll~ge~~~~~~~~~~~~~~~  109 (205)
                      |+.+|.+|+.+|||..+||..+|||+.+|++||+|...+|++++++|.+.|+.++-.   +|.+..-...........  
T Consensus       127 g~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i~~~Idil~~~~~~~~~~~~~~~~--  204 (319)
T PRK04140        127 GDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPLTKPIDILDSAERVEDDEKTLEEP--  204 (319)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC--
T ss_conf             799999999819888899998498699999997068866499999999983873235520223201254334576787--


Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-------C-------CCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             46777999999999729838999999779999999974148-------8-------9998999999998289999952
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-------T-------IPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~-------~-------~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      .....-.++-......|+.-...   -.-|-..++.-+...       .       .-....+..|+++++...=++.
T Consensus       205 ~~~~~e~~i~~~L~~iG~~v~~~---~kAPFdavs~~e~~~~~lLTgi~~~~~~~~~rrA~~~~~is~v~~s~sv~I~  279 (319)
T PRK04140        205 EDDPFEKEVIEILSRLGFDVLPT---KKAPFDAVAEDEKDENSLLTGISEFRTEETKRRARIVSSISEVTNSESVFIL  279 (319)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEE---CCCCHHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             65415679999999649646773---2597777510235564467545333328899999999999998668539998


No 31 
>PRK04140 hypothetical protein; Provisional
Probab=98.68  E-value=7e-08  Score=68.52  Aligned_cols=56  Identities=30%  Similarity=0.464  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             79999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      =|.+||..|+++|||..+||+.+|+|+.|+++||+|...++++.+.+|.++||..+
T Consensus       126 dg~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i  181 (319)
T PRK04140        126 DGDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPL  181 (319)
T ss_pred             CHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC
T ss_conf             47999999998198888999984986999999970688664999999999838732


No 32 
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.65  E-value=9.6e-08  Score=67.65  Aligned_cols=67  Identities=16%  Similarity=0.280  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHH-----CCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             999999999998599889999984-----8999999988779988899999999998289999961453221
Q gi|254781218|r   31 DVGTRIKDIRKANNKTQKEMAIGA-----NQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID   97 (205)
Q Consensus        31 ~iG~rik~lR~~~gltQ~elA~~~-----gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~   97 (205)
                      -.++|++.+++.+|++|.+|+..+     -+.+++||+|++|+..|.-+.+--||..++|+.+||++|+...
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (518)
T PRK13355          5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLGGESES   76 (518)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf             089999999987699689999999981755047888777338864421179999999688978860799765


No 33 
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.55  E-value=4e-07  Score=63.84  Aligned_cols=67  Identities=19%  Similarity=0.311  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHH---C--CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             779999999997298389999997---7--999999997414889998999999998289999952472102
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLL---G--MPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVI  179 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~l---g--is~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~  179 (205)
                      ..++||+++|+.+||+|.+|+...   |  +.++.+|+|++|++.|.-+.+..+|.+|+|+.+||+.|+...
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (518)
T PRK13355          5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLGGESES   76 (518)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf             089999999987699689999999981755047888777338864421179999999688978860799765


No 34 
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430    Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=98.45  E-value=4.7e-07  Score=63.38  Aligned_cols=55  Identities=15%  Similarity=0.135  Sum_probs=32.3

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             9999859988999998489999999887799888999999999982899999614
Q gi|254781218|r   38 DIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD   92 (205)
Q Consensus        38 ~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~   92 (205)
                      +.-+-.|+|+.+||+++|||+++||++=||++.+|.++.++||++|+.|.++-|+
T Consensus        14 EfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WLn   68 (81)
T TIGR02607        14 EFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWLN   68 (81)
T ss_pred             HHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf             7521047068999987099978888887448998888999999973898768998


No 35 
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. 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.
Probab=98.42  E-value=1e-06  Score=61.25  Aligned_cols=62  Identities=24%  Similarity=0.366  Sum_probs=51.3

Q ss_pred             HHHHHHHHCCCC-HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             999999972983-899999977999999997414889998999999998289999952472102
Q gi|254781218|r  117 RLKSIRKDKGMS-QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVI  179 (205)
Q Consensus       117 rLk~lR~~~gls-q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~  179 (205)
                      .|..+.+..|.+ +.|||+.+||++++++.|-...+. +.+.+.+++..+|+++|||++|+..+
T Consensus         2 vi~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~-P~e~iv~~~~~tGvsl~WL~~G~G~~   64 (65)
T pfam07022         2 VIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSF-PAEWVIRCALETGVSLDWLATGDGEL   64 (65)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-CHHHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf             8999999968886999999969888889999986999-89999999999882999997089999


No 36 
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.39  E-value=7.9e-07  Score=62.01  Aligned_cols=48  Identities=33%  Similarity=0.557  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             999999999729838999999779999999974148899989999999
Q gi|254781218|r  115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIK  162 (205)
Q Consensus       115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa  162 (205)
                      +..|+.+|+..||||.+||..+|++.+|+++||+|+..|+-..+.-+.
T Consensus        46 ~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~AlkLL~   93 (104)
T COG2944          46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALKLLR   93 (104)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHH
T ss_conf             899999999828889999999888799999998178589979999999


No 37 
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.39  E-value=9.9e-07  Score=61.39  Aligned_cols=55  Identities=18%  Similarity=0.310  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             9999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      |+++|..|+++|+|..+||.-+|+|+.+|++||+|...||++...+|-+.|+..+
T Consensus       127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~i  181 (313)
T COG1395         127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDI  181 (313)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHHHCCHH
T ss_conf             2999999998086787889883846888987624777732999999999856222


No 38 
>KOG3398 consensus
Probab=98.39  E-value=6.1e-07  Score=62.70  Aligned_cols=108  Identities=22%  Similarity=0.291  Sum_probs=78.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             8899999848999999988779988--89999999999828999996145322100002321345546777999999999
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCS--TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~--psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      .+-.-|...|+...+.-+|-.|...  |+-..+.+            +++|.-+....       .-+..+|.-|.+.|.
T Consensus        23 ~~vnaa~r~g~~v~t~~k~~~g~nkq~~~~~~t~k------------lD~etE~~~~~-------~v~~~Vg~aIq~aR~   83 (135)
T KOG3398          23 KAVNAARRAGVDVETVKKFPAGLNKQHPSTQSTAK------------LDRETEELGHD-------RVPLEVGKAIQQARA   83 (135)
T ss_pred             HHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCHHH------------CCCCCCCCCCC-------CCCHHHHHHHHHHHH
T ss_conf             99999997264024354220345566865421120------------24665323523-------014789999999888


Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             7298389999997799999999741488999899999999828999995
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      .+||||++||..++-.++.+..||+|+..|.-..|.++.++|||.++|=
T Consensus        84 ~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk  132 (135)
T KOG3398          84 QKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGK  132 (135)
T ss_pred             HCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECCCC
T ss_conf             6375488999996028613655750356741999999999853112465


No 39 
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.36  E-value=1.2e-06  Score=60.83  Aligned_cols=63  Identities=22%  Similarity=0.438  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC----CHHHHHCCC
Q ss_conf             799999999972983899999977999999997414889998999999998289----999952472
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK----HLDWIYFGD  176 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv----s~d~L~~G~  176 (205)
                      -|.+||+.|.++|+|..++|..+|+|+.++++||+|.+.|+++.+.++-.+||.    ++|||-.-+
T Consensus       126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv~~Idi~~~~~  192 (313)
T COG1395         126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIVKPIDILKIPE  192 (313)
T ss_pred             CHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHHHCCHHHCCEECCCCCC
T ss_conf             4299999999808678788988384688898762477773299999999985622203200113667


No 40 
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=98.35  E-value=9e-07  Score=61.66  Aligned_cols=74  Identities=15%  Similarity=0.169  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf             99999999999999998599889999984899999998877998889999999999828999996145322100
Q gi|254781218|r   26 RQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR   99 (205)
Q Consensus        26 ~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~   99 (205)
                      .+..++.|.=||.-|+.+||||++||++++.-.|.|.++|+-...|..+.+-.|=+.|+|++-+-+..+...+.
T Consensus        78 ~elvEdyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~~~eks  151 (169)
T TIGR00270        78 EELVEDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEEKLEKS  151 (169)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECC
T ss_conf             66664322542200014687878999987410678888754037988899999888835010023571000015


No 41 
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.34  E-value=1.4e-06  Score=60.54  Aligned_cols=60  Identities=18%  Similarity=0.372  Sum_probs=52.8

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC------CCHHHHHCC
Q ss_conf             999999997298389999997799999999741488999899999999828------999995247
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK------KHLDWIYFG  175 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg------vs~d~L~~G  175 (205)
                      +-||..|+..|+||++||+..|+|+..+.++|.|+..|.++++.+|-++|.      ++-+-++.-
T Consensus         8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s   73 (187)
T COG3620           8 EDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS   73 (187)
T ss_pred             HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEHHHHCCC
T ss_conf             999999987597789999870864888999863887930899999999999854666757665358


No 42 
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430    Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=98.32  E-value=1.6e-06  Score=60.18  Aligned_cols=62  Identities=23%  Similarity=0.217  Sum_probs=56.7

Q ss_pred             HHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             77799999-999972983899999977999999997414889998999999998289999952
Q gi|254781218|r  112 YAIGARLK-SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       112 ~~iG~rLk-~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      --.|+.|+ ++.+..|||+.+||+.+|||+++++++.+|++-.+.+.+.+||++||.|++|-+
T Consensus         5 ~HPGE~L~eEfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WL   67 (81)
T TIGR02607         5 AHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWL   67 (81)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf             788413287752104706899998709997888888744899888899999997389876899


No 43 
>KOG3398 consensus
Probab=98.29  E-value=1.2e-06  Score=60.91  Aligned_cols=77  Identities=16%  Similarity=0.184  Sum_probs=65.1

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf             6543331000156689999999999999999859988999998489999999887799888999999999982899999
Q gi|254781218|r   11 LKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW   89 (205)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~   89 (205)
                      .+.+-+.|-+..++  -...++|.-|...|.++||||++||.+++-.++.|..||+|+.-|.-.+|-++-.+|+|-++|
T Consensus        55 t~klD~etE~~~~~--~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrg  131 (135)
T KOG3398          55 TAKLDRETEELGHD--RVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRG  131 (135)
T ss_pred             HHHCCCCCCCCCCC--CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECCC
T ss_conf             12024665323523--014789999999888637548899999602861365575035674199999999985311246


No 44 
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.29  E-value=1.4e-06  Score=60.40  Aligned_cols=43  Identities=28%  Similarity=0.122  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf             9999999998599889999984899999998877998889999
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY   75 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~   75 (205)
                      |..|+.+|+..|+||.+||..+|+|.+++++||.|...|+---
T Consensus        46 ~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~A   88 (104)
T COG2944          46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAA   88 (104)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHH
T ss_conf             8999999998288899999998887999999981785899799


No 45 
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.27  E-value=7.6e-07  Score=62.12  Aligned_cols=75  Identities=21%  Similarity=0.237  Sum_probs=59.5

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             100015668999999999999999985998899999848999999988779988-89999999999828999996145
Q gi|254781218|r   17 YTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        17 ~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      .+.-|.+|+ -+.++.|+-+|++|+.-+.||.+||..+|+|+|.||.||.|++. |.+..+.++.++| +++|.==+|
T Consensus        14 va~rIaGdI-vlS~~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL-IeID~eRGg   89 (241)
T COG1709          14 LAKRIAGDI-VLSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL-IEIDEERGG   89 (241)
T ss_pred             HHHHHHCCE-EECCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHCCCCCCCCHHHHHHHHHHH-HHHHHHHCC
T ss_conf             988820427-8607825899999998182499999872899100312112575686178999999999-866686156


No 46 
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.21  E-value=1.9e-06  Score=59.67  Aligned_cols=53  Identities=32%  Similarity=0.465  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHH
Q ss_conf             7799999999972983899999977999999997414889-9989999999982
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI-PEIKPARKIKQVT  165 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~-Ps~~~l~kIa~~l  165 (205)
                      ..|+-||.+|...+.||.|+|..+|++++.+|.||.|++. |....+.++-.+|
T Consensus        27 ~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          27 DPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             825899999998182499999872899100312112575686178999999999


No 47 
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.18  E-value=5.9e-06  Score=56.61  Aligned_cols=52  Identities=19%  Similarity=0.161  Sum_probs=36.0

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             8599889999984899999998877998889999999999828999996145
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      -.||||.+||+.+||++.+||++=||++..+.++.++|+++|+.|.+.-++-
T Consensus        21 p~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlNl   72 (104)
T COG3093          21 PLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLNL   72 (104)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf             2169899999993998999999983776789999999999929989999999


No 48 
>PRK10072 putative transcriptional regulator; Provisional
Probab=98.16  E-value=5.9e-06  Score=56.61  Aligned_cols=54  Identities=17%  Similarity=0.410  Sum_probs=44.3

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf             9999999729838999999779999999974148899989999999982899999
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW  171 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~  171 (205)
                      -++++|+..|++|.+||+.+|+|.+++..||.+++.|+-..+.-++ +..-++..
T Consensus        37 dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~klL~-li~~nP~l   90 (96)
T PRK10072         37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMR-LIQANPAL   90 (96)
T ss_pred             CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHH-HHHHCHHH
T ss_conf             3999998809999999999777799999999678789839999999-99879799


No 49 
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.15  E-value=1e-05  Score=55.10  Aligned_cols=64  Identities=22%  Similarity=0.314  Sum_probs=57.9

Q ss_pred             HHHHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             6777999999-999729838999999779999999974148899989999999982899999524
Q gi|254781218|r  111 PYAIGARLKS-IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYF  174 (205)
Q Consensus       111 ~~~iG~rLk~-lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~  174 (205)
                      |.-.|+-|+. +.+-.|+|+.++|+.+|+++.+++.+.+|++..+.+.+.+|+++||+++++.+.
T Consensus         7 P~~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlN   71 (104)
T COG3093           7 PAHPGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLN   71 (104)
T ss_pred             CCCCHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf             99941889999845216989999999399899999998377678999999999992998999999


No 50 
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.10  E-value=2.1e-05  Score=53.14  Aligned_cols=65  Identities=26%  Similarity=0.363  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf             99999999998599889999984899999998877998-889999999999828999996145322
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMC-STSIRYALYLRNEYEISFDWIYDGEVI   96 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~-~psi~~l~~la~~~~vs~d~Ll~ge~~   96 (205)
                      +|.+++.+|+..|+||+++|..+|++..+++.||+|.. .|++..+..++..|++...+++.....
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLEEEEE   67 (120)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             789999999986999999998939889999999807877846999999999969789988400222


No 51 
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.05  E-value=1.5e-05  Score=54.16  Aligned_cols=64  Identities=16%  Similarity=0.208  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH------HHHHHHHHHHCCCHHHHHCC
Q ss_conf             99999999999985998899999848999999988779988899------99999999828999996145
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSI------RYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi------~~l~~la~~~~vs~d~Ll~g   93 (205)
                      +.+|+++|..|+.+|||++++|.+++|..+++-.+|+|...--.      .++...|++++++.|.|+..
T Consensus         2 ~~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~   71 (284)
T COG1426           2 KTLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQA   71 (284)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             6778999999998499999999885775999999866770106415767899999999968998999998


No 52 
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. 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.
Probab=97.96  E-value=3.4e-05  Score=51.92  Aligned_cols=59  Identities=19%  Similarity=0.249  Sum_probs=49.7

Q ss_pred             HHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf             9999998599-88999998489999999887799888999999999982899999614532
Q gi|254781218|r   36 IKDIRKANNK-TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEV   95 (205)
Q Consensus        36 ik~lR~~~gl-tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~   95 (205)
                      |..+-+..|. ||.|||..+||++++||.|-..-.. +.+.+++++...+||+|||+.|+-
T Consensus         3 i~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~-P~e~iv~~~~~tGvsl~WL~~G~G   62 (65)
T pfam07022         3 IERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSF-PAEWVIRCALETGVSLDWLATGDG   62 (65)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-CHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf             999999968886999999969888889999986999-899999999998829999970899


No 53 
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=97.95  E-value=1.4e-05  Score=54.28  Aligned_cols=71  Identities=20%  Similarity=0.165  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             34554677799999999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r  106 KKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD  176 (205)
Q Consensus       106 ~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~  176 (205)
                      ...+-...+|.-||..|+.+|||++|||+.+..-.+++.++|+....|....+.+|-+.|++++-.=+..+
T Consensus        76 t~~elvEdyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~  146 (169)
T TIGR00270        76 TVEELVEDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEE  146 (169)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             35666643225422000146878789999874106788887540379888999998888350100235710


No 54 
>PRK10856 hypothetical protein; Provisional
Probab=97.94  E-value=4.9e-05  Score=50.92  Aligned_cols=64  Identities=17%  Similarity=0.120  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC------CHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             999999999999859988999998489999999887799888------9999999999828999996145
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST------SIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~p------si~~l~~la~~~~vs~d~Ll~g   93 (205)
                      .-+|.+||..|+++|||++++|.+++++.+.|-.+|+|....      ---++...|+.++++.+.|+..
T Consensus        13 ~t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~   82 (332)
T PRK10856         13 LTTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPG   82 (332)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             6887999999998599999999870898999999857822108703647999999999978897996542


No 55 
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=97.92  E-value=0.00011  Score=48.78  Aligned_cols=63  Identities=37%  Similarity=0.560  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             79999999997298389999997799999999741488-9998999999998289999952472
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVTKKHLDWIYFGD  176 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~-~Ps~~~l~kIa~~lgvs~d~L~~G~  176 (205)
                      +|.+++.+|+..|++|.++|..+|++..+++.||+|.. .|....+..++..+++...+++...
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLEEE   65 (120)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             7899999999869999999989398899999998078778469999999999697899884002


No 56 
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435    Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=97.86  E-value=2.9e-05  Score=52.30  Aligned_cols=56  Identities=14%  Similarity=0.221  Sum_probs=31.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC--CCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             999999859988999998489999999887799--88899999999998289999961
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGM--CSTSIRYALYLRNEYEISFDWIY   91 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~G~--~~psi~~l~~la~~~~vs~d~Ll   91 (205)
                      ||.+|+..|||-.+||..+||+++.|..+|+..  ...+++.|-.-|+++||.+=|-|
T Consensus        30 vR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYaf   87 (150)
T TIGR02612        30 VRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAF   87 (150)
T ss_pred             HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEC
T ss_conf             6889877251578876652897377999888875553558889999998598443401


No 57 
>PRK10072 putative transcriptional regulator; Provisional
Probab=97.85  E-value=4.4e-05  Score=51.23  Aligned_cols=49  Identities=14%  Similarity=0.063  Sum_probs=40.8

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             99999998599889999984899999998877998889999999999828
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE   84 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~   84 (205)
                      -++.+|+..|++|.+||..+|+|.++|-.||.|++.|+-.-+ +|-....
T Consensus        37 dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~-klL~li~   85 (96)
T PRK10072         37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAEL-KLMRLIQ   85 (96)
T ss_pred             CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHH-HHHHHHH
T ss_conf             399999880999999999977779999999967878983999-9999998


No 58 
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435    Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=97.84  E-value=1.6e-05  Score=53.95  Aligned_cols=78  Identities=21%  Similarity=0.282  Sum_probs=61.2

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC--CCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999997298389999997799999999741488--9998999999998289999952472102545677754235678
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT--IPEIKPARKIKQVTKKHLDWIYFGDEVIVPKSIKRAKGNQSSK  194 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~--~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~~~~~~~~~~~~~~  194 (205)
                      =||.+|+.+|||-.+||..+||.++.|..+|...-  ..++.++.+-|+++||..=|=|=-     +.++...-.++..+
T Consensus        29 WvR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYafVP-----~~sLE~t~~~QArK  103 (150)
T TIGR02612        29 WVRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAFVP-----KTSLEATVRAQARK  103 (150)
T ss_pred             CHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECCC-----CCCHHHHHHHHHHH
T ss_conf             1688987725157887665289737799988887555355888999999859844340188-----60278999999999


Q ss_pred             HHHHH
Q ss_conf             77654
Q gi|254781218|r  195 KSKKD  199 (205)
Q Consensus       195 ~sk~d  199 (205)
                      .++..
T Consensus       104 vA~~~  108 (150)
T TIGR02612       104 VAKEI  108 (150)
T ss_pred             HHHHH
T ss_conf             99999


No 59 
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=97.83  E-value=9.3e-05  Score=49.21  Aligned_cols=65  Identities=23%  Similarity=0.250  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCH----HHHHHHHHHHCCCHHHHHCCCC
Q ss_conf             7799999999972983899999977999999997414889--998----9999999982899999524721
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI--PEI----KPARKIKQVTKKHLDWIYFGDE  177 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~--Ps~----~~l~kIa~~lgvs~d~L~~G~e  177 (205)
                      .+|++||+.|+.+|||+.|++..++|.++.+..+|+|.-.  |..    ..++..|+++|++.|-|+-.-+
T Consensus         3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~~~   73 (284)
T COG1426           3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQAFE   73 (284)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             77899999999849999999988577599999986677010641576789999999996899899999864


No 60 
>PRK10856 hypothetical protein; Provisional
Probab=97.70  E-value=0.00019  Score=47.33  Aligned_cols=67  Identities=19%  Similarity=0.226  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CC----HHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             4677799999999972983899999977999999997414889--99----8999999998289999952472
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI--PE----IKPARKIKQVTKKHLDWIYFGD  176 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~--Ps----~~~l~kIa~~lgvs~d~L~~G~  176 (205)
                      +...+|.+||+.|+.+|||+.|+|+.+.++...+..+|+|...  |.    -..++..|+.||++.+-|+..-
T Consensus        11 ~~~t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~~   83 (332)
T PRK10856         11 EALTTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGL   83 (332)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             6568879999999985999999998708989999998578221087036479999999999788979965421


No 61 
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.63  E-value=0.00015  Score=47.98  Aligned_cols=61  Identities=13%  Similarity=0.076  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             999999999859988999998489999999887799-8889999999999828999996145
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      ..++..+.-.+++++.+||+.+|+|.+++|.+.+|+ ...++++|-+||.+++|.+..|+.-
T Consensus         4 ~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley   65 (73)
T COG3655           4 AVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEY   65 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEEE
T ss_conf             37679999997501778999984369899999728866044899999999838984054577


No 62 
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.47  E-value=0.00034  Score=45.77  Aligned_cols=62  Identities=21%  Similarity=0.267  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             799999999972983899999977999999997414889-99899999999828999995247
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI-PEIKPARKIKQVTKKHLDWIYFG  175 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~-Ps~~~l~kIa~~lgvs~d~L~~G  175 (205)
                      +..++..++.+++++..|+|+.+|++..+++...+|+.. .+.++|.+||++|++.+.-|+--
T Consensus         3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley   65 (73)
T COG3655           3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEY   65 (73)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEEE
T ss_conf             137679999997501778999984369899999728866044899999999838984054577


No 63 
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   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 , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=97.38  E-value=0.00037  Score=45.49  Aligned_cols=123  Identities=20%  Similarity=0.254  Sum_probs=78.7

Q ss_pred             HHHCCC-HHHHH------------HHHHHHHHHHHHHHHC------CCCHHHHHHHHCCCHHH-HHHHHCCCCCCCHHHH
Q ss_conf             100015-66899------------9999999999999985------99889999984899999-9988779988899999
Q gi|254781218|r   17 YTLIIT-PEIRQ------------YWKDVGTRIKDIRKAN------NKTQKEMAIGANQLESA-VNLFENGMCSTSIRYA   76 (205)
Q Consensus        17 ~~~~~~-~~~~~------------~~~~iG~rik~lR~~~------gltQ~elA~~~gis~~~-is~~E~G~~~psi~~l   76 (205)
                      |||||= +|++=            ..|++|.+|++-|+..      .=|-.|||+.+|+++-. |...|.+...-++.-.
T Consensus        67 YAVPmI~GEIkRFLRDDG~ikVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~t  146 (231)
T TIGR02885        67 YAVPMIMGEIKRFLRDDGIIKVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDT  146 (231)
T ss_pred             CCCCHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCE
T ss_conf             12220221222310268855751527899999987799999983899888999887587887866442025761011001


Q ss_pred             HHHHHHHCCCHHHHHCCCCCCCCCCCC--CCHHHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             999998289999961453221000023--21345546777999999----------999729838999999779999999
Q gi|254781218|r   77 LYLRNEYEISFDWIYDGEVIDRRYEDV--TNKKRLDPYAIGARLKS----------IRKDKGMSQIEFGKLLGMPNSTLS  144 (205)
Q Consensus        77 ~~la~~~~vs~d~Ll~ge~~~~~~~~~--~~~~~~d~~~iG~rLk~----------lR~~~glsq~elA~~lgis~~tis  144 (205)
                      +   +.=+=++=+|++     .. .|.  ......+..++-+-|.+          +|=-+..||.|+|+.+|||+-.+|
T Consensus       147 v---h~dDGdPi~LlD-----~i-~d~~~~~~~~~~ki~Lke~i~~Ld~rer~ii~LRYFKDkTQ~eVA~~LGISQVQVS  217 (231)
T TIGR02885       147 V---HEDDGDPILLLD-----QI-ADKGSEDSDLLEKIALKEAISKLDERERQIIMLRYFKDKTQTEVAKMLGISQVQVS  217 (231)
T ss_pred             E---ECCCCCHHHHHH-----HH-CCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCCHHH
T ss_conf             1---417946446766-----52-12577136899989999998612522678977410140017999977185700122


Q ss_pred             HHHC
Q ss_conf             9741
Q gi|254781218|r  145 NYEQ  148 (205)
Q Consensus       145 ~~E~  148 (205)
                      ++|+
T Consensus       218 RlEk  221 (231)
T TIGR02885       218 RLEK  221 (231)
T ss_pred             HHHH
T ss_conf             7899


No 64 
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057   Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=97.34  E-value=0.00065  Score=44.01  Aligned_cols=59  Identities=27%  Similarity=0.390  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             4677799999999972983899999977999999997414889998999999998289999
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD  170 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d  170 (205)
                      ||.-|-.-|=.+=+.+||||  +|+.+|+++.++.+=.+++..|+.+++.++.++||+.+.
T Consensus        31 Dp~~~~~ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L~   89 (91)
T TIGR02684        31 DPALIAAALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKLT   89 (91)
T ss_pred             CHHHHHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf             98899999889986516578--999828767887887356889566888999984086020


No 65 
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.30  E-value=0.00062  Score=44.11  Aligned_cols=57  Identities=18%  Similarity=0.298  Sum_probs=49.3

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             9999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      +-|+.++...|+|+.+||..+| |++.+|++.+|++.-+++.++++.+-||++.|-|+
T Consensus        63 e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI  119 (120)
T COG5499          63 EVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI  119 (120)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf             9999999993871888899867-61889999732067669999999998695888753


No 66 
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.25  E-value=0.00077  Score=43.54  Aligned_cols=73  Identities=19%  Similarity=0.165  Sum_probs=60.5

Q ss_pred             HHCCCHHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             000156689999999---99999999985998899999848999999988779988899999999998289999961
Q gi|254781218|r   18 TLIITPEIRQYWKDV---GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY   91 (205)
Q Consensus        18 ~~~~~~~~~~~~~~i---G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll   91 (205)
                      +++-.+|.++|...-   =+-|+.+..+.|+|+.+||..+| |.+.+|++-+|++..++++..+|...|+|+.|-|+
T Consensus        44 tl~eAyE~kh~~i~aP~pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI  119 (120)
T COG5499          44 TLIEAYEFKHYPIAAPDPVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI  119 (120)
T ss_pred             HHHHHHHHHHCHHHCCCHHHHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf             99860665514031688889999999993871888899867-61889999732067669999999998695888753


No 67 
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=97.23  E-value=0.0026  Score=40.29  Aligned_cols=64  Identities=14%  Similarity=0.212  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCHH----HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             467779999999997298389----9999977999999997414889998999999998289999952
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQI----EFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~----elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      |...+..|+|++....|+...    .+++.||+|.+...+-.+|.+-=.+..+.+||+.||+++..||
T Consensus         2 ~~~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~   69 (146)
T pfam08667         2 DDLIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILL   69 (146)
T ss_pred             CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf             01899999999998639975677889999978748988787358997449999999999597999992


No 68 
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.20  E-value=0.0019  Score=41.17  Aligned_cols=59  Identities=17%  Similarity=0.085  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             689999999999999999859988999998489999999887799888999999999982
Q gi|254781218|r   24 EIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        24 ~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~   83 (205)
                      ++.+..+++|.-++.+-.++|||..+||+..|+..|++.++-+| +.|.+++|.+|.+..
T Consensus         9 ~~ies~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti   67 (170)
T COG4800           9 ECIESGEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI   67 (170)
T ss_pred             HHHHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf             99964007999999999981999899988709989999999817-996577899999999


No 69 
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=96.80  E-value=0.008  Score=37.26  Aligned_cols=54  Identities=24%  Similarity=0.354  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             6777999999999729838999999779999999974148899989999999982
Q gi|254781218|r  111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       111 ~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      ...+|+-++.+..++||+..|||+..|++.+|+.++..| +.|..+++.+|-+..
T Consensus        14 ~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti   67 (170)
T COG4800          14 GEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI   67 (170)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf             007999999999981999899988709989999999817-996577899999999


No 70 
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=96.71  E-value=0.0025  Score=40.40  Aligned_cols=36  Identities=17%  Similarity=0.238  Sum_probs=24.5

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf             983899999977999999997414889998999999
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI  161 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI  161 (205)
                      -|+++++|+.+|++.+|||+.-+|+..-+..-++.+
T Consensus       349 PL~lkdiA~~lglheSTVSRav~~Kyi~tp~G~~~l  384 (461)
T PRK05932        349 PLVLKDIAEALGMHESTISRATTNKYMATPRGIFEL  384 (461)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHCCEECCCCCEEEH
T ss_conf             763999998739981258898716611489744669


No 71 
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.69  E-value=0.0075  Score=37.44  Aligned_cols=58  Identities=12%  Similarity=0.046  Sum_probs=36.4

Q ss_pred             HHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHH
Q ss_conf             999999-9999985998899999848999999988779988-8999999999982899999
Q gi|254781218|r   31 DVGTRI-KDIRKANNKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDW   89 (205)
Q Consensus        31 ~iG~ri-k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~   89 (205)
                      -|-..+ +.+|.. |+||.+.|+.+|+||++||+|=+|.+. ..++.+..+.+....-+..
T Consensus         9 aiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~~~~~~~~e~~e~i~~l~~~   68 (119)
T COG2522           9 AIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGSARLEDIGETDEEIRSLVAE   68 (119)
T ss_pred             HHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999995-88699999996888999999973677368899999899999999999


No 72 
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. 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.
Probab=96.65  E-value=0.0045  Score=38.79  Aligned_cols=136  Identities=21%  Similarity=0.175  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             77766654333100015668999999999999999985998899999848999999988779988899999999998289
Q gi|254781218|r    6 FLETSLKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI   85 (205)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v   85 (205)
                      ++-.+++-++.--+.++..+-++.++.=..  .-..-+-||.+++|+.+|++.||||+.-+|+.--+..-++.|...|.-
T Consensus        13 ~li~~i~~R~~Tl~~V~~~Iv~~Q~~Ff~~--g~~~l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~fFs~   90 (160)
T pfam04552        13 WLIRSLEQRAETLLKVAREIVRRQEDFLEK--GPEALRPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKYFFSS   90 (160)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHHC
T ss_conf             999999999999999999999997999847--853575761999998809981069999961397679951659998501


Q ss_pred             CHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH----CCCCHHHHHHHHC-----CCHHHHHHHHCCCCCCCHH
Q ss_conf             999961453221000023213455467779999999997----2983899999977-----9999999974148899989
Q gi|254781218|r   86 SFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKD----KGMSQIEFGKLLG-----MPNSTLSNYEQGRTIPEIK  156 (205)
Q Consensus        86 s~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~----~glsq~elA~~lg-----is~~tis~~E~g~~~Ps~~  156 (205)
                      .+.        .....      ..+...|-.+|+++-..    +-+|-.++++.+.     |++.|+.+|-..-..|+..
T Consensus        91 ~~~--------~~~~~------~~S~~~ik~~I~~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYR~~L~Ip~s~  156 (160)
T pfam04552        91 AVS--------TSGGG------EASATAIRALIKKLIAAEDPKKPLSDDKIVELLKEQGIDIARRTVAKYREALNIPSSS  156 (160)
T ss_pred             CCC--------CCCCC------CHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHCCCCCHH
T ss_conf             367--------88863------0229999999999998247899999999999999779952146199999883999665


Q ss_pred             H
Q ss_conf             9
Q gi|254781218|r  157 P  157 (205)
Q Consensus       157 ~  157 (205)
                      .
T Consensus       157 ~  157 (160)
T pfam04552       157 Q  157 (160)
T ss_pred             H
T ss_conf             3


No 73 
>PHA00542 putative Cro-like protein
Probab=96.61  E-value=0.0065  Score=37.83  Aligned_cols=57  Identities=9%  Similarity=-0.004  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHH
Q ss_conf             999999999999999859988999998489999999887799-888999999999982
Q gi|254781218|r   27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEY   83 (205)
Q Consensus        27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~   83 (205)
                      ..++.--..|-..-...||||.+++...||+++.||++-.|+ ..|.+.++.+|.+.|
T Consensus        14 ~~y~k~P~E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L~   71 (82)
T PHA00542         14 AAYTQRPDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             7653298999999998225699999860877036899980887897206999999998


No 74 
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=96.60  E-value=0.06  Score=31.85  Aligned_cols=137  Identities=12%  Similarity=0.091  Sum_probs=67.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH---CCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf             156689999999999999999859--988999998489999999887---799888999999999982899999614532
Q gi|254781218|r   21 ITPEIRQYWKDVGTRIKDIRKANN--KTQKEMAIGANQLESAVNLFE---NGMCSTSIRYALYLRNEYEISFDWIYDGEV   95 (205)
Q Consensus        21 ~~~~~~~~~~~iG~rik~lR~~~g--ltQ~elA~~~gis~~~is~~E---~G~~~psi~~l~~la~~~~vs~d~Ll~ge~   95 (205)
                      ++..+.+....+-.-.+.++...|  -|-+++|+.+|++...+..+.   .+....|++..+.=-..-.+++..++.++.
T Consensus       104 iP~~~~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~SLd~~~~~~~d~~~~l~d~l~d~~  183 (256)
T PRK07408        104 IPRRWLELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPLSLDAPVSQDEDGSTSLGDLLPDPR  183 (256)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCHHHHHCCCCC
T ss_conf             36999999999999999999987899989999989596999999999987278873056647799987611777558999


Q ss_pred             CCCCCCCCCCHHHHHHH---HHHHHHH---HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             21000023213455467---7799999---9999729838999999779999999974148899989999999982
Q gi|254781218|r   96 IDRRYEDVTNKKRLDPY---AIGARLK---SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus        96 ~~~~~~~~~~~~~~d~~---~iG~rLk---~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      .+. ..........-..   .+..|=+   .+|-..++|+.|.|+.+|||+..+++++.       ..+.++-+.|
T Consensus       184 ~~~-~~~~~e~~~~L~~~l~~L~eREr~Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~-------~AL~kLR~~L  251 (256)
T PRK07408        184 YRS-FQLAQEDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVK-------KGLQQLKKLL  251 (256)
T ss_pred             CCH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf             753-8899999999999985699999999999963799899999897989999999999-------9999999972


No 75 
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057   Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=96.50  E-value=0.0042  Score=39.00  Aligned_cols=54  Identities=13%  Similarity=0.129  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      |-.=|=.+=+.+||||  +|++.|+++-++.+==++..+|+++++++++++|||.+
T Consensus        35 ~~~ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L   88 (91)
T TIGR02684        35 IAAALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKL   88 (91)
T ss_pred             HHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf             9999889986516578--99982876788788735688956688899998408602


No 76 
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.35  E-value=0.013  Score=35.94  Aligned_cols=40  Identities=33%  Similarity=0.478  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
Q ss_conf             7999999999729838999999779999999974148899
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIP  153 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~P  153 (205)
                      |-..|......+|+||.+.|+++|+++..+|+|-.|++.|
T Consensus        10 iRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522          10 IRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCH
T ss_conf             9999999999958869999999688899999997367736


No 77 
>PRK02866 cyanate hydratase; Validated
Probab=96.26  E-value=0.097  Score=30.58  Aligned_cols=62  Identities=15%  Similarity=0.040  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             99999999999985998899999848999999988779988899999999998289999961
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY   91 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll   91 (205)
                      .++-++|-..+..+|||-+++|+.+|.|.-.+...=-|+...+-+..-+++..|+.+-+..-
T Consensus         4 ~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~~   65 (147)
T PRK02866          4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA   65 (147)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf             99999999999984998999998949899999999846778999999999997499999999


No 78 
>PRK02866 cyanate hydratase; Validated
Probab=96.23  E-value=0.038  Score=33.09  Aligned_cols=64  Identities=13%  Similarity=0.223  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             4677799999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      +...+-++|-..+..+|+|-.++|+.+|.+.-.+....-|....+.+.+.+++++|+.+-+-.-
T Consensus         2 ~r~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~~   65 (147)
T PRK02866          2 KREELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA   65 (147)
T ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf             8899999999999984998999998949899999999846778999999999997499999999


No 79 
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=96.21  E-value=0.095  Score=30.61  Aligned_cols=131  Identities=13%  Similarity=0.132  Sum_probs=62.9

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHH---CCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             100015668999999999999999985--9988999998489999999887---79988899999999998289999961
Q gi|254781218|r   17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFE---NGMCSTSIRYALYLRNEYEISFDWIY   91 (205)
Q Consensus        17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E---~G~~~psi~~l~~la~~~~vs~d~Ll   91 (205)
                      .++-++...++....|..-...+....  .-|-.++|+.+|++...|...-   +.....|++....-.......+...+
T Consensus       113 ~~IRlP~~~~~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~~~~~v~~~l~~~~~~~~~SlD~~~~~~~~~~~~l~d~~  192 (263)
T PRK07122        113 WSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSSYNTLSIDSGGGSGDDDARAIADTL  192 (263)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf             75465799999989999999999998688999999998969399999999987335898778788888886520354641


Q ss_pred             CCCCCCCCCCCCCCHHHHHH--HHHH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             45322100002321345546--7779---9999999972983899999977999999997414
Q gi|254781218|r   92 DGEVIDRRYEDVTNKKRLDP--YAIG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        92 ~ge~~~~~~~~~~~~~~~d~--~~iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ...  +.....+.....+..  ..+-   ..|=.+|=..++|+.|.|+.+|||+..++++++.
T Consensus       193 ~d~--~~~~e~~~~~~~L~~~l~~L~eREr~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~  253 (263)
T PRK07122        193 GDV--DAGLDHIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAK  253 (263)
T ss_pred             CCC--CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             697--6428999999999999975999999999999569998999999989799999999999


No 80 
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=96.14  E-value=0.0062  Score=37.95  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             2983899999977999999997414889998999999998
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV  164 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~  164 (205)
                      +-|+++++|+.+|++.+|||+.-+|+..-+..-++.+...
T Consensus       362 kPL~lkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~F  401 (475)
T PRK12469        362 KPLVLRDVAEELGLHESTVSRATGNKYMATPRGTFEFKHF  401 (475)
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHHCCCEECCCCCEEEHHHH
T ss_conf             6734999999819982037688627502379854669986


No 81 
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=96.11  E-value=0.069  Score=31.47  Aligned_cols=102  Identities=20%  Similarity=0.207  Sum_probs=69.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-
Q ss_conf             9889999984899999998877998889999999999828999996145322100002321345546777999999999-
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK-  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~-  123 (205)
                      |+.+++|..+|++.|||||.=+++.--+..-+..|...|-..+..=-+|+..+             ..+|-++|+++-. 
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLk~FFs~~i~s~~gg~~~S-------------~~~Ik~~Ik~lI~~  397 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASS-------------TEAIKALIKKLIEA  397 (444)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCCCC-------------HHHHHHHHHHHHHH
T ss_conf             31999998837128889999825410488633448988777416788876444-------------89999999998753


Q ss_pred             ---HCCCCHHHHHHHH-----CCCHHHHHHHHCCCCCCCHHHHH
Q ss_conf             ---7298389999997-----79999999974148899989999
Q gi|254781218|r  124 ---DKGMSQIEFGKLL-----GMPNSTLSNYEQGRTIPEIKPAR  159 (205)
Q Consensus       124 ---~~glsq~elA~~l-----gis~~tis~~E~g~~~Ps~~~l~  159 (205)
                         .+-+|-..+++++     .|++.|+.+|-..-++|+...-+
T Consensus       398 E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe~L~I~sS~~Rk  441 (444)
T COG1508         398 EDKKKPLSDSKIAELLKEKGIDVARRTVAKYREELNIPSSSQRK  441 (444)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             16778887899999999719842588599999880899565540


No 82 
>KOG3802 consensus
Probab=96.05  E-value=0.055  Score=32.07  Aligned_cols=126  Identities=17%  Similarity=0.193  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf             999999999999999985998899999848------99999998877998889999999999828999996145322100
Q gi|254781218|r   26 RQYWKDVGTRIKDIRKANNKTQKEMAIGAN------QLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR   99 (205)
Q Consensus        26 ~~~~~~iG~rik~lR~~~gltQ~elA~~~g------is~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~   99 (205)
                      .+-.+.+++.+|..|...|+||.+++.++|      .|+.+|+|+|.=  ..|...+.+|--.|+   -||=.-|.....
T Consensus       205 leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKLKPLL~---KWLeEAes~~~~  279 (398)
T KOG3802         205 LEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKLKPLLE---KWLEEAESREST  279 (398)
T ss_pred             HHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH--CCCHHHHHHHHHHHH---HHHHHHHCCCCC
T ss_conf             999999999987650003644267888987650764430266676762--547787766379999---999998603345


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             00232134554677799999999972983899999977999999997414889998999999998289999
Q gi|254781218|r  100 YEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD  170 (205)
Q Consensus       100 ~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d  170 (205)
                       .....-.     .|+.--   |+++.-|=.|...     +..+.+.--..-.|+.+.+-.||+-|+..-|
T Consensus       280 -~~~~~~e-----~i~a~~---RkRKKRTSie~~v-----r~aLE~~F~~npKPt~qEIt~iA~~L~leKE  336 (398)
T KOG3802         280 -GSPNSIE-----KIGAQS---RKRKKRTSIEVNV-----RGALEKHFLKNPKPTSQEITHIAESLQLEKE  336 (398)
T ss_pred             -CCCCCHH-----HHHCCC---CCCCCCCCEEHHH-----HHHHHHHHHHCCCCCHHHHHHHHHHHCCCCC
T ss_conf             -7777788-----861343---3344345210889-----9999999986889988999999998466643


No 83 
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209   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 , .    The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage.   Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=96.05  E-value=0.003  Score=39.89  Aligned_cols=25  Identities=32%  Similarity=0.239  Sum_probs=18.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             8599889999984899999998877
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      ...-||.|.|+.+|||+|+|||||+
T Consensus       193 ~~~~tQREIA~~LgISRSYVSRIEK  217 (228)
T TIGR02846       193 GREKTQREIAKILGISRSYVSRIEK  217 (228)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             8954178998770865004548889


No 84 
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=96.03  E-value=0.055  Score=32.08  Aligned_cols=63  Identities=8%  Similarity=-0.028  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHHCCCCHH----HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             9999999999998599889----99998489999999887799888999999999982899999614
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQK----EMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD   92 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~----elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~   92 (205)
                      .-|.+|+|++-...|+.-.    .++..+|+|.|...+==+|...=.++.+.+++.+|++++..||+
T Consensus         4 ~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~~   70 (146)
T pfam08667         4 LIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILLI   70 (146)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
T ss_conf             8999999999986399756778899999787489887873589974499999999995979999927


No 85 
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.90  E-value=0.084  Score=30.95  Aligned_cols=43  Identities=21%  Similarity=0.392  Sum_probs=32.7

