Query         gi|254780693|ref|YP_003065106.1| transcriptional regulator protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 235
No_of_seqs    120 out of 7465
Neff          9.5 
Searched_HMMs 39220
Date          Mon May 30 02:40:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780693.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK13870 transcriptional regul 100.0 3.1E-36 7.8E-41  277.5  25.2  215   12-234    16-234 (234)
  2 PRK10188 DNA-binding transcrip 100.0 1.1E-35 2.9E-40  273.5  23.0  219    8-234    17-240 (240)
  3 TIGR03541 reg_near_HchA LuxR f 100.0 1.2E-34 3.1E-39  266.1  25.3  222    7-234    10-232 (232)
  4 TIGR03020 EpsA transcriptional  99.9 2.6E-19 6.7E-24  156.8  19.6  214    9-230    17-247 (247)
  5 PRK04841 transcriptional regul  99.8 7.7E-19   2E-23  153.5   8.5   60  172-231   837-896 (903)
  6 PRK09483 response regulator; P  99.8 5.8E-18 1.5E-22  147.2   9.7   66  169-234   144-209 (216)
  7 PRK09935 transcriptional regul  99.7 1.8E-17 4.5E-22  143.8   9.6   63  172-234   148-210 (210)
  8 PRK10100 DNA-binding transcrip  99.7 2.9E-17 7.3E-22  142.3  10.4   62  170-231   152-213 (216)
  9 PRK10840 transcriptional regul  99.7 4.6E-17 1.2E-21  140.8  10.6   64  171-234   148-211 (216)
 10 PRK10651 transcriptional regul  99.7 5.7E-17 1.5E-21  140.1  10.7   63  171-233   153-215 (216)
 11 PRK09390 fixJ response regulat  99.7 3.4E-17 8.7E-22  141.7   8.7   63  172-234   140-202 (202)
 12 COG2197 CitB Response regulato  99.7 3.7E-17 9.5E-22  141.4   8.8   63  172-234   147-209 (211)
 13 PRK09958 DNA-binding transcrip  99.7 1.1E-16 2.9E-21  138.0  10.5   63  171-233   141-203 (204)
 14 PRK10403 transcriptional regul  99.7 1.1E-16 2.7E-21  138.2   9.0   62  170-231   150-211 (215)
 15 PRK10360 DNA-binding transcrip  99.7 2.1E-16 5.4E-21  136.1   9.0   62  171-233   135-196 (196)
 16 COG2909 MalT ATP-dependent tra  99.7 6.4E-17 1.6E-21  139.8   6.1   62  173-234   831-892 (894)
 17 pfam00196 GerE Bacterial regul  99.6 4.2E-15 1.1E-19  126.8   7.5   57  172-228     2-58  (58)
 18 cd06170 LuxR_C_like C-terminal  99.6 1.1E-14 2.9E-19  123.7   7.9   57  174-230     1-57  (57)
 19 smart00421 HTH_LUXR helix_turn  99.5 3.2E-14 8.1E-19  120.6   7.3   57  172-228     2-58  (58)
 20 PRK11475 DNA-binding transcrip  99.5 2.7E-13 6.9E-18  114.0  10.8   62  170-231   131-192 (205)
 21 COG4566 TtrR Response regulato  99.4 2.4E-12 6.2E-17  107.1   8.8   63  171-233   140-202 (202)
 22 COG2771 CsgD DNA-binding HTH d  99.4 2.4E-12   6E-17  107.2   8.4   63  172-234     3-65  (65)
 23 pfam03472 Autoind_bind Autoind  99.3 2.6E-10 6.7E-15   92.7  15.4  129   13-147     1-129 (146)
 24 TIGR02985 Sig70_bacteroi1 RNA   98.5 3.7E-07 9.5E-12   70.2   5.8   46  172-217   118-164 (167)
 25 PRK06930 positive control sigm  98.2 3.2E-06 8.2E-11   63.5   5.7   46  173-218   114-160 (170)
 26 pfam07638 Sigma70_ECF ECF sigm  98.2 5.4E-06 1.4E-10   61.9   6.2   45  173-217   135-180 (185)
 27 PRK12523 RNA polymerase sigma   98.2 5.6E-06 1.4E-10   61.8   6.3   45  172-216   118-163 (172)
 28 TIGR02937 sigma70-ECF RNA poly  98.1 8.4E-06 2.1E-10   60.5   6.1   45  173-217   114-159 (162)
 29 PRK08295 RNA polymerase factor  98.1 4.6E-05 1.2E-09   55.3   9.6   45  173-217   155-199 (209)
 30 PRK12527 RNA polymerase sigma   98.1   1E-05 2.6E-10   59.9   6.2   46  173-218   105-151 (159)
 31 PRK07037 extracytoplasmic-func  98.1   1E-05 2.6E-10   59.9   6.1   45  172-216   122-167 (183)
 32 PRK12525 RNA polymerase sigma   98.1 1.2E-05   3E-10   59.5   6.2   44  173-216   118-162 (168)
 33 PRK09646 RNA polymerase sigma   98.0 1.1E-05 2.7E-10   59.8   5.8   45  172-216   141-186 (194)