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             99999999729838999999779999999974148899989999999982
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      +.+-.+|-..++||+|.|+.+|||.+.+|+++.       ..+.+|-+.|
T Consensus       202 k~Vl~l~y~eelt~kEI~~~LgISes~VSql~k-------kai~kLr~~l  244 (247)
T COG1191         202 KLVLVLRYKEELTQKEIAEVLGISESRVSRLHK-------KAIKKLRKEL  244 (247)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf             999999997015799999994914989999999-------9999999986


No 86 
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=95.83  E-value=0.02  Score=34.81  Aligned_cols=94  Identities=18%  Similarity=0.273  Sum_probs=62.9

Q ss_pred             CCCHHHHHHHHCCCHHHHHHH------HCCCCCC----------CHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf             998899999848999999988------7799888----------999999999982899999614532210000232134
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLF------ENGMCST----------SIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKK  107 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~------E~G~~~p----------si~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~  107 (205)
                      =|||+++|..+++|..+|+++      |+|..-|          ++.+=-.+++.|       +.|    ...+++....
T Consensus       105 lLT~~Dla~LL~~S~~TI~~~ik~ye~~~g~vvPtRG~i~DiGp~vTHK~iiv~~~-------lkg----~~t~eiaR~t  173 (220)
T pfam07900       105 LLTHADIAILLGVSTTTISRHVKEYEERTGEVVPTRGIIKDIGPSVTHKRKIVELY-------LKG----YQTSEIARLT  173 (220)
T ss_pred             EEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHH-------HCC----CCHHHHHHHH
T ss_conf             51176699998898889999999999970966357872034587620689999999-------826----8888999985


Q ss_pred             HHHHHHHHHHHHHH-----HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             55467779999999-----997298389999997799999999741
Q gi|254781218|r  108 RLDPYAIGARLKSI-----RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       108 ~~d~~~iG~rLk~l-----R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .+++.+|-.-|+..     -..+||+-.+.|-.+|+|...+..|+.
T Consensus       174 ~HS~~AvdRYi~df~rV~~l~~kg~~~~ei~~~tG~s~~lv~eY~~  219 (220)
T pfam07900       174 NHSPESIDRYIKDFTRVEKLTEKGMSEEEIRYITGISERLVEEYVE  219 (220)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             3798999999987689999998678799999997765899999972


No 87 
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322   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 , .    This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=95.83  E-value=0.0082  Score=37.19  Aligned_cols=118  Identities=22%  Similarity=0.329  Sum_probs=72.6

Q ss_pred             HHHHHCCC-HHHHHHHHH------HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             33100015-668999999------99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   15 QEYTLIIT-PEIRQYWKD------VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        15 ~~~~~~~~-~~~~~~~~~------iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      --|+|||= +|++=|-.+      |--|+|+++-+-+-..++|+..+|=             .|++   -.||+.++||.
T Consensus        58 ~tyAVPtI~GEIkR~fRD~~W~vrVPRrlkEl~~~~~~a~eeL~~~lgR-------------~Pt~---~EiAe~L~~s~  121 (229)
T TIGR02980        58 STYAVPTIMGEIKRFFRDDTWAVRVPRRLKELRLKINKATEELTQRLGR-------------SPTV---AEIAEELGVSE  121 (229)
T ss_pred             CCCCCCCEEEEEEEEEECCCCEEECCHHHHHHHHHHHHHHHHHHHHHCC-------------CCCH---HHHHHHHCCCH
T ss_conf             6410460233231334248732660513898899999999999998288-------------9887---89998858899


Q ss_pred             HHHHCC----CC-----CCCCC---CCCCCHHHHHH--------------HHHHHHHH----------HHHHHCCCCHHH
Q ss_conf             996145----32-----21000---02321345546--------------77799999----------999972983899
Q gi|254781218|r   88 DWIYDG----EV-----IDRRY---EDVTNKKRLDP--------------YAIGARLK----------SIRKDKGMSQIE  131 (205)
Q Consensus        88 d~Ll~g----e~-----~~~~~---~~~~~~~~~d~--------------~~iG~rLk----------~lR~~~glsq~e  131 (205)
                      ++.+-+    ..     +|...   .|-...+.+|.              .++=.-|.          .+|=-.+|||.|
T Consensus       122 EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~D~lG~~D~~~e~~~~~~aLk~~l~~LpeRER~il~lRFf~~~TQ~e  201 (229)
T TIGR02980       122 EEVVEALEAGNSYSALSLDATIEADDDGDPIALLDTLGDEDDALETVEDRLALKPLLAALPERERRILLLRFFEDKTQSE  201 (229)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEEECCCCHHH
T ss_conf             99999998654178611200045588884245664440224326789999999999850790270761000106977899


Q ss_pred             HHHHHCCCHHHHHHHHC
Q ss_conf             99997799999999741
Q gi|254781218|r  132 FGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       132 lA~~lgis~~tis~~E~  148 (205)
                      .|+.+|||+..+|++++
T Consensus       202 iA~~lGiSQMhVSRl~~  218 (229)
T TIGR02980       202 IAERLGISQMHVSRLLR  218 (229)
T ss_pred             HHHHCCCCHHHHHHHHH
T ss_conf             99781843678899999


No 88 
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=95.76  E-value=0.12  Score=29.95  Aligned_cols=125  Identities=15%  Similarity=0.175  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCC---CHHHHHHH--HHHHCCCHHHHHCCCCCC
Q ss_conf             8999999999999999985--9988999998489999999887799888---99999999--998289999961453221
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCST---SIRYALYL--RNEYEISFDWIYDGEVID   97 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~p---si~~l~~l--a~~~~vs~d~Ll~ge~~~   97 (205)
                      +.+....+-.-.+.++...  .-|-.++|+.+|++...+..+.......   |++.-...  -..-++++...+.++..+
T Consensus       105 ~~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~d~~~~~~l~d~i~d~~~~  184 (257)
T PRK05911        105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPSQSDDEAGLALEERIADERAE  184 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCHHHHCCCCCCC
T ss_conf             99999999999999999868899999999883979999999998535522230578888788887653077746798889


Q ss_pred             CCCCCCCCHHHH--HHHH---HH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             000023213455--4677---79---9999999972983899999977999999997414
Q gi|254781218|r   98 RRYEDVTNKKRL--DPYA---IG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        98 ~~~~~~~~~~~~--d~~~---iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .....+......  ...+   +-   ..|-.+|-..++|++|.|+.+|+|+..+++++..
T Consensus       185 ~~~~~~~~~~~~~~L~~al~~L~erEr~Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~  244 (257)
T PRK05911        185 TGYDVVDKKEFSSILANAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSK  244 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             989999999999999999865899999999987489878999998979889999999999


No 89 
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=95.72  E-value=0.022  Score=34.57  Aligned_cols=53  Identities=15%  Similarity=0.108  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             999999999999985998899999848------9999999887799888999999999982
Q gi|254781218|r   29 WKDVGTRIKDIRKANNKTQKEMAIGAN------QLESAVNLFENGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        29 ~~~iG~rik~lR~~~gltQ~elA~~~g------is~~~is~~E~G~~~psi~~l~~la~~~   83 (205)
                      .+.+...+|..|...|+||.++|.++|      .|+++|+++|+=.  .|...+.+|--.+
T Consensus         9 le~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~--LS~kn~~kLkPiL   67 (75)
T smart00352        9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL   67 (75)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf             9999999999898737759999999998618643146888988605--4798899889999


No 90 
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.69  E-value=0.16  Score=29.28  Aligned_cols=125  Identities=17%  Similarity=0.155  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCC---CCCCCHHHHHHHHHH-HCCCHHHHHCCCCCCC
Q ss_conf             899999999999999998--5998899999848999999988779---988899999999998-2899999614532210
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENG---MCSTSIRYALYLRNE-YEISFDWIYDGEVIDR   98 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G---~~~psi~~l~~la~~-~~vs~d~Ll~ge~~~~   98 (205)
                      +.+....+...++.+...  +.-|.+++|+.+|++...+..+...   ....|++..+..... =++++-..+.++....
T Consensus       109 ~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~d~l~d~~~~~  188 (261)
T PRK06288        109 VRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVSGTSVVSLNDLLFLGDENDEVSLMDTLEDPAAMN  188 (261)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC
T ss_conf             99999999999999999868999878888781999999999999972699747677765799986430878705889899


Q ss_pred             CCCCCCCHHHH--HHHH---H---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             00023213455--4677---7---99999999972983899999977999999997414
Q gi|254781218|r   99 RYEDVTNKKRL--DPYA---I---GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        99 ~~~~~~~~~~~--d~~~---i---G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      +..........  ...+   +   -..|=.+|-..++|+.+.|+.+|||+..++++|..
T Consensus       189 p~~~~e~~~~~~~l~~~l~~L~erEr~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~  247 (261)
T PRK06288        189 PDEIIEKEEIKRVIVEAINTLPEREKKVITLYYYEDLTLKEIGEVLGVTESRISQIHTK  247 (261)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999999999999870899999999998079988999999979789999999999


No 91 
>PHA00542 putative Cro-like protein
Probab=95.52  E-value=0.038  Score=33.05  Aligned_cols=49  Identities=18%  Similarity=0.251  Sum_probs=41.9

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHH
Q ss_conf             99999997298389999997799999999741488-99989999999982
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVT  165 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~-~Ps~~~l~kIa~~l  165 (205)
                      .|-......|++|.+.++.+|+++.+++++..|+. .|.+..+.++...+
T Consensus        22 E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L~   71 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             99999998225699999860877036899980887897206999999998


No 92 
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=95.46  E-value=0.075  Score=31.24  Aligned_cols=56  Identities=16%  Similarity=0.179  Sum_probs=43.3

Q ss_pred             HHHHHHHHHH---HHH-CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             9999999999---998-5998899999848999999988779988899999999998289
Q gi|254781218|r   30 KDVGTRIKDI---RKA-NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI   85 (205)
Q Consensus        30 ~~iG~rik~l---R~~-~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v   85 (205)
                      +.+..|++-.   |.- .-+|-+||++.+|+..+.++||-||..-||.+....|-+.++-
T Consensus         5 e~~~~~L~av~~LR~lK~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~   64 (238)
T PRK08558          5 EKLRLQLDAVRYLRSLKKTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKP   64 (238)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             899999999999999850268999998879799998505348878758999999998421


No 93 
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=95.43  E-value=0.21  Score=28.43  Aligned_cols=113  Identities=14%  Similarity=0.111  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCC
Q ss_conf             999999999999999985--998899999848999999988779988899999999998289999961453221000023
Q gi|254781218|r   26 RQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDV  103 (205)
Q Consensus        26 ~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~  103 (205)
                      ++..+.+..-.+.++...  .=|-.++|+.+|++...+..+......           ..-+|+|..+.++.........
T Consensus        95 r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~-----------~~~~sld~~~~~e~~~~~~~~~  163 (229)
T PRK12427         95 RQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENA-----------GAMESLDEILALEAHNDILQSR  163 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCC-----------CCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99999999999999998588999999998919999999999998736-----------6875723344578876545676


Q ss_pred             C-CHHHH----HHHH---HHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             2-13455----4677---7999---99999972983899999977999999997414
Q gi|254781218|r  104 T-NKKRL----DPYA---IGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       104 ~-~~~~~----d~~~---iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      . .....    ...+   +.+|   +=.++=..++|++|.|+.+|+|.+.++++++.
T Consensus       164 ~~~e~~~~~~~L~~al~~L~erEr~Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~k  220 (229)
T PRK12427        164 DLEENIIIEDNLKQAISQLDEREQMILHLYYQQELSMKEIAQVLDLTEARICQLNKK  220 (229)
T ss_pred             CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             646789999999999971999999999998058998999999979889999999999


No 94 
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=95.43  E-value=0.021  Score=34.65  Aligned_cols=53  Identities=15%  Similarity=0.142  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCC------CHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999999859988999998489------999999887799888999999999982
Q gi|254781218|r   29 WKDVGTRIKDIRKANNKTQKEMAIGANQ------LESAVNLFENGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        29 ~~~iG~rik~lR~~~gltQ~elA~~~gi------s~~~is~~E~G~~~psi~~l~~la~~~   83 (205)
                      .+......|..|...|+||.+++.++|.      |+++|+++|+=.  .|.....+|--.+
T Consensus         9 le~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~--Ls~kn~~kLkP~L   67 (75)
T pfam00157         9 LEQFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ--LSFKNMCKLKPLL   67 (75)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf             9999999999898737759999999998708654235888888504--4799899889999


No 95 
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=95.42  E-value=0.025  Score=34.24  Aligned_cols=61  Identities=15%  Similarity=0.035  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHH
Q ss_conf             99999999999999859988999998489999999887799-88899999999998289999
Q gi|254781218|r   28 YWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFD   88 (205)
Q Consensus        28 ~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d   88 (205)
                      ..-.++..|+.+-++++++|++.|+.+||+++.+|.+-+|+ ...+++-|+....+.+-.++
T Consensus        25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~   86 (91)
T COG5606          25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID   86 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999999999999978779999998388873188998361457669999999997598552


No 96 
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.16  E-value=0.034  Score=33.37  Aligned_cols=32  Identities=19%  Similarity=0.177  Sum_probs=26.8

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             999998599889999984899999998877998
Q gi|254781218|r   37 KDIRKANNKTQKEMAIGANQLESAVNLFENGMC   69 (205)
Q Consensus        37 k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~   69 (205)
                      =.+| .+|+||.+.|..+|.|++.||.+|+.-+
T Consensus        13 L~lR-~~G~tQ~eIA~~lgTSraNvs~iEk~A~   44 (139)
T PRK03975         13 LRLR-KRGLTQQEIADILGTSRANISIIEKRAR   44 (139)
T ss_pred             HHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999-8289799999997732889999999999


No 97 
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=94.96  E-value=0.3  Score=27.56  Aligned_cols=127  Identities=15%  Similarity=0.144  Sum_probs=59.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHH-CCCC--CCCHHHHHHHH-HHHCCCHHHHHCC
Q ss_conf             015668999999999999999985--9988999998489999999887-7998--88999999999-9828999996145
Q gi|254781218|r   20 IITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFE-NGMC--STSIRYALYLR-NEYEISFDWIYDG   93 (205)
Q Consensus        20 ~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E-~G~~--~psi~~l~~la-~~~~vs~d~Ll~g   93 (205)
                      -++..+.+....|-.-...+....  .-|-+++|+.+|++...|...- .+..  ..|++..+.-. +...+++...+..
T Consensus       106 r~P~~~~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~~~~~~~~Sld~~~~~d~d~~~~~~~d~~~~  185 (257)
T PRK08583        106 HVPRRIKELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQ  185 (257)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCC
T ss_conf             35499999988899999999998089987999998959599999999997516897027888877888771204330489


Q ss_pred             CCCCCCCCCCCCHHHHHHHH---HHHHHH---HHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             32210000232134554677---799999---999972983899999977999999997414
Q gi|254781218|r   94 EVIDRRYEDVTNKKRLDPYA---IGARLK---SIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        94 e~~~~~~~~~~~~~~~d~~~---iG~rLk---~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .  +..+... ........+   +..|=+   .+|-..++|+.+.|+.+|||+..++++++.
T Consensus       186 ~--e~~~e~~-e~~~~l~~~l~~L~erEr~Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~  244 (257)
T PRK08583        186 Q--EDGYELT-EQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQ  244 (257)
T ss_pred             C--CCHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             6--6247899-999999999954999999999999579999999999989699999999999


No 98 
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=94.95  E-value=0.16  Score=29.29  Aligned_cols=127  Identities=14%  Similarity=0.163  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCCC--C
Q ss_conf             8999999999999999985--998899999848999999988779988---89999999999828999996145322--1
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS---TSIRYALYLRNEYEISFDWIYDGEVI--D   97 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~---psi~~l~~la~~~~vs~d~Ll~ge~~--~   97 (205)
                      +.+..+.|...++.+....  .-|.+++|+.+|++...|...-.....   .|++..       ..+-+.+......  +
T Consensus        90 ~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~-------~~~~~~~~~~~~~~~~  162 (234)
T PRK06986         90 VRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDL-------GESGELLTDEDQSEHE  162 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCC-------CCCCCCCCCCCCCCCC
T ss_conf             999999999999999998787998999998959499999999998505778687767-------7664311122245789


Q ss_pred             CCCCCCCCHHHHHH--H---HHH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             00002321345546--7---779---99999999729838999999779999999974148899989999999982
Q gi|254781218|r   98 RRYEDVTNKKRLDP--Y---AIG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus        98 ~~~~~~~~~~~~d~--~---~iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      .+..++........  .   .+-   ..|-.+|-..++|+.|.|+.+|+|+..++++|+.       .+.++-+.|
T Consensus       163 ~~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~-------AL~kLR~~L  231 (234)
T PRK06986        163 DPLQQLEDEELREALVEAIEKLPEREQLVLSLYYDEELNLKEIGAVLGVSESRVSQIHSQ-------AIKRLRARL  231 (234)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf             999999999999999999980999999999987389989999999979789999999999-------999999987


No 99 
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=94.92  E-value=0.11  Score=30.25  Aligned_cols=54  Identities=22%  Similarity=0.260  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf             554677799999999972983899999977999999997414889998999999
Q gi|254781218|r  108 RLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI  161 (205)
Q Consensus       108 ~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI  161 (205)
                      ..|+-.+.+-||..+..++++|.++++.+|++++.+|+|.|-..-.....-..+
T Consensus       110 ~~d~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkGt~Mk~~kr~al  163 (177)
T pfam04814       110 REDPWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKGTPMKTQKRAAL  163 (177)
T ss_pred             HHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             728499999999999876884667876106559999999966884078999999


No 100
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322   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 , .    This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.79  E-value=0.015  Score=35.60  Aligned_cols=31  Identities=26%  Similarity=0.137  Sum_probs=23.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999998599889999984899999998877
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      |=.+|=-.++||.|+|+.+||||=+|||+|+
T Consensus       188 il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~  218 (229)
T TIGR02980       188 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR  218 (229)
T ss_pred             EEEEEEECCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             6100010697789999781843678899999


No 101
>PRK09526 lacI lac repressor; Reviewed
Probab=94.69  E-value=0.058  Score=31.97  Aligned_cols=48  Identities=17%  Similarity=-0.032  Sum_probs=37.6

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH---HHHHHCCCHH
Q ss_conf             98599889999984899999998877998889999999---9998289999
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALY---LRNEYEISFD   88 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~---la~~~~vs~d   88 (205)
                      +++..|-+++|+.+|+|.+|||++=||....|-++-.+   .++.++-.++
T Consensus         2 ~~k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn   52 (342)
T PRK09526          2 KSKPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPN   52 (342)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             989976999999989699999999789799999999999999998399978


No 102
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=94.68  E-value=0.28  Score=27.70  Aligned_cols=117  Identities=16%  Similarity=0.151  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf             99999999998--5998899999848999999988779988---899999999998289999961453221000023213
Q gi|254781218|r   32 VGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENGMCS---TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK  106 (205)
Q Consensus        32 iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G~~~---psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~  106 (205)
                      |-.-++.+...  +.-|-+++|+.+|+++..|..+-+....   .|++....- ..-+.++...+.++....+.......
T Consensus       107 i~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sld~~~~~-~~~~~~~~~~~~d~~~~~pe~~~~~~  185 (250)
T PRK07670        107 VEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSIDEKLHD-QDDGENVQVMIRDDKAVTPEEKLVKE  185 (250)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCHHHHHHHCCCCCCHHHHHHHH
T ss_conf             99999999998389998889987719999999999998754798036777778-88850477888524679999999999


Q ss_pred             HHHHH--H---HHHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             45546--7---77999---99999972983899999977999999997414
Q gi|254781218|r  107 KRLDP--Y---AIGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       107 ~~~d~--~---~iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .....  .   .+-.|   |=.+|-..++|+.+.|+.+|||+..+++++..
T Consensus       186 ~~~~~L~~~l~~L~~rEr~Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~  236 (250)
T PRK07670        186 ELIEQLAEKIKELNEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSK  236 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999855899999999997489868999999989799999999999


No 103
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=94.63  E-value=0.16  Score=29.23  Aligned_cols=56  Identities=20%  Similarity=0.229  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             7779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      .-|..-+-.+-..+||+|  +|+..|+++..+.+-.+....|++.++-++.+++|.-+
T Consensus        37 a~i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl   92 (100)
T COG3636          37 ALIAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL   92 (100)
T ss_pred             HHHHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf             999999999998657899--99994966999999847899975899999999808654


No 104
>PRK09492 treR trehalose repressor; Provisional
Probab=94.61  E-value=0.09  Score=30.77  Aligned_cols=48  Identities=23%  Similarity=0.004  Sum_probs=37.4

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH---HHHHHHHCCCHHH
Q ss_conf             85998899999848999999988779988899999---9999982899999
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA---LYLRNEYEISFDW   89 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l---~~la~~~~vs~d~   89 (205)
                      .+.+|.+++|+.+|+|.+|||++=||....|-++-   .+.++.++-.++-
T Consensus         2 ~kkvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn~   52 (315)
T PRK09492          2 QNKLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPSK   52 (315)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf             898879999999897999999997898999999999999999996998077


No 105
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.60  E-value=0.075  Score=31.27  Aligned_cols=48  Identities=21%  Similarity=0.115  Sum_probs=37.8

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH---HHHHHHHCCCHH
Q ss_conf             985998899999848999999988779988899999---999998289999
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA---LYLRNEYEISFD   88 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l---~~la~~~~vs~d   88 (205)
                      +.+.+|.+++|+.+|||.+|||++=||....|-++-   .+.++.++-.++
T Consensus         3 ~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~pn   53 (342)
T PRK10014          3 TAKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN   53 (342)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             999887999999989699999999779899999999999999999489978


No 106
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=94.55  E-value=0.091  Score=30.74  Aligned_cols=71  Identities=14%  Similarity=0.157  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH-----HCCCC--------CCCHHHHHHHHHHHCCCHHH
Q ss_conf             668999999999999999985998899999848999999988-----77998--------88999999999982899999
Q gi|254781218|r   23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF-----ENGMC--------STSIRYALYLRNEYEISFDW   89 (205)
Q Consensus        23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~-----E~G~~--------~psi~~l~~la~~~~vs~d~   89 (205)
                      ++......+.-.++..+.-..|+||.|+|+++|+|+.+++++     +.|..        ..+.+.--.|.+.|++.--+
T Consensus         5 ~~~~~~~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~   84 (321)
T COG2390           5 PDMLMEEERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAI   84 (321)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             30012689999999999984688799999883988999999999999879389996798765399999999965997699


Q ss_pred             HHCC
Q ss_conf             6145
Q gi|254781218|r   90 IYDG   93 (205)
Q Consensus        90 Ll~g   93 (205)
                      ...+
T Consensus        85 VVp~   88 (321)
T COG2390          85 VVPS   88 (321)
T ss_pred             EECC
T ss_conf             9748


No 107
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335   The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.   This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=94.46  E-value=0.071  Score=31.40  Aligned_cols=57  Identities=16%  Similarity=0.253  Sum_probs=42.5

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf             100015668999999999999999985--998899999848999999988779988899999
Q gi|254781218|r   17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYA   76 (205)
Q Consensus        17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l   76 (205)
                      +++..+++   -.++||.|++-++.-.  ++||.|++.++|+|-.+|.|==|.....+.+.-
T Consensus        30 L~L~Lt~~---Er~dl~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRGSn~Lk~~D~~~~   88 (95)
T TIGR01321        30 LELLLTAD---EREDLGSRVRIVEELLEGEMSQREIAEKLGVSIATITRGSNALKALDPEFK   88 (95)
T ss_pred             HHHHCCHH---HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHH
T ss_conf             99736863---799998799999999614897478888637616678787887516987889


No 108
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=94.45  E-value=0.027  Score=33.99  Aligned_cols=28  Identities=21%  Similarity=0.190  Sum_probs=24.8

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             8599889999984899999998877998
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGMC   69 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~~   69 (205)
                      .+||+|++.|+.++.|++.||.+|+--.
T Consensus        19 ~kGl~Q~eIAk~LkTtRaNvS~iEkrA~   46 (142)
T TIGR00721        19 EKGLKQKEIAKILKTTRANVSIIEKRAL   46 (142)
T ss_pred             HCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             3388878898772672013789888744


No 109
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.42  E-value=0.091  Score=30.73  Aligned_cols=36  Identities=17%  Similarity=0.144  Sum_probs=14.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             298389999997799999999741488999899999
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARK  160 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~k  160 (205)
                      +.+|..|+|+.+|+|..|+|+..||....+.++..+
T Consensus         5 kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~r   40 (342)
T PRK10014          5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGER   40 (342)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
T ss_conf             988799999998969999999977989999999999


No 110
>PRK09492 treR trehalose repressor; Provisional
Probab=94.32  E-value=0.12  Score=29.98  Aligned_cols=45  Identities=11%  Similarity=0.110  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHH
Q ss_conf             983899999977999999997414889998999999---998289999
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLD  170 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d  170 (205)
                      .+|.+|+|+.+|+|..|+|+..||....+.++-++|   ++.||..++
T Consensus         4 kvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn   51 (315)
T PRK09492          4 KLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPS   51 (315)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             887999999989799999999789899999999999999999699807


No 111
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors  are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor ,  required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions:  A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.19  E-value=0.02  Score=34.85  Aligned_cols=104  Identities=20%  Similarity=0.174  Sum_probs=72.5

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99859988999998489999999887799888999999999982899999614532210000232134554677799999
Q gi|254781218|r   40 RKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLK  119 (205)
Q Consensus        40 R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk  119 (205)
                      +.-+=||.+++|..+|++.|||||.=+|+.--+-.-++.|-..|-=.+..=-.+             ...+..+|=..|+
T Consensus       361 ~~LkPL~L~~vA~el~~heSTiSRai~~KYl~T~~G~f~Lk~FFS~~v~~~~~~-------------~~~S~~~ik~~~~  427 (477)
T TIGR02395       361 AALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSSGVSTESAE-------------GEASSTAIKALIK  427 (477)
T ss_pred             HCCCCCCHHHHHHHHCCCCCCEEEEECCCEEECCCCCHHHHHHCCHHHCCCCCC-------------HHHHHHHHHHHHH
T ss_conf             006886389999885889872463317735760764033654312012034565-------------0346999999999


Q ss_pred             HH----HHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHH
Q ss_conf             99----9972983899999977------9999999974148899989
Q gi|254781218|r  120 SI----RKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIK  156 (205)
Q Consensus       120 ~l----R~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~  156 (205)
                      ++    .+.+-||=.++|+.+.      |++.||.+|=.--.+|+-.
T Consensus       428 ~lI~~E~k~kPLSD~~i~~~L~e~G~i~~ARRTVaKYRe~L~ipss~  474 (477)
T TIGR02395       428 ELIAAEDKRKPLSDQKIAELLKEKGGIKIARRTVAKYREELGIPSSS  474 (477)
T ss_pred             HHHHCCCCCCCCCHHHHHHHHHHCCCEEEEEECHHHHHHHCCCCCCC
T ss_conf             99970178999766899999986298589960228989634889723


No 112
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=94.10  E-value=0.34  Score=27.17  Aligned_cols=90  Identities=12%  Similarity=0.116  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf             99999999999999859988999998489999999887799888999999999982899999614532210000232134
Q gi|254781218|r   28 YWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKK  107 (205)
Q Consensus        28 ~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~  107 (205)
                      |..++=+|+=...+ .|.|-.+.|...+||.++|.+|-+....-+                      ....+    ....
T Consensus         3 YS~DlR~rVl~~ve-~G~S~~eaA~~F~Is~~Tv~rWlkr~~~~~----------------------~~~~~----r~~~   55 (120)
T pfam01710         3 YSLDLRKKVIDYIE-SGGSITEASKVFQIGRATIYRWLKREKLGA----------------------LKVEP----RGRH   55 (120)
T ss_pred             CCHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHCHHCCC----------------------CCCCC----CCCC
T ss_conf             76899999999998-699999999993702999999985500147----------------------78888----8988


Q ss_pred             HHHHHHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             554677799999-99997298389999997799999999741
Q gi|254781218|r  108 RLDPYAIGARLK-SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       108 ~~d~~~iG~rLk-~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      ++|.    +.|+ .+...-++++.|.|+.+||++++|++...
T Consensus        56 Kid~----~~L~~~V~~~pD~tl~E~A~~~gVs~~tI~~aLk   93 (120)
T pfam01710        56 KIDR----DALKNDVKDNPDAYLKERAKKFGVTPSSIHYALK   93 (120)
T ss_pred             CCCH----HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             7789----9999999988672099999983987999999999


No 113
>PRK09526 lacI lac repressor; Reviewed
Probab=93.98  E-value=0.13  Score=29.83  Aligned_cols=37  Identities=16%  Similarity=0.208  Sum_probs=16.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf             2983899999977999999997414889998999999
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI  161 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI  161 (205)
                      +..|.+|.|+.+|+|.+|+|+..||....+.++-.+|
T Consensus         4 k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV   40 (342)
T PRK09526          4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKV   40 (342)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             9976999999989699999999789799999999999


No 114
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=93.98  E-value=0.31  Score=27.45  Aligned_cols=43  Identities=35%  Similarity=0.607  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             2983899999977999999997414889998999999998289
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK  167 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv  167 (205)
                      .-+|-+||++.+|++.+.+++|-||+..|+.+.+..|-..++-
T Consensus        22 ~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~   64 (238)
T PRK08558         22 KTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKP   64 (238)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             0268999998879799998505348878758999999998421


No 115
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   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 , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=93.95  E-value=0.02  Score=34.86  Aligned_cols=28  Identities=29%  Similarity=0.249  Sum_probs=16.6

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9998599889999984899999998877
Q gi|254781218|r   39 IRKANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        39 lR~~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      +|=-+..||.|+|..+||||=+|||+|+
T Consensus       194 LRYFKDkTQ~eVA~~LGISQVQVSRlEk  221 (231)
T TIGR02885       194 LRYFKDKTQTEVAKMLGISQVQVSRLEK  221 (231)
T ss_pred             EECCCCCHHHHHHHHCCCCCCHHHHHHH
T ss_conf             4101400179999771857001227899


No 116
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=93.87  E-value=0.24  Score=28.17  Aligned_cols=57  Identities=21%  Similarity=0.150  Sum_probs=46.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             999999997298389999997799999999741488999899999999828999995
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      .+||....++--+|..||..+|++..+++.-.+++..=....+.+.++.||++.|-+
T Consensus         6 ~kLrgrI~Ek~gtq~~Fa~~lg~se~tlslkln~~v~w~q~ei~kai~lL~i~~d~i   62 (69)
T pfam05339         6 SKLKGRILEKYGTQYNFASAIGLSERSLSLKLNDKVIWVANEIEKAIDLLGIPKDDI   62 (69)
T ss_pred             HHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
T ss_conf             886032889956798999995811768889876867753999999999968998887


No 117
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=93.87  E-value=0.11  Score=30.22  Aligned_cols=61  Identities=18%  Similarity=0.242  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHH
Q ss_conf             46777999999999729838999999779999999974148-89998999999998289999
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKHLD  170 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs~d  170 (205)
                      ...+++.-|+.+.+..+|+|.+.|+.+|++++.+|..-+|+ ...++..|.-.....|..++
T Consensus        25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~   86 (91)
T COG5606          25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID   86 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999999999999978779999998388873188998361457669999999997598552


No 118
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=93.85  E-value=0.29  Score=27.67  Aligned_cols=64  Identities=19%  Similarity=0.298  Sum_probs=46.4

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             100015668999999999999999985--9988999998489999999887799888999999999982
Q gi|254781218|r   17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~   83 (205)
                      +++.++|+   -++.+|.|++.+++-.  .++|.|++.++|++-.+|.|=-|.....+.+.--.+.+.+
T Consensus        34 L~llLTpd---EReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l   99 (103)
T COG2973          34 LTLLLTPD---EREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL   99 (103)
T ss_pred             HHHHCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCHHHHCCCCHHHHHHHHHHH
T ss_conf             99976876---8999999999999999563539999998586256550444442359878999999973


No 119
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=93.63  E-value=0.17  Score=29.00  Aligned_cols=46  Identities=15%  Similarity=0.090  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCC---CC---HHHHHHHHHHHCCCHHHH
Q ss_conf             98899999848999999988779988---89---999999999828999996
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCS---TS---IRYALYLRNEYEISFDWI   90 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~---ps---i~~l~~la~~~~vs~d~L   90 (205)
                      +|-+++|+++|||.+|||+.=||...   .|   -+...+.++.++-.++..
T Consensus         1 vTikDVA~~AGVS~aTVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~   52 (330)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGKAKQYRISDKTVEKVMAVVREHNYHPNAV   52 (330)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf             9789999997979989988838999888769999999999999968994888


No 120
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=93.53  E-value=0.46  Score=26.40  Aligned_cols=54  Identities=7%  Similarity=0.042  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      |..-+-.+-..+|+||  +|++.|+++..+.+-=+...+|+++++.++++++++-+
T Consensus        39 i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl   92 (100)
T COG3636          39 IAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL   92 (100)
T ss_pred             HHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf             9999999998657899--99994966999999847899975899999999808654


No 121
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=93.52  E-value=0.19  Score=28.78  Aligned_cols=35  Identities=14%  Similarity=0.209  Sum_probs=18.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             38999999779999999974148899989999999
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIK  162 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa  162 (205)
                      |..|+|+..|+|..|+|+..||....+.++-.+|-
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~   35 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVE   35 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             99999999897999999998797989999999999


No 122
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=93.49  E-value=0.61  Score=25.64  Aligned_cols=129  Identities=13%  Similarity=0.165  Sum_probs=56.7

Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf             0015668999999999999999985--998899999848999999988779988-8999999999982899999614532
Q gi|254781218|r   19 LIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDGEV   95 (205)
Q Consensus        19 ~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~ge~   95 (205)
                      +-++.-+.+....+..-.+.+....  .-|-+++|+.+|++...|..+..-... .|++.-  +...-+.++..++.++.
T Consensus       235 IRiP~h~~e~~~k~~r~~~~l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~--vg~d~~~~l~d~i~D~~  312 (398)
T PRK05901        235 IRIPVHMVETINKLGRIERELLQELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKT--IGDEGDSQFGDFIEDSE  312 (398)
T ss_pred             EECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCC--CCCCCCCCHHHHCCCCC
T ss_conf             5233239999999999999999984899999999988199999999999972898556787--78998651866416999


Q ss_pred             CCCCCCCCCC---HHHHHH--HHHHHHHHHH-HHH------CCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             2100002321---345546--7779999999-997------2983899999977999999997414
Q gi|254781218|r   96 IDRRYEDVTN---KKRLDP--YAIGARLKSI-RKD------KGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        96 ~~~~~~~~~~---~~~~d~--~~iG~rLk~l-R~~------~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ...+......   ...+..  ..+..|=+.+ +..      ..+|..++|+.+|+|+..+.++|..
T Consensus       313 ~~~p~~~~~~~~l~~~l~~~L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~k  378 (398)
T PRK05901        313 AVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESK  378 (398)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999999999998389999999999975899989603999998979699999999999


No 123
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=93.38  E-value=0.12  Score=29.97  Aligned_cols=15  Identities=20%  Similarity=0.317  Sum_probs=5.8

Q ss_pred             CCHHHHHHHHCCCHH
Q ss_conf             838999999779999
Q gi|254781218|r  127 MSQIEFGKLLGMPNS  141 (205)
Q Consensus       127 lsq~elA~~lgis~~  141 (205)
                      -|-.|+|+.+|++..
T Consensus       127 pt~~EIA~~L~i~~e  141 (247)
T COG1191         127 PTDEEIAEELGIDKE  141 (247)
T ss_pred             CCHHHHHHHHCCCHH
T ss_conf             868999989698999


No 124
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=93.08  E-value=0.15  Score=29.34  Aligned_cols=52  Identities=25%  Similarity=0.362  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             77799999999972983899999977------9999999974148899989999999982
Q gi|254781218|r  112 YAIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       112 ~~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      ..+....|+.|...|+||.+++..+|      .|+++|+++|+=.  .+...+.++.-+|
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~--LS~kn~~kLkPiL   67 (75)
T smart00352       10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL   67 (75)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf             999999999898737759999999998618643146888988605--4798899889999


No 125
>TIGR00673 cynS cyanate hydratase; InterPro: IPR008076   Cyanase, an enzyme found in bacteria and plants, catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate .    The cyanate lyase monomer is composed of two domains: an N-terminal domain that shows structural similarity to the DNA-binding alpha-helix bundle motif, and a C-terminal domain that has an 'open fold' that shows no structural similarity to other proteins .    The enzyme is active as a homodecamer of 17kDa subunits, and displays half-site binding of substrates or substrate analogues. The dimer structure reveals the C-terminal domains to be intertwined; the decamer is formed from a pentamer of these dimers. The active site of the enzyme is located between dimers and comprises residues from four adjacent subunits of the homodecamer.     Synonym(s): cyanase lyase, cyanase hydrolase ; GO: 0016836 hydro-lyase activity, 0008152 metabolic process.
Probab=93.08  E-value=0.7  Score=25.25  Aligned_cols=106  Identities=14%  Similarity=0.083  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf             99999999999999985998899999848999999988779988899999999998289999961453221000023213
Q gi|254781218|r   27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK  106 (205)
Q Consensus        27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~  106 (205)
                      +-.-+|...|=...+.+|||-++++..+|.++-.|...=-|....+.+-...+++.|+.+=|.+.--...+.. ..+...
T Consensus         9 nirldl~~~lle~Kk~kgltfad~~~~lG~~ev~~aa~~ygqa~a~~dea~~v~~~L~L~ed~~~eL~~aP~r-~~~~pv   87 (156)
T TIGR00673         9 NIRLDLAKKLLEAKKKKGLTFADVEDKLGKAEVYVAAVLYGQAAADADEAKKVAELLDLEEDEVAELKDAPLR-EGLDPV   87 (156)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC-CCCCCC
T ss_conf             2577789999998873599789986531875999999998420688889999998709981134665406666-888898


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             45546777999999999729838999999
Q gi|254781218|r  107 KRLDPYAIGARLKSIRKDKGMSQIEFGKL  135 (205)
Q Consensus       107 ~~~d~~~iG~rLk~lR~~~glsq~elA~~  135 (205)
                      -..||..  .|+=++..-.|++.++++..
T Consensus        88 ~PTDP~~--YRfYE~~~vYG~~lK~v~HE  114 (156)
T TIGR00673        88 VPTDPLV--YRFYEVLQVYGTALKEVVHE  114 (156)
T ss_pred             CCCCCHH--HHHHHHHHHHCHHHHHHHHH
T ss_conf             9677606--77788888716036776422


No 126
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=93.07  E-value=0.26  Score=27.89  Aligned_cols=37  Identities=19%  Similarity=-0.014  Sum_probs=30.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             8899999848999999988779988899999999998
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNE   82 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~   82 (205)
                      |-+++|+.+|+|.++||++=||....+-++-.++-.+
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~~~   37 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVEAA   37 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             9999999989799999999879798999999999999


No 127
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=92.97  E-value=0.73  Score=25.15  Aligned_cols=107  Identities=16%  Similarity=0.263  Sum_probs=55.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHH-HHCCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CC
Q ss_conf             599889999984899999998-87799------888999999999982---8999996145---------3221----00
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNL-FENGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RR   99 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~-~E~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~   99 (205)
                      +.-|..+.|.++|++...+-+ ++.|.      ....+..++.||+-|   +++++.|+..         +-+|    .+
T Consensus        55 ~~~~~~~~a~a~~~~~~~l~~~~~~g~~A~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~r  134 (318)
T PRK07405         55 REPSDLEWAKAAKLSEEELRRAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYR  134 (318)
T ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             78746788876045689999987627999999999819999999986657997988999986899999999709765980


Q ss_pred             CC---------------CCCCHHHHHHHHHHHHHHHHH-------HH--CCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             00---------------232134554677799999999-------97--2983899999977999999997414
Q gi|254781218|r  100 YE---------------DVTNKKRLDPYAIGARLKSIR-------KD--KGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       100 ~~---------------~~~~~~~~d~~~iG~rLk~lR-------~~--~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      |+               .........|..+..++..++       ..  +.-|..++|+.+|++...+..+..-
T Consensus       135 FSTYA~wWIrq~I~r~i~~~~r~IRlP~~~~~~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~  208 (318)
T PRK07405        135 FSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLER  208 (318)
T ss_pred             EEEEHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             22200999999999999976985168778999999999999999987189864899998859999999999998


No 128
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=92.84  E-value=0.28  Score=27.68  Aligned_cols=44  Identities=16%  Similarity=-0.043  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH---HHHHHHCCCHH
Q ss_conf             988999998489999999887799888999999---99998289999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYAL---YLRNEYEISFD   88 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~---~la~~~~vs~d   88 (205)
                      .|-+++|+.+|||.+|||+.=||....+-++--   ..++.++-.++
T Consensus         2 vTi~DVA~~AGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~eLgY~Pn   48 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNNSALVSPDTREAVMKAVSELGYRPN   48 (346)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             97899999989799999999779499999999999999999499848


No 129
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=92.84  E-value=0.27  Score=27.78  Aligned_cols=27  Identities=30%  Similarity=0.168  Sum_probs=15.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             889999984899999998877998889
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCSTS   72 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~ps   72 (205)
                      |.+|+|+.+|+|.+++|++=||....+
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs   28 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNGNGRVS   28 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCC
T ss_conf             899999998959999999977999899


No 130
>KOG1168 consensus
Probab=92.77  E-value=0.065  Score=31.65  Aligned_cols=128  Identities=16%  Similarity=0.180  Sum_probs=68.8

Q ss_pred             HHHHH---HHHHHHHHHHHHHHHCCCCHHHHHHHH---------CCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             66899---999999999999998599889999984---------899999998877998889999999999828999996
Q gi|254781218|r   23 PEIRQ---YWKDVGTRIKDIRKANNKTQKEMAIGA---------NQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI   90 (205)
Q Consensus        23 ~~~~~---~~~~iG~rik~lR~~~gltQ~elA~~~---------gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L   90 (205)
                      +++..   -.+.+++|.|+.|...|.||.++++++         .+|+++|-++|+=.-  |-..++.|--.+.   .||
T Consensus       210 sD~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTL--SHNNMiALKPILq---aWL  284 (385)
T KOG1168         210 SDMDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTL--SHNNMIALKPILQ---AWL  284 (385)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHH---HHH
T ss_conf             55678889999999998754543064277778898727688755323121332100002--4576310668999---999


Q ss_pred             HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             145322100002321345546777999999999729838999999779999999974148899989999999982899
Q gi|254781218|r   91 YDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus        91 l~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      =..|..-+.-..++.-..+  +.-|++=   |+.-.+        .---+.++-.|-.-.-.|+-+.+..||+-|+..
T Consensus       285 EeAE~a~keK~~~pd~~~l--~~~~ekK---RKRTSI--------AAPEKRsLEayFavQPRPS~EkIAaIAekLDLK  349 (385)
T KOG1168         285 EEAEAAMKEKDTKPDINEL--LPGGEKK---RKRTSI--------AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK  349 (385)
T ss_pred             HHHHHHHHHHCCCCCHHHC--CCCCCCC---CCCCCC--------CCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999998742358862321--6763111---102332--------484201288885448998600789999863211


No 131
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=92.77  E-value=0.78  Score=24.97  Aligned_cols=125  Identities=13%  Similarity=0.140  Sum_probs=66.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCC---HHHHHH--HHHHH
Q ss_conf             59988999998489999999887799-8889999999999828999996145322100002321---345546--77799
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTN---KKRLDP--YAIGA  116 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~---~~~~d~--~~iG~  116 (205)
                      +.-|-+++|+.+|++...|..+-.-. ...|++.-+  ..-=+.++-.++.++....+......   ...+..  ..+..
T Consensus       191 r~pt~eEIA~~lg~~~~~v~~~l~~~~~~~SLD~pv--~~d~~~tl~d~l~D~~~~~pd~~~~~~~l~~~l~~~L~~L~~  268 (328)
T PRK05657        191 HEPSAEEIAELLDKPVDDVSRMLALNERITSLDAPL--GGDPEKSLLDILADDQENGPEDTTQDDDLKQSIVKWLFELND  268 (328)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCC--CCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf             999899999996959999999997458763444535--899851178886277899999999999999999999806999


Q ss_pred             HHHHHHH-------HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             9999999-------72983899999977999999997414889998999999998289999952
Q gi|254781218|r  117 RLKSIRK-------DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       117 rLk~lR~-------~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      |=+.+..       ...+|+.++|+.+|+|+..+.++|+.    -+..|.+..+.-|++.|.||
T Consensus       269 REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~----AL~KLR~~l~~~~l~~~~~~  328 (328)
T PRK05657        269 KQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSKDALF  328 (328)
T ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCCHHHCC
T ss_conf             9999999980889989605999998969799999999999----99998799998699734249


No 132
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=92.68  E-value=0.072  Score=31.38  Aligned_cols=47  Identities=19%  Similarity=0.191  Sum_probs=32.3

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHH---HHHHHHHHHCCCHH
Q ss_conf             9859988999998489999999887799888999---99999998289999
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIR---YALYLRNEYEISFD   88 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~---~l~~la~~~~vs~d   88 (205)
                      ..+||||++.|..++.++..||.+|+.-.. .|+   .-+.|.+.++-++.
T Consensus        20 RekG~tQ~eIA~~L~TTraNvSaIEkrA~e-nIekarnTL~l~~~i~spv~   69 (143)
T COG1356          20 REKGLTQSEIARILKTTRANVSAIEKRALE-NIEKARNTLLLWEQINSPVS   69 (143)
T ss_pred             HHCCCCHHHHHHHHCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHCCCEE
T ss_conf             640564899999975451017999999999-89999889999998469758


No 133
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=92.66  E-value=0.32  Score=27.35  Aligned_cols=45  Identities=13%  Similarity=0.150  Sum_probs=36.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHHH
Q ss_conf             3899999977999999997414889998999999---99828999995
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLDWI  172 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d~L  172 (205)
                      |..|+|+..|+|..|+|+..||....+.++-.+|   ++.+|..++..
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV~~~a~~lgY~pn~~   49 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNRV   49 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf             899999998959999999977999899999999999999978998999


No 134
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=92.59  E-value=0.7  Score=25.25  Aligned_cols=67  Identities=19%  Similarity=0.173  Sum_probs=46.1

Q ss_pred             HHHHHHHHHH-HHHHHCCCHHHHHHHH----HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
Q ss_conf             7777666543-3310001566899999----99999999999859988999998489999999887799888
Q gi|254781218|r    5 PFLETSLKSL-QEYTLIITPEIRQYWK----DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST   71 (205)
Q Consensus         5 ~~~~~~~~~~-~~~~~~~~~~~~~~~~----~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~p   71 (205)
                      |=++.+++.+ +|.+.....++.++..    .+.+-||..-.++++.|.+++...|+++|+||.+-|--..+
T Consensus        84 pPi~kele~l~~EEaa~qra~Ve~ll~~d~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkGt~M  155 (177)
T pfam04814        84 PPILKELERLSPEEAAHQRAEVDRLLREDPWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKGTPM  155 (177)
T ss_pred             CCCCHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCCCCC
T ss_conf             876603222582588888999999997284999999999998768846678761065599999999668840


No 135
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=92.58  E-value=0.31  Score=27.45  Aligned_cols=44  Identities=16%  Similarity=-0.062  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHH
Q ss_conf             9889999984899999998877998889999---9999998289999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFD   88 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d   88 (205)
                      -|-+++|+.+|||.+|||+.=||....+-++   ....++.++-.++
T Consensus         2 aTIkDIA~~AGVS~sTVSrvLN~~~~Vs~~Tr~rV~~aa~eLgY~Pn   48 (342)
T PRK10727          2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPN   48 (342)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             98899999979699999999779799999999999999999399858


No 136
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=92.45  E-value=0.86  Score=24.72  Aligned_cols=130  Identities=14%  Similarity=0.148  Sum_probs=55.9

Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             00015668999999999999999985--998899999848999999988779988-899999999998289999961453
Q gi|254781218|r   18 TLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDGE   94 (205)
Q Consensus        18 ~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~ge   94 (205)
                      ++-++..+.+....+-.--+.+....  .-|.+++|+.+|++...|..+.+-... .|++.-  +...-+.++..++..+
T Consensus       205 ~IRiPvh~~e~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~e~V~~i~~~~~~~~SLd~p--vg~e~~s~l~d~i~D~  282 (368)
T PRK09210        205 TIRIPVHMVETINKLIRVQRQLLQELGRDPTPEEIAEEMDMPPEKVREILKIAQEPVSLETP--IGEEDDSHLGDFIEDQ  282 (368)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCC--CCCCCCCHHHHHHCCC
T ss_conf             51354249999999999999999983899988999989499899999999853888566886--7887755287552489


Q ss_pred             CCCCCCCCCCC---HHHHHH--HHHHHHHHHH-HHHCC------CCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             22100002321---345546--7779999999-99729------83899999977999999997414
Q gi|254781218|r   95 VIDRRYEDVTN---KKRLDP--YAIGARLKSI-RKDKG------MSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus        95 ~~~~~~~~~~~---~~~~d~--~~iG~rLk~l-R~~~g------lsq~elA~~lgis~~tis~~E~g  149 (205)
                      ....+......   +..+..  ..+..|=+.+ +...|      +|..++|+.+|+|+..+.++|..
T Consensus       283 ~~~~p~e~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~k  349 (368)
T PRK09210        283 DATSPADHAAYELLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK  349 (368)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999899999999999999998179999999999975999689614999998969798999999999


No 137
>pfam02376 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein .
Probab=92.36  E-value=0.3  Score=27.56  Aligned_cols=40  Identities=30%  Similarity=0.422  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCHHHHHHHHC
Q ss_conf             5467779999999997298389999997-799999999741
Q gi|254781218|r  109 LDPYAIGARLKSIRKDKGMSQIEFGKLL-GMPNSTLSNYEQ  148 (205)
Q Consensus       109 ~d~~~iG~rLk~lR~~~glsq~elA~~l-gis~~tis~~E~  148 (205)
                      +|...|..+|++..+.++++|.-||+.+ |.++.++|...+
T Consensus         3 ldT~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~   43 (81)
T pfam02376         3 LDTAEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR   43 (81)
T ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf             88999999999999994976999999997318378999881


No 138
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=92.30  E-value=0.36  Score=27.07  Aligned_cols=46  Identities=17%  Similarity=-0.086  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHH
Q ss_conf             998899999848999999988779988899999999---9982899999
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL---RNEYEISFDW   89 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~l---a~~~~vs~d~   89 (205)
                      .-|-+++|+.+|||.+|||+.=||....|-++-.++   ++.++-.++.
T Consensus         9 MaTikDIA~~aGVS~sTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~   57 (341)
T PRK11041          9 MATMKDVALKAGVSTATVSRALMNPEKVSQSTRNRVEQAVLEVGYSPQS   57 (341)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf             8889999999797999999997898999999999999999981998388


No 139
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=92.24  E-value=0.36  Score=27.04  Aligned_cols=44  Identities=18%  Similarity=-0.032  Sum_probs=34.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHHH
Q ss_conf             889999984899999998877998889999---99999982899999
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFDW   89 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d~   89 (205)
                      |-+++|+.+|||.+|||+.=||....|-++   ....++.++=.++.
T Consensus         3 TikDIA~~AGVS~aTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~   49 (335)
T PRK10703          3 TIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA   49 (335)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf             88999999798999999996896998999999999999982999787


No 140
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=92.02  E-value=0.59  Score=25.73  Aligned_cols=55  Identities=16%  Similarity=0.068  Sum_probs=49.8

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHH
Q ss_conf             9999999859988999998489999999887799-888999999999982899999
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDW   89 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~   89 (205)
                      -++..|++.|++..++|...|+++.+.+..-+|+ .+||...|..|.+.+++.+.-
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   61 (411)
T PRK08099          6 YLKTAIKQQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR   61 (411)
T ss_pred             HHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHH
T ss_conf             99999998488298876542340999999862524894378999999995886402


No 141
>PRK01381 Trp operon repressor; Provisional
Probab=91.93  E-value=0.38  Score=26.88  Aligned_cols=64  Identities=17%  Similarity=0.276  Sum_probs=44.7

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHH-HCC-CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             1000156689999999999999999-859-988999998489999999887799888999999999982
Q gi|254781218|r   17 YTLIITPEIRQYWKDVGTRIKDIRK-ANN-KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        17 ~~~~~~~~~~~~~~~iG~rik~lR~-~~g-ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~   83 (205)
                      +++.++|+   -.+.||.|++.++. .+| ++|.++|+.+|++-.+|.|=-|-....+.+.-..|.+.+
T Consensus        29 l~~lLTp~---Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~~~l   94 (99)
T PRK01381         29 LTLLLTPD---EREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQLL   94 (99)
T ss_pred             HHHHCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHHHHH
T ss_conf             99978999---9999999999999999487649999998497402000026988539999999999986


No 142
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=91.89  E-value=0.44  Score=26.51  Aligned_cols=43  Identities=21%  Similarity=0.002  Sum_probs=33.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCH
Q ss_conf             98899999848999999988779988899999999---99828999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL---RNEYEISF   87 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~l---a~~~~vs~   87 (205)
                      .|.+++|+.+|||.+|+|+.-||....|-++--++   ++.++--+
T Consensus         1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~p   46 (333)
T COG1609           1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRP   46 (333)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             9689999996899989889877999879999999999999978998


No 143
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=91.83  E-value=0.19  Score=28.81  Aligned_cols=28  Identities=25%  Similarity=0.405  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             8389999997799999999741488999
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQGRTIPE  154 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g~~~Ps  154 (205)
                      |+..|+|+.+|+++.|+.+|+.....|.
T Consensus         1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~   28 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLKA   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCE
T ss_conf             9889999997989999999998799431


No 144
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=91.73  E-value=0.51  Score=26.11  Aligned_cols=42  Identities=21%  Similarity=0.124  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCC--CCC---HHHHHHHHHHHCCC
Q ss_conf             9889999984899999998877998--889---99999999982899
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMC--STS---IRYALYLRNEYEIS   86 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~--~ps---i~~l~~la~~~~vs   86 (205)
                      -|-+++|+.+|||.+|||++=||..  ..+   -+...+.++.++-.
T Consensus         2 aTikDVA~~AGVS~sTVSrvLn~~~~~~V~~~Tr~rV~~aa~elgY~   48 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYK   48 (327)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             96899999978889999999589899996899999999999996899


No 145
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=91.60  E-value=0.15  Score=29.36  Aligned_cols=69  Identities=10%  Similarity=0.267  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      |+-.|||++.|++..+|-.||+ |.-.|+-..--.    |              ..|.    ......  + .-|+.++.
T Consensus         1 M~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g----~--------------r~Y~----~~~v~r--L-~~Ir~l~~   55 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPN----Q--------------AEYS----EAHVER--L-RLIRALQQ   55 (95)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCC----C--------------EECC----HHHHHH--H-HHHHHHHH
T ss_conf             97899999989789999999997899987769998----7--------------1549----999999--9-99999999


Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             729838999999779
Q gi|254781218|r  124 DKGMSQIEFGKLLGM  138 (205)
Q Consensus       124 ~~glsq~elA~~lgi  138 (205)
                      ..||+..+..+.++.
T Consensus        56 ~lG~sL~eIr~lL~~   70 (95)
T cd04780          56 EGGLPISQIKEVLDA   70 (95)
T ss_pred             HCCCCHHHHHHHHHC
T ss_conf             369999999999843


No 146
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=91.42  E-value=0.54  Score=25.95  Aligned_cols=12  Identities=8%  Similarity=-0.100  Sum_probs=3.8

Q ss_pred             HHHHHHHHCCCC
Q ss_conf             999999985998
Q gi|254781218|r   35 RIKDIRKANNKT   46 (205)
Q Consensus        35 rik~lR~~~glt   46 (205)
                      ||+..=++.|+.
T Consensus        35 rV~~aa~eLgY~   46 (335)
T PRK10703         35 AVWAAIKELHYS   46 (335)
T ss_pred             HHHHHHHHHCCC
T ss_conf             999999982999


No 147
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=91.25  E-value=0.6  Score=25.66  Aligned_cols=47  Identities=19%  Similarity=0.065  Sum_probs=33.3

Q ss_pred             HHHHHHHHCCCCHHHHHHHHC--CCHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             999999985998899999848--99999998877998889999999999
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGAN--QLESAVNLFENGMCSTSIRYALYLRN   81 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~g--is~~~is~~E~G~~~psi~~l~~la~   81 (205)
                      .+..+|+..-||-.|-|..++  ++..+-.+||+|...++.++.-++..
T Consensus         4 ELQAlR~if~mti~EaA~~I~~~~~s~~Wq~WE~G~~~IP~~i~~~~~~   52 (117)
T pfam08965         4 ELQALRKILFLTIVEAAELIGQSVSSRTWQRWEKGDIAIPDEVEAKLRK   52 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             8999999999649999999946888899999975898899999999999


No 148
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=91.23  E-value=0.53  Score=26.02  Aligned_cols=46  Identities=15%  Similarity=0.162  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHHH
Q ss_conf             83899999977999999997414889998999999---99828999995
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLDWI  172 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d~L  172 (205)
                      .|.+|+|+..|+|++|+|+..||....+-++-++|   ++.||..++..
T Consensus         1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~pn~~   49 (333)
T COG1609           1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAV   49 (333)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf             9689999996899989889877999879999999999999978998989


No 149
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=91.16  E-value=0.35  Score=27.09  Aligned_cols=51  Identities=24%  Similarity=0.361  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             7799999999972983899999977------9999999974148899989999999982
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      .+....|+.|...|+||.+++..+|      .|+++|+++|+=.  .+...+.++--+|
T Consensus        11 ~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~--Ls~kn~~kLkP~L   67 (75)
T pfam00157        11 QFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ--LSFKNMCKLKPLL   67 (75)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf             99999999898737759999999998708654235888888504--4799899889999


No 150
>KOG3802 consensus
Probab=91.15  E-value=0.25  Score=28.00  Aligned_cols=59  Identities=22%  Similarity=0.397  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             4677799999999972983899999977------999999997414889998999999998289999952
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      +-..+++-.|+.|...|+||.|++-.+|      .|+.||+|+|.=.  .+...+-||.=+|.   .||=
T Consensus       207 ELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALq--LSFKNMCKLKPLL~---KWLe  271 (398)
T KOG3802         207 ELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQ--LSFKNMCKLKPLLE---KWLE  271 (398)
T ss_pred             HHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHC--CCHHHHHHHHHHHH---HHHH
T ss_conf             99999999876500036442678889876507644302666767625--47787766379999---9999


No 151
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=91.05  E-value=0.22  Score=28.33  Aligned_cols=113  Identities=16%  Similarity=0.240  Sum_probs=53.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC---HHHHHCCCCCCC-CCCCC---CCHHHHHHHH---HH
Q ss_conf             88999998489999999887799888999999999982899---999614532210-00023---2134554677---79
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEIS---FDWIYDGEVIDR-RYEDV---TNKKRLDPYA---IG  115 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs---~d~Ll~ge~~~~-~~~~~---~~~~~~d~~~---iG  115 (205)
                      +.+++|+.+|++...|..++.....+++..-..+...=+-+   +|.+.+....+. .....   .........+   +-
T Consensus       150 ~~~eiA~~l~~~~~~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~d~~~~p~~~~e~~~~~~~~~~~L~~~l~~L~  229 (289)
T PRK07500        150 IHREIATALGVSLSDVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLVDDSPLPDEIVESSIDGERRRQWLTQALQTLN  229 (289)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             39999988099999999999997379866668067877774015554046889838999999999999999999985499


Q ss_pred             HHHHH---HH--HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             99999---99--9729838999999779999999974148899989999999982
Q gi|254781218|r  116 ARLKS---IR--KDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       116 ~rLk~---lR--~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      .|=+.   +|  ...++|+.|+|+.+|+|+..++++|+       ..+.+|-+.|
T Consensus       230 eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQIe~-------kAL~KLR~~L  277 (289)
T PRK07500        230 ERELFIIRERRLREDGATLEALGEELGISKERVRQIEA-------RALEKLRRAL  277 (289)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf             99999999976689985899999997979999999999-------9999999999


No 152
>PRK05572 sporulation sigma factor SigF; Validated
Probab=91.02  E-value=1.2  Score=23.75  Aligned_cols=121  Identities=18%  Similarity=0.166  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf             566899999999999999998--599889999984899999998877998889999999999828999996145322100
Q gi|254781218|r   22 TPEIRQYWKDVGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR   99 (205)
Q Consensus        22 ~~~~~~~~~~iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~   99 (205)
                      +..+.+....+..-...+...  +.-|-.++|+.+|++...|...-.....+.  .+......=+-+...+++. ..+  
T Consensus       108 p~~~~~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~~~~--sl~~~~~~~d~~~~~l~d~-~~~--  182 (251)
T PRK05572        108 SRSLKELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASRSPQ--SIHETVHENDGDPITLLDQ-IAD--  182 (251)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCCHHHHHHH-CCC--
T ss_conf             68899999889999999999878899899999997939999999998817987--5346666789971566541-268--


Q ss_pred             CCCCCCHHHHHHHH-------HHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             00232134554677-------7999---99999972983899999977999999997414
Q gi|254781218|r  100 YEDVTNKKRLDPYA-------IGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       100 ~~~~~~~~~~d~~~-------iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                        +.......+...       +-.|   |=.+|-..++|+.|.|+.+|+|+..++++++.
T Consensus       183 --~~~~~~~~~~~~L~~~l~~L~~rEr~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~  240 (251)
T PRK05572        183 --QSEEDDWFDKIALKEAIRELDERERLIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKK  240 (251)
T ss_pred             --CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             --7346899999999999972899999999998178988999999979799999999999


No 153
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=90.63  E-value=1.3  Score=23.53  Aligned_cols=70  Identities=23%  Similarity=0.333  Sum_probs=43.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      +|-.++|+.+|+|.++|-.|| .|.-.|. ..    .+.|.+              |+    ...+.   -=.+|..++.
T Consensus         1 ytIgevA~~~Gvs~~tlRyYE~~GLl~P~-R~----~~gyR~--------------Y~----~~dl~---rL~~I~~l~~   54 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPE-RS----EGRYRL--------------YS----EEDLK---RLERILRLRE   54 (96)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-CC----CCCCCC--------------CC----HHHHH---HHHHHHHHHH
T ss_conf             94889999989799999999987998998-69----999823--------------59----99999---9999999999


Q ss_pred             HCCCCHHHHHHHHCCCH
Q ss_conf             72983899999977999
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPN  140 (205)
Q Consensus       124 ~~glsq~elA~~lgis~  140 (205)
                      ..|+|..+..+.+..+.
T Consensus        55 ~lGfsL~eIk~lL~~~~   71 (96)
T cd04774          55 VLGFSLQEVTHFLERPL   71 (96)
T ss_pred             HCCCCHHHHHHHHCCCC
T ss_conf             57998999999981988


No 154
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=90.58  E-value=0.55  Score=25.92  Aligned_cols=38  Identities=13%  Similarity=0.136  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             999999999999--98599889999984899999998877
Q gi|254781218|r   29 WKDVGTRIKDIR--KANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        29 ~~~iG~rik~lR--~~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      .+.+++|++-.+  -..+.||.++|+.+|+|-.+|+|.-+
T Consensus        32 ~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr   71 (88)
T pfam01371        32 REALAQRLRIAKELLRGELSQREIAQELGASIATITRGSN   71 (88)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999999997899899999985985231478899


No 155
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=90.52  E-value=1.2  Score=23.76  Aligned_cols=69  Identities=14%  Similarity=0.140  Sum_probs=40.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99889999984899999998877998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      .||.+++|..+|+|++++++.=+              +.+++++..++..                  ..+ ...+.+..
T Consensus         1 plsl~~lA~~~~~S~~~l~~~f~--------------~~~g~s~~~~i~~------------------~Rl-~~a~~~L~   47 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFK--------------KETGTTPKQYLRD------------------RRL-ERARRLLR   47 (84)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH--------------HHHCCCHHHHHHH------------------HHH-HHHHHHHH
T ss_conf             98999999988909999999999--------------9889399999999------------------999-99999998


Q ss_pred             HCCCCHHHHHHHHCC-CHHHHHH
Q ss_conf             729838999999779-9999999
Q gi|254781218|r  124 DKGMSQIEFGKLLGM-PNSTLSN  145 (205)
Q Consensus       124 ~~glsq~elA~~lgi-s~~tis~  145 (205)
                      .-+++..++|..+|. +.+.+.+
T Consensus        48 ~~~~~i~~ia~~~Gy~~~s~f~r   70 (84)
T smart00342       48 DTDLSVTEIALRVGFSSQSYFSR   70 (84)
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHH
T ss_conf             57634999988819999999999


No 156
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=90.41  E-value=0.31  Score=27.43  Aligned_cols=44  Identities=20%  Similarity=0.327  Sum_probs=22.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHHH
Q ss_conf             89999997799999999741488999899999999828--999995
Q gi|254781218|r  129 QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK--KHLDWI  172 (205)
Q Consensus       129 q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg--vs~d~L  172 (205)
                      |..||.++|+++.++++|-+|.+.......-.|.++.+  |+...|
T Consensus        15 q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~el   60 (96)
T COG4197          15 QKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREEL   60 (96)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHH
T ss_conf             8999999726814788776520104755332899985377159997


No 157
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=90.23  E-value=1.2  Score=23.89  Aligned_cols=54  Identities=22%  Similarity=0.128  Sum_probs=34.8

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      .|......+|.|...++...|++.+|+.+-   -..|-..--.-||+++||.+..+-
T Consensus        12 DIiAAL~KrG~sLa~Lsr~aGls~sTL~nA---L~rpwPKgE~iIA~aLGv~P~eIW   65 (90)
T PRK10344         12 DIIAGLRKKGTSMAAESRRNGLSSSTLANA---LSRPWPKGEMIIAKALGTDPWVIW   65 (90)
T ss_pred             HHHHHHHHCCCCHHHHHHHCCCCHHHHHHH---HCCCCCHHHHHHHHHHCCCHHHCC
T ss_conf             999999986886999999909986889998---748995679999999787988809


No 158
>pfam08535 KorB KorB domain. This family consists of 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.
Probab=89.94  E-value=0.92  Score=24.52  Aligned_cols=44  Identities=25%  Similarity=0.227  Sum_probs=29.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH--------------CCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             59988999998489999999887--------------7998889999999999828999
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFE--------------NGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E--------------~G~~~psi~~l~~la~~~~vs~   87 (205)
                      .|++|.++|+.+|-+.+.||++-              +|.. -+++.|..|...+.-.+
T Consensus         2 ~G~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~~-~dv~~l~eL~~~~~k~p   59 (93)
T pfam08535         2 KGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGRC-SDIRALYELRRAARKHP   59 (93)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCCC-CCHHHHHHHHHHHHHCH
T ss_conf             98779999999788988999999983486999999874776-87999999999999799


No 159
>PHA00675 hypothetical protein
Probab=89.53  E-value=0.6  Score=25.65  Aligned_cols=35  Identities=11%  Similarity=0.216  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             79999999997298389999997799999999741
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-.+||.+|+..||+-..||...+++++++.++.+
T Consensus        27 ~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkICq   61 (78)
T PHA00675         27 EVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999987284389999997275689999988


No 160
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209   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 , .    The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage.   Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=89.53  E-value=0.2  Score=28.57  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             98389999997799999999741
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~  148 (205)
                      ..||.|.|..+|||++.+|++|.
T Consensus       195 ~~tQREIA~~LgISRSYVSRIEK  217 (228)
T TIGR02846       195 EKTQREIAKILGISRSYVSRIEK  217 (228)
T ss_pred             CCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             54178998770865004548889


No 161
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=89.52  E-value=0.8  Score=24.89  Aligned_cols=42  Identities=19%  Similarity=-0.092  Sum_probs=32.9

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHHH
Q ss_conf             9999984899999998877998889999---99999982899999
Q gi|254781218|r   48 KEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFDW   89 (205)
Q Consensus        48 ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d~   89 (205)
                      +++|+.+|||.+|||+.=||....|-++   ....++.++=.++.
T Consensus         2 kDIA~~AGVS~sTVSrvLn~~~~Vs~~tr~rV~~aa~elgY~pn~   46 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSA   46 (327)
T ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf             689878698999999997895999999999999999982998688


No 162
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=89.48  E-value=1.6  Score=23.06  Aligned_cols=56  Identities=25%  Similarity=0.255  Sum_probs=38.3

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             99999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG  175 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G  175 (205)
                      -|....+.+|.|...++...|++.+|+..-.. +.-|..  -.-||.++||++..+--+
T Consensus        12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~-rp~pkg--EriIA~algv~P~eIWp~   67 (82)
T COG3423          12 DIIAALKKKGTSLAALSREAGLSSSTLANALD-RPWPKG--ERIIADALGVPPEEIWPS   67 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHC-CCCCHH--HHHHHHHHCCCHHHHCCH
T ss_conf             99999998564299999880878789999874-788718--899999958988881834


No 163
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=89.48  E-value=0.73  Score=25.14  Aligned_cols=34  Identities=12%  Similarity=0.227  Sum_probs=18.4

Q ss_pred             HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             9999977999999997414889998999999998
Q gi|254781218|r  131 EFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV  164 (205)
Q Consensus       131 elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~  164 (205)
                      |+|+.+|+|..|+|+..|+....+.++..+|-++
T Consensus         2 diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I~~~   35 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAA   35 (52)
T ss_pred             HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             2888878599999999879898999999999999


No 164
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=89.32  E-value=0.39  Score=26.82  Aligned_cols=28  Identities=25%  Similarity=0.516  Sum_probs=25.2

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             9729838999999779999999974148
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      ..+||+|.|.|+.+|.|+..+|-+|..-
T Consensus        16 R~~G~tQ~eIA~~lgTSraNvs~iEk~A   43 (139)
T PRK03975         16 RKRGLTQQEIADILGTSRANISIIEKRA   43 (139)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9828979999999773288999999999


No 165
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=89.19  E-value=0.37  Score=27.00  Aligned_cols=38  Identities=21%  Similarity=0.267  Sum_probs=22.6

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             999729838999999779999999974148899989999999982
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      +..-.||+|.|-|+..|||+.|++++-..       .-.|||++|
T Consensus        47 L~D~egl~QeeaA~~MgVSR~Tf~ril~~-------ARkKvA~aL   84 (100)
T pfam02001        47 LVDYEDYTQEEAAKLMGISRRTVWRLLTS-------ARKKIADAL   84 (100)
T ss_pred             HHHHCCCCHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf             87360798999998849769999999999-------999999998


No 166
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=89.15  E-value=1.7  Score=22.80  Aligned_cols=23  Identities=9%  Similarity=0.258  Sum_probs=15.0

Q ss_pred             CCCHHHHHHHHHHH---CCCHHHHHC
Q ss_conf             88999999999982---899999614
Q gi|254781218|r   70 STSIRYALYLRNEY---EISFDWIYD   92 (205)
Q Consensus        70 ~psi~~l~~la~~~---~vs~d~Ll~   92 (205)
                      ...+..++.||+-|   ++++..|+-
T Consensus       177 ~aNLRLVVsIAkkY~~rGl~l~DLIQ  202 (410)
T PRK07598        177 KANLRLVVSVAKKYQNRGLELLDLVQ  202 (410)
T ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             99899999999865789989899998


No 167
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=89.06  E-value=1.6  Score=23.05  Aligned_cols=27  Identities=26%  Similarity=0.234  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf             988999998489999999887-799888
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCST   71 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~p   71 (205)
                      +|-.|+|+..|+|.++|-.|| .|.-.|
T Consensus         2 ~~Ige~A~~~gvs~~TlRyYe~~GLl~~   29 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKLGLITG   29 (102)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             8099999998979999999998699898


No 168
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=89.02  E-value=1.8  Score=22.75  Aligned_cols=22  Identities=23%  Similarity=0.451  Sum_probs=12.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             8389999997799999999741
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~  148 (205)
                      +|..|+|+.+|||+..+.++|+
T Consensus       279 ~TL~EIg~~lgvSrERVRQIE~  300 (320)
T PRK07921        279 RTLDQIGKLFGLSRERVRQIER  300 (320)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             4799999897969999999999


No 169
>PHA00675 hypothetical protein
Probab=89.00  E-value=0.7  Score=25.27  Aligned_cols=35  Identities=14%  Similarity=0.168  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999999999985998899999848999999988
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      -..=++||++|+..||+-..||...+++.++|.+|
T Consensus        25 d~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkI   59 (78)
T PHA00675         25 DAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKI   59 (78)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             89999999999872843899999972756899999


No 170
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=88.95  E-value=0.45  Score=26.46  Aligned_cols=47  Identities=19%  Similarity=0.114  Sum_probs=42.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHHHHC
Q ss_conf             889999984899999998877998889999999999828--99999614
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE--ISFDWIYD   92 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~--vs~d~Ll~   92 (205)
                      .|+.+|..+|+++.++|.|-+|.+..+.+....|..+-+  |+-..|-.
T Consensus        14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~elrp   62 (96)
T COG4197          14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREELRP   62 (96)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHHCC
T ss_conf             3899999972681478877652010475533289998537715999766


No 171
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=88.95  E-value=1.6  Score=23.07  Aligned_cols=28  Identities=21%  Similarity=0.348  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf             9988999998489999999887-799888
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLFE-NGMCST   71 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~E-~G~~~p   71 (205)
                      .||-.++|+..|+|.++|-.|| .|.-.|
T Consensus         1 ~mtIgelA~~~gvs~~tiRyYE~~GLl~p   29 (139)
T cd01110           1 ELSVGEVAKRSGVAVSALHFYEQKGLIAS   29 (139)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             99789999998878899999998788466


No 172
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are 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.
Probab=88.90  E-value=0.54  Score=25.96  Aligned_cols=28  Identities=18%  Similarity=0.096  Sum_probs=14.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999859988999998489999999887
Q gi|254781218|r   38 DIRKANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        38 ~lR~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      .+|-..|+|+.|+|+.+|+|+++|++.+
T Consensus        14 ~l~y~~~~t~~EIA~~lgis~~~V~~~~   41 (50)
T pfam04545        14 VLRFGEGLTLEEIGERLGISRERVRQIE   41 (50)
T ss_pred             HHHCCCCCHHHHHHHHHCCCHHHHHHHH
T ss_conf             9870688249999999897999999999


No 173
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=88.88  E-value=0.62  Score=25.58  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=9.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHH
Q ss_conf             83899999977999999997
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~  146 (205)
                      =|..|+|+.+|++...+..+
T Consensus       116 Pt~~EiA~~l~is~~~v~~~  135 (229)
T PRK12427        116 PNFEEISAELNLTADEYQEY  135 (229)
T ss_pred             CCHHHHHHHHCCCHHHHHHH
T ss_conf             99999998919999999999


No 174
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=88.68  E-value=1.9  Score=22.60  Aligned_cols=30  Identities=23%  Similarity=0.444  Sum_probs=25.4

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             999972983899999977999999997414
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ..|-..|+|+.|+|+.+|+|+..++++|+.
T Consensus       219 ~~ry~~~~Tl~eIa~~lGvSreRVrQie~~  248 (257)
T PRK08215        219 NLRFFQGKTQMEVADEIGISQAQVSRLEKA  248 (257)
T ss_pred             HHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999479998999999989699999999999


No 175
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=88.60  E-value=0.56  Score=25.88  Aligned_cols=27  Identities=19%  Similarity=-0.043  Sum_probs=23.4

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             998599889999984899999998877
Q gi|254781218|r   40 RKANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        40 R~~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      -.-.||+|+|-|.++|||++|++++=.
T Consensus        48 ~D~egl~QeeaA~~MgVSR~Tf~ril~   74 (100)
T pfam02001        48 VDYEDYTQEEAAKLMGISRRTVWRLLT   74 (100)
T ss_pred             HHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             736079899999884976999999999


No 176
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=88.43  E-value=2  Score=22.50  Aligned_cols=24  Identities=25%  Similarity=0.451  Sum_probs=21.1

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             729838999999779999999974
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ...+|..|+|+.+|+|+.|..+|.
T Consensus       171 ~~~~Taeela~~~giSRvTaRRYL  194 (224)
T COG4565         171 DQELTAEELAQALGISRVTARRYL  194 (224)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             776479999988372199999999


No 177
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759   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 , .    This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=88.29  E-value=0.82  Score=24.83  Aligned_cols=127  Identities=12%  Similarity=0.174  Sum_probs=80.0

Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHH---HC--C-CCHH---HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH-C----
Q ss_conf             00156689999999999999999---85--9-9889---99998489999999887799888999999999982-8----
Q gi|254781218|r   19 LIITPEIRQYWKDVGTRIKDIRK---AN--N-KTQK---EMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY-E----   84 (205)
Q Consensus        19 ~~~~~~~~~~~~~iG~rik~lR~---~~--g-ltQ~---elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~-~----   84 (205)
                      |.|+.+.-|--  +==+||.-++   ..  | ++++   .+|..+||+..-|...|+-.+.+++..=...-+.= +    
T Consensus       111 VKvATTkaQrK--LFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV~eMe~RlsG~D~~L~~~~~~~~~~~~~~  188 (279)
T TIGR02392       111 VKVATTKAQRK--LFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEVLEMESRLSGRDISLNASIDDDEDDGGSD  188 (279)
T ss_pred             HHHHCCHHHHH--HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf             88852776788--8765888999863101579898999999976389888998875145537733478876553456311


Q ss_pred             -CCHHHHHCC-C-CCCCCCCCCCCHHHHHHHHHHH----------HH---HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             -999996145-3-2210000232134554677799----------99---9999972-9838999999779999999974
Q gi|254781218|r   85 -ISFDWIYDG-E-VIDRRYEDVTNKKRLDPYAIGA----------RL---KSIRKDK-GMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus        85 -vs~d~Ll~g-e-~~~~~~~~~~~~~~~d~~~iG~----------rL---k~lR~~~-glsq~elA~~lgis~~tis~~E  147 (205)
                       -+++||-+. . ..........+.. .-...+..          +|   |.+. +. +.|..+||...|||..-|.++|
T Consensus       189 ~~~~~yL~D~~~~~~~~~l~~~~~~~-~~~~~L~~AL~~Ld~RsR~I~~~RwL~-d~~~~TL~~LA~eygvSaERiRQiE  266 (279)
T TIGR02392       189 FAPIAYLADKATSDPEATLEEEQWEE-LQTQKLANALESLDARSRRIIEARWLD-DDGKLTLHELAAEYGVSAERIRQIE  266 (279)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             45788630477778889999989999-999999999885228879999873027-8899647899988487466799999


Q ss_pred             CC
Q ss_conf             14
Q gi|254781218|r  148 QG  149 (205)
Q Consensus       148 ~g  149 (205)
                      ..
T Consensus       267 ~~  268 (279)
T TIGR02392       267 KN  268 (279)
T ss_pred             HH
T ss_conf             99


No 178
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=88.17  E-value=1.6  Score=23.00  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf             988999998489999999887-799888
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCST   71 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~p   71 (205)
                      ||-.|||+..|+|.+||-.|| .|.-.|
T Consensus         1 mtIgelA~~~gvs~~TiRyYE~~GLl~~   28 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEKGLIAS   28 (120)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             9689999998868898989996498065


No 179
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=88.08  E-value=2.1  Score=22.36  Aligned_cols=46  Identities=13%  Similarity=0.213  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHH
Q ss_conf             988999998489999999887-799888999----------------9999999828999996
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWI   90 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~L   90 (205)
                      |+-.+||++.|++..+|-.|| .|.-.|+..                .+++-|+.++.|++.+
T Consensus         1 M~IgelAk~tGv~~~TIRyYE~~GLl~~~~R~~~GyR~Y~~~~l~rL~fI~~ar~lGfsL~EI   63 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES   63 (135)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             968999999896999999999838977343289992177899999999999998879999999


No 180
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=88.03  E-value=0.86  Score=24.70  Aligned_cols=35  Identities=14%  Similarity=0.438  Sum_probs=21.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             38999999779999999974148899989999999982
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      ++..+|+.+||+++.+++|  |...|.... .+|.++.
T Consensus        12 sk~klA~aLgIs~~aVsqW--ge~IPE~rA-y~le~iT   46 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVPEGRA-MRLQEAS   46 (75)
T ss_pred             CHHHHHHHHCCCHHHHHHH--HHHCCHHHH-HHHHHHH
T ss_conf             2999999949987999887--401606889-9999985


No 181
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200   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 , .    Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.94  E-value=0.29  Score=27.64  Aligned_cols=24  Identities=33%  Similarity=0.452  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             983899999977999999997414
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .-+|+++|+++|++++.+++.|..
T Consensus       198 e~tqk~vad~lGisqsyisrlek~  221 (234)
T TIGR02835       198 EKTQKEVADLLGISQSYISRLEKR  221 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             146788898862468999999999


No 182
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212   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 , .    Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.90  E-value=0.9  Score=24.58  Aligned_cols=32  Identities=22%  Similarity=0.420  Sum_probs=27.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             99999972983899999977999999997414
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      |-..|--.|-||-|+|+.+|+++..+++.|..
T Consensus       214 il~~rff~G~tqmeva~eiGisqaqvsrlek~  245 (254)
T TIGR02850       214 ILKLRFFEGKTQMEVAEEIGISQAQVSRLEKA  245 (254)
T ss_pred             HHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             77755314631334565403016888888899


No 183
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=87.78  E-value=0.87  Score=24.69  Aligned_cols=28  Identities=18%  Similarity=0.252  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ++-.+||+..|++..+|-.|| .|.-.|.
T Consensus         2 ~~Ige~A~~~gvs~~tiRyYE~~GLl~~~   30 (140)
T PRK09514          2 YRIGELAKLCEVTPDTLRFYEKQGLMDPS   30 (140)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             86999999989689999999986999865


No 184
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=87.67  E-value=0.79  Score=24.94  Aligned_cols=26  Identities=27%  Similarity=0.419  Sum_probs=22.4

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             72983899999977999999997414
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ...+|+.|.|+.+|+|+..++++|.-
T Consensus       201 ~~~~Tl~EIa~~lgISrerVrQIe~~  226 (239)
T PRK08301        201 GEEKTQKEVADMLGISQSYISRLEKR  226 (239)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             98406999999989789999999999


No 185
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304   This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=87.64  E-value=0.45  Score=26.43  Aligned_cols=30  Identities=33%  Similarity=0.490  Sum_probs=16.1

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHH-HHHHCCC
Q ss_conf             99972983899999977999999-9974148
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTL-SNYEQGR  150 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~ti-s~~E~g~  150 (205)
                      +-+-.|+||+++|+.+|+|.+.. |+.-+|+
T Consensus       111 L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR  141 (170)
T TIGR02959       111 LTELEGLSQKEIAEKLGLSLSGAKSRVQRGR  141 (170)
T ss_pred             HHHCCCCCHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             8750799827998761753351567889999


No 186
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=87.62  E-value=2.2  Score=22.19  Aligned_cols=112  Identities=14%  Similarity=0.163  Sum_probs=50.9

Q ss_pred             HHHHHHHC----CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC---CHHHHHCCCCCCCCCCCCCCHH-
Q ss_conf             99999985----998899999848999999988779988899999999998289---9999614532210000232134-
Q gi|254781218|r   36 IKDIRKAN----NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI---SFDWIYDGEVIDRRYEDVTNKK-  107 (205)
Q Consensus        36 ik~lR~~~----gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v---s~d~Ll~ge~~~~~~~~~~~~~-  107 (205)
                      ++.++...    .-+.+++|+.+|++...|..++.-....++..-..+...=+-   ..|+|-+. ..+ +.....+.. 
T Consensus       139 lr~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~-~~~-~~~~~~~~~~  216 (284)
T PRK06596        139 LRKAKKRLGWLNPEEVEMIAEELGVSEEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDK-SSD-PAAVLEEDNW  216 (284)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CCC-HHHHHHHHHH
T ss_conf             99999987145986299999997919999999999853798202378888877754246651467-898-6789999999


Q ss_pred             ------HHHH--HHHHHHHHHH---HH--HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             ------5546--7779999999---99--72983899999977999999997414
Q gi|254781218|r  108 ------RLDP--YAIGARLKSI---RK--DKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       108 ------~~d~--~~iG~rLk~l---R~--~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                            .+..  ..+..|=+.+   |-  ..++|+.|+|+.+|+|+..++++|+.
T Consensus       217 ~~~~~~~L~~al~~L~~REr~Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~k  271 (284)
T PRK06596        217 EDQRRELLADALETLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERIRQIEKN  271 (284)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999999999986099999999999767999948999999979799999999999


No 187
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=87.47  E-value=0.79  Score=24.95  Aligned_cols=29  Identities=21%  Similarity=0.327  Sum_probs=25.1

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99997298389999997799999999741
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      -++.-.|||+.|.|+.+|||.+|+.++..
T Consensus       137 ~L~r~eGls~~EIAe~LgiS~~tV~~~l~  165 (178)
T PRK12529        137 LMATLDGMKQKDIAQALDIALPTVKKYIH  165 (178)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             79988299999999998959999999999


No 188
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=87.16  E-value=0.98  Score=24.35  Aligned_cols=33  Identities=12%  Similarity=-0.158  Sum_probs=27.4

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             999999972983899999977999999997414
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .+-.++--.|+|+.|.|+.+|+|..++..|.+.
T Consensus       113 ~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~  145 (154)
T PRK06759        113 YIIFERFFVGKTMGEIALETEMTYYQVRWIYRQ  145 (154)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999996998999999989899999999999


No 189
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=86.98  E-value=2.4  Score=21.97  Aligned_cols=30  Identities=17%  Similarity=0.234  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC-CCCCCC
Q ss_conf             599889999984899999998877-998889
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFEN-GMCSTS   72 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~-G~~~ps   72 (205)
                      .+++-.+||+..|++..+|-.||+ |.-.|+
T Consensus         6 ~~m~IgelAk~~gvs~~tIRyYE~~GLl~~~   36 (144)
T PRK13752          6 ENLTIGVFAKAAGVNVETIRFYQRKGLLPEP   36 (144)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             2382999999978984566798725997987


No 190
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.88  E-value=2.4  Score=21.93  Aligned_cols=109  Identities=18%  Similarity=0.280  Sum_probs=59.3

Q ss_pred             CCCCHHHHHHHHCCCHHH-HHHHHCCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CC
Q ss_conf             599889999984899999-99887799------888999999999982---8999996145---------3221----00
Q gi|254781218|r   43 NNKTQKEMAIGANQLESA-VNLFENGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RR   99 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~-is~~E~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~   99 (205)
                      +.-|-.+.|.++|++... -..++.|.      ....+..++.||+-|   +++++.|+-.         +-+|    .+
T Consensus        64 ~~~~~~ewa~~~~~~~~~l~~~~~~g~~A~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~R  143 (327)
T PRK05949         64 REPSLPEWADAVNLSETELKQALKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYK  143 (327)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             89756889987266789999998758999999999819999999986436998989999985899999999809655971


Q ss_pred             CC---------------CCCCHHHHHHHHHHHHHHHHHH---------HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             00---------------2321345546777999999999---------7298389999997799999999741488
Q gi|254781218|r  100 YE---------------DVTNKKRLDPYAIGARLKSIRK---------DKGMSQIEFGKLLGMPNSTLSNYEQGRT  151 (205)
Q Consensus       100 ~~---------------~~~~~~~~d~~~iG~rLk~lR~---------~~glsq~elA~~lgis~~tis~~E~g~~  151 (205)
                      |+               .........|..+..++..+++         .+.-+..|+|+.+|++...+..+..-..
T Consensus       144 FSTYA~wWIRq~I~r~i~~~~r~IRlP~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~  219 (327)
T PRK05949        144 FSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMAR  219 (327)
T ss_pred             EEEEHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             3420099998999999998288744637899999999999999999818899889999894999999999998418


No 191
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=86.84  E-value=2.4  Score=21.92  Aligned_cols=28  Identities=14%  Similarity=0.108  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +|-.+||+..|||..++-.|| .|.-.|.
T Consensus         1 y~Ige~Ak~~gvs~~TLRyYe~~GLl~p~   29 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDKIGLFKPE   29 (97)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999989699999999966998986