 34 PRK09637 RNA polymerase sigma   98.0 1.6E-05 4.2E-10   58.5   6.2   46  172-217   105-151 (181)
 35 PRK11922 RNA polymerase sigma   98.0 1.6E-05 4.1E-10   58.5   6.2   44  173-216   149-193 (231)
 36 PRK13919 putative RNA polymera  98.0   2E-05 5.1E-10   57.9   6.3   45  173-217   136-181 (187)
 37 PRK09645 RNA polymerase sigma   98.0 1.9E-05 4.9E-10   58.0   6.2   46  172-217   115-161 (171)
 38 PRK09047 RNA polymerase factor  98.0 1.8E-05 4.7E-10   58.1   6.0   45  173-217   106-151 (161)
 39 PRK12519 RNA polymerase sigma   98.0   2E-05   5E-10   57.9   5.9   46  172-217   140-186 (194)
 40 PRK09651 RNA polymerase sigma   98.0 2.2E-05 5.7E-10   57.5   6.2   45  172-216   118-163 (172)
 41 PRK09652 RNA polymerase sigma   98.0 2.1E-05 5.5E-10   57.6   6.0   45  173-217   137-182 (192)
 42 PRK09638 RNA polymerase sigma   97.9 2.5E-05 6.4E-10   57.2   6.2   46  172-217   126-172 (177)
 43 PRK09639 RNA polymerase sigma   97.9 2.3E-05 5.9E-10   57.4   6.0   45  173-217   112-156 (166)
 44 PRK12515 RNA polymerase sigma   97.9 3.8E-05 9.7E-10   55.9   7.0   57  173-233   131-188 (189)
 45 PRK12526 RNA polymerase sigma   97.9 2.8E-05 7.2E-10   56.8   6.3   45  173-217   153-198 (206)
 46 PRK05602 RNA polymerase sigma   97.9 2.6E-05 6.7E-10   57.0   6.1   46  172-217   127-173 (186)
 47 PRK12524 RNA polymerase sigma   97.9 2.7E-05 6.8E-10   56.9   6.1   46  172-217   135-181 (196)
 48 PRK12537 RNA polymerase sigma   97.9 2.6E-05 6.7E-10   57.0   6.0   45  173-217   135-180 (184)
 49 pfam08281 Sigma70_r4_2 Sigma-7  97.9 2.3E-05 5.8E-10   57.4   5.7   45  172-216     9-54  (54)
 50 PRK12516 RNA polymerase sigma   97.9   3E-05 7.6E-10   56.6   6.1   45  173-217   119-164 (190)
 51 PRK12529 RNA polymerase sigma   97.9 3.1E-05   8E-10   56.5   6.2   44  172-215   126-170 (178)
 52 PRK12512 RNA polymerase sigma   97.9 3.2E-05 8.2E-10   56.4   6.2   46  173-218   131-177 (184)
 53 PRK12541 RNA polymerase sigma   97.9 3.3E-05 8.5E-10   56.3   6.2   45  173-217   112-157 (161)
 54 PRK12543 RNA polymerase sigma   97.9 3.6E-05 9.1E-10   56.1   6.3   44  173-216   129-173 (190)
 55 PRK12514 RNA polymerase sigma   97.9 3.3E-05 8.4E-10   56.3   6.0   45  173-217   129-174 (179)
 56 cd06171 Sigma70_r4 Sigma70, re  97.9 3.7E-05 9.4E-10   55.9   6.2   46  172-217     9-55  (55)
 57 PRK09641 RNA polymerase sigma   97.9 3.9E-05   1E-09   55.8   6.0   45  173-217   136-181 (187)
 58 PRK09643 RNA polymerase sigma   97.9 4.4E-05 1.1E-09   55.4   6.2   45  173-217   131-176 (197)
 59 PRK12547 RNA polymerase sigma   97.9 4.5E-05 1.1E-09   55.3   6.2   45  173-217   112-157 (164)
 60 PRK12528 RNA polymerase sigma   97.8 4.7E-05 1.2E-09   55.2   6.2   45  172-216   118-163 (167)
 61 PRK12534 RNA polymerase sigma   97.8 4.8E-05 1.2E-09   55.1   6.2   45  173-217   137-182 (187)
 62 PRK12538 RNA polymerase sigma   97.8 4.8E-05 1.2E-09   55.1   6.2   45  173-217   171-216 (233)
 63 PRK12517 RNA polymerase sigma   97.8 5.7E-05 1.5E-09   54.6   6.3   45  173-217   128-173 (188)
 64 PRK12513 RNA polymerase sigma   97.8 5.7E-05 1.5E-09   54.6   6.2   45  173-217   139-184 (194)
 65 PRK12542 RNA polymerase sigma   97.8 5.4E-05 1.4E-09   54.8   6.1   44  173-216   122-166 (185)
 66 PRK11924 RNA polymerase sigma   97.8 5.5E-05 1.4E-09   54.7   6.1   45  173-217   125-170 (180)
 67 PRK09648 RNA polymerase sigma   97.8   6E-05 1.5E-09   54.4   6.3   46  172-217   136-182 (187)
 68 PRK11923 algU RNA polymerase s  97.8   6E-05 1.5E-09   54.4   6.3   45  173-217   138-183 (193)
 69 PRK09647 RNA polymerase sigma   97.8 6.1E-05 1.6E-09   54.4   6.2   46  172-217   156-202 (222)
 70 PRK12531 RNA polymerase sigma   97.8 6.6E-05 1.7E-09   54.2   6.2   46  172-217   140-186 (194)