No 192
>pfam05269 Phage_CII Bacteriophage CII protein. This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages.
Probab=86.70  E-value=0.48  Score=26.28  Aligned_cols=44  Identities=14%  Similarity=0.105  Sum_probs=27.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             5998899999848999999988779988899999999998289999
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD   88 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d   88 (205)
                      .-++|..+|+.+|+..+.||+|-.+.. |-..+|+.+-+ |+|.-|
T Consensus        22 a~~gq~~~A~~~Gv~es~ISRwK~~~~-~~~smllAvLE-~Gv~dd   65 (91)
T pfam05269        22 AMLGQRKTAEAVGVDESQISRWKRDWI-PKFSMLLAVLE-WGVVDD   65 (91)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHH-HHHHHHHHHHH-HCCCCH
T ss_conf             998436689996888998634443069-99999999999-555654


No 193
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=86.48  E-value=1.2  Score=23.80  Aligned_cols=25  Identities=36%  Similarity=0.440  Sum_probs=16.5

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9972983899999977999999997
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +...|.+..++|..+|||++|+.+|
T Consensus        17 l~~~G~~~~~iA~~~GVsr~Tiyr~   41 (42)
T cd00569          17 LLAAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9997898999999979799999865


No 194
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=86.38  E-value=2.6  Score=21.77  Aligned_cols=103  Identities=16%  Similarity=0.036  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHH
Q ss_conf             99999999999998599889999984899999998877998889999999999828999996145322100002321345
Q gi|254781218|r   29 WKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKR  108 (205)
Q Consensus        29 ~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~  108 (205)
                      .-++.+.+-...+.+|||-++++..+|.+.-.+...=-|....+.+....+++.++.+-|.+.--...+.+.. +...-.
T Consensus         6 i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygq~~~~~~ear~v~e~L~L~~~~v~~L~~~p~rg~-l~~~~P   84 (151)
T COG1513           6 ILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAILLLQMIPLRGC-LGPVIP   84 (151)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCCC-CCCCCC
T ss_conf             8999999999787549969999755083399999999762028999999999981998788998421675677-899899


Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             54677799999999972983899999
Q gi|254781218|r  109 LDPYAIGARLKSIRKDKGMSQIEFGK  134 (205)
Q Consensus       109 ~d~~~iG~rLk~lR~~~glsq~elA~  134 (205)
                      .||.  -.|.-++..-.|.+.+++..
T Consensus        85 TDP~--iYRfYE~~qvYG~~lK~lih  108 (151)
T COG1513          85 TDPL--IYRFYEMLQVYGTTLKALIH  108 (151)
T ss_pred             CCHH--HHHHHHHHHHHCHHHHHHHH
T ss_conf             9718--99999999997645999999


No 195
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284   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 , .    This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=86.26  E-value=1  Score=24.18  Aligned_cols=32  Identities=22%  Similarity=0.372  Sum_probs=26.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999997298389999997799999999741
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .+=.++--.|+|+.|.|+.+|+|..++.....
T Consensus       121 ~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~  152 (162)
T TIGR02937       121 EVLVLRYLEGLSYKEIAEILGISEGTVKSRLK  152 (162)
T ss_pred             HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999997189988999986899999999999


No 196
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=85.96  E-value=2.7  Score=21.63  Aligned_cols=98  Identities=11%  Similarity=0.014  Sum_probs=49.6

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC-C----HHHHHCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             99985998899999848999999988779988899999999998289-9----999614532210000232134554677
Q gi|254781218|r   39 IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI-S----FDWIYDGEVIDRRYEDVTNKKRLDPYA  113 (205)
Q Consensus        39 lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v-s----~d~Ll~ge~~~~~~~~~~~~~~~d~~~  113 (205)
                      +-.+..+|+.+||+.+|||..||-+-        |..+-..-+...+ +    --|.+.-.. +..+....+...   ..
T Consensus        12 lL~~~~lt~~eLA~~L~VS~RTIR~D--------I~~iN~~L~~~~i~~~~~~~GY~L~i~d-~~~~~~ll~~~~---~~   79 (585)
T PRK09863         12 LLEQQDRSGGELAQQLGVSRRTIVRD--------IAYINFTLNGKAIGSISGSAKYHLEILN-RRSLFQLLQKSD---NE   79 (585)
T ss_pred             HHHCCCCCHHHHHHHCCCCCHHHHHH--------HHHHHHHHHHCCEEEEECCCCEEEEECC-HHHHHHHHHCCH---HH
T ss_conf             99759999899998749971178999--------9999999841851898468752888678-788987754355---57


Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             79999999997298389999997799999999741
Q gi|254781218|r  114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-.-+..+.....++..|||+.+-+|++|+.+...
T Consensus        80 ~~~il~~lL~~~~i~l~dLAd~lfVSrsTi~~dl~  114 (585)
T PRK09863         80 DRLLLLNLLLNTFTPMGQLASALFLSRTWVAERLP  114 (585)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89999998626898899999985839999999999


No 197
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=85.69  E-value=0.66  Score=25.41  Aligned_cols=38  Identities=24%  Similarity=0.384  Sum_probs=30.3

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             997298389999997799999999741488999899999999828
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK  166 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg  166 (205)
                      ...+||+|.+.|..|+.+++-+|-+|.--       ++.|.++.+
T Consensus        17 lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA-------~EnIeKa~N   54 (142)
T TIGR00721        17 LREKGLKQKEIAKILKTTRANVSIIEKRA-------LENIEKAKN   54 (142)
T ss_pred             HHHCCCCHHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf             86338887889877267201378988874-------432377663


No 198
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=85.52  E-value=0.6  Score=25.66  Aligned_cols=66  Identities=21%  Similarity=0.293  Sum_probs=39.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCC-CCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             98899999848999999988779-98889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENG-MCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G-~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      .|-.|+|+.+|++..++-.||+. .-.|+ ..    .+.+              ..|+    ...+.   .-..|+.+| 
T Consensus         1 YtI~eva~~~Gv~~~tLRyyEk~~~l~~~-R~----~~G~--------------R~Ys----~~di~---~l~~I~~l~-   53 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIP-RT----ENGR--------------RYYT----DEDIE---LLKKIKTLL-   53 (67)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-CC----CCCC--------------CCCC----HHHHH---HHHHHHHHH-
T ss_conf             97899999988687899999873799999-69----9989--------------5239----99999---999999999-


Q ss_pred             HCCCCHHHHHHHHC
Q ss_conf             72983899999977
Q gi|254781218|r  124 DKGMSQIEFGKLLG  137 (205)
Q Consensus       124 ~~glsq~elA~~lg  137 (205)
                      ..|+|.++..+.++
T Consensus        54 ~~G~sl~~Ik~~LN   67 (67)
T cd04764          54 EKGLSIKEIKEILN   67 (67)
T ss_pred             HCCCCHHHHHHHHC
T ss_conf             96998999999859


No 199
>PRK04217 hypothetical protein; Provisional
Probab=85.47  E-value=1.1  Score=24.14  Aligned_cols=38  Identities=24%  Similarity=0.349  Sum_probs=24.8

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             999729838999999779999999974148899989999999982
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      +..-.||+|.|-|+..|||+.|+.++...       .-.+||.+|
T Consensus        53 L~D~egl~qeeaA~~M~VSR~Tf~ril~~-------AR~KvA~aL   90 (110)
T PRK04217         53 LVDYEGLTQEEAGKRMGVSRGTVWRALTS-------ARKKVAQML   90 (110)
T ss_pred             HHHHCCCCHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf             87360798999998849769999999999-------999999998


No 200
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=85.20  E-value=1.3  Score=23.50  Aligned_cols=48  Identities=6%  Similarity=-0.132  Sum_probs=36.2

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             9998599889999984899999998877998889999999999828999
Q gi|254781218|r   39 IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF   87 (205)
Q Consensus        39 lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~   87 (205)
                      .++..+++++++++..|.++ ++..|.++...+|...+-...+.++..-
T Consensus         7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g   54 (201)
T COG1974           7 RQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKG   54 (201)
T ss_pred             HHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCCCCHHHHHHHHHHHHCCC
T ss_conf             89998999999999728993-0899987517898489999999973088


No 201
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=85.06  E-value=3  Score=21.38  Aligned_cols=74  Identities=19%  Similarity=0.282  Sum_probs=46.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      .+-.++|+.+|+++.++-.|| .|...|.-+      +.+              +.|+    ...++  .+ ..|+.+.+
T Consensus         2 y~Ig~vA~l~gv~~~TLR~YEr~GLi~P~R~------~G~--------------RlYs----~~Di~--rL-rfIkrL~~   54 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERHGLIKPARR------NGQ--------------RLYS----NNDLK--RL-RFIKKLIN   54 (120)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCC--------------CCCC----HHHHH--HH-HHHHHHHH
T ss_conf             2489999997868899999998589688888------982--------------2779----99999--99-99999999


Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             72983899999977999999997414
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      +.|++..+....+.+    +..|++-
T Consensus        55 e~G~nlagI~~iLsl----~~c~~~~   76 (120)
T cd04767          55 EKGLNIAGVKQILSM----YPCWSIR   76 (120)
T ss_pred             HCCCCHHHHHHHHHC----CCCHHHH
T ss_conf             759689999999806----3231232


No 202
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=84.73  E-value=1.3  Score=23.55  Aligned_cols=29  Identities=24%  Similarity=0.369  Sum_probs=25.4

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99997298389999997799999999741
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .++...|+|+.|.|+.+|||.+++..+-.
T Consensus       129 ~L~~~eGls~~EIA~~LgiS~~tVk~~l~  157 (172)
T PRK12523        129 LYNRLDGMGHAEIAERLGVSVSRVRQYLA  157 (172)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999399999999998939999999999


No 203
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain  with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.  A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=84.70  E-value=3.1  Score=21.27  Aligned_cols=69  Identities=20%  Similarity=0.294  Sum_probs=39.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      +|-.++|+.+|+++.++-.||. |.-.|.-.     .           +|   -..|+      ..| ...-..|+.+.+
T Consensus         2 YtIgevA~~~Gvs~~tLR~yE~~GLl~P~R~-----~-----------~g---~R~Ys------~~d-i~~l~~I~~L~~   55 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYERLGLLSPSRT-----D-----------GG---TRRYS------ERD-IERLRRIQRLTQ   55 (91)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC-----C-----------CC---CEECC------HHH-HHHHHHHHHHHH
T ss_conf             6589999998929999999998599798839-----9-----------99---97447------999-999999999999


Q ss_pred             HCCCCHHHHHHHHCCC
Q ss_conf             7298389999997799
Q gi|254781218|r  124 DKGMSQIEFGKLLGMP  139 (205)
Q Consensus       124 ~~glsq~elA~~lgis  139 (205)
                      ..|++..+....+...
T Consensus        56 ~~G~sl~~I~~~L~l~   71 (91)
T cd04766          56 ELGVNLAGVKRILELE   71 (91)
T ss_pred             HCCCCHHHHHHHHHHH
T ss_conf             8699899999999808


No 204
>KOG1168 consensus
Probab=84.65  E-value=0.55  Score=25.89  Aligned_cols=38  Identities=34%  Similarity=0.525  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHH--------C-CCHHHHHHHHCC
Q ss_conf             7779999999997298389999997--------7-999999997414
Q gi|254781218|r  112 YAIGARLKSIRKDKGMSQIEFGKLL--------G-MPNSTLSNYEQG  149 (205)
Q Consensus       112 ~~iG~rLk~lR~~~glsq~elA~~l--------g-is~~tis~~E~g  149 (205)
                      .++++|.|+.|.+.|.||.|++..+        | ++++||.++|+=
T Consensus       220 EaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESL  266 (385)
T KOG1168         220 EAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESL  266 (385)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEE
T ss_conf             99999987545430642777788987276887553231213321000


No 205
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=84.48  E-value=1.3  Score=23.59  Aligned_cols=27  Identities=19%  Similarity=0.000  Sum_probs=12.6

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999985998899999848999999988
Q gi|254781218|r   38 DIRKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        38 ~lR~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      .+...-+++|.+||+.+++++++++++
T Consensus        11 ~l~~~~~~s~~~la~~~~~~~~~vs~~   37 (59)
T pfam01047        11 ILYEHGPLTVSELAEKLGVDRSTVTRV   37 (59)
T ss_pred             HHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999469929999999988586549999


No 206
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.47  E-value=3.2  Score=21.21  Aligned_cols=102  Identities=16%  Similarity=0.131  Sum_probs=52.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC------C----CCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             599889999984899999998877------9----988899999999998289999961453221000023213455467
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFEN------G----MCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPY  112 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~------G----~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~  112 (205)
                      .-.|.+|+|...+++...|++.-+      +    ...| .+++.++|..|+++-+..-.-..+-....+..-.....|.
T Consensus       181 ~prtl~Eia~~~~i~~k~i~r~~~~l~~~l~~~~~~~~p-~~~i~Rf~s~L~l~~~v~~~a~~i~~~~~~~~i~~Gr~P~  259 (310)
T PRK00423        181 VPRTLDEIAEVSRVSRKEIGRTYRFLARELNLKLPPTDP-IDYVPRFASELKLSGEVQKKAIEILRKAKERGLTSGKGPT  259 (310)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             997499999995988999999999999984678888899-9999999988699989999999999999972776795868


Q ss_pred             HH---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             77---9999999997298389999997799999999
Q gi|254781218|r  113 AI---GARLKSIRKDKGMSQIEFGKLLGMPNSTLSN  145 (205)
Q Consensus       113 ~i---G~rLk~lR~~~glsq~elA~~lgis~~tis~  145 (205)
                      .+   .--|.......+.||.++|+.+|++..|+.+
T Consensus       260 siaAaaIyla~~~~~~~~t~~~Ia~v~~vsevTIr~  295 (310)
T PRK00423        260 GLAAAAIYIASLLEGERRTQREVAEVAGVTEVTVRN  295 (310)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             999999999999948898999999896988999999


No 207
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=84.24  E-value=2.7  Score=21.63  Aligned_cols=54  Identities=17%  Similarity=0.127  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH-HHHHHHCCC
Q ss_conf             9999999999859988999998489999999887799888999999-999982899
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYAL-YLRNEYEIS   86 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~-~la~~~~vs   86 (205)
                      .=+.+|+.-+..+++|+.+|..+|+++.++|+|=|| ..+.....- +|+..++-.
T Consensus         7 ~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~   61 (297)
T COG2842           7 EIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKK   61 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHCCC
T ss_conf             999999999861666999998736684457878437-6741777899999997277


No 208
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=84.08  E-value=2.1  Score=22.32  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=26.0

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999997298389999997799999999741
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      +=.++...|+|++|.|+.+|||.+|+.++..
T Consensus       127 vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~  157 (167)
T PRK12528        127 AFLLAQVDGLGYGEIATELGISLATVKRYLN  157 (167)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999998298999999997979999999999


No 209
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=83.89  E-value=1.4  Score=23.36  Aligned_cols=52  Identities=19%  Similarity=0.284  Sum_probs=30.8

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf             99729838999999779999999974148-89998999999998289999952
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKHLDWIY  173 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs~d~L~  173 (205)
                      -+..|+|-.++|..+|++...+..+-... ..|....+.--|-.|.-...|++
T Consensus        67 aK~~GFSD~~IA~l~~~~e~~Ir~~R~~~~i~P~yk~VDTcAaEF~a~TpY~Y  119 (122)
T pfam02787        67 AKKLGFSDAQIAKLLGVTEEEVRKLRKELGIRPVYKMVDTCAAEFEAKTPYYY  119 (122)
T ss_pred             HHHHCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             99949998999988398699999999987991226210385205577998555


No 210
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093   An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=83.88  E-value=1  Score=24.25  Aligned_cols=31  Identities=19%  Similarity=0.314  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf             8389999997799999999741488999899
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKP  157 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~  157 (205)
                      ||-+|.|+.+|++++|+.+|-..+..|....
T Consensus         2 lTv~EaA~yLgv~~~t~~~l~~~g~l~~~~~   32 (49)
T TIGR01764         2 LTVEEAAEYLGVSKSTVYRLIEEGELPAYRV   32 (49)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHCCCCCEEEC
T ss_conf             8778899771999057899997189850006


No 211
>PHA01083 hypothetical protein
Probab=83.66  E-value=2.4  Score=21.99  Aligned_cols=63  Identities=22%  Similarity=0.220  Sum_probs=50.1

Q ss_pred             HHHHHHHCCCCH-HHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCCCCCC
Q ss_conf             999999859988-9999984899999998877998-88999999999982899999614532210
Q gi|254781218|r   36 IKDIRKANNKTQ-KEMAIGANQLESAVNLFENGMC-STSIRYALYLRNEYEISFDWIYDGEVIDR   98 (205)
Q Consensus        36 ik~lR~~~gltQ-~elA~~~gis~~~is~~E~G~~-~psi~~l~~la~~~~vs~d~Ll~ge~~~~   98 (205)
                      +....+.++..| +++|..+|++++.||.+-+|.+ ..+-+..+-||+.-+++.+--+-|-.-|+
T Consensus         5 ldAYK~aknYvQdKQIAhDlg~~pq~iS~~RkG~R~Ylsd~eAifLAe~~GiD~E~aLlG~hADr   69 (153)
T PHA01083          5 LDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIALLGCHADR   69 (153)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             99999999888899999980999899999981237643538899989870998888899854112


No 212
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress 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.
Probab=83.57  E-value=1.5  Score=23.27  Aligned_cols=32  Identities=19%  Similarity=0.242  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf             83899999977999999997414889998999
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA  158 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~l  158 (205)
                      +...|+++.+|++++|+.++++....|..-.+
T Consensus         4 lr~~eV~~~~glsrstiyr~i~~G~FP~pikl   35 (51)
T pfam05930         4 LRLKEVEQLTGLSRSTIYRLIKDGEFPKPIKL   35 (51)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEEE
T ss_conf             37999999989899999999987999998760


No 213
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.37  E-value=1.1  Score=23.97  Aligned_cols=20  Identities=20%  Similarity=0.039  Sum_probs=9.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHH
Q ss_conf             98899999848999999988
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~   64 (205)
                      +||+++|..+|+++.++|+.
T Consensus         9 lt~~~iA~~lG~tretvsR~   28 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRT   28 (48)
T ss_pred             CCHHHHHHHHCCCHHHHHHH
T ss_conf             79999999979979999999


No 214
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=83.36  E-value=1.3  Score=23.59  Aligned_cols=38  Identities=16%  Similarity=0.245  Sum_probs=26.1

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             999729838999999779999999974148899989999999982
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      +....||+|.|.|...|||++|+.+..+       ....|+|.+|
T Consensus        44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~-------sAR~KvA~aL   81 (99)
T COG1342          44 LVDYEGLTQEEAALRMGISRQTFWRLLT-------SARKKVADAL   81 (99)
T ss_pred             HHHHHHCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf             8868610578999984642999999999-------9999999998


No 215
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517   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 , .    This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=82.90  E-value=1.8  Score=22.79  Aligned_cols=32  Identities=25%  Similarity=0.406  Sum_probs=28.6

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH-HH
Q ss_conf             999999997298389999997799999999-74
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSN-YE  147 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~-~E  147 (205)
                      .+|=++|---||+..|.|+.+|||..|+.+ |.
T Consensus       151 a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~Rdw~  183 (194)
T TIGR02999       151 AEVVELRFFAGLTVEEIAELLGVSVRTVERDWR  183 (194)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             998853110488989999986888878998799


No 216
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=82.46  E-value=1.1  Score=24.08  Aligned_cols=22  Identities=18%  Similarity=0.137  Sum_probs=19.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9889999984899999998877
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~   66 (205)
                      ||-+|||...|.|+++|++|-+
T Consensus         1 mT~eELa~~~G~srQtINkwaR   22 (122)
T pfam07037         1 MTPEELAELTGYSRQTINRWVR   22 (122)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHH
T ss_conf             9878998874712999999999


No 217
>COG2512 Predicted membrane-associated trancriptional regulator    [Transcription]
Probab=82.45  E-value=1.6  Score=22.98  Aligned_cols=33  Identities=30%  Similarity=0.486  Sum_probs=28.8

Q ss_pred             HHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999999729-8389999997799999999741
Q gi|254781218|r  116 ARLKSIRKDKG-MSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       116 ~rLk~lR~~~g-lsq~elA~~lgis~~tis~~E~  148 (205)
                      +-|+-+|..-| ++|.|+.+.+|.|+.|+++.-+
T Consensus       199 ~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~  232 (258)
T COG2512         199 EILDLIRERGGRITQAELRRALGLSKTTVSRILR  232 (258)
T ss_pred             HHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999858978699988860997677999999


No 218
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=82.04  E-value=4  Score=20.60  Aligned_cols=99  Identities=16%  Similarity=0.112  Sum_probs=62.6

Q ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHH
Q ss_conf             99998877998889999999999828999996145322100002321345546777---999999999729838999999
Q gi|254781218|r   59 SAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAI---GARLKSIRKDKGMSQIEFGKL  135 (205)
Q Consensus        59 ~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~i---G~rLk~lR~~~glsq~elA~~  135 (205)
                      ..-..+|+..+.--|..+.+.-..|+||++.|...-+.   ..|...........+   ..-+..+.+.+.|..++++..
T Consensus       120 ~~~~~~e~~~~~eEI~~f~~~L~eygIsf~dLv~~sPK---H~DtR~~~i~iA~~i~~~~~l~~~l~~kK~LPikeL~~~  196 (237)
T PRK08311        120 EYEEEIENEERREEILEFQKELKEFGITFEDLVEESPK---HRDTRENAIKIAKTIAENEELLEKLKRKKKLPLKELEKR  196 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCC---CHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf             99999988999999999999999939759999772999---878999999999998649999999999288879999988


Q ss_pred             HCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             779999999974148899989999999982899
Q gi|254781218|r  136 LGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       136 lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      +++++.|+-++   +     ..+..++-+|.-.
T Consensus       197 ~~VsrKtlER~---R-----KYIIAv~lIl~~d  221 (237)
T PRK08311        197 VKVSRKTLERN---R-----KYIIAVAIILAGD  221 (237)
T ss_pred             CCCCHHHHHHH---H-----HHHHHHHHHHHCC
T ss_conf             59889999742---3-----9999999999199


No 219
>PRK07773 replicative DNA helicase; Validated
Probab=82.00  E-value=3.4  Score=21.01  Aligned_cols=53  Identities=11%  Similarity=0.217  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             67779999999997298389999997799999999741488999899999999828
Q gi|254781218|r  111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK  166 (205)
Q Consensus       111 ~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg  166 (205)
                      |..+-..++..+.+.|+|..+|++.+|+.....+.|   +..|+-..+.++|.+++
T Consensus       709 P~evw~~Vr~a~~~~g~t~r~~~~~~g~~~~g~~~~---k~~~SR~Rl~~~A~~l~  761 (868)
T PRK07773        709 PKKVWKQVRPRLQAKQMTTRQLHEPIGTSYCGSTLW---KHSPSRERAHRVAARIQ  761 (868)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHH---CCCCCHHHHHHHHHHHC
T ss_conf             589999999999860654899998725454640132---03422778999998747


No 220
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=81.95  E-value=1.8  Score=22.69  Aligned_cols=28  Identities=25%  Similarity=0.204  Sum_probs=22.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ||-.|+|+.+|+|.++|-.|| .|.-.|.
T Consensus         1 mtIgelAk~~gvs~~tlRyYE~~GLl~p~   29 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKEGLLSPD   29 (108)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             96899999989799999999977982998


No 221
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=81.83  E-value=2.1  Score=22.36  Aligned_cols=28  Identities=25%  Similarity=0.502  Sum_probs=23.9

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      -++...|+|..|.|+.+|||.+|+.+..
T Consensus       128 lL~~~eGlsy~EIAe~LgIS~~tV~~~l  155 (168)
T PRK12525        128 LMSQLEGLTYVEIGERLGVSLSRIHQYM  155 (168)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999929999999999897999999999


No 222
>pfam00376 MerR MerR family regulatory protein.
Probab=81.75  E-value=1.8  Score=22.70  Aligned_cols=27  Identities=37%  Similarity=0.481  Sum_probs=19.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             389999997799999999741488999
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPE  154 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps  154 (205)
                      |..|+|+++|++..++..||.-.-.|+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~Gli~~   27 (38)
T pfam00376         1 TIGEVAKLLGVSPRTLRYYEKIGLLPP   27 (38)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             989999998879999999998689899


No 223
>PRK09954 hypothetical protein; Provisional
Probab=81.56  E-value=1.9  Score=22.56  Aligned_cols=28  Identities=21%  Similarity=0.069  Sum_probs=24.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999998599889999984899999998
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      ++.+|+.=-++|.|||..+|+|+++|.-
T Consensus         9 l~~i~~~p~i~q~ela~~lgisrs~va~   36 (362)
T PRK09954          9 LAILRRNPLIQQNEIADILQISRSRVAA   36 (362)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             9999878995899999997987999999


No 224
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=81.43  E-value=1.9  Score=22.57  Aligned_cols=28  Identities=32%  Similarity=0.364  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             8389999997799999999741488999
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQGRTIPE  154 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g~~~Ps  154 (205)
                      ++..|+|+.+|++..++..||.-.-.|+
T Consensus         1 ytI~eva~~~gvs~~tlR~ye~~gLl~p   28 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLSP   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             9588999998939999999999799898


No 225
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=81.38  E-value=2  Score=22.47  Aligned_cols=68  Identities=24%  Similarity=0.219  Sum_probs=40.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      +|-.|+|+.+|++.++|-.|| .|.-.|+...-    +               ...+-     ...| ...-..|+.+| 
T Consensus         1 ytI~e~a~~~gvs~~tlR~ye~~Gll~p~~r~~----~---------------g~R~Y-----~~~d-i~~l~~I~~lr-   54 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE----G---------------GYRLY-----SDED-LERLRFIKRLK-   54 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC----C---------------CCEEC-----CHHH-HHHHHHHHHHH-
T ss_conf             978899999896999999999858989984489----9---------------97443-----9999-99999999999-


Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             729838999999779
Q gi|254781218|r  124 DKGMSQIEFGKLLGM  138 (205)
Q Consensus       124 ~~glsq~elA~~lgi  138 (205)
                      ..|++..+..+.+.+
T Consensus        55 ~~G~~l~~Ik~~l~l   69 (70)
T smart00422       55 ELGFSLEEIKELLEL   69 (70)
T ss_pred             HCCCCHHHHHHHHHC
T ss_conf             978999999999962


No 226
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=81.16  E-value=4.3  Score=20.41  Aligned_cols=108  Identities=14%  Similarity=0.160  Sum_probs=59.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH-CCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CCC
Q ss_conf             9988999998489999999887-799------888999999999982---8999996145---------3221----000
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLFE-NGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RRY  100 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~E-~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~~  100 (205)
                      --|..+.|+.+|++...+.+.- .|.      ....+..++.||+-|   +++++.|+-.         +-+|    .+|
T Consensus       122 ~p~~~ewa~~~~~~~~~l~~~~~~g~~Ar~~LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RF  201 (385)
T PRK07406        122 FPSVEEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKF  201 (385)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCE
T ss_conf             54279999880888899999998799999999999899999999865689989889999858999999998196548822


Q ss_pred             C---------------CCCCHHHHHHHHHHHHHHHHHH-------H--CCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             0---------------2321345546777999999999-------7--298389999997799999999741488
Q gi|254781218|r  101 E---------------DVTNKKRLDPYAIGARLKSIRK-------D--KGMSQIEFGKLLGMPNSTLSNYEQGRT  151 (205)
Q Consensus       101 ~---------------~~~~~~~~d~~~iG~rLk~lR~-------~--~glsq~elA~~lgis~~tis~~E~g~~  151 (205)
                      +               .........|..+...+..+++       .  +.-|..++|+.+|++...+..+.+...
T Consensus       202 STYA~WWIRqaI~RaI~~~sr~IRlP~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~  276 (385)
T PRK07406        202 STYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQ  276 (385)
T ss_pred             EEHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             110299999999999997386120208999999999999999998708998699999993999999999998548


No 227
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771   Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate.   This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=81.05  E-value=0.71  Score=25.22  Aligned_cols=31  Identities=29%  Similarity=0.109  Sum_probs=15.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf             9889999984899999998877998889999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRY   75 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~   75 (205)
                      ||-++.|+..||+.|||||.=|+...-++++
T Consensus         2 LTIkDIArLagVgKSTVSRVLnNe~~V~~~t   32 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNNESKVSIET   32 (311)
T ss_pred             CHHHHHHHHHCCCCEEEEEEEECCCCCCCHH
T ss_conf             6177769770886202331561688887203


No 228
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=80.94  E-value=4.3  Score=20.36  Aligned_cols=61  Identities=20%  Similarity=0.154  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHH
Q ss_conf             9999999982899999614532210000232134554677799999999972983899999977-99999999
Q gi|254781218|r   74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG-MPNSTLSN  145 (205)
Q Consensus        74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg-is~~tis~  145 (205)
                      ..+-.+|++|+|+.+.|++..-.         +....+..++  +--+|+..|+|..+.|..+| -+++|+..
T Consensus         3 ~I~~~Va~~~~v~~~~i~~~~R~---------~~~~~aR~ia--~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~   64 (90)
T cd06571           3 LIIEAVAEYFGISVEDLRSKSRK---------KEIALARQIA--MYLARELTGLSLPEIGRAFGGRDHSTVLH   64 (90)
T ss_pred             HHHHHHHHHHCCCHHHHHCCCCC---------CHHHHHHHHH--HHHHHHHHCCCHHHHHHHHCCCCHHHHHH
T ss_conf             89999999979989998469887---------1378999999--99999997889999999958997149999


No 229
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=80.67  E-value=4.4  Score=20.31  Aligned_cols=141  Identities=13%  Similarity=0.201  Sum_probs=100.0

Q ss_pred             HHHHHH--CCCCHHHHHHHHCCCHHHHH-HHH--------------------CCC------CCCCHHHHHHHHHHH---C
Q ss_conf             999998--59988999998489999999-887--------------------799------888999999999982---8
Q gi|254781218|r   37 KDIRKA--NNKTQKEMAIGANQLESAVN-LFE--------------------NGM------CSTSIRYALYLRNEY---E   84 (205)
Q Consensus        37 k~lR~~--~gltQ~elA~~~gis~~~is-~~E--------------------~G~------~~psi~~l~~la~~~---~   84 (205)
                      ..++..  +..|.+++|+.+|+|...+. .+.                    .|.      ....+..++.||+-|   |
T Consensus        55 ~~l~~~~g~~ps~~ewA~~~~~~~~~l~~~l~G~~aWA~~a~l~leLk~~~r~G~RAK~kMi~ANLRLVVSvAKKYq~Rg  134 (336)
T TIGR02997        55 EELEEQLGREPSKEEWAAALGLSEAELRQRLRGLQAWAEAAQLELELKLVLRQGQRAKEKMIKANLRLVVSVAKKYQNRG  134 (336)
T ss_pred             HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf             99998508999878999871899889999987657889984225899999997899999998760226889999851368


Q ss_pred             CCHHHHH---------CCCCCC----CCCC---------------CCCCHHHHHHHHHHHHHHHHHHH---------CCC
Q ss_conf             9999961---------453221----0000---------------23213455467779999999997---------298
Q gi|254781218|r   85 ISFDWIY---------DGEVID----RRYE---------------DVTNKKRLDPYAIGARLKSIRKD---------KGM  127 (205)
Q Consensus        85 vs~d~Ll---------~ge~~~----~~~~---------------~~~~~~~~d~~~iG~rLk~lR~~---------~gl  127 (205)
                      +.+=.|+         .-|-+|    ++||               ....+++-.|.-|-++|..+++.         +-=
T Consensus       135 lElLDLIQEG~lGL~RAVEKFDPtrGYKFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~EKLnkiKK~qReL~q~lGR~P  214 (336)
T TIGR02997       135 LELLDLIQEGTLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRRP  214 (336)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             83356887634312211233577778863301246875688999843688324741076666899899899999838897


Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH-HHHHCCCHHHHHCC-CCC
Q ss_conf             3899999977999999997414889998999999-99828999995247-210
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI-KQVTKKHLDWIYFG-DEV  178 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI-a~~lgvs~d~L~~G-~e~  178 (205)
                      |..|+|+.++++...+..+-.-... +++.=.++ -+-=++.+-.|+-. +..
T Consensus       215 s~~EiAe~lel~~~qvR~~l~~~~~-p~SLd~~VrG~e~dt~LgdLl~d~~~~  266 (336)
T TIGR02997       215 SEAEIAEALELEPEQVRELLQRARQ-PVSLDTRVRGDEEDTELGDLLEDEDGE  266 (336)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHCC-CCCCCCCCCCCCCCCHHHHHCCCCCCC
T ss_conf             8689998838898899999997078-744577326888542265432688899


No 230
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288   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 , .    This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes  and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=80.56  E-value=0.75  Score=25.07  Aligned_cols=136  Identities=19%  Similarity=0.210  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHCCC-HHHHHHHHH-------------HHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHH-HHHCCC
Q ss_conf             6654333100015-668999999-------------999999999985------9988999998489999999-887799
Q gi|254781218|r   10 SLKSLQEYTLIIT-PEIRQYWKD-------------VGTRIKDIRKAN------NKTQKEMAIGANQLESAVN-LFENGM   68 (205)
Q Consensus        10 ~~~~~~~~~~~~~-~~~~~~~~~-------------iG~rik~lR~~~------gltQ~elA~~~gis~~~is-~~E~G~   68 (205)
                      =..+---|++|.- +|++-|.++             ||-|||..=...      -=+-.|.|..+|+|.--|- -.|-|.
T Consensus        79 ~g~~FE~FaiPTiiGEIKrylRDKTWsvHVPRRIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~  158 (256)
T TIGR02941        79 YGKAFEAFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQ  158 (256)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf             04565662366100101121115643001574110037720145566444421487065464121774888987761477


Q ss_pred             --CCCCHHHHHHHHHH-HCCCHHHHHCCCCCCCCCCCCCCHHHHHHH---HHHHH---HHHHHHHCCCCHHHHHHHHCCC
Q ss_conf             --88899999999998-289999961453221000023213455467---77999---9999997298389999997799
Q gi|254781218|r   69 --CSTSIRYALYLRNE-YEISFDWIYDGEVIDRRYEDVTNKKRLDPY---AIGAR---LKSIRKDKGMSQIEFGKLLGMP  139 (205)
Q Consensus        69 --~~psi~~l~~la~~-~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~---~iG~r---Lk~lR~~~glsq~elA~~lgis  139 (205)
                        +..|++..+.=+.= =-|.+=.+++-   .....|..++.-+...   .+..|   |=+.-=..||+|+|-++.+|||
T Consensus       159 sY~alSvD~~iEadsDGStVa~ld~vG~---~edgYd~tE~Rm~LekIlpiLserE~~ii~c~f~enlsQKeTGErlGiS  235 (256)
T TIGR02941       159 SYKALSVDDKIEADSDGSTVALLDLVGE---VEDGYDQTEKRMVLEKILPILSEREKEIIECTFIENLSQKETGERLGIS  235 (256)
T ss_pred             CCCEEECCCCCCCCCCCCCCHHHHHHCC---CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHCCHH
T ss_conf             7433322530003688851111112167---6665457888888887410005445676665531478730023222403


Q ss_pred             HHHHHHHHC
Q ss_conf             999999741
Q gi|254781218|r  140 NSTLSNYEQ  148 (205)
Q Consensus       140 ~~tis~~E~  148 (205)
                      +..+|++-+
T Consensus       236 QMHVSRl~R  244 (256)
T TIGR02941       236 QMHVSRLQR  244 (256)
T ss_pred             HHHHHHHHH
T ss_conf             556778889


No 231
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=80.30  E-value=2.4  Score=21.94  Aligned_cols=29  Identities=10%  Similarity=0.180  Sum_probs=22.2

Q ss_pred             HHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999999-85998899999848999999988
Q gi|254781218|r   36 IKDIRK-ANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        36 ik~lR~-~~gltQ~elA~~~gis~~~is~~   64 (205)
                      +..+.. .-|+||.+||..+|+.++++++.
T Consensus        37 L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~   66 (144)
T PRK03573         37 LHNIHQLPPDQSQIQLAKAIGIEQPSLVRT   66 (144)
T ss_pred             HHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999997398989999999979878369999


No 232
>KOG2252 consensus
Probab=80.25  E-value=2.8  Score=21.57  Aligned_cols=119  Identities=15%  Similarity=0.105  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC
Q ss_conf             999999999999998599889999984-8999999988779988-----8999999999982899999614532210000
Q gi|254781218|r   28 YWKDVGTRIKDIRKANNKTQKEMAIGA-NQLESAVNLFENGMCS-----TSIRYALYLRNEYEISFDWIYDGEVIDRRYE  101 (205)
Q Consensus        28 ~~~~iG~rik~lR~~~gltQ~elA~~~-gis~~~is~~E~G~~~-----psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~  101 (205)
                      .-++|..||+..-+..++.|.=||+.+ |.|+.++|..=+.-..     .--++..+.++-|+ ..+.            
T Consensus       327 dTkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~WL~-eP~~------------  393 (558)
T KOG2252         327 DTKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMANWLE-EPEF------------  393 (558)
T ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCCCCHHHHCCCCHHHHHHHHHHC-CHHH------------
T ss_conf             189999999999864577378888888612522299996389952544032099999998742-7877------------


Q ss_pred             CCCCHHHHHHHHHHHH-HHHHHHHC-----C-------CCHHHH-HHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             2321345546777999-99999972-----9-------838999-99977999999997414889998999999998289
Q gi|254781218|r  102 DVTNKKRLDPYAIGAR-LKSIRKDK-----G-------MSQIEF-GKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK  167 (205)
Q Consensus       102 ~~~~~~~~d~~~iG~r-Lk~lR~~~-----g-------lsq~el-A~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv  167 (205)
                                    .| ++.+|++.     +       ..++.- .-.+.+-+.|+..+-...-.|+-+..+.|+.-|+.
T Consensus       394 --------------~r~m~~L~~~a~kRke~ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L  459 (558)
T KOG2252         394 --------------QRLMSALRKKACKRKEQEPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNL  459 (558)
T ss_pred             --------------HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf             --------------899998778876401268873335667886156458899999999861789879999999998587


Q ss_pred             CH----HHHH
Q ss_conf             99----9952
Q gi|254781218|r  168 HL----DWIY  173 (205)
Q Consensus       168 s~----d~L~  173 (205)
                      .+    +||+
T Consensus       460 ~~sTV~NfFm  469 (558)
T KOG2252         460 ELSTVINFFM  469 (558)
T ss_pred             CHHHHHHHHH
T ss_conf             6888999877


No 233
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=80.24  E-value=2.6  Score=21.71  Aligned_cols=20  Identities=25%  Similarity=0.373  Sum_probs=10.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHH
Q ss_conf             83899999977999999997
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~  146 (205)
                      +|-.++|+.+|+|..|+.+.
T Consensus        16 vt~~~La~~l~VSr~TV~rd   35 (55)
T pfam08279        16 ISGQELAEKLGVSRRTIRRD   35 (55)
T ss_pred             CCHHHHHHHHCCCHHHHHHH
T ss_conf             18999999969889999999


No 234
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=80.18  E-value=4.6  Score=20.21  Aligned_cols=67  Identities=16%  Similarity=0.047  Sum_probs=39.2

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877--99888999999999982899999614532210000232134554677799999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIR  122 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR  122 (205)
                      .|-.|+|+.+|++++++-.||.  |...|.-.                   +.--+.|+      ..| ...-..|+.+.
T Consensus         1 ysIgEva~~~gv~~~tLRywE~~~~~~~P~r~-------------------~~g~R~Ys------~~d-i~~l~~Ik~Ll   54 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKR-------------------AGGRRYYR------PKD-VELLLLIKHLL   54 (99)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCC-------------------CCCCCCCC------HHH-HHHHHHHHHHH
T ss_conf             97889999989499999999987477488758-------------------99885068------999-99999999999


Q ss_pred             HHCCCCHHHHHHHHC
Q ss_conf             972983899999977
Q gi|254781218|r  123 KDKGMSQIEFGKLLG  137 (205)
Q Consensus       123 ~~~glsq~elA~~lg  137 (205)
                      ++.|+|....-+.+.
T Consensus        55 ~~~G~ti~~~k~~L~   69 (99)
T cd04765          55 YEKGYTIEGAKQALK   69 (99)
T ss_pred             HHCCCCHHHHHHHHH
T ss_conf             987987999999998


No 235
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147; InterPro: IPR011873    This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised..
Probab=80.13  E-value=1.5  Score=23.19  Aligned_cols=43  Identities=12%  Similarity=0.015  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHCCCH--HHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             998899999848999--9999887799888999999999982899
Q gi|254781218|r   44 NKTQKEMAIGANQLE--SAVNLFENGMCSTSIRYALYLRNEYEIS   86 (205)
Q Consensus        44 gltQ~elA~~~gis~--~~is~~E~G~~~psi~~l~~la~~~~vs   86 (205)
                      -.|-..+|+++|.|.  +.++++=.|+...+...+.+++.+|+.+
T Consensus        27 ~FS~R~fa~KaGfsS~r~~~~~~~~GK~~Lt~~~i~k~~~~l~Ld   71 (281)
T TIGR02147        27 AFSWRSFAEKAGFSSKRSYLKRIIKGKKNLTKRMIPKFAEALGLD   71 (281)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             330899998648898777888998666753000357666552467


No 236
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain  HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=80.06  E-value=2.4  Score=21.99  Aligned_cols=28  Identities=18%  Similarity=0.127  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +|-.++|+.+|+|..+|-.|| .|.-.|.
T Consensus         1 ~tIge~Ak~~gvs~~tlRyYe~~GLl~p~   29 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPA   29 (96)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999988699999999843997987


No 237
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=79.74  E-value=2.8  Score=21.52  Aligned_cols=29  Identities=21%  Similarity=0.022  Sum_probs=19.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999985998899999848999999988
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      +..++..-++||.+||+.++++++++++.
T Consensus        46 L~~L~~~~~~t~~eLa~~l~id~~tvt~~   74 (144)
T PRK11512         46 LCSIRCAACITPVELKKVLSVDLGALTRM   74 (144)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999869979999999978888789999


No 238
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=79.58  E-value=4.8  Score=20.09  Aligned_cols=24  Identities=13%  Similarity=0.134  Sum_probs=21.2

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             729838999999779999999974
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..++|..|+|+.+|+|+.|..+|.
T Consensus       175 ~~~~ta~eva~~~giSrvTaRRYL  198 (225)
T PRK10046        175 GVQHTAETVAQALTISRTTARRYL  198 (225)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             998689999998585199999999


No 239
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA.  Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=79.56  E-value=2.9  Score=21.46  Aligned_cols=27  Identities=30%  Similarity=0.479  Sum_probs=14.5

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++-..|+|..|.|+.+|++.+++..+
T Consensus        20 ~l~y~~~~s~~EIa~~lgis~~tVk~~   46 (55)
T cd06171          20 LLRFGEGLSYEEIAEILGISRSTVRQR   46 (55)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999980999999999989599999999


No 240
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=79.20  E-value=4.9  Score=20.02  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=13.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             29838999999779999999974
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..||+.|+|+.+|++..|+|+..
T Consensus        24 l~ltr~eiA~~lG~t~eTVsR~l   46 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTL   46 (67)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             17799999999789099999999


No 241
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=79.18  E-value=2.3  Score=22.07  Aligned_cols=64  Identities=22%  Similarity=0.227  Sum_probs=37.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             889999984899999998877--998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      |-.++|+.+||++.++-.||+  |...|. ..                  +.--..|+      ..| ...-..|+.++ 
T Consensus         2 sI~eva~~~Gv~~~tLR~wE~~~~l~~p~-R~------------------~~g~R~Ys------~~d-i~~l~~I~~l~-   54 (68)
T cd04763           2 TIGEVALLTGIKPHVLRAWEREFGLLKPQ-RS------------------DGGHRLFN------DAD-IDRILEIKRWI-   54 (68)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCCCC-CC------------------CCCCCCCC------HHH-HHHHHHHHHHH-
T ss_conf             78899999887945758988705899986-79------------------99996549------999-99999999999-


Q ss_pred             HCCCCHHHHHHHH
Q ss_conf             7298389999997
Q gi|254781218|r  124 DKGMSQIEFGKLL  136 (205)
Q Consensus       124 ~~glsq~elA~~l  136 (205)
                      +.|++.++.++.+
T Consensus        55 ~~G~~i~~i~~lL   67 (68)
T cd04763          55 DNGVQVSKVKKLL   67 (68)
T ss_pred             HCCCCHHHHHHHH
T ss_conf             9799899999972


No 242
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=78.77  E-value=5.1  Score=19.93  Aligned_cols=103  Identities=15%  Similarity=0.210  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-HHHHCCCC-----------CCCCCCCCCCHHHHH
Q ss_conf             599889999984899999998877998889999999999828999-99614532-----------210000232134554
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF-DWIYDGEV-----------IDRRYEDVTNKKRLD  110 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~-d~Ll~ge~-----------~~~~~~~~~~~~~~d  110 (205)
                      +.=+-+++|+.+|++...|-.+++-... +++.=..+..--+-.+ |||-+...           ......++-..+ ++
T Consensus       204 r~p~~eeia~~l~~~~~~V~~m~~~~~~-~~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~-Lt  281 (342)
T COG0568         204 REPTPEEIAEELGVSPDKVREMLKRASE-PISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEA-LT  281 (342)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHCCC-CCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC-CC
T ss_conf             8997999999959999999999986536-767678488885207888764268789899999888999999998715-99


Q ss_pred             HHHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             6777999999999----72983899999977999999997414
Q gi|254781218|r  111 PYAIGARLKSIRK----DKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       111 ~~~iG~rLk~lR~----~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      +..  .++-..|-    ....|..++|+..|+++..+.++|+.
T Consensus       282 ~rE--~~Vi~~R~gl~~~~~~TLeevg~~~~vsrERvRQIE~k  322 (342)
T COG0568         282 ERE--RRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAK  322 (342)
T ss_pred             HHH--HHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999--99999995567999551999998959869999999999


No 243
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif  that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=78.68  E-value=2.7  Score=21.66  Aligned_cols=29  Identities=21%  Similarity=0.162  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCH
Q ss_conf             988999998489999999887-79988899
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSI   73 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi   73 (205)
                      +|-.++|+.+|||.++|-.|| .|.-.|..
T Consensus         1 ~tIgevAk~~gvs~~TlRyYE~~GLl~P~~   30 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAY   30 (108)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCE
T ss_conf             978999999895999999999859988541


No 244
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=78.68  E-value=5.1  Score=19.92  Aligned_cols=32  Identities=16%  Similarity=0.201  Sum_probs=24.0

Q ss_pred             HHHHH-HHHHC--CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999-99972--9838999999779999999974
Q gi|254781218|r  116 ARLKS-IRKDK--GMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       116 ~rLk~-lR~~~--glsq~elA~~lgis~~tis~~E  147 (205)
                      .+|.+ ++...  .+|..|+|+.+|+|+.|..+|.
T Consensus       165 ~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYL  199 (239)
T PRK10430        165 RTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYL  199 (239)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999998279998469999988585298899999


No 245
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=78.47  E-value=3.2  Score=21.15  Aligned_cols=29  Identities=14%  Similarity=0.016  Sum_probs=19.7

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999859988999998489999999887
Q gi|254781218|r   37 KDIRKANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        37 k~lR~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      ..+...-++||.++|..++++++++|+.=
T Consensus        17 ~~l~~~~~~t~~~la~~l~~~~~~vs~~v   45 (101)
T smart00347       17 RILYEEGPLSVSELAKRLGVSPSTVTRVL   45 (101)
T ss_pred             HHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99997699799999999896887999999


No 246
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=78.40  E-value=3.5  Score=20.95  Aligned_cols=29  Identities=28%  Similarity=0.359  Sum_probs=25.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +=.++...|||..|.|+.+|||..|+...
T Consensus       143 v~~L~~~eglS~~EIAe~Lgis~~TVk~r  171 (185)
T pfam07638       143 LVELRFFAGLSNDEIAERLGVSERTVERN  171 (185)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             98889975999999999979699899999


No 247
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=78.40  E-value=2.8  Score=21.52  Aligned_cols=28  Identities=21%  Similarity=0.296  Sum_probs=22.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      |+-.|||+..|+|..+|-.|| .|.-.|.
T Consensus         1 M~Ige~A~~~gvs~~TlRyYe~~GLl~p~   29 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTRIGLLRPT   29 (133)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             96899999989789999999985999886


No 248
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.08  E-value=5.3  Score=19.81  Aligned_cols=40  Identities=18%  Similarity=0.079  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             9999999999998599889999984899999998877998
Q gi|254781218|r   30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMC   69 (205)
Q Consensus        30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~   69 (205)
                      .+.=.++-..=...|+|..++|+.+|+|.++|-+|-+-..
T Consensus         7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415           7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             8999999999997685499999996922999999998733


No 249
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=77.91  E-value=3  Score=21.38  Aligned_cols=28  Identities=14%  Similarity=0.122  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ||-.++|+..|+|..+|-.|| .|.-.|.
T Consensus         1 M~Ige~Ak~~gvs~~tlRyYe~~GLl~p~   29 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPP   29 (127)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999989599999999985898986


No 250
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=77.84  E-value=2.9  Score=21.43  Aligned_cols=28  Identities=18%  Similarity=0.251  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ||-.+||+..|+|..+|-.|| .|.-.|+
T Consensus         1 m~IgevA~~~gvs~~TlRyYE~~GLl~~~   29 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQRRGLLPEP   29 (126)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999989398999999986998876


No 251
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=77.80  E-value=2.9  Score=21.44  Aligned_cols=28  Identities=21%  Similarity=0.221  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +|-.++|+..|||..++-.|| .|.-.|.
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~   29 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYERKGLLSPE   29 (124)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHCCCCCC
T ss_conf             95999999979699999999990899976


No 252
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=77.71  E-value=5.5  Score=19.74  Aligned_cols=84  Identities=7%  Similarity=0.000  Sum_probs=50.7

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             85998899999848999999988779988899999999998289999961453221000023213455467779999999
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI  121 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l  121 (205)
                      ...+|.++||+.+|+|++++++.=+..              +|+++-.-+..                  ..+ .+-+.+
T Consensus        23 ~~~lsl~~lA~~~~~S~~~l~r~Fk~~--------------~G~s~~~Yi~~------------------~Rl-~~A~~l   69 (127)
T PRK11511         23 ESPLSLEKVSERSGYSKWHLQRMFKKE--------------TGHSLGQYIRS------------------RKM-TEIAQK   69 (127)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH--------------HCCCHHHHHHH------------------HHH-HHHHHH
T ss_conf             899999999999895999999999999--------------89199999999------------------999-999999


Q ss_pred             HHHCCCCHHHHHHHHCCC-HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             997298389999997799-999999741488999899999999828999995
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMP-NSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       122 R~~~glsq~elA~~lgis-~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      ...-+++..+.|..+|.+ .+.+++              ...+.+|++|...
T Consensus        70 L~~t~~~I~~IA~~~Gf~~~~~F~r--------------~Fkk~~G~tP~~y  107 (127)
T PRK11511         70 LKESNEPILYLAERYGFESQQTLTR--------------TFKNYFDVPPHKY  107 (127)
T ss_pred             HHHCCCCHHHHHHHHCCCCHHHHHH--------------HHHHHHCCCHHHH
T ss_conf             9985998999999968998899999--------------9999889099999


No 253
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. 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.
Probab=77.66  E-value=4.5  Score=20.28  Aligned_cols=35  Identities=23%  Similarity=0.504  Sum_probs=27.2

Q ss_pred             HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             999999-99729838999999779999999974148
Q gi|254781218|r  116 ARLKSI-RKDKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       116 ~rLk~l-R~~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      +++.-+ |.+.|.|..++|...|+..+|++.|...+
T Consensus        11 eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knk   46 (53)
T pfam04218        11 EKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNK   46 (53)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             999999999858968899999698797999999809


No 254
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper),  CadR (cadmium),  PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=77.64  E-value=2.8  Score=21.51  Aligned_cols=27  Identities=19%  Similarity=0.292  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC-CCCCC
Q ss_conf             9889999984899999998877-99888
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN-GMCST   71 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~-G~~~p   71 (205)
                      ||-.+||+..|+|.++|-.||. |.-.|
T Consensus         1 m~Ige~A~~~gvs~~tlR~Ye~~GLl~~   28 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYERIGLLPP   28 (123)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             9689999998959999999998189875


No 255
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements.  A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=77.56  E-value=3.1  Score=21.26  Aligned_cols=67  Identities=22%  Similarity=0.274  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      +|-.+||+.+|+|.++|-.|| .|.-.|.-..     +.+              ..|.    ...   ...-..|+.+| 
T Consensus         1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~-----~g~--------------R~Y~----~~~---i~~l~~I~~lr-   53 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSE-----NGY--------------RLYS----EED---LERLRLIRRLR-   53 (100)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-----CCC--------------CCCC----HHH---HHHHHHHHHHH-
T ss_conf             97889999989599999999876999988358-----997--------------4256----999---99999999999-


Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             729838999999779
Q gi|254781218|r  124 DKGMSQIEFGKLLGM  138 (205)
Q Consensus       124 ~~glsq~elA~~lgi  138 (205)
                      ..|++..+..+.+..
T Consensus        54 ~~G~sl~~I~~~l~~   68 (100)
T cd00592          54 ELGLSLKEIRELLDA   68 (100)
T ss_pred             HCCCCHHHHHHHHHC
T ss_conf             979999999999835


No 256
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=77.51  E-value=4.8  Score=20.08  Aligned_cols=31  Identities=32%  Similarity=0.432  Sum_probs=18.6

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             9972983899999977999999997414889
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI  152 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~~~  152 (205)
                      |...|++..+.|+.+|.+.+|+.++-.|...
T Consensus        57 rekag~Ti~EIAeelG~TeqTir~hlkgetk   87 (182)
T COG1318          57 REKAGMTISEIAEELGRTEQTVRNHLKGETK   87 (182)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHCCHH
T ss_conf             9870374999999968779999999751403


No 257
>PRK06930 positive control sigma-like factor; Validated
Probab=77.32  E-value=4.7  Score=20.17  Aligned_cols=43  Identities=21%  Similarity=0.356  Sum_probs=32.5

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             99997298389999997799999999741488999899999999828999
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      -+....|+|+.|.|+.+||+.+|+..+-.       ....+|++-++.++
T Consensus       124 ll~~~~glsy~EIA~~L~Is~~tV~~~l~-------RA~~Ki~~~~~~~L  166 (170)
T PRK06930        124 LMHRGYGLSYSEIAAYLNIKKSTVQSMIE-------RAEKKIAKQINESL  166 (170)
T ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHCCCC
T ss_conf             88976188899999997988999999999-------99999999854053


No 258
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=77.17  E-value=3.1  Score=21.23  Aligned_cols=29  Identities=24%  Similarity=0.358  Sum_probs=24.4

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             99729838999999779999999974148
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      ....|+|..++|+.+|+|++|+.+|-.-.
T Consensus       168 ~~~~g~s~~~iak~~gvsrsTvyR~lK~~  196 (200)
T PRK13413        168 ELKKGTTKSEIAKKLKVSRTTLARFLKTM  196 (200)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99888999999999892999999999744


No 259
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=76.97  E-value=5.7  Score=19.61  Aligned_cols=39  Identities=28%  Similarity=0.414  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             7799999999972983899999977999999997414889
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI  152 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~  152 (205)
                      .+..-|..+|... ||+...|..-||+++|+.+..+|...
T Consensus         4 ~l~~Al~av~~g~-~S~~kAa~~ygIP~sTL~~r~~g~~~   42 (45)
T pfam05225         4 DLAEALEAVRNGK-MSLRKAARKYGIPRSTLWRRLRGKYS   42 (45)
T ss_pred             HHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf             9999999999199-67999999978985899999756343


No 260
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=76.90  E-value=5.8  Score=19.60  Aligned_cols=33  Identities=9%  Similarity=-0.004  Sum_probs=24.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHH
Q ss_conf             729838999999779999999974148899989
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK  156 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~  156 (205)
                      ...+|..++|+.+|+|++.+++.-....--++.
T Consensus       197 ~~~isl~~lA~~~~lS~s~l~rlFk~~~G~sp~  229 (290)
T PRK10572        197 ASEFDIESVAQHVCLSPSRLSHLFRQQLGISVL  229 (290)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf             799999999989697999999999986498999


No 261
>pfam07471 Phage_Nu1 Phage DNA packaging protein Nu1. 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.
Probab=76.76  E-value=2.6  Score=21.71  Aligned_cols=24  Identities=8%  Similarity=0.039  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             599889999984899999998877
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      ..++.++||+.+|||..+|.+|-.
T Consensus         1 ~~vnk~elA~~~gVS~~tv~~W~~   24 (164)
T pfam07471         1 MEVNKKQLAEIFGVSIRTIDNWQS   24 (164)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             967899999996988889999998


No 262
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=76.75  E-value=3.6  Score=20.86  Aligned_cols=29  Identities=21%  Similarity=0.327  Sum_probs=25.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++...|+|..|.|+.+|||.+|+..+-
T Consensus       128 ~~L~~~egls~~EIA~~lgiS~~tVk~~l  156 (172)
T PRK09651        128 FLLSQLDGLTYSEIAHKLGVSISSVKKYV  156 (172)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99998839999999999893999999999


No 263
>PRK11753 cAMP-regulatory protein; Provisional
Probab=76.72  E-value=5.8  Score=19.57  Aligned_cols=23  Identities=13%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             98389999997799999999741
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~  148 (205)
                      .+||.|+|..+|+++.++++..+
T Consensus       168 ~lt~~eLA~~lG~sretvsR~L~  190 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLK  190 (211)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             46999999886998999999999


No 264
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.64  E-value=5.9  Score=19.56  Aligned_cols=42  Identities=14%  Similarity=0.198  Sum_probs=34.3

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             9999729838999999779999999974148899989999999982899
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      .++...|+|..|.|+.+|++..|+...-       -..+.+|.+.||||
T Consensus       152 ~L~~~~g~s~~EIA~~Lgis~~TVk~rl-------~rA~~~LR~~LG~~  193 (194)
T PRK09646        152 TLAYYGGLTYREVAERLAVPLGTVKTRM-------RDGLRRLRDCLGVS  193 (194)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH-------HHHHHHHHHHHCCC
T ss_conf             9999939999999999891999999999-------99999999983789


No 265
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium.  Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=76.42  E-value=3.2  Score=21.15  Aligned_cols=65  Identities=14%  Similarity=0.112  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877--99888999999999982899999614532210000232134554677799999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIR  122 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR  122 (205)
                      .|-.++|+.+|+++.++-.||+  |.-.|.-.                   +..-+.|++    .   ....-..|+.++
T Consensus         1 YtI~eva~~~gv~~~tLR~wE~~~~l~~p~R~-------------------~~g~R~Ys~----~---dv~~l~~I~~l~   54 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRT-------------------DGGHRLYSE----A---DVARLRLIRRLT   54 (68)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCC-------------------CCCCEECCH----H---HHHHHHHHHHHH
T ss_conf             97899999988298999999985799999749-------------------999850499----9---999999999999


Q ss_pred             HHCCCCHHHHHHHH
Q ss_conf             97298389999997
Q gi|254781218|r  123 KDKGMSQIEFGKLL  136 (205)
Q Consensus       123 ~~~glsq~elA~~l  136 (205)
                       +.|++..+.+++.
T Consensus        55 -~~G~~l~~I~~l~   67 (68)
T cd01104          55 -SEGVRISQAAALA   67 (68)
T ss_pred             -HCCCCHHHHHHHH
T ss_conf             -9789999999870


No 266
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845   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 , .     Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.
Probab=76.25  E-value=6  Score=19.49  Aligned_cols=117  Identities=17%  Similarity=0.153  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH-----CCCHHHHHCCCCCC
Q ss_conf             8999999999999999985--9988999998489999999887799888999999999982-----89999961453221
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY-----EISFDWIYDGEVID   97 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~-----~vs~d~Ll~ge~~~   97 (205)
                      .++--++|..=++.+....  .=|-+|+|+.+|++..-|.++.+....-.+-.|=.+-.-.     ..++..++..+...
T Consensus        78 ~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~  157 (227)
T TIGR02479        78 LRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIEDDKSE  157 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCC
T ss_conf             89998689999999999869898888999983999989999999988998764899984146322345323100143576


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHH--------------HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             00002321345546777999999999--------------729838999999779999999974
Q gi|254781218|r   98 RRYEDVTNKKRLDPYAIGARLKSIRK--------------DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus        98 ~~~~~~~~~~~~d~~~iG~rLk~lR~--------------~~glsq~elA~~lgis~~tis~~E  147 (205)
                            .+...+....+-..|.++.+              ..+|+.+|.|+.+|+|.+-||++-
T Consensus       158 ------~P~~~~~~~~L~~~l~~ai~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiH  215 (227)
T TIGR02479       158 ------DPEEELEREELREALAEAIEKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIH  215 (227)
T ss_pred             ------CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             ------8135899999999999997406855788888864127668899988378705799999


No 267
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=76.24  E-value=3.2  Score=21.22  Aligned_cols=28  Identities=25%  Similarity=0.455  Sum_probs=21.3

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             9972983899999977999999997414
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      +-+.|++..++|+..||+++|+.+|.++
T Consensus        17 L~~~G~~i~~IA~~~~vsrsTvYRyl~~   44 (45)
T pfam02796        17 LLEEGISIKQIAKIFGISRSTVYRYLAA   44 (45)
T ss_pred             HHHCCCCHHHHHHHHCCHHHHHHHHCCC
T ss_conf             9987994999999986008888764458


No 268
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=76.18  E-value=2.8  Score=21.52  Aligned_cols=23  Identities=30%  Similarity=0.404  Sum_probs=13.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             29838999999779999999974
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E  147 (205)
                      ++.+..|+|+.+||+++|++...
T Consensus        22 R~~~l~elA~~lgis~sT~~~hL   44 (53)
T pfam04967        22 RRVTLKDLAKELGISKSTLSEHL   44 (53)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             76889999999698999999999


No 269
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=76.10  E-value=3.5  Score=20.91  Aligned_cols=28  Identities=14%  Similarity=0.182  Sum_probs=22.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ||-.+||+..|+|..+|-.|| .|.-.|+
T Consensus         1 m~IgelA~~~gvs~~tlRyYE~~GLl~~~   29 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYESIGLLPEP   29 (126)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             96899999989499999999984998987


No 270
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=76.07  E-value=3.3  Score=21.08  Aligned_cols=66  Identities=18%  Similarity=0.225  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      |.-.|+|+..|+|..+|-.|| .|.-.|.-.. -. -..|+                     ...   ..--..|+.+|.
T Consensus         1 M~IgevAk~~gvs~~TlRyYE~~GLl~~~~r~-~~-yR~Y~---------------------~~~---l~~l~~I~~~r~   54 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRS-GN-YRVYD---------------------AQH---VECLRFIKEARQ   54 (116)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-CC-CCCCC---------------------HHH---HHHHHHHHHHHH
T ss_conf             96899999989699999999986999987577-77-33228---------------------999---999999999999


Q ss_pred             HCCCCHHHHHHHHC
Q ss_conf             72983899999977
Q gi|254781218|r  124 DKGMSQIEFGKLLG  137 (205)
Q Consensus       124 ~~glsq~elA~~lg  137 (205)
                       .|+|..|+.+.+.
T Consensus        55 -~GfsL~eI~~ll~   67 (116)
T cd04769          55 -LGFTLAELKAIFA   67 (116)
T ss_pred             -CCCCHHHHHHHHH
T ss_conf             -7999999999996


No 271
>TIGR00160 MGSA methylglyoxal synthase; InterPro: IPR004363   Methylglyoxal synthase (MGS)  catalyzes the conversion of dihydroxyacetone phosphate to methylglyoxal and phosphate:  Glycerone phosphate = methylglyoxal + phosphate  It provides bacteria with an alternative to triosephosphate isomerase for metabolizing dihydroxyacetone phosphate. MGS is a small protein of about 13 to 17 kDa. An aspartate residue is involved in the catalytic mechanism. Methylglyoxal synthase contains a domain shared by other enzymes. Other proteins containing this domain include purine biosynthesis protein PurH and carbamoyl phosphate synthetase.; GO: 0008929 methylglyoxal synthase activity, 0019242 methylglyoxal biosynthetic process, 0005737 cytoplasm.
Probab=75.72  E-value=1.6  Score=23.01  Aligned_cols=25  Identities=20%  Similarity=0.364  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHHHHHCCCH-------HHHHCC
Q ss_conf             8889999999999828999-------996145
Q gi|254781218|r   69 CSTSIRYALYLRNEYEISF-------DWIYDG   93 (205)
Q Consensus        69 ~~psi~~l~~la~~~~vs~-------d~Ll~g   93 (205)
                      .+|+++.|++||.+|+|++       |-|+.+
T Consensus        89 HEPDV~ALlRLc~V~nIPlAtN~~TA~~li~~  120 (143)
T TIGR00160        89 HEPDVKALLRLCDVYNIPLATNVATADILIKS  120 (143)
T ss_pred             CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             88007889878645025034405667887730


No 272
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=75.63  E-value=3.6  Score=20.84  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=24.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +=.++...|+|..|.|+.+|||.+|+...
T Consensus       113 v~~L~~~egls~~EIA~~lgis~~tVk~~  141 (159)
T PRK12527        113 SFLLRKLEGLSHQQIAEHLGISRSLVEKH  141 (159)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99889873979999999989199999999


No 273
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=75.54  E-value=5.6  Score=19.68  Aligned_cols=27  Identities=22%  Similarity=0.347  Sum_probs=19.0

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             972983899999977999999997414
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ..-|.|..++|..+||+.+++.+|-+-
T Consensus        20 ~~~g~sv~~var~~gi~~~~l~~W~k~   46 (75)
T pfam01527        20 LEPGASVSELAREHGVSPATLYKWRKK   46 (75)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             809984999999989599999999999


No 274
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=75.24  E-value=3.9  Score=20.64  Aligned_cols=21  Identities=14%  Similarity=0.170  Sum_probs=12.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHC
Q ss_conf             889999984899999998877
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~   66 (205)
                      +-.|+|+..|+|.++|-.||.
T Consensus         2 ri~ElA~~~Gvs~~tiR~YE~   22 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNYES   22 (99)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             789999998969999999999


No 275
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=75.01  E-value=5.7  Score=19.64  Aligned_cols=31  Identities=19%  Similarity=0.293  Sum_probs=23.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999999972983899999977999999997
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      ..|.+..+..+..+.+.|+.+||+++++.+-
T Consensus         8 ~~I~~aL~~~~gn~~~aA~~LGisr~tL~~k   38 (42)
T pfam02954         8 ELIEAALERTGGNKSKAARLLGISRRTLYRK   38 (42)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9999999994997999999979699999999


No 276
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=74.62  E-value=4.8  Score=20.10  Aligned_cols=26  Identities=35%  Similarity=0.408  Sum_probs=21.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             72983899999977999999997414
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      ...+|+.|.|+.+|+|+..++++|..
T Consensus       192 ~~~~Tl~eIg~~lgiSrERVRQIe~~  217 (228)
T PRK05803        192 GKEKTQREIAKALGISRSYVSRIEKK  217 (228)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99715999999989799999999999


No 277
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=74.61  E-value=4.2  Score=20.46  Aligned_cols=67  Identities=15%  Similarity=0.240  Sum_probs=39.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      |+-.+||+..|+|..+|-.|| .|.-.|.     .-.+.|.+              |.    ...+   .--..|+.+| 
T Consensus         1 M~Ige~a~~~gvs~~tlRyYe~~GLl~p~-----r~~~gyR~--------------Y~----~~~~---~~l~~I~~lr-   53 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEEQGLLVPE-----RSANGYRD--------------YD----EAAV---DRVRQIRRLL-   53 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-----CCCCCCEE--------------CC----HHHH---HHHHHHHHHH-
T ss_conf             96899999989799999999984899998-----08998700--------------59----9999---9999999999-


Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             729838999999779
Q gi|254781218|r  124 DKGMSQIEFGKLLGM  138 (205)
Q Consensus       124 ~~glsq~elA~~lgi  138 (205)
                      ..|||..|..+.+.+
T Consensus        54 ~~G~sl~eI~~~l~~   68 (112)
T cd01282          54 AAGLTLEEIREFLPC   68 (112)
T ss_pred             HCCCCHHHHHHHHHH
T ss_conf             969999999999987


No 278
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=74.60  E-value=6.3  Score=19.38  Aligned_cols=29  Identities=7%  Similarity=0.166  Sum_probs=25.0

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99997298389999997799999999741
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .++...|+|+.|.|+.+|||..|+..+-.
T Consensus       133 ~L~~~eg~s~~EIAe~LgiS~~tVk~~l~  161 (183)
T PRK07037        133 EMVRLRGETLQDIARELNVSQTLVNFMIR  161 (183)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98987398999999998929999999999


No 279
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=74.30  E-value=6.7  Score=19.18  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             298389999997799999999741
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~  148 (205)
                      ..|||.|+|+++|+++.|+++..+
T Consensus       183 l~lt~~dLA~~lG~trEtVsR~L~  206 (235)
T PRK11161        183 LTMTRGDIGNYLGLTVETISRLLG  206 (235)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             237899999887898999999999


No 280
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.  A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=74.23  E-value=4.2  Score=20.46  Aligned_cols=67  Identities=12%  Similarity=0.017  Sum_probs=41.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      +|-.++|+.+|++.++|-.|| .|...|....-                   .....     +.. +....-..|+.++ 
T Consensus         2 ~tIgeva~~~gvs~~tLRyye~~gli~p~~~~~-------------------~g~R~-----Ys~-~dl~~l~~I~~l~-   55 (88)
T cd01105           2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDG-------------------GGQRK-----YSL-ADVDRLLVIKELL-   55 (88)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC-------------------CCCEE-----CCH-HHHHHHHHHHHHH-
T ss_conf             678999999895999999999949989987699-------------------98214-----799-9999999999999-


Q ss_pred             HCCCCHHHHHHHHC
Q ss_conf             72983899999977
Q gi|254781218|r  124 DKGMSQIEFGKLLG  137 (205)
Q Consensus       124 ~~glsq~elA~~lg  137 (205)
                      +.|++..+.++.+.
T Consensus        56 ~~G~sl~~i~~~L~   69 (88)
T cd01105          56 DEGFTLAAAVEKLR   69 (88)
T ss_pred             HCCCCHHHHHHHHH
T ss_conf             97998999999999


No 281
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789    This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=74.22  E-value=6.8  Score=19.17  Aligned_cols=78  Identities=10%  Similarity=0.126  Sum_probs=51.8

Q ss_pred             HHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHHHCC----CCCCCCCCCCCC
Q ss_conf             8999998489999999887-799888999----------------9999999828999996145----322100002321
Q gi|254781218|r   47 QKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWIYDG----EVIDRRYEDVTN  105 (205)
Q Consensus        47 Q~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~Ll~g----e~~~~~~~~~~~  105 (205)
                      --++|+..|+|-.+|--|| .|...|++.                .|+.=|+.+|-|++++=.-    ....+...||+.
T Consensus         3 Ig~~AK~tglssK~IR~YE~kGLi~Pp~Rse~GYR~Y~~~h~~~L~li~raR~~GFSLeEc~~ll~L~ndp~R~SAdVK~   82 (127)
T TIGR02044         3 IGQVAKLTGLSSKSIRYYEEKGLIPPPLRSEGGYRTYTDKHVDELRLISRARSVGFSLEECKELLSLWNDPNRTSADVKA   82 (127)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf             67775014772688988776326799886888885638767888899999987189889999998752288898878899


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             3455467779999999997
Q gi|254781218|r  106 KKRLDPYAIGARLKSIRKD  124 (205)
Q Consensus       106 ~~~~d~~~iG~rLk~lR~~  124 (205)
                      .+.-.-..|-.+|.++...
T Consensus        83 rtl~k~~E~~~kI~eL~~m  101 (127)
T TIGR02044        83 RTLEKVAELERKISELQEM  101 (127)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             9998899999999999889


No 282
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=74.13  E-value=4.4  Score=20.36  Aligned_cols=28  Identities=21%  Similarity=0.334  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      |+-.+||+..|+|.++|-.|| .|.-.|+
T Consensus         1 M~IgelA~~~gvs~~tlR~YE~~GLl~p~   29 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEAEGLLSSV   29 (131)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999988788999999977998987


No 283
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=73.82  E-value=3.9  Score=20.62  Aligned_cols=27  Identities=22%  Similarity=0.298  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf             988999998489999999887-799888
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCST   71 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~p   71 (205)
                      .|-.|||+..|+|.++|-.|| -|.-.|
T Consensus         1 ytIgelA~~~gvs~~tlRyYe~~GLl~~   28 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEGLLPP   28 (113)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             9788999998959999999998389799


No 284
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an  N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=73.38  E-value=4.6  Score=20.21  Aligned_cols=28  Identities=18%  Similarity=0.158  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +|-.++|+.+|+|.+++-.|| .|.-.|.
T Consensus         1 ytIge~a~~~gvs~~tlRyYe~~GLl~p~   29 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPS   29 (103)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97889999989699999999853897886


No 285
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=73.37  E-value=5.2  Score=19.88  Aligned_cols=27  Identities=7%  Similarity=0.111  Sum_probs=18.3

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             999999859988999998489999999
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVN   62 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is   62 (205)
                      |+.|.+.-.+|-.++|+++|+|++++.
T Consensus        15 L~~Lq~d~R~s~~eiA~~lglS~stv~   41 (153)
T PRK11179         15 LEALMENARTPYAELAKQFGVSPGTIH   41 (153)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf             999998489999999999892999999


No 286
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=73.33  E-value=4.3  Score=20.39  Aligned_cols=34  Identities=21%  Similarity=0.249  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf             2983899999977999999997414889998999
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA  158 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l  158 (205)
                      +-+...|+++.+|++++|+.++.+.+..|..-.+
T Consensus        12 r~lrl~ev~~~~GlSrstiYr~i~~~~FPkpvkl   45 (70)
T COG3311          12 RLLRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKL   45 (70)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCEEC
T ss_conf             1520899999977668999999804779998622


No 287
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=73.23  E-value=7.2  Score=19.02  Aligned_cols=71  Identities=14%  Similarity=0.271  Sum_probs=41.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~  123 (205)
                      ++-.++|+.+|++++++-.||+ |...|.-                 -.|-  -..|+      ..| ...-..|+.+.+
T Consensus         2 Y~IgevA~l~Gv~~~tLR~yEr~gli~P~R-----------------t~gG--~R~Ys------~~D-l~~L~~I~~L~~   55 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDRLGLVSPAR-----------------TNGG--GRRYS------NND-LELLRQVQRLSQ   55 (98)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCC-----------------CCCC--CCCCC------HHH-HHHHHHHHHHHH
T ss_conf             358999999798999999999938978661-----------------8999--94349------999-999999999999


Q ss_pred             HCCCCHHHHHHHHCCCHH
Q ss_conf             729838999999779999
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNS  141 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~  141 (205)
                      ..|++....-..+.+..+
T Consensus        56 ~~G~~l~gik~iL~l~~q   73 (98)
T cd01279          56 DEGFNLAGIKRIIELYPQ   73 (98)
T ss_pred             HCCCCHHHHHHHHHHHHH
T ss_conf             589889999999998999


No 288
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=72.91  E-value=5.4  Score=19.77  Aligned_cols=27  Identities=7%  Similarity=0.151  Sum_probs=14.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             999999859988999998489999999
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVN   62 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is   62 (205)
                      |+.|++.-.+|..++|+++|+|++++.
T Consensus        20 L~~Lq~daR~s~~eLA~~vglS~stv~   46 (164)
T PRK11169         20 LNELQKDGRISNVELSKRVGLSPTPCL   46 (164)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf             999998489999999999892999999


No 289
>PRK09775 hypothetical protein; Provisional
Probab=72.69  E-value=5.2  Score=19.88  Aligned_cols=31  Identities=6%  Similarity=0.019  Sum_probs=27.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999859988999998489999999887
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      -|+.++.+--++-.+|+..+|||+.|+|+-=
T Consensus         3 ~l~~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l   33 (443)
T PRK09775          3 LLTTLLLQGPLSAAELAQRLGISQATLSRLL   33 (443)
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             6899997399359999998688888899999


No 290
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=72.49  E-value=4.9  Score=20.04  Aligned_cols=28  Identities=14%  Similarity=0.228  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      |.-.+||+..|+|..+|-.|| .|.-.|+
T Consensus         1 M~Ige~a~~~gvs~~tlRyYE~~GLl~~~   29 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEKEGLLPAP   29 (127)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             96899999989499999999985898875


No 291
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=71.87  E-value=5.3  Score=19.84  Aligned_cols=25  Identities=20%  Similarity=0.158  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf             988999998489999999887-7998
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMC   69 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~   69 (205)
                      +|-.++|+..|+|.++|-.|| .|.-
T Consensus         2 ~~Ige~a~~~gis~~tlRyYe~~GLl   27 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYESIGLI   27 (102)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf             87899999989499999999987999


No 292
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.71  E-value=5.9  Score=19.55  Aligned_cols=28  Identities=14%  Similarity=0.107  Sum_probs=20.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999998599889999984899999998
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      ++.+++....++.++|+.+|+|++++.+
T Consensus        14 L~~L~~d~r~~~~eia~~lglS~~~v~~   41 (154)
T COG1522          14 LRLLQEDARISNAELAERVGLSPSTVLR   41 (154)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             9999972765799999997979899999


No 293
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=71.42  E-value=4  Score=20.60  Aligned_cols=41  Identities=10%  Similarity=0.147  Sum_probs=31.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHCC-------------CCCCCHHHHHHHHHHHC
Q ss_conf             983899999977999999997414-------------88999899999999828
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYEQG-------------RTIPEIKPARKIKQVTK  166 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E~g-------------~~~Ps~~~l~kIa~~lg  166 (205)
                      .+|++|+|.++|.++.|+++..+.             -...+.+.|.+||+.=|
T Consensus       145 ~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~~I~I~D~~~L~~lAe~~g  198 (201)
T PRK13918        145 YATHDELAAAVGSVRETVTKVVGELSREGVIRSGYGKIQLLDLKALKELAESRG  198 (201)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHCC
T ss_conf             579999998859868999999999998898896799899928999999987447


No 294
>PRK13749 transcriptional regulator MerD; Provisional
Probab=70.91  E-value=6.8  Score=19.16  Aligned_cols=48  Identities=19%  Similarity=0.117  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHH
Q ss_conf             59988999998489999999887-799888999----------------9999999828999996
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWI   90 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~L   90 (205)
                      ..+|-.+||+..|+|..+|-.|| .|.-.|+-.                ..++-|..+++++|.|
T Consensus         2 ~aytIg~LA~~aGVsv~tIR~Y~~~GLL~p~~Rt~gGyRlyd~~~l~RL~FIR~a~elGf~LdeI   66 (121)
T PRK13749          2 NAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL   66 (121)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             84209999999599735548898768989988899884367899999999999999908989999


No 295
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=70.74  E-value=4.3  Score=20.39  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=20.6

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             729838999999779999999974
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ...+|+.|+|.++|+++.++++..
T Consensus       171 ~l~lT~~dLA~~lG~trETVsR~L  194 (224)
T PRK09391        171 ALPMSRRDIADYLGLTIETVSRAL  194 (224)
T ss_pred             ECCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             715799999988799799999999


No 296
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327   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 , .    This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=70.49  E-value=6.7  Score=19.21  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=21.5

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+-...|||-+|.|+.+|||..||-..
T Consensus       129 ~lsr~eg~s~~EIA~~L~iS~~TVe~h  155 (167)
T TIGR02985       129 ILSRFEGLSNKEIAEELGISVKTVEYH  155 (167)
T ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             998861798678998848988899999


No 297
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=70.47  E-value=6.8  Score=19.17  Aligned_cols=27  Identities=19%  Similarity=0.256  Sum_probs=16.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             999999859988999998489999999
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVN   62 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is   62 (205)
                      |+.+++.-.+|-.++|+.+|+|++++.
T Consensus         9 l~~L~~n~R~s~~~iA~~lg~S~~tv~   35 (108)
T smart00344        9 LEELQKDARISLAELAKKVGLSPSTVH   35 (108)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf             999998289999999999893999999


No 298
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=70.21  E-value=8.3  Score=18.63  Aligned_cols=29  Identities=28%  Similarity=0.423  Sum_probs=17.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +=.++.-.|+|..|.|+.+|++.+++..+
T Consensus        18 ~~~l~~~~~~s~~eIA~~lg~s~~tVk~~   46 (54)
T pfam08281        18 VFLLRYLEGLSYAEIAELLGISEGTVKSR   46 (54)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             96879987859999999989499999999


No 299
>PRK13503 transcriptional activator RhaS; Provisional
Probab=69.81  E-value=8.6  Score=18.54  Aligned_cols=41  Identities=10%  Similarity=-0.003  Sum_probs=28.5

Q ss_pred             HHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf             99999997--298389999997799999999741488999899
Q gi|254781218|r  117 RLKSIRKD--KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKP  157 (205)
Q Consensus       117 rLk~lR~~--~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~  157 (205)
                      -+.-+...  ..++..++|+.+|+++..++++-+...--+...
T Consensus       176 i~~yI~~hy~~~isl~~lA~~~~lS~~~l~r~FK~~tG~t~~~  218 (278)
T PRK13503        176 LLAWLEDHFAEEVNWEAVADQFSLSLRTLHRQLKQQTGLTPQR  218 (278)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf             9999999757999999999897959999999999988938999


No 300
>pfam08299 Bac_DnaA_C domain.
Probab=69.74  E-value=8.6  Score=18.53  Aligned_cols=61  Identities=15%  Similarity=0.230  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHH
Q ss_conf             9999999982899999614532210000232134554677799999999972983899999977-99999999
Q gi|254781218|r   74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG-MPNSTLSN  145 (205)
Q Consensus        74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg-is~~tis~  145 (205)
                      +.+-.+|+.|+|+.+.|....-         .+....+..++-  --+|+..++|..+.+..+| -+++|+..
T Consensus         4 ~I~~~Va~~f~v~~~~i~s~~R---------~~~i~~aR~iam--yL~r~~t~~s~~~IG~~fg~RdHsTVi~   65 (70)
T pfam08299         4 NIQEIVAEYYNITVEDLLSKSR---------TRSVVRARQIAM--YLLRELTNLSLPEIGEIFGGRDHTTVLH   65 (70)
T ss_pred             HHHHHHHHHHCCCHHHHHCCCC---------CCHHHHHHHHHH--HHHHHHHCCCHHHHHHHHCCCCCHHHHH
T ss_conf             9999999882996999837898---------811578999999--9999986799999999938997379999


No 301
>PHA00361 cI Repressor
Probab=69.46  E-value=2.3  Score=22.03  Aligned_cols=19  Identities=16%  Similarity=0.144  Sum_probs=16.5

Q ss_pred             HHHHHHCCCHHHHHCCCCC
Q ss_conf             9999828999996145322
Q gi|254781218|r   78 YLRNEYEISFDWIYDGEVI   96 (205)
Q Consensus        78 ~la~~~~vs~d~Ll~ge~~   96 (205)
                      +||++|+|+++||+.|...
T Consensus         1 ~lA~~Lg~s~~~Ll~g~~~   19 (165)
T PHA00361          1 KLAKALGTSVDDLLQEDLS   19 (165)
T ss_pred             CHHHHHCCCHHHHHCCCCC
T ss_conf             9568669899998557556


No 302
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=69.00  E-value=6.5  Score=19.27  Aligned_cols=47  Identities=21%  Similarity=0.155  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHHH
Q ss_conf             988999998489999999887-799888999----------------99999998289999961
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWIY   91 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~Ll   91 (205)
                      +|-.++|+.+|+|..++-.|| .|.-.|+-.                ..+...+.+|+|++.+-
T Consensus         2 ~tI~e~Ak~~gvs~~TLRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eIk   65 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIR   65 (172)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             9789999998949889999998879899884999870779999999999999998799999999


No 303
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor; InterPro: IPR012781    Members of this family belong the lacI helix-turn-helix family of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterised members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.; GO: 0003677 DNA binding, 0006355 regulation of transcription DNA-dependent, 0009750 response to fructose stimulus, 0045449 regulation of transcription.
Probab=68.86  E-value=4  Score=20.56  Aligned_cols=48  Identities=13%  Similarity=0.079  Sum_probs=36.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCC------CCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             889999984899999998877998------889999999999828999996145
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFENGMC------STSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E~G~~------~psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      |..|.|+.+|||..|.|.+=||+.      .-+.+.+..+++.++=.++---.|
T Consensus         1 tL~dIA~LAGVS~TTASyViNGka~~~Ris~~T~erV~Avv~e~~Y~Pn~~A~s   54 (335)
T TIGR02417         1 TLDDIAKLAGVSKTTASYVINGKAKEYRISEETVERVMAVVEEQGYKPNVAAAS   54 (335)
T ss_pred             CCHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             900576660823232212000431110136787889999898737857755420


No 304
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=68.37  E-value=6.3  Score=19.38  Aligned_cols=23  Identities=13%  Similarity=-0.172  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99889999984899999998877
Q gi|254781218|r   44 NKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        44 gltQ~elA~~~gis~~~is~~E~   66 (205)
                      .|+-++.|+.+||+..++-+|=+
T Consensus         1 ~m~~~e~~~~lgis~~Tl~rw~r   23 (193)
T COG2452           1 LLRPKEACQLLGISYSTLLRWIR   23 (193)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98889999983947999999987


No 305
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794    This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=68.30  E-value=1.6  Score=23.12  Aligned_cols=21  Identities=24%  Similarity=0.408  Sum_probs=14.4

Q ss_pred             HHHHHHHCCCHHHHHHHH-CCC
Q ss_conf             999998489999999887-799
Q gi|254781218|r   48 KEMAIGANQLESAVNLFE-NGM   68 (205)
Q Consensus        48 ~elA~~~gis~~~is~~E-~G~   68 (205)
                      .+||+++||..-||-.|| +|.
T Consensus         3 g~LA~~~GVNvETiRyYeRkGL   24 (126)
T TIGR02051         3 GELAKAAGVNVETIRYYERKGL   24 (126)
T ss_pred             HHHHHHCCCCEEEEEHHHHCCC
T ss_conf             1136666897012210010077


No 306
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain.  For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization.  For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=68.12  E-value=6.1  Score=19.46  Aligned_cols=23  Identities=22%  Similarity=0.462  Sum_probs=11.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             72983899999977999999997
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~  146 (205)
                      ..|++-.|.|+.+|++..|+..+
T Consensus        13 ~~G~s~~eIA~~L~is~~TV~~~   35 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTH   35 (57)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             80799999999989789999999


No 307
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle 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=67.80  E-value=5.3  Score=19.83  Aligned_cols=28  Identities=18%  Similarity=0.246  Sum_probs=21.8

Q ss_pred             HHHHHHHHH--CCCCHHHHHHHHC-CCHHHH
Q ss_conf             999999998--5998899999848-999999
Q gi|254781218|r   34 TRIKDIRKA--NNKTQKEMAIGAN-QLESAV   61 (205)
Q Consensus        34 ~rik~lR~~--~gltQ~elA~~~g-is~~~i   61 (205)
                      +||..|++.  .|+|..++|+.+| ||+++|
T Consensus         6 Erve~LkkLW~eGlSaSqIA~~LGgvTRNAV   36 (162)
T pfam07750         6 ERVELLKKLWLEGLSASQIAAQLGGVSRNAV   36 (162)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCCCCCE
T ss_conf             9999999999853659999999765540000


No 308
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=67.35  E-value=5.8  Score=19.59  Aligned_cols=69  Identities=17%  Similarity=0.102  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHCCCHHHHH-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH------HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999999998289999961-4532210000232134554677799999999------97298389999997799999999
Q gi|254781218|r   73 IRYALYLRNEYEISFDWIY-DGEVIDRRYEDVTNKKRLDPYAIGARLKSIR------KDKGMSQIEFGKLLGMPNSTLSN  145 (205)
Q Consensus        73 i~~l~~la~~~~vs~d~Ll-~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR------~~~glsq~elA~~lgis~~tis~  145 (205)
                      ...+..+++.+.....+.. ..........+.+.++..       -|+.+-      --+..+..|+|+.+||+++|++.
T Consensus       125 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~-------vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e  197 (215)
T COG3413         125 KDELRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLE-------VLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE  197 (215)
T ss_pred             HHHHHHHHHHHCCCCHHEECCCCCCCCCCCCCCHHHHH-------HHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             78999999884323101021344234564469999999-------99999985898887658999999995998889999