 71 PRK06811 RNA polymerase factor  97.8 7.2E-05 1.8E-09   53.9   6.3   45  172-216   127-172 (185)
 72 PRK12539 RNA polymerase sigma   97.8 7.9E-05   2E-09   53.6   6.2   46  172-217   130-176 (184)
 73 PRK12533 RNA polymerase sigma   97.8   8E-05   2E-09   53.6   6.2   45  173-217   137-182 (217)
 74 PRK12522 RNA polymerase sigma   97.8 8.5E-05 2.2E-09   53.4   6.3   45  173-217   119-164 (173)
 75 PRK09644 RNA polymerase sigma   97.8 7.3E-05 1.9E-09   53.8   5.9   45  173-217   108-153 (165)
 76 PRK12520 RNA polymerase sigma   97.7 7.8E-05   2E-09   53.6   5.9   45  173-217   131-176 (191)
 77 PRK12536 RNA polymerase sigma   97.7 9.4E-05 2.4E-09   53.1   6.3   45  173-217   126-171 (178)
 78 PRK12546 RNA polymerase sigma   97.7 9.1E-05 2.3E-09   53.1   6.2   45  173-217   113-158 (188)
 79 PRK12511 RNA polymerase sigma   97.7 3.6E-05 9.1E-10   56.0   4.0   45  173-217   111-156 (182)
 80 PRK12518 RNA polymerase sigma   97.7 9.8E-05 2.5E-09   52.9   6.2   45  173-217   120-165 (175)
 81 PRK09640 RNA polymerase sigma   97.7 0.00012 2.9E-09   52.4   6.2   45  173-217   134-179 (188)
 82 PRK12540 RNA polymerase sigma   97.7 0.00011 2.9E-09   52.4   6.2   45  173-217   111-156 (181)
 83 PRK09415 RNA polymerase factor  97.7 0.00012 3.1E-09   52.3   6.3   45  173-217   127-172 (177)
 84 PRK06759 RNA polymerase factor  97.7 0.00013 3.3E-09   52.0   6.4   45  173-217   106-151 (154)
 85 PRK09642 RNA polymerase sigma   97.7 0.00014 3.6E-09   51.8   6.2   45  173-217   106-151 (160)
 86 PRK12535 RNA polymerase sigma   97.6 0.00014 3.7E-09   51.7   6.1   45  173-217   132-177 (195)
 87 PRK12532 RNA polymerase sigma   97.6 0.00018 4.6E-09   51.0   6.2   45  173-217   136-181 (195)
 88 PRK09649 RNA polymerase sigma   97.6 0.00019 4.8E-09   50.9   6.3   46  173-218   130-176 (185)
 89 PRK12544 RNA polymerase sigma   97.6 0.00018 4.6E-09   51.0   6.1   45  173-217   149-194 (207)
 90 PRK12530 RNA polymerase sigma   97.6 0.00025 6.5E-09   50.0   6.3   45  173-217   136-181 (191)
 91 COG3413 Predicted DNA binding   97.6  0.0009 2.3E-08   46.1   9.1   45  172-216   154-206 (215)
 92 COG1595 RpoE DNA-directed RNA   97.5 0.00028 7.1E-09   49.7   6.1   45  173-217   127-172 (182)
 93 pfam04545 Sigma70_r4 Sigma-70,  97.4  0.0003 7.7E-09   49.4   5.6   46  172-217     3-49  (50)
 94 pfam04967 HTH_10 HTH DNA bindi  97.4 0.00064 1.6E-08   47.1   6.3   43  174-216     1-51  (53)
 95 PRK12545 RNA polymerase sigma   97.2  0.0057 1.4E-07   40.4  10.1   45  173-217   139-184 (201)
 96 PRK09636 RNA polymerase sigma   97.2  0.0042 1.1E-07   41.3   9.0   49  172-220   110-159 (289)
 97 PRK13558 bacterio-opsin activa  97.1 0.00088 2.2E-08   46.1   5.2   44  173-216   616-667 (674)
 98 TIGR02983 SigE-fam_strep RNA p  97.1 0.00046 1.2E-08   48.2   3.7   45  173-218   113-159 (165)
 99 PRK08583 RNA polymerase sigma   97.1  0.0015 3.8E-08   44.5   6.0   46  172-217   204-250 (257)
100 PRK07408 RNA polymerase sigma   97.0  0.0019   5E-08   43.7   6.1   46  172-217   202-248 (256)
101 TIGR02999 Sig-70_X6 RNA polyme  97.0  0.0015 3.9E-08   44.4   5.5   46  173-218   145-191 (194)
102 PRK07670 RNA polymerase sigma   97.0  0.0084 2.1E-07   39.2   8.9   45  173-217   197-242 (250)
103 PRK07122 RNA polymerase sigma   97.0  0.0025 6.3E-08   42.9   6.0   45  173-217   214-259 (263)
104 PRK12427 flagellar biosynthesi  96.9  0.0022 5.7E-08   43.2   5.7   47  172-218   180-227 (229)
105 TIGR01884 cas_HTH CRISPR locus  96.8   0.003 7.7E-08   42.3   5.7   47  169-215   162-211 (231)
106 PRK08215 sporulation sigma fac  96.8  0.0037 9.4E-08   41.7   6.0   45  173-217   209-254 (257)
107 TIGR02952 Sig70_famx2 RNA poly  96.8  0.0066 1.7E-07   39.9   7.2   45  173-217   123-168 (171)
108 PRK05572 sporulation sigma fac  96.8  0.0038 9.8E-08   41.6   6.0   45  173-217   201-246 (251)
109 PRK07500 rpoH2 RNA polymerase   96.8   0.018 4.5E-07   36.8   9.1   45  173-217   227-274 (289)
110 PRK06288 RNA polymerase sigma   96.7  0.0041   1E-07   41.4   5.7   45  173-217   208-253 (261)
111 PRK08301 sporulation sigma fac  96.7  0.0041   1E-07   41.4   5.7   45  172-216   182-231 (239)
112 PRK05803 sporulation sigma fac  96.7  0.0048 1.2E-07   40.9   5.7   46  172-217   173-223 (228)
113 PRK06596 RNA polymerase factor  96.7   0.027 6.8E-07   35.6   9.5   45  173-217   230-277 (284)
114 PRK09635 sigI RNA polymerase s  96.7   0.024 6.2E-07   35.9   9.2   48  173-220   118-166 (290)
115 PRK06986 fliA flagellar biosyn  96.7  0.0058 1.5E-07   40.3   6.0   45  173-217   183-228 (234)
116 PRK10336 DNA-binding transcrip  96.6  0.0048 1.2E-07   40.9   5.1   48  172-219   148-204 (219)
117 PRK03975 tfx putative transcri  96.6  0.0034 8.8E-08   41.9   4.4   56  173-228     4-59  (139)
118 PRK08241 RNA polymerase factor  96.6   0.017 4.3E-07   37.0   7.9   46  173-218   156-202 (341)
119 PRK05911 RNA polymerase sigma   96.4   0.008   2E-07   39.3   5.5   46  172-217   204-250 (257)
120 PRK12423 LexA repressor; Provi  96.3  0.0064 1.6E-07   40.0   4.6   43  173-215     3-53  (202)
121 PRK00215 LexA repressor; Valid  96.3  0.0084 2.1E-07   39.2   5.2   42  174-215     2-51  (204)
122 PRK05949 RNA polymerase sigma   96.3   0.054 1.4E-06   33.4   9.4   47  173-219   266-317 (327)
123 PRK05657 RNA polymerase sigma   96.3   0.048 1.2E-06   33.8   9.0   48  173-220   265-317 (328)
124 pfam01726 LexA_DNA_bind LexA D  96.3  0.0098 2.5E-07   38.7   5.4   44  172-215     2-53  (65)
125 pfam02001 DUF134 Protein of un  96.3   0.012   3E-07   38.1   5.8   45  172-216    35-80  (100)
126 PRK07921 RNA polymerase sigma   96.2   0.091 2.3E-06   31.8  10.0   51  173-223   258-313 (320)
127 PRK13413 mpi multiple promoter  96.1   0.017 4.4E-07   36.9   5.8   41  174-214   158-198 (200)
128 PRK05901 RNA polymerase sigma   96.1   0.024 6.1E-07   35.9   6.4   52  173-224   335-391 (398)
129 PRK09210 RNA polymerase sigma   96.0    0.11 2.9E-06   31.1   9.7   52  173-224   306-362 (368)
130 PRK07598 RNA polymerase sigma   96.0   0.031   8E-07   35.1   6.8   53  173-225   345-402 (410)
131 PRK07406 RNA polymerase sigma   95.9   0.034 8.6E-07   34.8   6.7   54  172-225   322-380 (385)
132 COG1191 FliA DNA-directed RNA   95.9   0.023 5.8E-07   36.1   5.7   45  173-217   196-241 (247)
133 PRK04217 hypothetical protein;  95.8   0.027 6.8E-07   35.5   5.7   45  172-216    41-86  (110)
134 PRK07405 RNA polymerase sigma   95.8   0.028   7E-07   35.5   5.8   47  172-218   256-307 (318)
135 pfam09862 DUF2089 Protein of u  95.7   0.091 2.3E-06   31.8   8.2   64  171-234    31-103 (113)
136 TIGR02984 Sig-70_plancto1 RNA   95.7    0.12 3.1E-06   30.9   8.7   45  173-217   141-186 (190)
137 PRK10710 DNA-binding transcrip  95.6   0.028 7.2E-07   35.4   5.3   48  172-219   159-215 (240)
138 TIGR02997 Sig70-cyanoRpoD RNA   95.5    0.12 3.1E-06   30.8   8.3   44  173-216   287-335 (336)
139 pfam08279 HTH_11 HTH domain. T  95.5   0.035 8.8E-07   34.8   5.3   41  177-218     1-44  (55)
140 COG0856 Orotate phosphoribosyl  95.2   0.033 8.5E-07   34.9   4.4   41  180-220    10-50  (203)
141 cd00090 HTH_ARSR Arsenical Res  95.2   0.059 1.5E-06   33.1   5.7   41  174-214     4-46  (78)
142 TIGR02954 Sig70_famx3 RNA poly  95.1   0.015 3.7E-07   37.4   2.4   37  181-218   132-168 (173)
143 COG1342 Predicted DNA-binding   95.1   0.056 1.4E-06   33.2   5.4   46  171-216    31-77  (99)