Q ss_pred             HHC
Q ss_conf             741
Q gi|254781218|r  146 YEQ  148 (205)
Q Consensus       146 ~E~  148 (205)
                      +.+
T Consensus       198 hLR  200 (215)
T COG3413         198 HLR  200 (215)
T ss_pred             HHH
T ss_conf             999


No 309
>pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.
Probab=67.15  E-value=8.4  Score=18.59  Aligned_cols=30  Identities=17%  Similarity=0.013  Sum_probs=17.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             99998599889999984899999998877998
Q gi|254781218|r   38 DIRKANNKTQKEMAIGANQLESAVNLFENGMC   69 (205)
Q Consensus        38 ~lR~~~gltQ~elA~~~gis~~~is~~E~G~~   69 (205)
                      +.-+..|  |...|+.+|+.+++||+-=+-.+
T Consensus         7 dyv~~~G--Q~kaA~~lGV~Q~AISKAlragR   36 (58)
T pfam09048         7 DYVEEHG--QAKAAKDLGVNQSAISKALRAGR   36 (58)
T ss_pred             HHHHHHC--HHHHHHHCCCCHHHHHHHHHCCC
T ss_conf             9999976--59899982975899999996488


No 310
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=67.00  E-value=7.5  Score=18.89  Aligned_cols=64  Identities=31%  Similarity=0.370  Sum_probs=39.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH--
Q ss_conf             988999998489999999887-79988899999999998289999961453221000023213455467779999999--
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI--  121 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l--  121 (205)
                      +|-.++|+..|+|..+|-.|| .|.-.|.-+      +.+              ..|.         +..+ .+|+.+  
T Consensus         1 ytIge~A~~~gvs~~tlRyYe~~GLl~p~r~------~g~--------------R~Y~---------~~~~-~~l~~I~~   50 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDKGLLSPERR------GQT--------------RVYS---------RRDR-ARLKLILR   50 (118)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCC--------------CCCC---------HHHH-HHHHHHHH
T ss_conf             9588999998979999999998699875557------986--------------8608---------9999-99999999


Q ss_pred             HHHCCCCHHHHHHHHCC
Q ss_conf             99729838999999779
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGM  138 (205)
Q Consensus       122 R~~~glsq~elA~~lgi  138 (205)
                      -+..|+|..|..+.+.+
T Consensus        51 ~r~~G~sL~eI~~~L~l   67 (118)
T cd04776          51 GKRLGFSLEEIRELLDL   67 (118)
T ss_pred             HHHCCCCHHHHHHHHHH
T ss_conf             99829989999999964


No 311
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=66.69  E-value=4.2  Score=20.45  Aligned_cols=21  Identities=14%  Similarity=0.347  Sum_probs=11.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH
Q ss_conf             838999999779999999974
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E  147 (205)
                      ++..+.|+.||++.++|++|-
T Consensus        23 ~~l~~IA~~L~vs~~~IrkWK   43 (60)
T pfam10668        23 MKLKDIANKLNVSESQIRKWK   43 (60)
T ss_pred             EEHHHHHHHHCCCHHHHHHCC
T ss_conf             449999999687988876031


No 312
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745   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 , .    This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=66.48  E-value=4.3  Score=20.41  Aligned_cols=29  Identities=21%  Similarity=0.305  Sum_probs=20.1

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             99972983899999977999999997414
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      +.--.|+|..++|.+-+++++|+|+|-..
T Consensus       177 LHfv~~Ls~~r~g~my~~~~STvsR~~~~  205 (249)
T TIGR03001       177 LHFVEGLSMDRLGAMYQVHRSTVSRWVAQ  205 (249)
T ss_pred             HHHHCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             68820332999987745775078999999


No 313
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=65.78  E-value=7.1  Score=19.03  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=12.0

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             72983899999977999999997
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~  146 (205)
                      ..|++-.|.|+.+|++..|+..+
T Consensus        16 ~~G~s~~eIA~~L~is~~TV~~h   38 (58)
T pfam00196        16 AAGKSNKEIADILGISEKTVKVH   38 (58)
T ss_pred             HHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             80799999999978889999999


No 314
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=65.78  E-value=8  Score=18.73  Aligned_cols=42  Identities=24%  Similarity=0.285  Sum_probs=29.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             9999997298389999997799999999741488999899999999828
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK  166 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg  166 (205)
                      +=.++...|+|..|.|+.+|+|.+|+...-.       ....+|.+.|.
T Consensus       114 v~~L~~~eg~s~~EIA~~L~is~~tVksrl~-------RAr~~Lr~~LE  155 (181)
T PRK09637        114 ALRLTELEGLSQKEIAEKLGLSLSGAKSRVQ-------RGRVKLKELLE  155 (181)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHH
T ss_conf             9799988599999999998949999999999-------99999999997


No 315
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.57  E-value=7.4  Score=18.92  Aligned_cols=44  Identities=9%  Similarity=0.171  Sum_probs=30.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             999999729838999999779999999974148899989999999982899
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      +=.++...|+|.+|.|+.+|||..|+...-.       ....++.+.|++.
T Consensus       127 vl~L~~~egls~~EIAe~Lgis~~TVksrl~-------RAr~~Lr~~L~~~  170 (190)
T PRK12516        127 AIILIGASGFAYEEAAEICGCAVGTIKSRVS-------RARARLQEILQIE  170 (190)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHC
T ss_conf             9998998299999999998949999999999-------9999999999845


No 316
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=65.48  E-value=5.8  Score=19.59  Aligned_cols=23  Identities=9%  Similarity=-0.081  Sum_probs=19.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             98899999848999999988779
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENG   67 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G   67 (205)
                      |...++|+++|||+.+|.||-+-
T Consensus         1 mkT~~vAk~LGVspkTVQRWvKq   23 (178)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQ   23 (178)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             97178899939992999999999


No 317
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=65.45  E-value=10  Score=18.00  Aligned_cols=28  Identities=29%  Similarity=0.507  Sum_probs=24.2

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++...|+|..|.|+.+||+..|+..+-
T Consensus       146 ~L~~~~g~s~~EIA~~L~is~~TVk~~l  173 (187)
T PRK13919        146 EVLYYQGYTHREAARLLGLPLGTLKTWA  173 (187)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999859999999999893999999999


No 318
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, 
Probab=65.27  E-value=7.5  Score=18.90  Aligned_cols=28  Identities=14%  Similarity=0.154  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +|-.++|+..|+|..+|-.|| .|.-.|.
T Consensus         1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~   29 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLRGLLHPV   29 (107)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             95889999978894899899987898998


No 319
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=64.98  E-value=11  Score=17.96  Aligned_cols=58  Identities=14%  Similarity=0.045  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH-HHHHHH
Q ss_conf             999999999999999-9859988999998489999999887799888999999-999982
Q gi|254781218|r   26 RQYWKDVGTRIKDIR-KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYAL-YLRNEY   83 (205)
Q Consensus        26 ~~~~~~iG~rik~lR-~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~-~la~~~   83 (205)
                      ....+.|++-|-.-. +...+|-.+||+.+|+|+++|.|+=+-...-...-+. .|+..+
T Consensus        15 t~~Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~   74 (282)
T PRK11557         15 AQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEAL   74 (282)
T ss_pred             CHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             999999999998098999765699999896999889999999938998999999999998


No 320
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=64.94  E-value=6.6  Score=19.25  Aligned_cols=56  Identities=20%  Similarity=0.127  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHHHHC
Q ss_conf             99999999999-9985998899999848999999988779988899-99999999828
Q gi|254781218|r   29 WKDVGTRIKDI-RKANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRNEYE   84 (205)
Q Consensus        29 ~~~iG~rik~l-R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~~~~   84 (205)
                      .+.|++-|-.- .....+|-.+||+++|+|+++|.|+=+-...-.. ++=+.|+..+.
T Consensus        18 e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~~   75 (106)
T pfam01418        18 EKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGELA   75 (106)
T ss_pred             HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             9999999992999998833999998969989999999999589989999999999865


No 321
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=64.43  E-value=9.2  Score=18.36  Aligned_cols=28  Identities=18%  Similarity=0.160  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ++-.+||+..|||..+|-.|| .|.-.|.
T Consensus         1 y~Ige~Ak~~gvs~~tlRyYe~~GLl~p~   29 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDHIGLLSPS   29 (96)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             94889999989599999999973998988


No 322
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=64.25  E-value=8.9  Score=18.44  Aligned_cols=29  Identities=24%  Similarity=0.334  Sum_probs=24.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99997298389999997799999999741
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .++...|||..|.|+.+|+|..|+...-.
T Consensus       159 ~L~~~eglS~~EIA~~Lgis~~TVKsrL~  187 (231)
T PRK11922        159 VLRVVEELSVEETAQALGLPEETVKTRLH  187 (231)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999399999999998939999999999


No 323
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=63.98  E-value=8.3  Score=18.64  Aligned_cols=28  Identities=18%  Similarity=0.213  Sum_probs=23.8

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999972983899999977999999997
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      =.+|.-.|+|..|.|+.+|+|.+++...
T Consensus       121 ~~L~~~~g~s~~EIA~~lgis~~tVk~~  148 (161)
T PRK12541        121 LLLRDYYGFSYKEIAEMTGLSLAKVKIE  148 (161)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9989974999999999989399999999


No 324
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=63.91  E-value=7.2  Score=19.01  Aligned_cols=23  Identities=22%  Similarity=0.192  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             29838999999779999999974
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..+++.++|..+|+++.|+++..
T Consensus       172 l~~t~~~lA~~lG~tretvsR~L  194 (236)
T PRK09392        172 LPYEKRTLASYLGMTPENLSRAF  194 (236)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHH
T ss_conf             34789999998789899999999


No 325
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.85  E-value=8  Score=18.71  Aligned_cols=24  Identities=21%  Similarity=0.412  Sum_probs=13.3

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             972983899999977999999997
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~  146 (205)
                      -..|++..+.|+.+|++..|+..+
T Consensus        15 l~~G~s~~eIA~~L~is~~TV~~~   38 (58)
T smart00421       15 LAEGLTNKEIAERLGISEKTVKTH   38 (58)
T ss_pred             HHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             981799999998989789899999


No 326
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=63.41  E-value=6.5  Score=19.27  Aligned_cols=27  Identities=7%  Similarity=0.047  Sum_probs=22.8

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             859988999998489999999887799
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGM   68 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~   68 (205)
                      -.|+..+++|+++||++.+|-.|-+-.
T Consensus        17 l~gmk~~dIAeklGvspntiksWKrr~   43 (279)
T COG5484          17 LKGMKLKDIAEKLGVSPNTIKSWKRRD   43 (279)
T ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             843419999999689868888778740


No 327
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=63.39  E-value=7.3  Score=18.99  Aligned_cols=64  Identities=20%  Similarity=0.254  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH--
Q ss_conf             988999998489999999887-79988899999999998289999961453221000023213455467779999999--
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI--  121 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l--  121 (205)
                      |+-.+||+..|||..||-.|| .|.-.|.-.      +.     -+.++.       .           .+ .+|+-+  
T Consensus         1 m~Ige~Ak~~~vs~~TlRyYe~~GLl~P~~~------~g-----~r~Y~~-------~-----------d~-~~L~~I~~   50 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYIDLGLLIPEKK------GG-----QYFFDE-------K-----------CQ-DDLEFILE   50 (107)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CC-----CCCCCH-------H-----------HH-HHHHHHHH
T ss_conf             9689999996998988899998588688768------99-----466199-------9-----------99-99999999


Q ss_pred             HHHCCCCHHHHHHHHCC
Q ss_conf             99729838999999779
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGM  138 (205)
Q Consensus       122 R~~~glsq~elA~~lgi  138 (205)
                      -+..|+|..|..+.+.+
T Consensus        51 ~k~lgfsL~eIk~ll~l   67 (107)
T cd04777          51 LKGLGFSLIEIQKIFSY   67 (107)
T ss_pred             HHHCCCCHHHHHHHHHH
T ss_conf             98889989999999962


No 328
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=63.05  E-value=11  Score=17.86  Aligned_cols=27  Identities=26%  Similarity=0.209  Sum_probs=23.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++...|+|..|.|+.+|+|..++...
T Consensus       141 ~L~~~eg~s~~EIA~~lgis~~tVks~  167 (184)
T PRK12539        141 QAVKLDGLSVAEAATRSGMSESAVKVS  167 (184)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999994999999999989199999999


No 329
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=62.49  E-value=8.2  Score=18.67  Aligned_cols=34  Identities=15%  Similarity=0.113  Sum_probs=26.3

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf             9999999859988999998489999999887-7998
Q gi|254781218|r   35 RIKDIRKANNKTQKEMAIGANQLESAVNLFE-NGMC   69 (205)
Q Consensus        35 rik~lR~~~gltQ~elA~~~gis~~~is~~E-~G~~   69 (205)
                      +|..++ ..|+|-.++|..+|-.+||||+== +|..
T Consensus        15 ~I~~l~-~~~~S~reIA~~LgRh~sTIsRElkRn~~   49 (318)
T COG2826          15 EIERLL-KAKMSIREIAKQLNRHHSTISRELKRNRT   49 (318)
T ss_pred             HHHHHH-HCCCCHHHHHHHHCCCCCHHHHHHHCCCC
T ss_conf             999999-85998999999857686204279866875


No 330
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.32  E-value=9.4  Score=18.30  Aligned_cols=27  Identities=19%  Similarity=0.345  Sum_probs=21.1

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|...|+|..|.|+.+|+|.+++...
T Consensus       146 ~L~~~egls~~EIA~~lgis~~tVks~  172 (195)
T PRK12532        146 TLKEILGFSSDEIQQMCGISTSNYHTI  172 (195)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999981999999999989599999999


No 331
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=61.67  E-value=11  Score=17.99  Aligned_cols=29  Identities=17%  Similarity=0.184  Sum_probs=24.1

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++.-.|+|..|.|+.+|||..|+...-
T Consensus       137 i~L~~~eg~s~~EIA~~Lgis~~tVksrl  165 (188)
T PRK12517        137 LLLQVIGGFSGEEIAEILDLNKNTVMTRL  165 (188)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999839999999999893999999999


No 332
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=61.49  E-value=7.1  Score=19.04  Aligned_cols=26  Identities=31%  Similarity=0.422  Sum_probs=19.2

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             97298389999997799999999741
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      ...+++..|+|+.+|++++++.++-+
T Consensus        15 ~~~~~~l~eia~~~gl~kstv~RlL~   40 (52)
T pfam09339        15 APGGLSLTEIARRTGLPKSTAHRLLQ   40 (52)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89998999999998919999999999


No 333
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.46  E-value=11  Score=17.96  Aligned_cols=28  Identities=25%  Similarity=0.405  Sum_probs=18.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999997298389999997799999999
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSN  145 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~  145 (205)
                      +..+.+..-++..|+|+.+|+|..|+.+
T Consensus         6 l~~l~~~~~~~i~~La~~~~VS~~TiRR   33 (53)
T smart00420        6 LELLAQQGKVSVEELAELLGVSEMTIRR   33 (53)
T ss_pred             HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             9999986979799999998979999999


No 334
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.43  E-value=11  Score=17.93  Aligned_cols=28  Identities=18%  Similarity=0.103  Sum_probs=23.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++...|+|..|.|+.+|+|..|+...-
T Consensus       163 ~L~~~egls~~EIA~~l~is~~TVksrl  190 (206)
T PRK12526        163 KGVYFQELSQEQLAQQLNVPLGTVKSRL  190 (206)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999859999999999893999999999


No 335
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=60.89  E-value=13  Score=17.48  Aligned_cols=42  Identities=14%  Similarity=0.112  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH-------CCCCCCCHHHHHHHHHHHCC
Q ss_conf             9838999999779999999974-------14889998999999998289
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYE-------QGRTIPEIKPARKIKQVTKK  167 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E-------~g~~~Ps~~~l~kIa~~lgv  167 (205)
                      +++..|||+.+|++..-+-+..       +-....+.+.+..|++.||.
T Consensus         3 ~itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~ld~e~a~~i~~~~~~   51 (52)
T pfam04760         3 KIRVYELAKELGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFGV   51 (52)
T ss_pred             CEEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHHCC
T ss_conf             1739999999888899999999987985567774599999999998198


No 336
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=60.79  E-value=11  Score=17.90  Aligned_cols=51  Identities=12%  Similarity=0.252  Sum_probs=35.7

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf             9999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD  176 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~  176 (205)
                      =.++...|+|..|.|+.+|+|..|+...-.       ....+|.+.|+---.++=+|+
T Consensus       145 i~L~~~eg~s~~EIA~~lgis~~tVk~~l~-------Rark~Lr~~L~~~r~~~g~~~  195 (196)
T PRK12524        145 VVLRHIEGLSNPEIAEVMQIGVEAVESLTA-------RGKRALAALLAGQRAELGYGE  195 (196)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHHHHHCCCCC
T ss_conf             899998089999999998929999999999-------999999999871798749889


No 337
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=60.35  E-value=12  Score=17.74  Aligned_cols=30  Identities=23%  Similarity=0.242  Sum_probs=24.9

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.+|-..|||..|.|+.+|++.+|+...-
T Consensus       137 vi~L~~~~g~s~~EIA~~l~is~~tVk~rl  166 (190)
T PRK12543        137 VIILRYLHDYSQEEVAQILHIPIGTVKSRI  166 (190)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999859999999999893999999999


No 338
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=60.29  E-value=11  Score=17.89  Aligned_cols=27  Identities=22%  Similarity=0.310  Sum_probs=23.5

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             997298389999997799999999741
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-..|+|.+|.|+.+++|..|+..+-+
T Consensus       148 lia~G~snkeIA~~L~IS~~TVk~h~~  174 (196)
T PRK10360        148 KLAQGMAVKEIAAELGLSPKTVHVHRA  174 (196)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             998799999999996999999999999


No 339
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=60.24  E-value=11  Score=17.95  Aligned_cols=30  Identities=17%  Similarity=0.125  Sum_probs=25.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.++...|+|..|.|+.+|+|..|+...-
T Consensus       120 v~~L~~~~g~s~~EIA~~lgis~~tVksrl  149 (164)
T PRK12547        120 AIILIGASGFSYEEAAEICGCAVGTIKSRV  149 (164)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999899849999999999893999999999


No 340
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=59.69  E-value=11  Score=17.92  Aligned_cols=28  Identities=21%  Similarity=0.211  Sum_probs=23.9

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .+|...|||..|.|+.+|++..++....
T Consensus       167 ~Lr~~eglS~~EIAe~Lgis~gTVKsrl  194 (222)
T PRK09647        167 VLCDIEGLSYEEIAATLGVKLGTVRSRI  194 (222)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             8799639999999999893999999999


No 341
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=59.68  E-value=11  Score=17.86  Aligned_cols=33  Identities=24%  Similarity=0.295  Sum_probs=25.8

Q ss_pred             HHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             999999--997298389999997799999999741
Q gi|254781218|r  116 ARLKSI--RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       116 ~rLk~l--R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .|=+++  .-..|+|.+|.|+.+++|..|+..+-+
T Consensus       152 ~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~  186 (210)
T PRK09935        152 NREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKS  186 (210)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89999999998699999999894988999999999


No 342
>TIGR01529 argR_whole arginine repressor; InterPro: IPR001669   The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein .   Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=59.29  E-value=13  Score=17.42  Aligned_cols=32  Identities=22%  Similarity=0.162  Sum_probs=15.5

Q ss_pred             HHHHHHHHHCC-CCHHHHHHHH-----C-CCHHHHHHHH
Q ss_conf             99999999859-9889999984-----8-9999999887
Q gi|254781218|r   34 TRIKDIRKANN-KTQKEMAIGA-----N-QLESAVNLFE   65 (205)
Q Consensus        34 ~rik~lR~~~g-ltQ~elA~~~-----g-is~~~is~~E   65 (205)
                      ++||.+=...+ =||+||...+     . ++|+++||+=
T Consensus         5 ~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL   43 (155)
T TIGR01529         5 EAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDL   43 (155)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHH
T ss_conf             999999874376798899999986597511234067878


No 343
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=59.22  E-value=11  Score=17.83  Aligned_cols=41  Identities=5%  Similarity=0.224  Sum_probs=30.0

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             999999729838999999779999999974148899989999999982
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT  165 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l  165 (205)
                      +=.+|--.|||..|.|+.+|+|.+|+...-.       ....+|.+.+
T Consensus       130 v~~L~~~~gls~~EIA~~L~is~~tVk~rl~-------RArk~Lr~~L  170 (185)
T PRK12542        130 VFKYKVFYNLTYQEISSVMGITEANVRKQFE-------RARKRVQNMI  170 (185)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf             9767998399999999998929999999999-------9999999987


No 344
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=59.14  E-value=6.8  Score=19.17  Aligned_cols=32  Identities=25%  Similarity=0.465  Sum_probs=22.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             99997298389999997799999999741488
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT  151 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~  151 (205)
                      .+.--.|+|...+|.+-|.+++|+++|-.+-.
T Consensus        34 RLH~~~gLsldR~~~lY~~hrStvaR~v~~ar   65 (106)
T TIGR02233        34 RLHHVEGLSLDRLGTLYGVHRSTVARWVAGAR   65 (106)
T ss_pred             HHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             67762365589999884788616999999999


No 345
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=58.95  E-value=12  Score=17.74  Aligned_cols=28  Identities=25%  Similarity=0.183  Sum_probs=23.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++.-.|+|..|.|+.+|+|.+++...-
T Consensus       136 ~l~~~eg~s~~EIA~~lgis~~tVk~rl  163 (178)
T PRK12536        136 VHVKLEGLSVEETAQLTGLSESAVKVGI  163 (178)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9998859999999999892999999999


No 346
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=58.88  E-value=11  Score=17.96  Aligned_cols=29  Identities=10%  Similarity=0.067  Sum_probs=24.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +=.++...|+|..|.|+.+|+|.+++...
T Consensus       116 v~~L~~~~~~s~~EIA~~l~is~~tVk~r  144 (165)
T PRK09644        116 AILLCDVHELTYEEAASVLDLKENTYKSH  144 (165)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999998889999999989399999999


No 347
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=58.45  E-value=11  Score=17.87  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=23.4

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|.-.|||..|.|+.+|+|..++...
T Consensus       116 ~L~~~egls~~EIA~~l~is~~tVk~~  142 (161)
T PRK09047        116 LLRYWEDMDVAETAAAMGCSEGSVKTH  142 (161)
T ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999998779999999989699999999


No 348
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator; InterPro: IPR011791    This entry represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system , . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix ..
Probab=58.34  E-value=5.4  Score=19.78  Aligned_cols=25  Identities=12%  Similarity=0.110  Sum_probs=14.5

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             9999984899999998877998889
Q gi|254781218|r   48 KEMAIGANQLESAVNLFENGMCSTS   72 (205)
Q Consensus        48 ~elA~~~gis~~~is~~E~G~~~ps   72 (205)
                      -|||++.|++..||-.||.----|.
T Consensus         4 GeLA~~t~v~v~TIRFYE~~gLLPe   28 (127)
T TIGR02047         4 GELAKKTGVSVETIRFYEKEGLLPE   28 (127)
T ss_pred             HHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf             3454553344002246441378538


No 349
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=58.21  E-value=12  Score=17.66  Aligned_cols=42  Identities=12%  Similarity=0.193  Sum_probs=29.4

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             9999729838999999779999999974148899989999999982899
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      .++.-.|+|..|.|+.+||+..|+...-.-       ...++.+.|+..
T Consensus       123 ~L~~~egls~~EIAe~Lgis~gTVKsRL~R-------AR~~Lr~~Le~~  164 (188)
T PRK12546        123 ILVGASGFSYEEAAEMCGVAVGTVKSRANR-------ARARLAELLQLE  164 (188)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHCC
T ss_conf             879982989999999989399999999999-------999999987272


No 350
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=57.92  E-value=13  Score=17.35  Aligned_cols=28  Identities=32%  Similarity=0.450  Sum_probs=23.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++-..|+|..|.|+.+|++..|+....
T Consensus       151 ~L~~~eg~s~~EIA~~lgis~~tVk~rl  178 (194)
T PRK12519        151 ELAYYEGLSQSEIAKRLGIPLGTVKARA  178 (194)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999819999999999894999999999


No 351
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=57.91  E-value=14  Score=17.17  Aligned_cols=24  Identities=17%  Similarity=-0.111  Sum_probs=14.3

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             859988999998489999999887
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      .+.||..++|..+.+|++.+++.=
T Consensus       156 ~~~wsL~dIA~~L~MSpS~LkKkL  179 (274)
T PRK09978        156 AHEWTLARIASELLMSPSLLKKKL  179 (274)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             036139999988727999999999


No 352
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=57.91  E-value=14  Score=17.17  Aligned_cols=58  Identities=21%  Similarity=0.122  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH-HHHHHHHC
Q ss_conf             9999999999999-9985998899999848999999988779988899999-99999828
Q gi|254781218|r   27 QYWKDVGTRIKDI-RKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA-LYLRNEYE   84 (205)
Q Consensus        27 ~~~~~iG~rik~l-R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l-~~la~~~~   84 (205)
                      ...+.|+.-|-.- -....+|-.+||+++|+|+++|.|+=+-.......-+ +.|+..+.
T Consensus        16 ~~Ek~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~l~~~l~   75 (284)
T PRK11302         16 KSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLAQSLA   75 (284)
T ss_pred             HHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             999999999980989997666999998969988899999999578978999999999975


No 353
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=57.82  E-value=13  Score=17.33  Aligned_cols=23  Identities=26%  Similarity=0.485  Sum_probs=12.0

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             72983899999977999999997
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~  146 (205)
                      +..++..|+|+.+|++++++++.
T Consensus         8 ~~~~~~~ela~~l~is~~tvs~H   30 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHH   30 (66)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             39966999999988298888799


No 354
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704   At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=57.79  E-value=13  Score=17.49  Aligned_cols=36  Identities=14%  Similarity=0.085  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             779999999997298389999997799999999741
Q gi|254781218|r  113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      ....-+++..+..+=...-.|+.+|||+.|+++|.+
T Consensus       622 v~a~~~~~aL~~~~G~~~a~a~~LGiSrTTLWRrL~  657 (658)
T TIGR02329       622 VEALAVRAALERFQGDRAAAAKALGISRTTLWRRLK  657 (658)
T ss_pred             CCHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHC
T ss_conf             335768999987278968998542764245777613


No 355
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=57.73  E-value=14  Score=17.18  Aligned_cols=27  Identities=11%  Similarity=0.186  Sum_probs=21.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             88999998489999999887-7998889
Q gi|254781218|r   46 TQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        46 tQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      +-.++|+..|+|..+|-.|| .|.-.|.
T Consensus         2 ~IgelA~~~gvs~~TlRyYe~~GLl~p~   29 (134)
T cd04779           2 RIGQLAHLAGVSKRTIDYYTNLGLLTPE   29 (134)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             5889999988688999999977997999


No 356
>PRK10403 transcriptional regulator NarP; Provisional
Probab=57.60  E-value=12  Score=17.55  Aligned_cols=36  Identities=14%  Similarity=0.250  Sum_probs=28.0

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             99729838999999779999999974148899989999999982899
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      .-..|+|-+|.|+.++++..|+..+           +..|.+-||++
T Consensus       164 lla~G~snkeIA~~L~iS~~TV~~h-----------~~~I~~KLgv~  199 (215)
T PRK10403        164 ELAQGLSNKQIASVLNISEQTVKVH-----------IRNLLRKLNVR  199 (215)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH-----------HHHHHHHHCCC
T ss_conf             9986999999999979829999999-----------99999986899


No 357
>PHA01082 putative transcription regulator
Probab=57.56  E-value=6.4  Score=19.33  Aligned_cols=40  Identities=15%  Similarity=0.103  Sum_probs=27.6

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHH
Q ss_conf             85998899999848999999988779988899-99999999
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRN   81 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~   81 (205)
                      ..|||-+|-|+.+=-|.++|-.|..|+.-|+. ..|++.-.
T Consensus        28 eCgLsveeaA~LCfKtVrtVk~WD~G~~IPPeCkRLMRm~~   68 (133)
T PHA01082         28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRMNK   68 (133)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC
T ss_conf             13763999999999978888630489949879999998851


No 358
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=57.42  E-value=13  Score=17.45  Aligned_cols=27  Identities=19%  Similarity=0.250  Sum_probs=23.1

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             997298389999997799999999741
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-..|+|.+|.|+.+++|..|+..|-+
T Consensus       154 ll~~G~snkeIA~~L~iS~~TV~~h~~  180 (204)
T PRK09958        154 YILDGKDNNDIAEKMFISNKTVSTYKS  180 (204)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             998699999999897889999999999


No 359
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=57.36  E-value=15  Score=17.11  Aligned_cols=30  Identities=27%  Similarity=0.335  Sum_probs=24.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.++.-.|++..|.|+.+|++.+++..+-
T Consensus       133 il~l~~~~g~s~~eIA~~lgis~~tv~~~l  162 (180)
T PRK11924        133 VFLLRYVEGLSYQEIADQLGVPLGTVKSRL  162 (180)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999968599999999894999999999


No 360
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=57.21  E-value=13  Score=17.47  Aligned_cols=28  Identities=21%  Similarity=0.264  Sum_probs=21.3

Q ss_pred             HHHHHHHC--CCCHHHHHHHHCCCHHHHHH
Q ss_conf             99999985--99889999984899999998
Q gi|254781218|r   36 IKDIRKAN--NKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~--gltQ~elA~~~gis~~~is~   63 (205)
                      ||.++...  |+.|-|+-+..|.|.|++|.
T Consensus        10 ir~Lk~a~~~GI~Q~eIeel~GlSKStvSE   39 (321)
T COG3888          10 IRELKRAGPEGIDQTEIEELMGLSKSTVSE   39 (321)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             999986287776587889885745647999


No 361
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). 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.
Probab=56.73  E-value=11  Score=17.91  Aligned_cols=29  Identities=17%  Similarity=0.279  Sum_probs=20.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             72983899999977999999997414889
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTI  152 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g~~~  152 (205)
                      -+|.+..+.|+.+|++..|+..|-.-..=
T Consensus        11 ~qg~~~~eIA~~Lg~~~~tVysWk~r~~W   39 (58)
T pfam06056        11 WQGYRPAEIAQELGLKARTVYSWKDRDKW   39 (58)
T ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHHCCC
T ss_conf             96898999999978993145658652483


No 362
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=56.72  E-value=13  Score=17.33  Aligned_cols=28  Identities=14%  Similarity=0.010  Sum_probs=23.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .+|.-.|||..|.|+.+|++.+++....
T Consensus       159 ~Lr~~eglS~~EIAe~Lgis~~tVks~L  186 (207)
T PRK12544        159 MMREFIELETPEICHNEDLTVSNLNVML  186 (207)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999819999999999797999999999


No 363
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=56.69  E-value=15  Score=17.04  Aligned_cols=29  Identities=21%  Similarity=0.394  Sum_probs=24.4

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++-..|+|..|.|+.+|+|..|+...-
T Consensus       137 ~~L~~~~g~s~~EIA~~l~is~~tVk~~l  165 (186)
T PRK05602        137 IVLQYYQGLSNIEAARVMGLSVDALESLL  165 (186)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99998638999999999893999999999


No 364
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=56.31  E-value=15  Score=17.00  Aligned_cols=47  Identities=17%  Similarity=0.155  Sum_probs=30.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             999999729838999999779999999974148899989999999982899
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      +=.++--.|+|.+|.|+.+|+|..|+...-.-    ....|.+.-+-.||+
T Consensus       124 v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~r----a~~~Lr~~L~~~gi~  170 (171)
T PRK09645        124 VLVRSYYRGWSTAQIAADLGIPEGTVKSRLHY----AVRALRLTLQEMGVT  170 (171)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCC
T ss_conf             98999986999999999989299999999999----999999999970999


No 365
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=56.29  E-value=12  Score=17.72  Aligned_cols=57  Identities=16%  Similarity=0.123  Sum_probs=36.4

Q ss_pred             HHHHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHHHHCC
Q ss_conf             99999999-9999985998899999848999999988779988899-999999998289
Q gi|254781218|r   29 WKDVGTRI-KDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRNEYEI   85 (205)
Q Consensus        29 ~~~iG~ri-k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~~~~v   85 (205)
                      .+.|++-| ....+...+|-.+||+.+|||+++|.|+=+-...-.. ++=..|+..+..
T Consensus        20 er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l~~   78 (281)
T COG1737          20 ERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQELAE   78 (281)
T ss_pred             HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999939678856149999988199888999999985999889999999999763


No 366
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=56.27  E-value=15  Score=17.00  Aligned_cols=23  Identities=26%  Similarity=0.095  Sum_probs=12.6

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             98599889999984899999998
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~   63 (205)
                      ....+|..++|+.+|.++|++++
T Consensus        39 ~~~~~tvdelae~lnr~rStv~r   61 (126)
T COG3355          39 ENGPLTVDELAEILNRSRSTVYR   61 (126)
T ss_pred             HCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             46995799999997831999999


No 367
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=56.16  E-value=15  Score=16.99  Aligned_cols=26  Identities=19%  Similarity=0.036  Sum_probs=21.9

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99729838999999779999999974
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +--.|+|..|.|+.+|+|..++....
T Consensus       166 ~~~eg~s~~EIA~~l~is~~tV~~~l  191 (209)
T PRK08295        166 LYLDGKSYQEIAEELNRHVKSIDNAL  191 (209)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99869999999999892999999999


No 368
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=55.75  E-value=14  Score=17.22  Aligned_cols=27  Identities=19%  Similarity=0.247  Sum_probs=23.9

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             997298389999997799999999741
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-..|+|-+|.|+.+++|..|+..+-+
T Consensus       159 lla~G~snkeIA~~L~iS~~TVk~h~~  185 (211)
T COG2197         159 LLAEGLSNKEIAEELNLSEKTVKTHVS  185 (211)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             998799889999997878989999999


No 369
>PRK13502 transcriptional activator RhaR; Provisional
Probab=55.63  E-value=16  Score=16.93  Aligned_cols=28  Identities=11%  Similarity=0.024  Sum_probs=20.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             7298389999997799999999741488
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYEQGRT  151 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E~g~~  151 (205)
                      ...++..++|+.+|+|+..+++.-+...
T Consensus       190 ~~~isl~~lA~~~~~S~~~lsr~FK~~t  217 (282)
T PRK13502        190 ECPFALDAFCQQEQCSERVLRQQFRAQT  217 (282)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             6998899999897979999999999998


No 370
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=55.56  E-value=14  Score=17.22  Aligned_cols=42  Identities=12%  Similarity=0.146  Sum_probs=29.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             9999729838999999779999999974148899989999999982899
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs  168 (205)
                      .++...|+|..|.|+.+|+|..|+...-.       ....++.+.|..+
T Consensus       121 ~L~~~egls~~EIA~iL~is~gTVKsRL~-------RAr~kLr~~L~~~  162 (181)
T PRK12540        121 ILVGASGFSYEDAAAICGCAVGTIKSRVN-------RARSKLSALLYVD  162 (181)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHC
T ss_conf             87998099999999998949999999999-------9999999998746


No 371
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=55.53  E-value=15  Score=17.11  Aligned_cols=27  Identities=15%  Similarity=0.076  Sum_probs=23.3

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|.-.|+|..|.|+.+|+|.+++...
T Consensus       146 ~Lr~~~~ls~~EIA~~l~is~~tVksr  172 (191)
T PRK12530        146 MMREFLELSSEQICQECHITTSNLHVL  172 (191)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999992999999999989699999999


No 372
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=55.30  E-value=15  Score=17.10  Aligned_cols=47  Identities=13%  Similarity=0.017  Sum_probs=30.9

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHCCC
Q ss_conf             9972983899999977999999997414----8899989999999982899
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQG----RTIPEIKPARKIKQVTKKH  168 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g----~~~Ps~~~l~kIa~~lgvs  168 (205)
                      .-..|+|-+|.|+.+++|..|+..+-+.    -..-+.-.|...+..+|..
T Consensus       161 lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~~~gl~  211 (216)
T PRK10840        161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLS  211 (216)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
T ss_conf             998699999999896989999999999999982999899999999986999


No 373
>PRK09483 response regulator; Provisional
Probab=55.03  E-value=15  Score=17.03  Aligned_cols=51  Identities=14%  Similarity=0.109  Sum_probs=32.7

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHC-CCHHHH
Q ss_conf             99729838999999779999999974148----8999899999999828-999995
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR----TIPEIKPARKIKQVTK-KHLDWI  172 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~----~~Ps~~~l~kIa~~lg-vs~d~L  172 (205)
                      .-..|+|-+|.|+.+++|..|+..+-+.-    ..-+.-.+...|.-.| ++.|.|
T Consensus       159 ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~gli~~~~~  214 (216)
T PRK09483        159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLLNAETL  214 (216)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHC
T ss_conf             99879999999999698999999999999998099999999999999599188884


No 374
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=54.34  E-value=16  Score=16.80  Aligned_cols=54  Identities=11%  Similarity=0.108  Sum_probs=34.2

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCC------------------------------CCCHHHHHHHHHHHCCCHHHH
Q ss_conf             97298389999997799999999741488------------------------------999899999999828999995
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNYEQGRT------------------------------IPEIKPARKIKQVTKKHLDWI  172 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~E~g~~------------------------------~Ps~~~l~kIa~~lgvs~d~L  172 (205)
                      ...|=|...+|...|++...+.+|-+-..                              .=+-++|..||+.|||+++-|
T Consensus       348 Vr~GDtL~~IA~ky~vsv~~L~~~N~L~~~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vk~GDTL~~IArry~Vsv~~L  427 (449)
T PRK10783        348 VRSGDTLSGIASRLGVSTKDLQQWNNLRGSTLKVGQSLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHGVNIKDV  427 (449)
T ss_pred             ECCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHCCCHHHH
T ss_conf             58999899999997979999999839994447899878737887555565678965899899997999999969899999


Q ss_pred             HCCC
Q ss_conf             2472
Q gi|254781218|r  173 YFGD  176 (205)
Q Consensus       173 ~~G~  176 (205)
                      ..=+
T Consensus       428 ~~wN  431 (449)
T PRK10783        428 MRWN  431 (449)
T ss_pred             HHHC
T ss_conf             9865


No 375
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=54.25  E-value=13  Score=17.32  Aligned_cols=26  Identities=23%  Similarity=0.054  Sum_probs=21.8

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99859988999998489999999887
Q gi|254781218|r   40 RKANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        40 R~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      +.+-...|+|.|+++|||.+.||.+=
T Consensus        21 ~~qp~v~q~eIA~~lgiT~QaVsehi   46 (260)
T COG1497          21 VRQPRVKQKEIAKKLGITLQAVSEHI   46 (260)
T ss_pred             HHCCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             75887788899987098799999999


No 376
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=53.93  E-value=17  Score=16.76  Aligned_cols=29  Identities=24%  Similarity=0.415  Sum_probs=19.4

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             99999997298389999997799999999
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSN  145 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~  145 (205)
                      -+..+....-++..|+|+.+++|..|+.+
T Consensus         5 Il~~l~~~~~v~i~~La~~f~VS~~TiRR   33 (57)
T pfam08220         5 ILELLKQQGTLSVEELAELLGVSEMTIRR   33 (57)
T ss_pred             HHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             99999986979799999998959999999


No 377
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=53.91  E-value=17  Score=16.76  Aligned_cols=29  Identities=10%  Similarity=0.138  Sum_probs=24.6

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++...|+|..|.|+.+|++..|+..+.
T Consensus       180 l~L~~~egls~~EIA~~Lgis~~TVKsrL  208 (233)
T PRK12538        180 VILSYHENMSNGEIAEVMDTTVAAVESLL  208 (233)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999849999999999892999999999


No 378
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=53.83  E-value=16  Score=16.79  Aligned_cols=30  Identities=17%  Similarity=0.035  Sum_probs=24.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.++.-.|+|..|.|+.+|+|.+++....
T Consensus       139 vi~L~~~~g~s~~EIA~~lgis~~tVk~~l  168 (184)
T PRK12512        139 VVQSIAVEGASIKETAAKLSMSEGAVRVAL  168 (184)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999998559799999999891999999999


No 379
>TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248   This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO)..
Probab=53.45  E-value=8.1  Score=18.70  Aligned_cols=20  Identities=10%  Similarity=0.244  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHCCCHHHHHCC
Q ss_conf             99999999828999996145
Q gi|254781218|r   74 RYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        74 ~~l~~la~~~~vs~d~Ll~g   93 (205)
                      ++|-+||+-|+|++|.|...
T Consensus         5 DtlWkiA~kygV~~~~Li~~   24 (44)
T TIGR02899         5 DTLWKIAKKYGVDLDELIQA   24 (44)
T ss_pred             CHHHHHHHHHCCCHHHHHHH
T ss_conf             21477787717876788641


No 380
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=53.44  E-value=17  Score=16.72  Aligned_cols=27  Identities=19%  Similarity=0.364  Sum_probs=23.6

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++...|+|..|.|+.+|+|..|+...
T Consensus       148 ~L~~~egls~~EIA~~l~is~~tVk~r  174 (193)
T PRK11923        148 TLREFDGLSYEDIASVMQCPVGTVRSR  174 (193)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999994999999999989299999999


No 381
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=53.40  E-value=16  Score=16.82  Aligned_cols=28  Identities=18%  Similarity=0.172  Sum_probs=23.9

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999972983899999977999999997
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      =.++...|+|..|.|+.+|+|.+|+...
T Consensus       128 i~L~~~~~~s~~EIA~~l~is~~tVksr  155 (173)
T PRK12522        128 LVLYYYEQYSYKEMSEILNIPIGTVKYR  155 (173)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9999983999999999989399999999


No 382
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=53.04  E-value=17  Score=16.77  Aligned_cols=30  Identities=13%  Similarity=0.067  Sum_probs=25.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999999972983899999977999999997
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+=.+|-..|+|..|.|+.+|++.+|+...
T Consensus       141 ~vl~L~~~~~ls~~EIA~~l~is~~tVksr  170 (188)
T PRK09640        141 EILVLRFVAELEFQEIADIMHMGLSATKMR  170 (188)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999999992999999999989299999999


No 383
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=52.97  E-value=16  Score=16.79  Aligned_cols=28  Identities=18%  Similarity=0.204  Sum_probs=23.0

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++-..|+|..|.|+.+|+|.+|+...-
T Consensus       139 ~l~~~eg~s~~EIA~~l~is~~tVk~~l  166 (179)
T PRK12514        139 RRAYLEGLSYKELAERHDVPLNTMRTWL  166 (179)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9996069989999998890999999999


No 384
>pfam11268 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=52.96  E-value=17  Score=16.67  Aligned_cols=28  Identities=25%  Similarity=0.444  Sum_probs=17.1

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +.|...|.|..++|+..|++...+.+|+
T Consensus        62 QarIRaGas~eevA~~~g~~~~rVerfa   89 (169)
T pfam11268        62 QARIRAGASAEEVAEAAGVPEERVERFE   89 (169)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHCC
T ss_conf             9998879999999999599999987422


No 385
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=52.84  E-value=17  Score=16.66  Aligned_cols=29  Identities=24%  Similarity=0.395  Sum_probs=24.3

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++-..|+|..|.|+.+|+|.+|+...-
T Consensus       136 ~~L~~~eg~s~~EIA~~l~is~~tVk~~l  164 (177)
T PRK09638        136 FILKHYYGYTYEEIAKMLGIPEGTVKSRV  164 (177)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999919999999999893999999999


No 386
>pfam07278 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.
Probab=52.76  E-value=17  Score=16.65  Aligned_cols=25  Identities=12%  Similarity=-0.001  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             9889999984899999998877998
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMC   69 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~   69 (205)
                      |+-.++|+..|+.++|+++=-.|..
T Consensus         2 lnI~qlA~~~GlhRqTV~~RL~~~~   26 (152)
T pfam07278         2 LNINQLAALTGLHRQTVAARLAGVN   26 (152)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf             8789999998532999999984599