144 TIGR02479 FliA_WhiG RNA polyme  95.0   0.065 1.7E-06   32.8   5.4   47  172-218   177-224 (227)
145 PRK00118 putative DNA-binding   94.9   0.099 2.5E-06   31.5   6.1   45  173-217    17-62  (105)
146 PRK13719 conjugal transfer tra  94.7    0.04   1E-06   34.3   3.8   60  175-234   147-206 (220)
147 pfam04297 UPF0122 Putative hel  94.7    0.11 2.8E-06   31.2   6.0   44  173-216    17-61  (101)
148 TIGR02980 SigBFG RNA polymeras  94.6   0.022 5.7E-07   36.1   2.3   45  173-217   180-225 (229)
149 COG0568 RpoD DNA-directed RNA   94.6   0.099 2.5E-06   31.5   5.5   50  174-223   280-335 (342)
150 cd00569 HTH_Hin_like Helix-tur  94.5   0.063 1.6E-06   32.9   4.4   38  172-209     4-42  (42)
151 TIGR02989 Sig-70_gvs1 RNA poly  94.4     0.1 2.6E-06   31.4   5.4   45  173-217   115-160 (163)
152 cd00383 trans_reg_C Effector d  94.4   0.093 2.4E-06   31.7   5.1   49  172-220    22-79  (95)
153 TIGR02960 SigX5 RNA polymerase  94.4   0.087 2.2E-06   31.9   4.8   47  173-219   143-190 (329)
154 TIGR02959 SigZ RNA polymerase   94.3   0.079   2E-06   32.2   4.5   44  173-216   100-144 (170)
155 COG3415 Transposase and inacti  94.2    0.11 2.7E-06   31.3   5.0   41  174-214     7-47  (138)
156 PRK10766 DNA-binding transcrip  94.2    0.14 3.6E-06   30.4   5.6   46  173-218   162-216 (224)
157 pfam00486 Trans_reg_C Transcri  94.2    0.12 2.9E-06   31.0   5.1   48  172-219     4-60  (77)
158 COG3355 Predicted transcriptio  94.1    0.16 4.2E-06   29.9   5.9   43  173-215    24-69  (126)
159 PRK09468 ompR osmolarity respo  94.1    0.11 2.8E-06   31.1   5.0   47  173-219   161-216 (239)
160 COG1710 Uncharacterized protei  94.1    0.09 2.3E-06   31.8   4.5   42  174-215    94-136 (139)
161 TIGR02859 spore_sigH RNA polym  94.0    0.16 4.1E-06   30.0   5.6   90  118-217   105-194 (198)
162 COG1318 Predicted transcriptio  93.9   0.035 8.9E-07   34.7   2.1   37  181-217    54-90  (182)
163 pfam02796 HTH_7 Helix-turn-hel  93.8    0.12 3.2E-06   30.8   4.7   39  172-210     4-43  (45)
164 smart00862 Trans_reg_C Transcr  93.7    0.15 3.9E-06   30.2   5.1   48  172-219     4-61  (78)
165 PRK09836 DNA-binding transcrip  93.7    0.15 3.7E-06   30.3   4.9   48  173-220   150-206 (226)
166 PRK11517 transcriptional regul  93.7    0.15 3.9E-06   30.2   5.0   47  173-219   147-202 (223)
167 PRK10701 DNA-binding transcrip  93.7    0.13 3.4E-06   30.6   4.7   47  173-219   161-216 (240)
168 PRK06704 RNA polymerase factor  93.6    0.15 3.8E-06   30.2   4.9   58  173-230   116-185 (228)
169 pfam03444 DUF293 Domain of unk  93.6    0.13 3.2E-06   30.7   4.5   45  173-218     1-52  (79)
170 PRK10643 DNA-binding transcrip  93.6    0.17 4.4E-06   29.8   5.2   47  172-218   148-203 (222)
171 PRK10955 DNA-binding transcrip  93.5    0.15 3.8E-06   30.2   4.7   47  173-219   156-211 (232)
172 smart00344 HTH_ASNC helix_turn  93.4    0.22 5.6E-06   29.1   5.4   48  176-224     3-52  (108)
173 COG2390 DeoR Transcriptional r  93.3    0.11 2.9E-06   31.1   3.9   37  198-234   261-303 (321)
174 PRK11083 DNA-binding response   93.3     0.2 5.2E-06   29.3   5.2   48  173-220   155-211 (229)
175 COG5625 Predicted transcriptio  93.1   0.094 2.4E-06   31.7   3.2   43  173-215    18-63  (113)
176 TIGR02941 Sigma_B RNA polymera  93.1    0.12 3.1E-06   30.9   3.7   45  173-217   206-251 (256)
177 PRK02277 orotate phosphoribosy  93.0   0.099 2.5E-06   31.5   3.2   30  182-211    12-41  (201)
178 PRK10161 transcriptional regul  93.0    0.23 5.7E-06   29.0   5.0   47  173-219   154-209 (229)
179 TIGR03001 Sig-70_gmx1 RNA poly  92.9     0.2 5.1E-06   29.3   4.6   56  172-227   165-221 (249)
180 PRK09191 two-component respons  92.8     0.3 7.6E-06   28.1   5.4   46  173-218    88-134 (261)
181 CHL00148 orf27 Ycf27; Reviewed  92.8    0.25 6.3E-06   28.7   5.0   47  173-219   161-218 (240)
182 PRK11557 putative DNA-binding   92.8    0.33 8.4E-06   27.8   5.6   19   20-38     50-68  (282)
183 COG0745 OmpR Response regulato  92.7    0.21 5.3E-06   29.2   4.5   48  173-220   153-209 (229)
184 TIGR02846 spore_sigmaK RNA pol  92.7    0.17 4.2E-06   29.9   4.0   45  173-217   175-224 (228)
185 TIGR00721 tfx DNA-binding prot  92.6    0.23 5.9E-06   28.8   4.7   46  172-217     5-50  (142)
186 pfam01978 TrmB Sugar-specific   92.5    0.46 1.2E-05   26.7   6.0   44  172-215     4-49  (68)
187 PRK11886 biotin--protein ligas  92.5    0.34 8.6E-06   27.7   5.3   37    4-40     17-54  (319)
188 pfam01371 Trp_repressor Trp re  92.4    0.22 5.5E-06   29.1   4.3   38  173-210    26-71  (88)
189 COG1356 tfx Transcriptional re  92.4   0.082 2.1E-06   32.1   2.1   52  171-222     6-57  (143)
190 COG3398 Uncharacterized protei  92.4    0.27 6.9E-06   28.4   4.7   35  179-213   177-213 (240)
191 PRK10816 DNA-binding transcrip  92.3     0.2   5E-06   29.4   3.9   47  173-219   149-204 (223)
192 pfam03811 Ins_element1 Inserti  92.2    0.19 4.8E-06   29.5   3.7   36  177-212    52-87  (88)
193 PRK11337 DNA-binding transcrip  92.0    0.47 1.2E-05   26.7   5.6   18   20-37     63-80  (293)
194 COG1737 RpiR Transcriptional r  92.0    0.45 1.1E-05   26.8   5.4   19   20-38     52-70  (281)
195 PRK10529 DNA-binding transcrip  91.9    0.34 8.6E-06   27.7   4.7   47  173-219   151-206 (225)
196 pfam01022 HTH_5 Bacterial regu  91.9    0.55 1.4E-05   26.2   5.8   38  177-214     3-41  (47)
197 smart00347 HTH_MARR helix_turn  91.6    0.55 1.4E-05   26.2   5.5   45  171-215     5-51  (101)
198 COG1522 Lrp Transcriptional re  91.3    0.68 1.7E-05   25.5   5.8   43  172-214     4-48  (154)
199 pfam01047 MarR MarR family. Th  91.1    0.69 1.8E-05   25.5   5.7   42  174-215     1-44  (59)
200 COG3877 Uncharacterized protei  91.0    0.56 1.4E-05   26.1   5.2   51  169-219    37-88  (122)
201 TIGR02957 SigX4 RNA polymerase  90.6     1.3 3.4E-05   23.5   8.7   48  173-220   109-158 (287)
202 PRK11179 DNA-binding transcrip  90.6    0.99 2.5E-05   24.4   6.0   40  174-213     7-48  (153)
203 COG2865 Predicted transcriptio  90.5    0.53 1.4E-05   26.3   4.6   42  173-214   399-442 (467)
204 PRK11173 two-component respons  90.4    0.59 1.5E-05   26.0   4.8   48  173-220   160-216 (237)
205 TIGR02233 Myxo_sigma_rel Myxoc  90.4    0.53 1.4E-05   26.3   4.5   56  172-227    23-79  (106)
206 COG2522 Predicted transcriptio  90.3    0.54 1.4E-05   26.3   4.5   35  177-211    11-45  (119)
207 pfam03965 Pencillinase_R Penic  90.2    0.78   2E-05   25.1   5.2   13  173-185   100-112 (115)
208 pfam08461 HTH_12 Ribonuclease   90.0    0.56 1.4E-05   26.2   4.4   34  180-213     2-43  (66)
209 pfam00126 HTH_1 Bacterial regu  89.9    0.97 2.5E-05   24.4   5.6   43  177-219     2-44  (60)
210 PRK05658 RNA polymerase sigma   89.7     1.6   4E-05   23.0  10.3   52  173-224   557-613 (620)
211 PRK11242 DNA-binding transcrip  89.6     1.1 2.8E-05   24.1   5.6   19   13-31     28-46  (292)
212 PRK11074 putative DNA-binding   89.5     1.4 3.5E-05   23.3   6.1   14   17-30     33-46  (300)
213 PRK13856 two-component respons  89.5    0.31 7.9E-06   28.0   2.8   48  172-219   154-210 (241)
214 pfam01418 HTH_6 Helix-turn-hel  89.2     1.1 2.8E-05   24.0   5.4   49  172-224    12-66  (106)
215 COG1654 BirA Biotin operon rep  89.0    0.86 2.2E-05   24.8   4.7   39  175-214     5-45  (79)
216 PRK12683 transcriptional regul  88.7     1.6 4.1E-05   22.9   6.0   26  173-198   279-304 (308)
217 smart00418 HTH_ARSR helix_turn  88.7    0.88 2.3E-05   24.7   4.6   34  181-214     2-36  (66)