No 387
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=52.69  E-value=17  Score=16.64  Aligned_cols=29  Identities=24%  Similarity=0.351  Sum_probs=24.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99997298389999997799999999741
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .++.-.|+|+.|.|+.+|++.+|+..+..
T Consensus       137 ~l~~~~gls~~EIA~~l~i~~~tVks~l~  165 (182)
T COG1595         137 LLRYLEGLSYEEIAEILGISVGTVKSRLH  165 (182)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99998599999999895999999999999


No 388
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=52.56  E-value=14  Score=17.26  Aligned_cols=55  Identities=22%  Similarity=0.230  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHH----HHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             999999999999--859988999998489999999----8877998889999999999828999996145
Q gi|254781218|r   30 KDVGTRIKDIRK--ANNKTQKEMAIGANQLESAVN----LFENGMCSTSIRYALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        30 ~~iG~rik~lR~--~~gltQ~elA~~~gis~~~is----~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g   93 (205)
                      ++|-+-|+..|+  .+|||..|.|..+|+|+.+..    +-+.+...|.         --+|.+||---|
T Consensus         2 k~IeeLi~kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~---------p~Di~i~W~siG   62 (203)
T COG0856           2 KNIEELIKKARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA---------PVDIKIDWRSIG   62 (203)
T ss_pred             CCHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC---------CCCEEEEHHHHC
T ss_conf             6589999999999877985777676641048778888754431147888---------752587326725


No 389
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=52.54  E-value=17  Score=16.63  Aligned_cols=28  Identities=25%  Similarity=0.284  Sum_probs=22.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++...|+|..|.|+.+|++..|+...-
T Consensus       145 ~l~~~eg~s~~EIA~~l~is~~TVk~rl  172 (184)
T PRK12537        145 LHAYVDGCSHAEIAQRLGAPLGTVKAWI  172 (184)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9988439999999999892999999999


No 390
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=52.45  E-value=18  Score=16.62  Aligned_cols=121  Identities=15%  Similarity=0.133  Sum_probs=69.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC
Q ss_conf             56689999999999999999859988999998489999999887799888999999999982899999614532210000
Q gi|254781218|r   22 TPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYE  101 (205)
Q Consensus        22 ~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~  101 (205)
                      ++.+.+|.+.|=.-.   ......+-.++|..+||++++++.           ++.+|.+.==|     ...   .+...
T Consensus         3 T~s~EdYLe~Iy~L~---~~~~~vr~~dIA~~L~Vs~~SVs~-----------mikkL~~~Glv-----~~~---~y~~i   60 (142)
T PRK03902          3 TPSMEDYIEQIYLLI---EEKGYARVSDIAEALSVHPSSVTK-----------MVQKLDKDEYL-----IYE---KYRGL   60 (142)
T ss_pred             CCHHHHHHHHHHHHH---HCCCCCCHHHHHHHHCCCCHHHHH-----------HHHHHHHCCCC-----EEC---CCCCE
T ss_conf             942999999999998---258971299999997899533999-----------99999987992-----455---89875


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH-HHCCCCCCCHHHHHHHHHHHC---CCHHHH
Q ss_conf             23213455467779999999997298389999997799999999-741488999899999999828---999995
Q gi|254781218|r  102 DVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSN-YEQGRTIPEIKPARKIKQVTK---KHLDWI  172 (205)
Q Consensus       102 ~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~-~E~g~~~Ps~~~l~kIa~~lg---vs~d~L  172 (205)
                      ..+        .-|.++......+.--...|=..+|++...... -+.=....|.+++.+|.+.++   ..+||+
T Consensus        61 ~LT--------~~G~~~A~~i~~rHrlle~FL~~LGv~~~~a~~eAc~lEH~iS~~~~~~l~~~l~~~~~~P~~~  127 (142)
T PRK03902         61 VLT--------PKGKKIGKRLVYRHELLEQFLRIIGVDESKIYNDVEGIEHHLSWNAIDRIGDLVQYFEEDPDRL  127 (142)
T ss_pred             EEC--------HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHCCHHH
T ss_conf             689--------8799999999999999999999919987699999988141698999999999973654296999


No 391
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=52.11  E-value=13  Score=17.50  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=16.0

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             729838999999779999999974
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..+++..|+|+.+|++++|+.++.
T Consensus        18 ~~~~sl~eia~~~~l~ksT~~RlL   41 (91)
T smart00346       18 PGGLTLAELAERLGLSKSTAHRLL   41 (91)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999899999999890999999999


No 392
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=51.95  E-value=18  Score=16.60  Aligned_cols=28  Identities=14%  Similarity=0.106  Sum_probs=23.9

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++.-.|||..|.|+.+|++..|+...-
T Consensus       142 ~L~~~~g~s~~EIA~ilgi~~gTVKsRl  169 (195)
T PRK12535        142 ILTQVLGYTYEEAAKIADVRVGTIRSRV  169 (195)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999829989999999893999999999


No 393
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=51.71  E-value=18  Score=16.60  Aligned_cols=28  Identities=18%  Similarity=0.235  Sum_probs=23.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      -++.-.|||..|.|+.+|+|..|+....
T Consensus       140 ~L~~~egls~~EIA~~lg~~~gTVKsRl  167 (185)
T PRK09649        140 LLTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9899729999999999893999999999


No 394
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=51.39  E-value=18  Score=16.51  Aligned_cols=28  Identities=25%  Similarity=0.389  Sum_probs=16.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      |..+. ..+++..|+|+.+|++++++++.
T Consensus        13 l~~L~-~~~~~~~eia~~l~is~~~vs~h   40 (78)
T cd00090          13 LRLLL-EGPLTVSELAERLGLSQSTVSRH   40 (78)
T ss_pred             HHHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99998-48906999987778487899999


No 395
>TIGR00491 aIF-2 translation initiation factor aIF-2; InterPro: IPR004544 Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 Kd which contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this family undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation.; GO: 0003743 translation initiation factor activity, 0005525 GTP binding, 0006413 translational initiation, 0005622 intracellular.
Probab=51.36  E-value=4.6  Score=20.23  Aligned_cols=47  Identities=21%  Similarity=0.183  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             99999999998599889999984899999998877998889999999999828
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE   84 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~   84 (205)
                      |..-+|.+|-..|+|..++      ..|++.+||||+.-||.+.+.+..+.+.
T Consensus       415 inkdmkrlrilfGmtrnev------nvsyyakyenGkeiPsyeivkkflnslk  461 (1145)
T TIGR00491       415 INKDMKRLRILFGMTRNEV------NVSYYAKYENGKEIPSYEIVKKFLNSLK  461 (1145)
T ss_pred             CHHHHHHHHHHHCCCCCCE------EEEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             3034455344321210003------4555543047863750899999985227


No 396
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113   This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.   In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=51.32  E-value=18  Score=16.51  Aligned_cols=30  Identities=23%  Similarity=0.355  Sum_probs=26.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999999997298389999997799999999
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSN  145 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~  145 (205)
                      +||-.++++-|+-|..-|.+||+++..+.-
T Consensus       533 ERli~AlE~aGWVQAKAARlLg~TPRQVgY  562 (574)
T TIGR01817       533 ERLIAALEKAGWVQAKAARLLGLTPRQVGY  562 (574)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHCCCHHHHHH
T ss_conf             899999975153799999973786558999


No 397
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=51.24  E-value=18  Score=16.50  Aligned_cols=42  Identities=7%  Similarity=0.038  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf             79999999997--2983899999977999999997414889998
Q gi|254781218|r  114 IGARLKSIRKD--KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI  155 (205)
Q Consensus       114 iG~rLk~lR~~--~glsq~elA~~lgis~~tis~~E~g~~~Ps~  155 (205)
                      +-.-|.-+.+.  ..+|..++|+.+|+++..++++-+...--+.
T Consensus       193 v~~il~YI~~hY~e~IsL~diA~~~~lS~~y~sr~FKk~tG~T~  236 (302)
T PRK10371        193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTM  236 (302)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf             99999999998289999999998979599999999999989099


No 398
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=51.17  E-value=18  Score=16.49  Aligned_cols=59  Identities=10%  Similarity=-0.024  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH-HHHHHHHCC
Q ss_conf             999999999999-99985998899999848999999988779988899999-999998289
Q gi|254781218|r   27 QYWKDVGTRIKD-IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA-LYLRNEYEI   85 (205)
Q Consensus        27 ~~~~~iG~rik~-lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l-~~la~~~~v   85 (205)
                      ...+.|++-|-. ......+|-.+||+.+|+|+++|.|+=+-...-...-+ ..|+..+..
T Consensus        29 ~sEk~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~~~   89 (293)
T PRK11337         29 ENESRVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALEDYFSQ   89 (293)
T ss_pred             HHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf             9999999999829899976669999989599888999999995789789999999999860


No 399
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=51.01  E-value=18  Score=16.48  Aligned_cols=27  Identities=19%  Similarity=0.311  Sum_probs=23.5

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++-..|+|..|.|+.+|+|.+|+...
T Consensus       146 ~L~~~~~~s~~EIA~~l~is~~tVk~~  172 (187)
T PRK09641        146 VLKYIEELSLKEISEILDLPVGTVKTR  172 (187)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999982998999999989399999999


No 400
>KOG3647 consensus
Probab=50.81  E-value=19  Score=16.46  Aligned_cols=136  Identities=16%  Similarity=0.198  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---------HHHHHHHHCCCHHHHHCCCC
Q ss_conf             899999999999999998599889999984899999998877998889999---------99999982899999614532
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY---------ALYLRNEYEISFDWIYDGEV   95 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~---------l~~la~~~~vs~d~Ll~ge~   95 (205)
                      ..||..-||.+|..+|+.+.     ||..+-.+..+|+..-+-.--.+-..         |...-+.+.+.+-.+...- 
T Consensus        48 ~~q~~~~i~~k~~e~r~~r~-----lat~l~~~g~~i~e~ls~~~~~~~~~~~aa~Rplel~e~Ekvlk~aIq~i~~~~-  121 (338)
T KOG3647          48 RDQYRSLIGDKIEELRKARE-----LATDLTQRGTTICEMLSKELLHKESLMSAAQRPLELLEVEKVLKSAIQAIQVRL-  121 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-----HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH-
T ss_conf             89999998789999999999-----874054111399999879999999999987177207889999999999999999-


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC---CCHHHH
Q ss_conf             21000023213455467779999999997298389999997799999999741488999899999999828---999995
Q gi|254781218|r   96 IDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK---KHLDWI  172 (205)
Q Consensus        96 ~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg---vs~d~L  172 (205)
                        .+..+.-+-...|..++|.+|...+.+.--+++-|+.+-.+-+..+..||.-.     +.|.++-+.|=   -.++||
T Consensus       122 --q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~E-----eeLqkly~~Y~l~f~nl~yL  194 (338)
T KOG3647         122 --QSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCE-----EELQKLYQRYFLRFHNLDYL  194 (338)
T ss_pred             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_conf             --99999998775378788779999999999999999998720658788898899-----99999999999987418999


Q ss_pred             H
Q ss_conf             2
Q gi|254781218|r  173 Y  173 (205)
Q Consensus       173 ~  173 (205)
                      -
T Consensus       195 ~  195 (338)
T KOG3647         195 K  195 (338)
T ss_pred             H
T ss_conf             9


No 401
>PRK10651 transcriptional regulator NarL; Provisional
Probab=50.35  E-value=19  Score=16.41  Aligned_cols=25  Identities=20%  Similarity=0.231  Sum_probs=22.0

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9729838999999779999999974
Q gi|254781218|r  123 KDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       123 ~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      -..|+|-++.|+.+++|..|+..+-
T Consensus       167 l~~G~snkeIA~~L~iS~~TV~~h~  191 (216)
T PRK10651        167 IAQGLSNKMIARRLDITESTVKVHV  191 (216)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9859999999999697899999999


No 402
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=50.34  E-value=19  Score=16.41  Aligned_cols=81  Identities=10%  Similarity=-0.053  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             999999999985--998899999848999999988779988899999999998289999961453221000023213455
Q gi|254781218|r   32 VGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRL  109 (205)
Q Consensus        32 iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~  109 (205)
                      |-.-+..+....  .+|.++||+.+|+|++++++.=+              ..++.++-..+..                
T Consensus         7 i~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk--------------~~~g~t~~~yi~~----------------   56 (107)
T PRK10219          7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFR--------------TVTHQTLGDYIRQ----------------   56 (107)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH--------------HHHCCCHHHHHHH----------------
T ss_conf             9999999998669999999999898939999999999--------------9989099999999----------------


Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHH
Q ss_conf             46777999999999729838999999779-9999999
Q gi|254781218|r  110 DPYAIGARLKSIRKDKGMSQIEFGKLLGM-PNSTLSN  145 (205)
Q Consensus       110 d~~~iG~rLk~lR~~~glsq~elA~~lgi-s~~tis~  145 (205)
                        ..+ .+-+.+...-+++..|.|..+|. +.+.+++
T Consensus        57 --~Rl-~~A~~lL~~t~~~I~eIA~~~Gf~~~~~Fsr   90 (107)
T PRK10219         57 --RRL-LLAAVELRTTERPIFDIAMDLGYVSQQTFSR   90 (107)
T ss_pred             --HHH-HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf             --999-9999998869998999999928998899999


No 403
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=50.08  E-value=19  Score=16.39  Aligned_cols=30  Identities=10%  Similarity=-0.043  Sum_probs=24.9

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.+|.-.|||..|.|+.+|++..++.-..
T Consensus       147 v~~Lr~~egls~~EIA~~L~is~~tVksrL  176 (201)
T PRK12545        147 VFMMREFLDFEIDDICTELTLTANHCSVLL  176 (201)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             989999928989999999896999999999


No 404
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=50.05  E-value=19  Score=16.38  Aligned_cols=33  Identities=21%  Similarity=0.128  Sum_probs=21.3

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             999999729838999999779999999974148
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      +..++....+++.+.|..+|++..++-+..+..
T Consensus         7 ~~dl~~~F~lpi~~AA~~Lgv~~T~LKk~CR~~   39 (52)
T pfam02042         7 LEDLSKYFHLPIKEAAKELGVCLTVLKKICRQL   39 (52)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             999999818759999999687799999999987


No 405
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=49.91  E-value=19  Score=16.37  Aligned_cols=48  Identities=19%  Similarity=0.248  Sum_probs=32.0

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf             9999729838999999779999999974148899989999999982899999
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW  171 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~  171 (205)
                      .++-..|+|..|.|+.+|+|..|+...-.-    ....|.+.-+..|+...|
T Consensus       141 ~l~~~e~~s~~EIA~~lgis~~tV~~~l~R----Ar~~Lr~~L~~~g~~~g~  188 (189)
T PRK12515        141 DLVYYHEKSVEEVGEIVGIPESTVKTRMFY----ARKKLAELLKAAGVERGW  188 (189)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHCCCCCC
T ss_conf             999984999999999989299999999999----999999999972833589


No 406
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=49.85  E-value=10  Score=18.13  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=22.5

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99972983899999977999999997
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      ++.-.|+|..|.|+.+|||..|+...
T Consensus       122 L~~~egls~~EIAe~Lgis~gTVKsr  147 (182)
T PRK12511        122 LVAIEGLSYQEAANVLGIPIGTLMSR  147 (182)
T ss_pred             EEEECCCCHHHHHHHHCCCHHHHHHH
T ss_conf             41007999999999989399999999


No 407
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator; InterPro: IPR011788    This entry represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix . .
Probab=49.70  E-value=7.7  Score=18.84  Aligned_cols=27  Identities=19%  Similarity=0.290  Sum_probs=21.7

Q ss_pred             HHHHHHHHCCCHHHHHHHH-CCCCCCCH
Q ss_conf             8999998489999999887-79988899
Q gi|254781218|r   47 QKEMAIGANQLESAVNLFE-NGMCSTSI   73 (205)
Q Consensus        47 Q~elA~~~gis~~~is~~E-~G~~~psi   73 (205)
                      --+||+..+|+.-|+-.|| +|...|+-
T Consensus         4 IGeLAklc~V~~DTlRfYEK~gl~~p~~   31 (132)
T TIGR02043         4 IGELAKLCDVTADTLRFYEKNGLLKPAE   31 (132)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHCCCCC
T ss_conf             0224766179843334776774305566


No 408
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=49.63  E-value=19  Score=16.34  Aligned_cols=19  Identities=16%  Similarity=0.004  Sum_probs=10.5

Q ss_pred             CCHHHHHHHHCCCHHHHHH
Q ss_conf             9889999984899999998
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~   63 (205)
                      .+.++||+.+|+|+.+|.+
T Consensus        20 ~SGe~La~~LgiSRtaVwK   38 (79)
T COG1654          20 VSGEKLAEELGISRTAVWK   38 (79)
T ss_pred             CCHHHHHHHHCCCHHHHHH
T ss_conf             6689999997865999999


No 409
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=49.27  E-value=20  Score=16.31  Aligned_cols=30  Identities=7%  Similarity=0.119  Sum_probs=24.9

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +-.++...|+|..|.|+.+|+|.+|+...-
T Consensus       149 vi~L~~~e~~s~~EIAe~l~is~~TVKsrl  178 (194)
T PRK12531        149 VLQAVYLEELPHQQVAEMFDIPLGTVKSRL  178 (194)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999998869999999999892999999999


No 410
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.11  E-value=15  Score=17.00  Aligned_cols=25  Identities=16%  Similarity=0.021  Sum_probs=21.9

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9985998899999848999999988
Q gi|254781218|r   40 RKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        40 R~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      +...++|..|+|..+|++++++.++
T Consensus        22 ~~~~~lslsela~~lglpksTv~Rl   46 (264)
T PRK09834         22 RLDGGATVGLLAELTGLHRTTVRRL   46 (264)
T ss_pred             HCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             1799979999999979099999999


No 411
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=48.88  E-value=20  Score=16.27  Aligned_cols=30  Identities=17%  Similarity=0.213  Sum_probs=25.0

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999729838999999779999999974
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      +=.++...|+|..|.|+.+|+|..|+....
T Consensus       139 vl~L~~~eg~s~~EIA~~lgis~~tVKsrl  168 (197)
T PRK09643        139 ALVAVDMQGYSVADTARMLGVAEGTVKSRC  168 (197)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999819999999999893999999999


No 412
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=48.22  E-value=7.5  Score=18.91  Aligned_cols=117  Identities=14%  Similarity=0.216  Sum_probs=83.4

Q ss_pred             HHHHHHHHCCCCCCCHHH---HHHHHHHH--CCCHHHHHCCCCCCCCC----CCCCCHHHH-H----H-H---HHHHHHH
Q ss_conf             999998877998889999---99999982--89999961453221000----023213455-4----6-7---7799999
Q gi|254781218|r   58 ESAVNLFENGMCSTSIRY---ALYLRNEY--EISFDWIYDGEVIDRRY----EDVTNKKRL-D----P-Y---AIGARLK  119 (205)
Q Consensus        58 ~~~is~~E~G~~~psi~~---l~~la~~~--~vs~d~Ll~ge~~~~~~----~~~~~~~~~-d----~-~---~iG~rLk  119 (205)
                      .-....++.-...|+-+.   +..|+++|  ++|+|.|+.--.+|.=|    ..+...... .    . .   .+-.-+=
T Consensus       416 ~~~~~~~~~~l~~p~d~RPYW~f~i~~Al~~G~~V~~~~ElT~ID~wFL~k~~~iV~~e~~l~~~~n~~~~I~~~~~e~L  495 (1089)
T TIGR01369       416 VESDEDLEEALKKPTDRRPYWIFAIAEALRRGVSVEEIHELTKIDRWFLHKIKNIVELEKELEELKNKLTGIEELDKELL  495 (1089)
T ss_pred             CCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             03578999997286988761899899998758868999865278888999999999999998753012445334898899


Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHH------HHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             99997298389999997799999------99974148-899989999999982899999524
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNST------LSNYEQGR-TIPEIKPARKIKQVTKKHLDWIYF  174 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~t------is~~E~g~-~~Ps~~~l~kIa~~lgvs~d~L~~  174 (205)
                      +--|.+|+|=.++|..++++...      +.++=... ..|..+.+--.|--|...+.||+.
T Consensus       496 ~~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi~Pv~K~vDTcAAEF~A~TpY~YS  557 (1089)
T TIGR01369       496 RKAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGIIPVYKRVDTCAAEFEAKTPYLYS  557 (1089)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf             99864188878999986897444200689999998469747787752321202015688525


No 413
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=48.09  E-value=16  Score=16.89  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=14.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9838999999779999999974
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~E  147 (205)
                      -||..|.|+.+|++..|+|+..
T Consensus         2 pmsrqdIadylGlt~ETVsR~l   23 (32)
T pfam00325         2 PMSRQEIADYLGLTRETVSRLL   23 (32)
T ss_pred             CCCHHHHHHHHCCHHHHHHHHH
T ss_conf             8658899998472599999999


No 414
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=47.68  E-value=21  Score=16.15  Aligned_cols=94  Identities=16%  Similarity=0.049  Sum_probs=49.8

Q ss_pred             CCCHHHHHHHHCCCCCCCHHHHHHHHHH-------HCCCHHHHHCCC--------CCCCCCCCCCCHHHHHHH----HH-
Q ss_conf             8999999988779988899999999998-------289999961453--------221000023213455467----77-
Q gi|254781218|r   55 NQLESAVNLFENGMCSTSIRYALYLRNE-------YEISFDWIYDGE--------VIDRRYEDVTNKKRLDPY----AI-  114 (205)
Q Consensus        55 gis~~~is~~E~G~~~psi~~l~~la~~-------~~vs~d~Ll~ge--------~~~~~~~~~~~~~~~d~~----~i-  114 (205)
                      ++++.++..+.+=.-.=.+.-|.++.+.       -.+.+|.++-..        .......+.......+-.    .+ 
T Consensus       208 ~~s~~a~~~L~~y~WPGNvrEL~n~ierav~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~E  287 (325)
T PRK11608        208 GFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRPPEEAIAVSEATSLPTLPLDLREFQHQQE  287 (325)
T ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             88999999996199996599999999999985688765555421371210565567787775456677868999999999


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             9999999997298389999997799999999741
Q gi|254781218|r  115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      -.-|....+..+..+...|+.+||++.|+.+..+
T Consensus       288 k~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~klk  321 (325)
T PRK11608        288 KELLQRSLQQAKFNQKRAAELLGLTYHQFRALLK  321 (325)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999399899999998889999999999


No 415
>PRK04182 cytidylate kinase; Provisional
Probab=47.67  E-value=21  Score=16.15  Aligned_cols=113  Identities=12%  Similarity=0.018  Sum_probs=55.0

Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH-----HHHHHHHHCCCHHHHHCC
Q ss_conf             001566899999999999999998599889999984899999998877998889999-----999999828999996145
Q gi|254781218|r   19 LIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY-----ALYLRNEYEISFDWIYDG   93 (205)
Q Consensus        19 ~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~-----l~~la~~~~vs~d~Ll~g   93 (205)
                      .++++...+--+.+++++-.---..|..-.++|+..|++...++++  +...|.++.     +..+|+.=+|    .+.|
T Consensus         7 g~~GSGk~tIak~LA~~lg~~~~d~g~i~r~~a~~~g~~~~~~~~~--~e~~~~id~~~~~~~~~~a~~~~~----Vi~G   80 (178)
T PRK04182          7 GPPGSGKTTVARLLAEKLGLKLVSAGDIFRELARERGMSLEEFNKY--AEEDPEIDKEIDRRQLELAKRGNV----VLEG   80 (178)
T ss_pred             CCCCCCHHHHHHHHHHHHCCEEECHHHHHHHHHHHCCCCHHHHHHH--HHCCHHHHHHHHHHHHHHHHCCCE----EEEC
T ss_conf             8998887999999999959938721299999999859999999999--851926899999999999853998----9983


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             32210000232134554677799999999972983899999977
Q gi|254781218|r   94 EVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG  137 (205)
Q Consensus        94 e~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg  137 (205)
                      -..+....+...........+..|++.+.+..|++..+..+.+-
T Consensus        81 R~~~~il~~~~~l~ifl~A~~e~R~~Ri~~r~~~~~~~a~~~i~  124 (178)
T PRK04182         81 RLAGWIVKNYADLKIYLKAPLEVRAKRIAEREGISVEEALEETI  124 (178)
T ss_pred             CCCCEEECCCCCEEEEEECCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             88876972798779999899999999999732999999999999


No 416
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=46.71  E-value=22  Score=16.06  Aligned_cols=53  Identities=13%  Similarity=0.142  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             9999999982899999614532210000232134554677799999999972983899999977
Q gi|254781218|r   74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG  137 (205)
Q Consensus        74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg  137 (205)
                      +.+-.+|+.|+|+.+.|....-         .+....+..++  .--+|+..++|..+.+..+|
T Consensus         4 ~I~~~Va~~~~v~~~~i~s~~R---------~~~i~~aR~ia--myL~r~~~~~s~~~IG~~fg   56 (60)
T smart00760        4 EIIEAVAEYFGVKPEDLKSKSR---------KREIVLARQIA--MYLARELTDLSLPEIGKIFG   56 (60)
T ss_pred             HHHHHHHHHHCCCHHHHHCCCC---------CHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHC
T ss_conf             9999999883997999856799---------81688899999--99999986799999999977


No 417
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=46.31  E-value=22  Score=16.03  Aligned_cols=25  Identities=4%  Similarity=0.037  Sum_probs=21.7

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9859988999998489999999887
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      ...++|..|+|+.+|++++++.++=
T Consensus        37 ~~~~ltl~eia~~lglpksT~~RlL   61 (271)
T PRK10163         37 SGGSSSVSDISLNLDLPLSTTFRLL   61 (271)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             7999799999999791999999999


No 418
>PRK01905 DNA-binding protein Fis; Provisional
Probab=46.05  E-value=22  Score=16.00  Aligned_cols=32  Identities=22%  Similarity=0.236  Sum_probs=26.9

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999999729838999999779999999974
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .=|..+.+.-+-.|...|+.+||++.|+.+-.
T Consensus        40 pLi~~vl~~~~gNQ~kAA~~LGinR~TLRkKl   71 (77)
T PRK01905         40 PLLEVVMEQAGGNQSLAAEYLGINRNTLRKKL   71 (77)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999845949999999786588899999


No 419
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=46.02  E-value=22  Score=16.00  Aligned_cols=25  Identities=28%  Similarity=0.504  Sum_probs=11.3

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             9999729838999999779999999
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLS  144 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis  144 (205)
                      .++..-+|...|+|+.+|+++++++
T Consensus        31 lL~~k~plNvneiAe~lgLpqst~s   55 (308)
T COG4189          31 LLHRKGPLNVNEIAEALGLPQSTMS   55 (308)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHH
T ss_conf             9987179878999988588656666


No 420
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=45.79  E-value=22  Score=15.97  Aligned_cols=33  Identities=15%  Similarity=0.101  Sum_probs=19.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             999999729838999999779999999974148
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      +=.-+--.+.|..++|+.+|+++.++.+|-.++
T Consensus         8 l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~~K   40 (47)
T pfam00440         8 LFAEKGYDATTVREIAKEAGVSKGALYRHFPSK   40 (47)
T ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCH
T ss_conf             999869150779999999796988999887699


No 421
>PRK11569 transcriptional repressor IclR; Provisional
Probab=45.54  E-value=22  Score=15.98  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=21.1

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             985998899999848999999988
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      ...++|..|+|+.+|++++++.++
T Consensus        40 ~~~~lsl~eia~~lglpksT~~Rl   63 (274)
T PRK11569         40 SNGSVALTELAQQAGLPNSTTHRL   63 (274)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             899989999999879199999999


No 422
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=44.65  E-value=23  Score=15.87  Aligned_cols=74  Identities=14%  Similarity=0.152  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH------HHHHHHHHCCCH----
Q ss_conf             015668999999999999999985--99889999984899999998877998889999------999999828999----
Q gi|254781218|r   20 IITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRY------ALYLRNEYEISF----   87 (205)
Q Consensus        20 ~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~------l~~la~~~~vs~----   87 (205)
                      .|+||.-.   .-..-+-.+|..-  -+.-..|...+|+|.+.+-.+|.|+-.|...-      |-+++....-.+    
T Consensus         6 ~itp~~l~---~~p~~L~~LR~~t~ppia~d~l~~lagvsk~lv~~le~~kl~~~~~~~~l~~~l~ki~~iI~~~lDpdi   82 (251)
T pfam09572         6 AITPDVLK---AYPLTLPTLRMLTCPPIARDRLVGLAGGSKNLVKSLEPKKLPPKMKADVLDEHLQKVVAVIEKMLDPDR   82 (251)
T ss_pred             CCCHHHHH---HCCHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             17889987---380477787861399830878766516667888764227898322243689999999999998518430


Q ss_pred             -HHHHCCCCC
Q ss_conf             -996145322
Q gi|254781218|r   88 -DWIYDGEVI   96 (205)
Q Consensus        88 -d~Ll~ge~~   96 (205)
                       .|+-.|...
T Consensus        83 F~Wl~~g~~p   92 (251)
T pfam09572        83 FPWVGRGRTP   92 (251)
T ss_pred             CCEECCCCCC
T ss_conf             1011589999


No 423
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=44.59  E-value=23  Score=15.86  Aligned_cols=57  Identities=12%  Similarity=0.090  Sum_probs=45.4

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH-HHHCC
Q ss_conf             9999972983899999977999999997414889998999999998289999-95247
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD-WIYFG  175 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d-~L~~G  175 (205)
                      ....++.|+++...+..++++++++|++.+=-...+.+.+..|.-+-++-.+ |+-..
T Consensus       170 A~~l~~~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aIGpAp~iGR~RW~~La  227 (325)
T TIGR03454       170 AQRLEDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAIGPAPGIGRPRWMELA  227 (325)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHHH
T ss_conf             9999984999999999988899999999999997899999973798734733799999


No 424
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=44.08  E-value=24  Score=15.81  Aligned_cols=21  Identities=10%  Similarity=0.143  Sum_probs=11.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHH
Q ss_conf             983899999977999999997
Q gi|254781218|r  126 GMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       126 glsq~elA~~lgis~~tis~~  146 (205)
                      .+.-.|+++.+|++++++|+.
T Consensus        28 elcV~eL~~~l~~sQs~vS~H   48 (106)
T PRK10141         28 ELCVCDLCTALDQSQPKISRH   48 (106)
T ss_pred             CCCHHHHHHHHCCCHHHHHHH
T ss_conf             956999998869988899999


No 425
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.94  E-value=24  Score=15.80  Aligned_cols=27  Identities=26%  Similarity=0.504  Sum_probs=22.2

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++--.|+|..|.|+.+|+|.+++...
T Consensus       147 ~l~~~~~~s~~EIA~~lgis~~tVk~~  173 (192)
T PRK09652        147 TLREIEGLSYEEIAEIMGCPIGTVRSR  173 (192)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             899972999999999989399999999


No 426
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.64  E-value=24  Score=15.77  Aligned_cols=27  Identities=33%  Similarity=0.284  Sum_probs=23.4

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|--.|+|..|.|+.+|+|.+|+...
T Consensus       138 ~l~~~~~~s~~EIA~~l~is~~tVk~r  164 (185)
T PRK06811        138 IKRYLLGESIEEIAKKLGLTRSAIDNR  164 (185)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999994999999999989299999999


No 427
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=43.51  E-value=24  Score=15.76  Aligned_cols=29  Identities=17%  Similarity=0.190  Sum_probs=23.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999972983899999977999999997
Q gi|254781218|r  118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       118 Lk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +=.++-..|+|..|.|+.+|+|..|+...
T Consensus       145 vi~l~~~eg~s~~EIA~~l~i~~gTVksr  173 (187)
T PRK12534        145 LIRTAFFEGITYEELAARTDTPIGTVKSW  173 (187)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999984999999999989199999999


No 428
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=42.68  E-value=25  Score=15.68  Aligned_cols=29  Identities=17%  Similarity=0.282  Sum_probs=24.5

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999729838999999779999999974
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      =.++...|+|..|.|+.+|+|.+|+...-
T Consensus       129 i~l~~~~~~s~~EIA~~l~is~~tVk~~l  157 (175)
T PRK12518        129 LVLHDLEDLPQKEIAEILNIPVGTVKSRL  157 (175)
T ss_pred             HHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999929999999999895999999999


No 429
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=42.56  E-value=25  Score=15.67  Aligned_cols=26  Identities=23%  Similarity=0.367  Sum_probs=17.1

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99729838999999779999999974
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..+.-++..|+|+.+|++++++|+..
T Consensus        11 L~~~~~~v~el~~~l~~sq~~vS~HL   36 (47)
T pfam01022        11 LSEGELCVCELAEILGLSQSTVSHHL   36 (47)
T ss_pred             HHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             98089969999999895886999999


No 430
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.55  E-value=25  Score=15.67  Aligned_cols=40  Identities=10%  Similarity=0.053  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHH
Q ss_conf             89999999999999999859988999998489-99999988
Q gi|254781218|r   25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQ-LESAVNLF   64 (205)
Q Consensus        25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gi-s~~~is~~   64 (205)
                      ++.|..+.-.++-.+....|.|..++|...|| +.+++.+|
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W   45 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKW   45 (116)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHH
T ss_conf             36489999999999998178359999999487753789999


No 431
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=42.50  E-value=25  Score=15.66  Aligned_cols=27  Identities=11%  Similarity=-0.141  Sum_probs=23.3

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .++--.|+|..|.|+.+|+|.+|+...
T Consensus       116 ~L~~~e~~s~~EIA~~l~is~~tVk~~  142 (160)
T PRK09642        116 LAHYLEEKSYQEIALQENIEVKTVEMK  142 (160)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999982999999999989199999999


No 432
>pfam02540 NAD_synthase NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.
Probab=42.39  E-value=25  Score=15.65  Aligned_cols=32  Identities=22%  Similarity=0.219  Sum_probs=17.7

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999999729838999999779999999974
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..+=....+.+++..+.++.+|++...+.++.
T Consensus       199 D~~l~~~~~~~~~~~~i~~~~g~~~~~v~~i~  230 (243)
T pfam02540       199 DQILKGLIEKKLSPEEIIGDLGLPAEVVERVE  230 (243)
T ss_pred             HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             99999998759999999987298999999999


No 433
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211   SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=42.06  E-value=12  Score=17.54  Aligned_cols=25  Identities=32%  Similarity=0.389  Sum_probs=20.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf             988999998489999999887-7998
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMC   69 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~   69 (205)
                      ||--+||+..||..|++..|| +|.-
T Consensus         2 lTvG~lA~R~GVAVSALHFYE~KGLI   27 (142)
T TIGR01950         2 LTVGELAKRAGVAVSALHFYESKGLI   27 (142)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf             86101655655788877654103561


No 434
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.97  E-value=26  Score=15.61  Aligned_cols=31  Identities=10%  Similarity=-0.045  Sum_probs=18.9

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             9972983899999977999999997414889
Q gi|254781218|r  122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI  152 (205)
Q Consensus       122 R~~~glsq~elA~~lgis~~tis~~E~g~~~  152 (205)
                      .-...++..++|+.+|+|..++.+.-+...-
T Consensus       228 ~l~~~ls~~~lA~~~~~S~R~l~R~Fk~~~G  258 (320)
T PRK09393        228 HLAQPHTVASLAARAAMSPRTFLRRFEAATG  258 (320)
T ss_pred             HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf             1114788999999978798799989978869


No 435
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus..
Probab=41.72  E-value=25  Score=15.68  Aligned_cols=27  Identities=15%  Similarity=0.026  Sum_probs=13.1

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999998599889999984899999998
Q gi|254781218|r   37 KDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        37 k~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      ..|-+.-..|-.+||+.++||+++|-+
T Consensus         8 ~~LL~~Gq~sA~~lA~~L~iSpQAvRr   34 (215)
T TIGR02702         8 EYLLKEGQASALALAEELAISPQAVRR   34 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             998860048899999972788678876


No 436
>pfam06413 Neugrin Neugrin. This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation.
Probab=40.89  E-value=27  Score=15.51  Aligned_cols=45  Identities=11%  Similarity=0.108  Sum_probs=39.1

Q ss_pred             HHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             9999999985--99889999984899999998877998889999999
Q gi|254781218|r   34 TRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALY   78 (205)
Q Consensus        34 ~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~   78 (205)
                      +.||.|+...  -||...||+...||+.+|.+|-+.+-.|+.+.-++
T Consensus        17 e~IR~Lh~~~Pe~~t~~~LAe~F~VSpeaIrRILKSKw~Pt~e~klK   63 (225)
T pfam06413        17 EQIRYLKQEFPEEWTVPRLAEGFDVSTDVIRRVLKSKFVPTLERKLK   63 (225)
T ss_pred             HHHHHHHHHCCHHCCHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf             99999987384011589998607889999999997157886888754


No 437
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=40.04  E-value=27  Score=15.42  Aligned_cols=30  Identities=20%  Similarity=0.133  Sum_probs=25.4

Q ss_pred             CC-CCHHHHHHHHCCCHHHHH----HHHCCCCCCC
Q ss_conf             59-988999998489999999----8877998889
Q gi|254781218|r   43 NN-KTQKEMAIGANQLESAVN----LFENGMCSTS   72 (205)
Q Consensus        43 ~g-ltQ~elA~~~gis~~~is----~~E~G~~~ps   72 (205)
                      .| |+-.++|..+||++..|.    +||.|...+.
T Consensus        17 eG~L~D~eIA~~LGVsr~nV~kmRqKwes~~dsv~   51 (181)
T pfam04645        17 EGSLSDAEIAKELGVSRVNVWRMRQKWESGEDSVN   51 (181)
T ss_pred             CCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             17875799999978309999999999981278855


No 438
>pfam04458 DUF505 Protein of unknown function (DUF505). Family of uncharacterized prokaryotic proteins.
Probab=39.94  E-value=27  Score=15.41  Aligned_cols=47  Identities=9%  Similarity=0.017  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999859988999998489999999887-799888999999999982
Q gi|254781218|r   32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEY   83 (205)
Q Consensus        32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~   83 (205)
                      ++.++-..-+.+|+.++     -|++.....-+| --...|-+..-..|+.+.
T Consensus       105 vp~~w~e~L~ERgla~e-----~~LT~~gk~lle~Y~et~P~l~vt~ela~~i  152 (591)
T pfam04458       105 VPERWEEALSERGLAEE-----GGLTEYGKAVLEIYRETHPKLYVTPEVAGYI  152 (591)
T ss_pred             CCHHHHHHHHHCCCCCC-----CCCCHHHHHHHHHHHHCCCEEEECHHHHHHH
T ss_conf             96779999987245322-----5734999999999986298299878999999


No 439
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=39.87  E-value=28  Score=15.41  Aligned_cols=115  Identities=10%  Similarity=-0.004  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCC
Q ss_conf             66899999999999999998599889999984899999998877998889999999999828999996145322100002
Q gi|254781218|r   23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYED  102 (205)
Q Consensus        23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~  102 (205)
                      +...+|.+.|=.-++   ..--....++|..++|++++++..           +.+|++.==|..        ..+....
T Consensus         6 ~~~edYL~~Iy~l~~---~~~~~~~~diA~~L~Vsp~sVt~m-----------l~rL~~~GlV~~--------~~y~gi~   63 (154)
T COG1321           6 ETEEDYLETIYELLE---EKGFARTKDIAERLKVSPPSVTEM-----------LKRLERLGLVEY--------EPYGGVT   63 (154)
T ss_pred             HHHHHHHHHHHHHHH---CCCCCCHHHHHHHHCCCCHHHHHH-----------HHHHHHCCCEEE--------ECCCCEE
T ss_conf             168999999999984---368751999999858992789999-----------999987899788--------4588867


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCHHH-HHHHHCCCHHHHHH-HHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             32134554677799999999972983899-99997799999999-7414889998999999998289
Q gi|254781218|r  103 VTNKKRLDPYAIGARLKSIRKDKGMSQIE-FGKLLGMPNSTLSN-YEQGRTIPEIKPARKIKQVTKK  167 (205)
Q Consensus       103 ~~~~~~~d~~~iG~rLk~lR~~~glsq~e-lA~~lgis~~tis~-~E~g~~~Ps~~~l~kIa~~lgv  167 (205)
                      ..        .-|.++..-.-.+...... |.+.+|++...... -+.=....+.+.+.+|.+.++-
T Consensus        64 LT--------~~G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~leh~~s~~~~~rl~~~l~~  122 (154)
T COG1321          64 LT--------EKGREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLEHALSDETAERLDELLGF  122 (154)
T ss_pred             EC--------CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             88--------354899999999999999999998589889999999888621999999999999579


No 440
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=39.64  E-value=20  Score=16.33  Aligned_cols=24  Identities=33%  Similarity=0.429  Sum_probs=15.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             389999997799999999741488
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRT  151 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~  151 (205)
                      |..|.|+.+|+++++|+++.++..
T Consensus        19 Si~~aak~l~~~~~~I~~~l~~~~   42 (53)
T smart00497       19 SIREAAKYLGISHSSISKYLNTGK   42 (53)
T ss_pred             HHHHHHHHHCCCCCCHHHHHCCCC
T ss_conf             799999985888323888706775


No 441
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=39.61  E-value=12  Score=17.60  Aligned_cols=116  Identities=10%  Similarity=0.141  Sum_probs=62.5

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH--CCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999848999999988779988899999999998289999961--453221-000023213455467779999999997
Q gi|254781218|r   48 KEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY--DGEVID-RRYEDVTNKKRLDPYAIGARLKSIRKD  124 (205)
Q Consensus        48 ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll--~ge~~~-~~~~~~~~~~~~d~~~iG~rLk~lR~~  124 (205)
                      .|||++||||+.|+-           |+|.+||+=     -||-  .|+++- +.+-+.....+++-.      -++  +
T Consensus        34 RELsElIGVTRTTLR-----------EVLQRLARD-----GWLTIQHGKPTKVNnfWETSGLNILeTL------~~L--D   89 (275)
T TIGR02812        34 RELSELIGVTRTTLR-----------EVLQRLARD-----GWLTIQHGKPTKVNNFWETSGLNILETL------IRL--D   89 (275)
T ss_pred             HHHHHHCCCCCCHHH-----------HHHHHHHHH-----CCCCCCCCCCCCCCCHHHCCCCCHHHHH------HHH--C
T ss_conf             657542376630378-----------999887641-----1343658899862762430273578999------861--8


Q ss_pred             CC----CCHHHHHHHHCCCHHHHHHHHCCCCCCC-----HHHHHHHHHHHCCCH--HHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             29----8389999997799999999741488999-----899999999828999--9952472102545677754235
Q gi|254781218|r  125 KG----MSQIEFGKLLGMPNSTLSNYEQGRTIPE-----IKPARKIKQVTKKHL--DWIYFGDEVIVPKSIKRAKGNQ  191 (205)
Q Consensus       125 ~g----lsq~elA~~lgis~~tis~~E~g~~~Ps-----~~~l~kIa~~lgvs~--d~L~~G~e~~~~~~~~~~~~~~  191 (205)
                      ..    +.-.=|+.+++||.-.+..=-+  ..|.     +..+.+=+++|.-.-  +-|+  +.....+.+++.-.+.
T Consensus        90 ~~~~P~l~dnLLSARTnIS~IYir~A~K--~np~~~~~~~~~VI~s~e~L~~~~s~~~F~--~~SP~~~~~~~~l~d~  163 (275)
T TIGR02812        90 GESVPSLIDNLLSARTNISAIYIRAAFK--NNPEESEELIENVIKSLEVLANAESFAEFV--EASPLAEKVKKELEDT  163 (275)
T ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHCCCCHHHHH--HHCCHHHHHHHHHHCC
T ss_conf             7777079999997764137788999862--283568999999999999983040179998--5082689999874203


No 442
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.29  E-value=28  Score=15.35  Aligned_cols=27  Identities=19%  Similarity=0.180  Sum_probs=22.7

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|--.|+|..|.|+.+|++..++...
T Consensus       147 ~L~~~~g~s~~EIA~~lg~s~~tVk~~  173 (187)
T PRK09648        147 ILRVVVGLSAEETAEAVGSTPGAVRVA  173 (187)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999984999999999989399999999