218 COG1846 MarR Transcriptional r  88.6     1.2 3.1E-05   23.8   5.3   42  174-215    20-63  (126)
219 COG5484 Uncharacterized conser  88.6    0.79   2E-05   25.1   4.3   19  172-190   152-170 (279)
220 pfam09339 HTH_IclR IclR helix-  88.3     1.5 3.9E-05   23.0   5.6   38  177-214     4-44  (52)
221 PRK12679 cbl transcriptional r  88.2       2   5E-05   22.3   6.2   25  174-198   280-304 (316)
222 TIGR02702 SufR_cyano iron-sulf  88.2    0.67 1.7E-05   25.6   3.7   28  185-212    11-39  (215)
223 COG1321 TroR Mn-dependent tran  87.9     1.4 3.5E-05   23.3   5.2   39  174-212     4-48  (154)
224 CHL00180 rbcR LysR transcripti  87.9     1.9 4.8E-05   22.4   5.9   19   13-31     32-50  (307)
225 PRK03573 transcriptional regul  87.7     2.1 5.4E-05   22.0   8.3   44  172-215    27-73  (144)
226 PRK11302 DNA-binding transcrip  87.5     1.7 4.4E-05   22.6   5.5   21   19-39     49-69  (284)
227 PRK10341 DNA-binding transcrip  87.5     1.8 4.7E-05   22.5   5.7   17   15-31     36-52  (312)
228 pfam06056 Terminase_5 Putative  87.2    0.94 2.4E-05   24.5   4.0   31  181-211     6-36  (58)
229 PRK12684 transcriptional regul  87.1     2.2 5.7E-05   21.8   5.9   25  174-198   280-304 (313)
230 cd04762 HTH_MerR-trunc Helix-T  87.1    0.61 1.6E-05   25.9   3.0   23  189-211     1-23  (49)
231 PRK11139 DNA-binding transcrip  86.5     2.4 6.2E-05   21.6   5.9   12   18-29     38-49  (295)
232 PRK10046 dpiA two-component re  86.4     1.1 2.7E-05   24.1   4.0   38  177-214   166-203 (225)
233 pfam11268 DUF3071 Protein of u  86.1     1.9 4.9E-05   22.4   5.1   42  170-213    52-93  (169)
234 PRK11013 DNA-binding transcrip  86.1     2.5 6.5E-05   21.5   6.0   17   15-31     33-49  (309)
235 TIGR02950 SigM_subfam RNA poly  86.0    0.72 1.8E-05   25.3   2.9   45  174-218   114-159 (162)
236 pfam07750 GcrA GcrA cell cycle  86.0    0.83 2.1E-05   24.9   3.2   19  120-140   120-138 (162)
237 PRK09801 transcriptional activ  86.0     2.6 6.6E-05   21.4   6.1   13  174-186   281-293 (310)
238 pfam07900 DUF1670 Protein of u  85.9     1.4 3.6E-05   23.3   4.4   30  180-209   189-218 (220)
239 COG1497 Predicted transcriptio  85.8     1.6 4.2E-05   22.8   4.6   15  198-212   231-245 (260)
240 PRK11151 DNA-binding transcrip  85.7     2.7 6.8E-05   21.3   5.9   17   15-31     30-46  (305)
241 pfam01527 Transposase_8 Transp  85.6     1.7 4.4E-05   22.7   4.7   38  180-217    14-52  (75)
242 PRK01381 Trp operon repressor;  85.3    0.99 2.5E-05   24.4   3.3   35  173-207    32-74  (99)
243 PRK09791 putative DNA-binding   85.2     2.8 7.1E-05   21.2   6.1   18   14-31     33-50  (302)
244 smart00346 HTH_ICLR helix_turn  84.9     2.9 7.3E-05   21.1   5.9   57  176-232     5-69  (91)
245 COG2739 Uncharacterized protei  84.9     2.5 6.3E-05   21.5   5.2   44  173-216    17-61  (105)
246 pfam07374 DUF1492 Protein of u  84.8     1.5 3.9E-05   23.0   4.1   42  176-217    58-100 (100)
247 PRK12680 transcriptional regul  84.4       3 7.7E-05   20.9   5.8   19   13-31     29-47  (327)
248 COG4565 CitB Response regulato  84.2       2   5E-05   22.2   4.5   41  173-213   154-198 (224)
249 PRK11169 leucine-responsive tr  84.2     1.5 3.9E-05   23.0   3.9   39  174-212    12-52  (164)
250 TIGR03298 argP transcriptional  84.2     3.1 7.8E-05   20.9   5.7   19   13-31     28-46  (292)
251 smart00419 HTH_CRP helix_turn_  84.0     1.5 3.7E-05   23.2   3.7   26  189-214     9-34  (48)
252 COG2964 Uncharacterized protei  83.8     1.2 3.1E-05   23.8   3.2   38  176-213   174-216 (220)
253 PRK10141 DNA-binding transcrip  83.4     2.9 7.5E-05   21.0   5.1   38  177-214    15-54  (106)