No 443
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=39.28  E-value=28  Score=15.35  Aligned_cols=28  Identities=25%  Similarity=0.355  Sum_probs=23.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .++-..|||..|.|+.+|+|.+|+...-
T Consensus       149 ~L~~~~g~s~~EIA~~l~is~~tVk~~l  176 (194)
T PRK12513        149 LLREHGDLSLEEIAQLTGVPLETVKSRL  176 (194)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999849999999999894999999999


No 444
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=38.82  E-value=29  Score=15.31  Aligned_cols=32  Identities=19%  Similarity=0.202  Sum_probs=26.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999999729838999999779999999974
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      .-|....+..+-.+.+.|+.+||+++|+.+..
T Consensus       408 ~~I~~aL~~~~gn~~~aA~~LGisR~tLyrKl  439 (441)
T PRK10365        408 EVILAALEKTGGNKTEAARQLGITRKTLLAKL  439 (441)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999939989999999788999999996


No 445
>PRK09409 insertion element IS2 transposase InsD; Reviewed
Probab=38.52  E-value=29  Score=15.28  Aligned_cols=26  Identities=4%  Similarity=-0.117  Sum_probs=21.2

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             98599889999984899999998877
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFEN   66 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E~   66 (205)
                      -+.|+.-+-++..+|||+|.+..|-+
T Consensus         8 ~a~g~~v~~~cr~LgVSRS~~y~~~~   33 (301)
T PRK09409          8 IARGWGVSLVSRCLRVSRAQLHVILR   33 (301)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf             96897499999997866877444302


No 446
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325   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 , .    This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=38.31  E-value=15  Score=16.97  Aligned_cols=59  Identities=17%  Similarity=0.127  Sum_probs=37.7

Q ss_pred             HHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             996145322100002321345546777999999----------99972983899999977999999997
Q gi|254781218|r   88 DWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKS----------IRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus        88 d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~----------lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +.+...+.+|-...+-......+...+-.-|+.          +|---+||-.|.|+.+|||..|+...
T Consensus        81 ~e~~~~~~Pd~~ga~d~~~~~~~r~~l~~AL~~LP~rQR~vvVLRY~eDlSe~~~A~~LG~SvGTVKS~  149 (165)
T TIGR02983        81 LELPTEELPDAAGAPDPAADVALRAALARALRRLPARQRAVVVLRYYEDLSEAEVAEVLGISVGTVKSR  149 (165)
T ss_pred             HHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHCCEEEEEECCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf             421466864888898753112269999999973564123672320457898689998819993228998


No 447
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305   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 , .    This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=38.25  E-value=29  Score=15.25  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=14.3

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             999729838999999779999999
Q gi|254781218|r  121 IRKDKGMSQIEFGKLLGMPNSTLS  144 (205)
Q Consensus       121 lR~~~glsq~elA~~lgis~~tis  144 (205)
                      +|+-.|++-.|.|+.+|.|..+++
T Consensus       154 LRdvlGw~A~E~A~~L~~s~ASVn  177 (329)
T TIGR02960       154 LRDVLGWKAAEVAELLGTSVASVN  177 (329)
T ss_pred             HHHHHCCCHHHHHHHHCCCHHHHH
T ss_conf             898835555689987438326786


No 448
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=37.80  E-value=30  Score=15.21  Aligned_cols=28  Identities=7%  Similarity=0.088  Sum_probs=23.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999998599889999984899999998
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      +..+++..-++-.+||+.+|+|..||-|
T Consensus        11 l~~l~~~g~v~v~eLa~~~~VS~~TIRR   38 (252)
T PRK10906         11 IELVKQQGYVSTEELVEHFSVSPQTIRR   38 (252)
T ss_pred             HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             9999986989999999987969989988


No 449
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.60  E-value=22  Score=16.01  Aligned_cols=33  Identities=21%  Similarity=0.072  Sum_probs=22.0

Q ss_pred             HHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999999999-85998899999848999999988
Q gi|254781218|r   32 VGTRIKDIRK-ANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        32 iG~rik~lR~-~~gltQ~elA~~~gis~~~is~~   64 (205)
                      +|.=.-.+=- ..-||..|+++.+|+|.+.+|.-
T Consensus        28 VG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~   61 (177)
T COG1510          28 VGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMG   61 (177)
T ss_pred             HHHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHH
T ss_conf             7778654000699966999999977780128899


No 450
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. 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.
Probab=37.38  E-value=30  Score=15.17  Aligned_cols=22  Identities=23%  Similarity=0.078  Sum_probs=13.1

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             8599889999984899999998
Q gi|254781218|r   42 ANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        42 ~~gltQ~elA~~~gis~~~is~   63 (205)
                      ...+|..|.|+..|||+++|..
T Consensus        31 ~eDlSL~EIAe~~~iSRQaV~D   52 (101)
T pfam04297        31 LDDLSLSEIAEEFNVSRQAVYD   52 (101)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHH
T ss_conf             7639899999881985999999


No 451
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=37.35  E-value=30  Score=15.16  Aligned_cols=29  Identities=3%  Similarity=-0.123  Sum_probs=24.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999985998899999848999999988
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      +..+++..-++-++||+.+|+|..||-|-
T Consensus        11 l~~L~~~g~v~v~eLa~~~~VS~~TIRRD   39 (251)
T PRK13509         11 LDMLAQLGFVTVEKVIERLGISPATARRD   39 (251)
T ss_pred             HHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf             99999869898999999989699899983


No 452
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=36.96  E-value=31  Score=15.13  Aligned_cols=28  Identities=7%  Similarity=0.107  Sum_probs=24.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999998599889999984899999998
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      +..+++..-++-.+||+.+|||..||-|
T Consensus        23 l~~L~~~g~v~v~eLae~~~VS~~TIRR   50 (269)
T PRK09802         23 IQRLRQQGSVQVNDLSALYGVSTVTIRN   50 (269)
T ss_pred             HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             9999986989999999987969889998


No 453
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.70  E-value=31  Score=15.10  Aligned_cols=28  Identities=21%  Similarity=0.245  Sum_probs=24.0

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999729838999999779999999974
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      -+|.-.|||..|.|+.+|++..|+....
T Consensus       147 ~Lr~~eglS~~EIAeiLgip~gTVKSRL  174 (217)
T PRK12533        147 VLRELEDMSYREIAAIADVPVGTVMSRL  174 (217)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999809999999999894999999999


No 454
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=36.31  E-value=31  Score=15.06  Aligned_cols=32  Identities=22%  Similarity=0.172  Sum_probs=27.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999999729838999999779999999974
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..|.......|..+.+.|+.+||+++|+.+..
T Consensus       594 ~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRKl  625 (639)
T PRK11388        594 QAIINAAQVCGGRIQEMAALLGIGRTTLWRKM  625 (639)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999949979999999898999999999


No 455
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=35.76  E-value=32  Score=15.01  Aligned_cols=22  Identities=18%  Similarity=0.108  Sum_probs=19.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             5998899999848999999988
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~   64 (205)
                      .+++..++|+++|++++++.++
T Consensus        18 ~~l~l~ela~~~glpksT~~Rl   39 (246)
T COG1414          18 GGLSLAELAERLGLPKSTVHRL   39 (246)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHH
T ss_conf             8887999999879198899999


No 456
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications.  Binding of the effector to GntR-like transcriptional regulators is 
Probab=35.74  E-value=32  Score=15.01  Aligned_cols=17  Identities=18%  Similarity=0.257  Sum_probs=7.5

Q ss_pred             CHHHHHHHHCCCHHHHH
Q ss_conf             88999998489999999
Q gi|254781218|r   46 TQKEMAIGANQLESAVN   62 (205)
Q Consensus        46 tQ~elA~~~gis~~~is   62 (205)
                      |..+||+..|+|+.+|.
T Consensus        27 s~~~La~~~~vSr~tvr   43 (66)
T cd07377          27 SERELAEELGVSRTTVR   43 (66)
T ss_pred             CHHHHHHHHCCCHHHHH
T ss_conf             79999999798889999


No 457
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=35.71  E-value=32  Score=15.00  Aligned_cols=24  Identities=25%  Similarity=0.290  Sum_probs=20.8

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             729838999999779999999974
Q gi|254781218|r  124 DKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       124 ~~glsq~elA~~lgis~~tis~~E  147 (205)
                      ..|+|..|.|+.+|+|.+|+...-
T Consensus       125 ~~g~s~~EIA~~l~is~~tVk~~l  148 (166)
T PRK09639        125 FSGYSYKEIAQALGIDESSVGTTL  148 (166)
T ss_pred             HHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             938999999999891999999999


No 458
>PRK13501 transcriptional activator RhaR; Provisional
Probab=35.53  E-value=32  Score=14.98  Aligned_cols=31  Identities=13%  Similarity=0.045  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf             2983899999977999999997414889998
Q gi|254781218|r  125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI  155 (205)
Q Consensus       125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~  155 (205)
                      ..++..++|+.+++++..++++-+..+--+.
T Consensus       191 ~~~~l~~lA~~~~lS~~~lsrlFK~~tG~T~  221 (290)
T PRK13501        191 AYFDMADFCHKNQLVERSLKQLFRQQTGMSI  221 (290)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf             8999999999969899999999999989399


No 459
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=35.46  E-value=24  Score=15.77  Aligned_cols=19  Identities=37%  Similarity=0.578  Sum_probs=10.3

Q ss_pred             CHHHHHHHHCCCHHHHHHH
Q ss_conf             3899999977999999997
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~  146 (205)
                      |..++|+.+|+++.+++++
T Consensus        18 Si~~aa~~L~i~~~tI~~~   36 (37)
T pfam07453        18 SIREAARALGISHSTINKY   36 (37)
T ss_pred             HHHHHHHHHCCCHHHHHCC
T ss_conf             7999999847646566502


No 460
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=34.53  E-value=31  Score=15.08  Aligned_cols=46  Identities=26%  Similarity=0.386  Sum_probs=24.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHH----HCCCCCCCHHHHHHHH-HHHCCCHHHHHCCCCC
Q ss_conf             83899999977999999997----4148899989999999-9828999995247210
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNY----EQGRTIPEIKPARKIK-QVTKKHLDWIYFGDEV  178 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~----E~g~~~Ps~~~l~kIa-~~lgvs~d~L~~G~e~  178 (205)
                      .|+.++|+.+|+|.+|+..-    +.+.-.      .+.. -++=++|+-+|-|++.
T Consensus        76 ~T~R~lae~~gvs~~TV~~tmK~L~e~~fI------kk~t~GvymiNP~i~~kG~~~  126 (165)
T pfam05732        76 MTQREIAEETGISLETVRQTMKALEEGNFL------KKKTSGVYMINPDLLFKGDDT  126 (165)
T ss_pred             EEHHHHHHHHCCCHHHHHHHHHHHHHCCCE------EEECCCEEEECHHHHHCCCHH
T ss_conf             878999998395299999999999758926------861387699885895068727


No 461
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=34.36  E-value=34  Score=14.87  Aligned_cols=61  Identities=21%  Similarity=0.232  Sum_probs=38.5

Q ss_pred             HHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999999982899999614532210000232134554677799999999972983899999977999999997
Q gi|254781218|r   75 YALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus        75 ~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +-..+.++|.     -++|+....-|..+-..-      =..=|..+.+.-+-.|...|+.+||++.|+.+-
T Consensus        31 V~~al~~Yf~-----~L~g~~~~~ly~~vl~ev------E~pLl~~vL~~t~gNqskAA~~LGInR~TLRkK   91 (98)
T PRK00430         31 VKQALKNYFA-----QLDGQDVNDLYELVLAEV------EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKK   91 (98)
T ss_pred             HHHHHHHHHH-----HCCCCCCHHHHHHHHHHH------HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9999999999-----749999206999999998------999999999996695999999978778899999


No 462
>COG0656 ARA1 Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]
Probab=34.31  E-value=34  Score=14.86  Aligned_cols=59  Identities=17%  Similarity=0.253  Sum_probs=42.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-----HHHHCCCCCCCHHHHHHH
Q ss_conf             89999997799999999741488999899999999828999-----995247210254567775
Q gi|254781218|r  129 QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL-----DWIYFGDEVIVPKSIKRA  187 (205)
Q Consensus       129 q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~-----d~L~~G~e~~~~~~~~~~  187 (205)
                      .-+||+.-||....+|-..+|.....-..+..||+.+|.|+     .|.+...-...|++.+..
T Consensus       175 l~~~~~~~gI~v~AysPL~~g~~l~~~~~l~~Ia~k~g~t~AQv~L~W~i~~gv~~Ipks~~~~  238 (280)
T COG0656         175 LLPFCQRHGIAVEAYSPLAKGGKLLDNPVLAEIAKKYGKTPAQVALRWHIQRGVIVIPKSTTPE  238 (280)
T ss_pred             HHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCEEECCCCCHH
T ss_conf             9999998799899978722366312586999999984898799999988757948755789889


No 463
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=34.13  E-value=34  Score=14.84  Aligned_cols=33  Identities=21%  Similarity=0.221  Sum_probs=27.4

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             999999997298389999997799999999741
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .-|.+..+..+..+.+.|+.+||+++|+.+..+
T Consensus       432 ~~I~~aL~~~~gn~~~aA~~LGisR~TLyrKlk  464 (469)
T PRK10923        432 TLLTTALRHTQGHKQEAARLLGWGRNTLTRKLK  464 (469)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999999099899999998989999999999


No 464
>pfam02084 Bindin Bindin.
Probab=33.99  E-value=34  Score=14.85  Aligned_cols=52  Identities=21%  Similarity=0.294  Sum_probs=38.2

Q ss_pred             HHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             988779988899999999998289999961453221000023213455467779999999997298
Q gi|254781218|r   62 NLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGM  127 (205)
Q Consensus        62 s~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~gl  127 (205)
                      |.++-+...+|.+++-+|-.+|+.+-        +|.      .--+.||+.+|--||.+|...+|
T Consensus        90 ss~~e~etTIsAkvm~~IKAVLGATK--------IDL------PVDINDPYDLGLLLRHLRHHSNL  141 (239)
T pfam02084        90 SSIEEGDTTISADVMEKIKAVLGATK--------IDL------PVDINDPYDLGLLLRHLRHHSNL  141 (239)
T ss_pred             CCCCCCCCEEEHHHHHHHHHHHCCCC--------CCC------CCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             22347875350999998999857543--------467------44368733678999998877778


No 465
>PRK00118 putative DNA-binding protein; Validated
Probab=33.91  E-value=34  Score=14.82  Aligned_cols=23  Identities=22%  Similarity=0.027  Sum_probs=14.8

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             98599889999984899999998
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~   63 (205)
                      -..++|-.|.|+..|||+++|+.
T Consensus        30 y~~DlSl~EIAe~~~iSRQaV~D   52 (105)
T PRK00118         30 YLDDYSLGEIAEEFNVSRQAVYD   52 (105)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             88549999998996985999999


No 466
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=33.90  E-value=34  Score=14.82  Aligned_cols=30  Identities=13%  Similarity=0.028  Sum_probs=24.2

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             985998899999848999999988779988
Q gi|254781218|r   41 KANNKTQKEMAIGANQLESAVNLFENGMCS   70 (205)
Q Consensus        41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~   70 (205)
                      .-.++|..++|+.+|||+.++.++=.++..
T Consensus        27 ~~~~iTt~~iA~~~gvs~aalYrHF~sK~~   56 (194)
T PRK09480         27 PGERITTAKLAARVGVSEAALYRHFPSKAR   56 (194)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHCCCHHH
T ss_conf             976422999998909978999997587999


No 467
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=33.48  E-value=35  Score=14.78  Aligned_cols=30  Identities=10%  Similarity=0.137  Sum_probs=25.6

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999999998599889999984899999998
Q gi|254781218|r   34 TRIKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        34 ~rik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      .=+..+++..-++-.+||+.+|+|..||-|
T Consensus        11 ~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR   40 (252)
T PRK10681         11 QLLQALKRSDKLHLKDAAALLGVSEMTIRR   40 (252)
T ss_pred             HHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             999999986979999999887979989987


No 468
>KOG0774 consensus
Probab=33.33  E-value=17  Score=16.72  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=11.6

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf             99999977999999997414889
Q gi|254781218|r  130 IEFGKLLGMPNSTLSNYEQGRTI  152 (205)
Q Consensus       130 ~elA~~lgis~~tis~~E~g~~~  152 (205)
                      .+||...||+.+.+++|.-.+++
T Consensus       222 ~eLAkqCnItvsQvsnwfgnkrI  244 (334)
T KOG0774         222 EELAKQCNITVSQVSNWFGNKRI  244 (334)
T ss_pred             HHHHHHCCCEEHHHCCCCCCCEE
T ss_conf             99998729340563232245403


No 469
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=33.12  E-value=35  Score=14.74  Aligned_cols=37  Identities=11%  Similarity=0.140  Sum_probs=19.7

Q ss_pred             HHHHHHHHHH---HCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             7999999999---729838999999779999999974148
Q gi|254781218|r  114 IGARLKSIRK---DKGMSQIEFGKLLGMPNSTLSNYEQGR  150 (205)
Q Consensus       114 iG~rLk~lR~---~~glsq~elA~~lgis~~tis~~E~g~  150 (205)
                      ++.+++.+-.   .+.++..++|+.+.++.+++.+.....
T Consensus       135 ~s~Kv~~II~sDis~~W~L~dIA~~L~mSEStLkRkLk~E  174 (253)
T PRK09940        135 VSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE  174 (253)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             5698999996483004609999988745899999999986


No 470
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=32.92  E-value=36  Score=14.72  Aligned_cols=27  Identities=15%  Similarity=0.164  Sum_probs=23.0

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999972983899999977999999997
Q gi|254781218|r  120 SIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       120 ~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+|-..|+|..|.|+.+|++.+++...
T Consensus       137 ~l~~~~~~s~~EIA~~l~is~~tV~~r  163 (177)
T PRK09415        137 YLFYYEELSIKEIATVTGVNENTIKTR  163 (177)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999980998999999889299999999


No 471
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=32.89  E-value=36  Score=14.72  Aligned_cols=45  Identities=13%  Similarity=0.268  Sum_probs=29.6

Q ss_pred             HCCCHHHHHHHHCCC---------------CCCCHHHHHHHHHHHCCCH-------HHHHCCCCCCC
Q ss_conf             489999999887799---------------8889999999999828999-------99614532210
Q gi|254781218|r   54 ANQLESAVNLFENGM---------------CSTSIRYALYLRNEYEISF-------DWIYDGEVIDR   98 (205)
Q Consensus        54 ~gis~~~is~~E~G~---------------~~psi~~l~~la~~~~vs~-------d~Ll~ge~~~~   98 (205)
                      +|=.++-=+++..|.               ..|++..|+++|..++|++       |.|+.+-..+.
T Consensus        62 lGGDqQIga~Ia~g~id~viFF~DPl~~~phd~Dv~aLlRlc~v~nIP~AtN~aTAe~li~~~~~~~  128 (146)
T PRK05234         62 LGGDQQIGALIAEGKIDMLIFFWDPLTAQPHDPDVKALLRLADVWNIPVATNRATADFLISSPLFND  128 (146)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCC
T ss_conf             4189999999983998789994088755777520999999998728764268978999970822365


No 472
>PRK04280 arginine repressor; Provisional
Probab=32.88  E-value=33  Score=14.89  Aligned_cols=29  Identities=24%  Similarity=0.224  Sum_probs=19.3

Q ss_pred             HHHHH-HHCCCCHHHHHHHH-----CCCHHHHHHH
Q ss_conf             99999-98599889999984-----8999999988
Q gi|254781218|r   36 IKDIR-KANNKTQKEMAIGA-----NQLESAVNLF   64 (205)
Q Consensus        36 ik~lR-~~~gltQ~elA~~~-----gis~~~is~~   64 (205)
                      |+.+= ...=-||+||.+.+     .+||.+|||-
T Consensus        10 I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRD   44 (149)
T PRK04280         10 IREIITNEEIETQDELVDRLREYGFNVTQATVSRD   44 (149)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHH
T ss_conf             99999748977899999999985975538988987


No 473
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=32.67  E-value=36  Score=14.70  Aligned_cols=26  Identities=15%  Similarity=0.005  Sum_probs=21.7

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999859988999998489999999887
Q gi|254781218|r   39 IRKANNKTQKEMAIGANQLESAVNLFE   65 (205)
Q Consensus        39 lR~~~gltQ~elA~~~gis~~~is~~E   65 (205)
                      .|. .++|-.+||+.+|+|+++.++|=
T Consensus        15 ~~~-~~~t~~ela~~l~~S~qta~R~l   40 (214)
T COG1339          15 VRG-VKVTSSELAKRLGVSSQTAARKL   40 (214)
T ss_pred             HCC-CCCCHHHHHHHHCCCCHHHHHHH
T ss_conf             037-60208999988574707788998


No 474
>PRK13500 transcriptional activator RhaR; Provisional
Probab=31.88  E-value=37  Score=14.62  Aligned_cols=42  Identities=10%  Similarity=0.040  Sum_probs=27.3

Q ss_pred             HHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf             7999999999--72983899999977999999997414889998
Q gi|254781218|r  114 IGARLKSIRK--DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI  155 (205)
Q Consensus       114 iG~rLk~lR~--~~glsq~elA~~lgis~~tis~~E~g~~~Ps~  155 (205)
                      +.+-|..+..  ..-++..+||+..|+|..++++.-+...--+.
T Consensus       208 L~~ll~~l~~~~~ep~~l~~lA~~~~lS~r~L~R~Fk~~tG~Tp  251 (312)
T PRK13500        208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI  251 (312)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf             99999999987449998999998978899999999999989199


No 475
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=31.77  E-value=37  Score=14.61  Aligned_cols=39  Identities=13%  Similarity=0.026  Sum_probs=27.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCC-------------CCCCCHHHHHHHHHHH
Q ss_conf             83899999977999999997414-------------8899989999999982
Q gi|254781218|r  127 MSQIEFGKLLGMPNSTLSNYEQG-------------RTIPEIKPARKIKQVT  165 (205)
Q Consensus       127 lsq~elA~~lgis~~tis~~E~g-------------~~~Ps~~~l~kIa~~l  165 (205)
                      .++.|+|+.+|+++.++++..+.             -..-+.+.|.+||.-+
T Consensus       157 ~~~~elA~~lG~Sretl~R~L~~f~~eGiI~~~~~~i~I~D~~~L~~LA~~~  208 (213)
T PRK10402        157 EKHTQAAEYLGVSYRHLLYVLAQFCQDGYLIKSKRGYLIKNRKQLSGLALEL  208 (213)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHC
T ss_conf             6799999997988999999999999889889749999995799999998644


No 476
>TIGR00651 pta phosphate acetyltransferase; InterPro: IPR004614 Phosphate acetyltransferase (2.3.1.8 from EC) catalyses the conversion of acetyl-CoA and phosphate to CoA and acetyl phosphate in the last two steps in the conversion of actetae to acetyl-CoA.; GO: 0016407 acetyltransferase activity.
Probab=31.50  E-value=38  Score=14.58  Aligned_cols=34  Identities=18%  Similarity=0.239  Sum_probs=23.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             1566899999999999999998599889999984
Q gi|254781218|r   21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGA   54 (205)
Q Consensus        21 ~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~   54 (205)
                      +.+......+...+++-++||.+|+|.++..+.+
T Consensus        55 ~~~~~~~~~E~Y~~~~~e~RK~KG~t~~~A~~~l   88 (322)
T TIGR00651        55 IDPDVSPDRESYAERYYELRKHKGVTLAQARKQL   88 (322)
T ss_pred             ECCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             2786742279999999987415560479999973


No 477
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=31.48  E-value=38  Score=14.58  Aligned_cols=33  Identities=18%  Similarity=0.266  Sum_probs=24.6

Q ss_pred             HHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf             999999--997298389999997799999999741
Q gi|254781218|r  116 ARLKSI--RKDKGMSQIEFGKLLGMPNSTLSNYEQ  148 (205)
Q Consensus       116 ~rLk~l--R~~~glsq~elA~~lgis~~tis~~E~  148 (205)
                      .|=+++  .-..|+|-++.|+.+++|..|+..+-.
T Consensus       144 ~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~  178 (202)
T PRK09390        144 ERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRA  178 (202)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89999999998389689999997987889999999


No 478
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=31.37  E-value=38  Score=14.56  Aligned_cols=29  Identities=10%  Similarity=0.103  Sum_probs=22.4

Q ss_pred             HHHHHHHH--CCCCHHHHHHHHCCCHHHHHH
Q ss_conf             99999998--599889999984899999998
Q gi|254781218|r   35 RIKDIRKA--NNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        35 rik~lR~~--~gltQ~elA~~~gis~~~is~   63 (205)
                      .+|.++..  .|++..+-|+++++||++||+
T Consensus         5 QLryf~~va~~~~n~t~AA~~L~iSQPavS~   35 (324)
T PRK12681          5 QLRYIVEVVNHNLNVSATAESLYTSQPGISK   35 (324)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             9999999997699999999997897779999


No 479
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=30.96  E-value=38  Score=14.52  Aligned_cols=36  Identities=14%  Similarity=0.235  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHCC-------CCHHHHHHHHCCCHHHHHH
Q ss_conf             99999999999999859-------9889999984899999998
Q gi|254781218|r   28 YWKDVGTRIKDIRKANN-------KTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        28 ~~~~iG~rik~lR~~~g-------ltQ~elA~~~gis~~~is~   63 (205)
                      -+.+|.++|+..=-..-       -|..+||..++|++.|+++
T Consensus        12 IY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~r   54 (125)
T COG1725          12 IYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQR   54 (125)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             7999999999999808868888897599999981989889999


No 480
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.76  E-value=39  Score=14.50  Aligned_cols=31  Identities=10%  Similarity=0.044  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999999998599889999984899999998
Q gi|254781218|r   33 GTRIKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        33 G~rik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      ..=+..+++..-++.++||+.+|||..||-|
T Consensus         8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR   38 (253)
T COG1349           8 QKILELLKEKGKVSVEELAELFGVSEMTIRR   38 (253)
T ss_pred             HHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             9999999985969799999885978999986


No 481
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=30.71  E-value=39  Score=14.50  Aligned_cols=49  Identities=8%  Similarity=-0.048  Sum_probs=20.4

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf             99999848999999988779988899999999998289999961453221
Q gi|254781218|r   48 KEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID   97 (205)
Q Consensus        48 ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~   97 (205)
                      .++.+.+|+..+...+|=+-.+. --..-+.||+++-+.+.+|+-+|.++
T Consensus       122 ~~~L~~VgL~~~~l~R~P~eLSG-GQ~QRiaIARAL~~~PklLIlDEptS  170 (252)
T COG1124         122 AELLDQVGLPPSFLDRRPHELSG-GQRQRIAIARALIPEPKLLILDEPTS  170 (252)
T ss_pred             HHHHHHCCCCHHHHHCCCHHCCH-HHHHHHHHHHHHCCCCCEEEECCCHH
T ss_conf             99999849998998539421281-68999999998636888799538234


No 482
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=30.07  E-value=40  Score=14.43  Aligned_cols=22  Identities=23%  Similarity=0.129  Sum_probs=13.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             5998899999848999999988
Q gi|254781218|r   43 NNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        43 ~gltQ~elA~~~gis~~~is~~   64 (205)
                      ...+..++|..+|+++++++..
T Consensus        19 ~~v~~~~iA~~L~Vs~~SVt~m   40 (58)
T pfam01325        19 GVVKTKDLAERLNVSPSTVSEM   40 (58)
T ss_pred             CCEEHHHHHHHHCCCCHHHHHH
T ss_conf             9612999999959992529999


No 483
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=30.05  E-value=40  Score=14.43  Aligned_cols=28  Identities=11%  Similarity=0.147  Sum_probs=23.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             9999998599889999984899999998
Q gi|254781218|r   36 IKDIRKANNKTQKEMAIGANQLESAVNL   63 (205)
Q Consensus        36 ik~lR~~~gltQ~elA~~~gis~~~is~   63 (205)
                      +..+++..-++-.+||+.+|||..||-|
T Consensus        11 l~~L~~~g~v~v~eLa~~l~VS~~TIRR   38 (256)
T PRK10434         11 LEYLQKQGKCSVEELAQYFDTTGTTIRK   38 (256)
T ss_pred             HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf             9999986979999999987969989998


No 484
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=29.73  E-value=40  Score=14.39  Aligned_cols=107  Identities=16%  Similarity=0.225  Sum_probs=65.6

Q ss_pred             HHCCCCCCCHHHHHHHHHHH--CCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH------------HHHHHCCCCH
Q ss_conf             87799888999999999982--899999614532210000232134554677799999------------9999729838
Q gi|254781218|r   64 FENGMCSTSIRYALYLRNEY--EISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLK------------SIRKDKGMSQ  129 (205)
Q Consensus        64 ~E~G~~~psi~~l~~la~~~--~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk------------~lR~~~glsq  129 (205)
                      ++.-...|+-..+..|+++|  +++++.+-.-..+|.=|...-+.=    ..+.++|+            ..-+..|+|-
T Consensus       419 l~~~L~~p~~~Rl~~i~eAlrrG~sveeI~elT~ID~wFL~ki~~I----v~~e~~l~~~~~~~l~~~~L~~aK~~GFSD  494 (1063)
T PRK05294        419 IRRELKKPTPERIFYIAEAFRRGASVEEIHELTKIDPWFLEQIEEI----VELEEELKEGGLPGLDAELLRELKRLGFSD  494 (1063)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHCCCCCCCHHHHHHHHHHCCCH
T ss_conf             9998637993599999999985999999999878769999999999----999999984898879999999999809985


Q ss_pred             HHHHHHHCCCHHHHHHHHCC-CCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf             99999977999999997414-8899989999999982899999524
Q gi|254781218|r  130 IEFGKLLGMPNSTLSNYEQG-RTIPEIKPARKIKQVTKKHLDWIYF  174 (205)
Q Consensus       130 ~elA~~lgis~~tis~~E~g-~~~Ps~~~l~kIa~~lgvs~d~L~~  174 (205)
                      .++|+.+|++...+.++-.. ...|....+.-.|-.|.-...|++.
T Consensus       495 ~~IA~l~~~~~~~Vr~~R~~~~I~P~yK~VDTcAgEF~a~T~Y~YS  540 (1063)
T PRK05294        495 ARIAKLLGVTEDEVRKLRKELGIHPVYKRVDTCAAEFEADTPYMYS  540 (1063)
T ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEEEE
T ss_conf             9999884999999999999879953898415632345667872676


No 485
>PRK13980 NAD synthetase; Provisional
Probab=29.55  E-value=40  Score=14.37  Aligned_cols=71  Identities=17%  Similarity=0.116  Sum_probs=32.0

Q ss_pred             HHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99999998289999961453221000023213455-4677799999999972983899999977999999997
Q gi|254781218|r   75 YALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRL-DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus        75 ~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~-d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      .+..||++++|+ +.++.-.+...-..++.....+ -+..+=..+=....+.+++..+.++.+|+++..+.++
T Consensus       167 ~V~~La~~l~vP-~~Ii~k~PSa~L~~~Q~DE~~LG~~Y~~lD~iL~~~ie~~~~~~~i~~~~g~~~~~v~~i  238 (264)
T PRK13980        167 QVRELARHLGVP-EDIIEKPPSADLWEGQTDEDELGFSYEEIDEILYALFDKKMPREEILAQLGIDEELVDRV  238 (264)
T ss_pred             HHHHHHHHHCCC-HHHEECCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf             999999993996-644036999776799998777199999999999999976999999998719899999999


No 486
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=29.44  E-value=41  Score=14.36  Aligned_cols=118  Identities=15%  Similarity=0.165  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf             999999999999985998899999848999999988779988--899999999998289999961453221000023213
Q gi|254781218|r   29 WKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCS--TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK  106 (205)
Q Consensus        29 ~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~--psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~  106 (205)
                      ..+.-.++|..=-..+++.+..|.+.||+.++--+|-..-..  -+-+.+-.-         ..+.|..++.     ..+
T Consensus         4 ~~e~r~~vR~~Yv~~~~~Le~aA~~~gV~~~TArrWK~~Ak~~GDDWDkaRaA---------~~maggg~ed-----var   69 (165)
T pfam08822         4 PKETRDAVRRLYVFDRLTLEVAAAKAGVSYSTARRWKREAKAKGDDWDKARAA---------YTLAGGGIED-----LAR   69 (165)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHH---------HHHHCCCHHH-----HHH
T ss_conf             68999999999996678799999880998888999999888758838999999---------9985687889-----999


Q ss_pred             HHHHHHH--HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH--CCCCCCCHHHHHH
Q ss_conf             4554677--7999999999729838999999779999999974--1488999899999
Q gi|254781218|r  107 KRLDPYA--IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE--QGRTIPEIKPARK  160 (205)
Q Consensus       107 ~~~d~~~--iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E--~g~~~Ps~~~l~k  160 (205)
                      ..+.-+.  .-.-+.+++..-.|+..+=++.+.-=..++++.-  +++..|.++.+--
T Consensus        70 ~~l~~f~~Q~~~tmeeL~~~~~l~~~~Kv~lLAsLaDsf~K~vaAskr~lPets~LA~  127 (165)
T pfam08822        70 QMLTGFVVQYQATMDELQEDEDLPPSDKAKLLASLADSFSKTVAASKRVLPETSKLAT  127 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             9999999999999999872556998899999999999999999987133841899999


No 487
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=29.41  E-value=41  Score=14.36  Aligned_cols=34  Identities=18%  Similarity=0.202  Sum_probs=28.6

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf             9999999972983899999977999999997414
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG  149 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g  149 (205)
                      .-|+.+....+-+....|+.+||+++|+.++..-
T Consensus       523 ~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk  556 (560)
T COG3829         523 HLIREALERHGGNKSKAAKELGISRTTLYRKLKK  556 (560)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999999982798989999969978999999998


No 488
>cd00086 homeodomain Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=29.39  E-value=41  Score=14.36  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=6.8

Q ss_pred             HHHHHHCCCHHHHHHHH
Q ss_conf             99999779999999974
Q gi|254781218|r  131 EFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       131 elA~~lgis~~tis~~E  147 (205)
                      ++|..+|++...|..|-
T Consensus        32 ~La~~~~l~~~qV~~WF   48 (59)
T cd00086          32 ELAKELGLTERQVKIWF   48 (59)
T ss_pred             HHHHHHCCCHHHHHHHH
T ss_conf             99999792999999999


No 489
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=29.38  E-value=41  Score=14.35  Aligned_cols=31  Identities=10%  Similarity=0.121  Sum_probs=25.9

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999729838999999779999999974
Q gi|254781218|r  117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE  147 (205)
Q Consensus       117 rLk~lR~~~glsq~elA~~lgis~~tis~~E  147 (205)
                      -|.+..+..+-.+.+.|+.+||+++|+.+..
T Consensus       421 ~i~~aL~~~~gn~~~aA~~LGisR~tLyrKl  451 (457)
T PRK11361        421 IIMEVLEQQEGNRTRTALMLGISRRALMYKL  451 (457)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999829989999999898999999999


No 490
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.37  E-value=41  Score=14.35  Aligned_cols=28  Identities=14%  Similarity=0.237  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf             988999998489999999887-7998889
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFE-NGMCSTS   72 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E-~G~~~ps   72 (205)
                      ++-.+||...|++..+|-.|+ .|.-.|+
T Consensus         2 y~i~eLa~~~g~~~rtiR~Y~~~GLlppp   30 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDRGLLPPP   30 (219)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHCCCCCCC
T ss_conf             75999999829981112798876899998


No 491
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=29.29  E-value=41  Score=14.35  Aligned_cols=34  Identities=15%  Similarity=-0.023  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999999999985998899999848999999988
Q gi|254781218|r   31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF   64 (205)
Q Consensus        31 ~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~   64 (205)
                      -+-.=|..+|..+.+|..+||+..+||..+|.+-
T Consensus         9 RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RD   42 (311)
T COG2378           9 RLLQIIQILRAKETVTAAELADEFEVSVRTIYRD   42 (311)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHH
T ss_conf             9999999998576045999998729889999999


No 492
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=28.86  E-value=42  Score=14.30  Aligned_cols=64  Identities=11%  Similarity=-0.020  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH----------CCCCHHHHHHHHCCCHHHHHHHHCC----------------CCCCCHHHH
Q ss_conf             66899999999999999998----------5998899999848999999988779----------------988899999
Q gi|254781218|r   23 PEIRQYWKDVGTRIKDIRKA----------NNKTQKEMAIGANQLESAVNLFENG----------------MCSTSIRYA   76 (205)
Q Consensus        23 ~~~~~~~~~iG~rik~lR~~----------~gltQ~elA~~~gis~~~is~~E~G----------------~~~psi~~l   76 (205)
                      ..|.+-..++.++|+.+|-.          +-+|-.|+|+.+||+.+++-+.+..                ++.=+++.+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~P~~~k~lR~Fs~~E~A~l~gvs~~~lR~~~~~g~~P~p~~~~~gr~~~rr~ytl~~i   87 (387)
T PHA02519          8 NSCIERGQEMTQAIAIAQFGDDSPEARAITRRWGITEVADLIGVTPQAIRDAEKSGRLPPPDFETRGRVERRAGYTIDQI   87 (387)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             99999899999999999721589633124477888999999599989998787568999997688887553343579999


Q ss_pred             HHHHHHHCCC
Q ss_conf             9999982899
Q gi|254781218|r   77 LYLRNEYEIS   86 (205)
Q Consensus        77 ~~la~~~~vs   86 (205)
                      ..|..+|+..
T Consensus        88 ~~lR~~l~~~   97 (387)
T PHA02519         88 SHMRDHFGNP   97 (387)
T ss_pred             HHHHHHHCCC
T ss_conf             9999986456


No 493
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=28.84  E-value=28  Score=15.32  Aligned_cols=46  Identities=13%  Similarity=0.286  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             933077776665433310001566----8999999999999999985998
Q gi|254781218|r    1 MFLNPFLETSLKSLQEYTLIITPE----IRQYWKDVGTRIKDIRKANNKT   46 (205)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iG~rik~lR~~~glt   46 (205)
                      .+|||.+--++++.++-|+.+...    +++.-.++-+||+..|++-+.-
T Consensus        12 ~~lN~~~IE~ie~~PDttItLinGkkyvVkEsveEVi~kI~~y~rkI~~~   61 (67)
T COG1582          12 FWLNAHHIETIEAFPDTTITLINGKKYVVKESVEEVINKIIEYRRKIGSL   61 (67)
T ss_pred             EEECHHHHHHHHCCCCCEEEEECCCEEEECCCHHHHHHHHHHHHHHHHEE
T ss_conf             25378784432216973899976828997023999999999999876230


No 494
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (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. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=28.59  E-value=42  Score=14.27  Aligned_cols=46  Identities=22%  Similarity=0.119  Sum_probs=26.6

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf             999999997298389999997799999999741488999899999999828999
Q gi|254781218|r  116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL  169 (205)
Q Consensus       116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~  169 (205)
                      +-|..+-.....+..+||+.+.+|.+|+.+.        +..+..+-+-+|+.+
T Consensus        20 ~il~~lf~~~~~s~~~~a~~l~iS~sTl~R~--------ik~l~~~L~~~~l~i   65 (87)
T pfam05043        20 QLLKFLFFHEFFSLTSLAQKLFISESTLYRL--------IKKLNKLLKEFDLSI   65 (87)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH--------HHHHHHHHHHCCEEE
T ss_conf             9999998189998999999978899999999--------999999999859688


No 495
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852    Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose .     Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=28.54  E-value=32  Score=14.99  Aligned_cols=27  Identities=19%  Similarity=0.487  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHCCCHH-----HHHHHHHHHHHH
Q ss_conf             665433310001566-----899999999999
Q gi|254781218|r   10 SLKSLQEYTLIITPE-----IRQYWKDVGTRI   36 (205)
Q Consensus        10 ~~~~~~~~~~~~~~~-----~~~~~~~iG~ri   36 (205)
                      -+.++++..+.++.|     --+||++||.+.
T Consensus       224 D~aaI~~Agl~lGvDPLGGa~v~YW~~Ia~~y  255 (553)
T TIGR01132       224 DLAAIRKAGLRLGVDPLGGAGVDYWKEIAEKY  255 (553)
T ss_pred             EHHHHHHCCCEECCCCCCCCCHHHHHHHHHHH
T ss_conf             06678658977723467778736789999875


No 496
>pfam00165 HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.
Probab=28.45  E-value=42  Score=14.26  Aligned_cols=36  Identities=11%  Similarity=-0.078  Sum_probs=0.0

Q ss_pred             HCCCCHHHHHHHHCC-CHHHHHHHHCCCCCCCHHHHH
Q ss_conf             859988999998489-999999887799888999999
Q gi|254781218|r   42 ANNKTQKEMAIGANQ-LESAVNLFENGMCSTSIRYAL   77 (205)
Q Consensus        42 ~~gltQ~elA~~~gi-s~~~is~~E~G~~~psi~~l~   77 (205)
                      ..+|+-.++|..+|. ++++.++.-+-....+.....
T Consensus         6 ~~~~~i~~IA~~~g~~s~~~f~r~fk~~~G~tP~~~r   42 (43)
T pfam00165         6 STNWTIADIAEELGFSSQSYFSRLFKKYTGVTPSQYR   42 (43)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHC
T ss_conf             0899799999996899768999999998890989982


No 497
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=28.28  E-value=38  Score=14.51  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHCCCH
Q ss_conf             889999999999828999
Q gi|254781218|r   70 STSIRYALYLRNEYEISF   87 (205)
Q Consensus        70 ~psi~~l~~la~~~~vs~   87 (205)
                      .|++..|+++|..++|++
T Consensus        87 ~~Di~aLlRlc~v~niP~  104 (115)
T cd01422          87 EPDVKALLRLCDVYNIPL  104 (115)
T ss_pred             CCCHHHHHHHHHHCCCCC
T ss_conf             702999999998619612


No 498
>PRK04435 hypothetical protein; Provisional
Probab=28.22  E-value=33  Score=14.89  Aligned_cols=28  Identities=25%  Similarity=0.307  Sum_probs=0.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9999972983899999977999999997
Q gi|254781218|r  119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY  146 (205)
Q Consensus       119 k~lR~~~glsq~elA~~lgis~~tis~~  146 (205)
                      +-+...+-.+..|.++.+|+|++++.+|
T Consensus        26 ~LL~~g~~~~i~EAvk~vGISRSafYKY   53 (146)
T PRK04435         26 ELLKSGKVKSITEAVKQVGISRSAFYKY   53 (146)
T ss_pred             HHHHCCCCCCHHHHHHHHCCCHHHEECC
T ss_conf             9997389774999999839652101123


No 499
>pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages.
Probab=28.19  E-value=43  Score=14.23  Aligned_cols=27  Identities=4%  Similarity=0.201  Sum_probs=0.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf             389999997799999999741488999
Q gi|254781218|r  128 SQIEFGKLLGMPNSTLSNYEQGRTIPE  154 (205)
Q Consensus       128 sq~elA~~lgis~~tis~~E~g~~~Ps  154 (205)
                      |..|+|+.+.+|+.+++-|-.....|.
T Consensus        16 TidElad~f~vs~~svs~WIknGk~~~   42 (134)
T pfam04936        16 TIDEIADMFDLSPHSIAGWIKNGKANK   42 (134)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHCCCCCC
T ss_conf             399999997457014478886488862


No 500
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=28.07  E-value=36  Score=14.65  Aligned_cols=18  Identities=28%  Similarity=0.243  Sum_probs=0.0

Q ss_pred             CHHHHHHHH-----CCCHHHHHH
Q ss_conf             889999984-----899999998
Q gi|254781218|r   46 TQKEMAIGA-----NQLESAVNL   63 (205)
Q Consensus        46 tQ~elA~~~-----gis~~~is~   63 (205)
                      ||+||...+     .+++++||+
T Consensus        21 tQ~eL~~~L~~~G~~vTQATlSR   43 (70)
T pfam01316        21 TQEELVALLKAEGINVTQATVSR   43 (70)
T ss_pred             CHHHHHHHHHHCCCCEEEHHHHH
T ss_conf             99999999997698564178887


Done!