254 smart00550 Zalpha Z-DNA-bindin  83.3     2.8 7.3E-05   21.1   5.0   42  178-219     8-53  (68)
255 PRK10430 DNA-binding transcrip  83.3     1.8 4.6E-05   22.5   3.9   42  173-214   158-204 (239)
256 PRK13348 chromosome replicatio  82.9     3.4 8.8E-05   20.5   6.1   20   13-32     29-48  (294)
257 PRK11233 nitrogen assimilation  82.2     3.6 9.3E-05   20.3   6.0   12   19-30     34-45  (305)
258 PRK03635 chromosome replicatio  82.1     3.7 9.4E-05   20.3   6.1   19   13-31     29-47  (295)
259 PRK04172 pheS phenylalanyl-tRN  82.1     3.7 9.4E-05   20.3   5.5   14  187-200   449-462 (501)
260 PRK09834 DNA-binding transcrip  82.1     3.7 9.4E-05   20.3   5.4   29  116-144   206-234 (264)
261 smart00354 HTH_LACI helix_turn  82.0    0.93 2.4E-05   24.6   2.1   44  190-234     2-45  (70)
262 PRK09906 DNA-binding transcrip  81.9     3.7 9.5E-05   20.3   5.5   18   14-31     29-46  (296)
263 COG0583 LysR Transcriptional r  81.9     3.8 9.6E-05   20.3   5.9   11  178-188   222-232 (297)
264 pfam01710 Transposase_14 Trans  81.7     3.3 8.4E-05   20.7   4.8   24  188-211    71-94  (120)
265 PRK10163 DNA-binding transcrip  81.7     3.8 9.7E-05   20.2   5.9   27  116-142   216-243 (271)
266 pfam10668 Phage_terminase Phag  81.6       1 2.7E-05   24.2   2.2   21  188-208    22-42  (60)
267 PRK00423 tfb transcription ini  81.5     3.8 9.8E-05   20.2   5.1   39  181-219   269-307 (310)
268 PRK10086 DNA-binding transcrip  81.5     3.9 9.9E-05   20.2   5.8   17   15-31     43-59  (311)
269 pfam04218 CENP-B_N CENP-B N-te  81.4     3.3 8.4E-05   20.6   4.7   43  173-215     6-49  (53)
270 pfam00376 MerR MerR family reg  81.1     1.7 4.3E-05   22.7   3.1   22  190-211     1-22  (38)
271 smart00420 HTH_DEOR helix_turn  81.0       3 7.7E-05   20.9   4.4   39  177-215     1-41  (53)
272 PRK11512 DNA-binding transcrip  80.9       4  0.0001   20.0   6.8   43  173-215    37-81  (144)
273 pfam00356 LacI Bacterial regul  80.8     1.2   3E-05   23.8   2.2   44  190-234     1-44  (46)
274 PRK03601 transcriptional regul  80.3     4.2 0.00011   19.9   5.7   18   14-31     29-46  (275)
275 PRK10082 putative DNA-binding   79.9     4.3 0.00011   19.8   5.6   16   16-31     41-56  (303)
276 COG2524 Predicted transcriptio  79.9     2.2 5.6E-05   21.9   3.4   29  179-207   221-249 (294)
277 PRK13509 transcriptional repre  79.8     4.4 0.00011   19.8   4.9   12   13-24     32-43  (251)
278 COG3711 BglG Transcriptional a  79.8     2.8 7.1E-05   21.2   3.9   28  189-216   101-128 (491)
279 PRK10632 putative DNA-binding   79.3     4.5 0.00012   19.7   5.8   14  174-187   277-290 (309)
280 pfam01325 Fe_dep_repress Iron   79.3       2 5.1E-05   22.2   3.0   26  189-214    21-46  (58)
281 PRK12681 cysB transcriptional   79.2     4.6 0.00012   19.6   5.8   27  174-200   280-306 (324)
282 PRK10411 DNA-binding transcrip  78.9     4.6 0.00012   19.6   4.8   13   13-25     31-43  (240)
283 PRK10837 putative DNA-binding   78.6     4.7 0.00012   19.5   6.3   20   13-32     30-49  (291)
284 TIGR01764 excise DNA binding d  78.3     1.9 4.9E-05   22.3   2.7   23  189-211     2-24  (49)
285 PRK12682 transcriptional regul  77.9       5 0.00013   19.4   6.0   18  174-191   280-297 (309)
286 cd00092 HTH_CRP helix_turn_hel  77.6     3.5 8.8E-05   20.5   3.8   28  187-214    24-51  (67)
287 COG1349 GlpR Transcriptional r  77.4     4.6 0.00012   19.6   4.4   11   11-21     19-29  (253)
288 cd04768 HTH_BmrR-like Helix-Tu  77.1     2.4 6.2E-05   21.6   2.9   29  181-209    50-78  (96)
289 pfam00440 TetR_N Bacterial reg  77.1     1.6 4.1E-05   22.9   2.0   27  186-212    14-40  (47)
290 cd04769 HTH_MerR2 Helix-Turn-H  76.6     2.6 6.5E-05   21.4   2.9   12  187-198    55-66  (116)
291 PRK00876 nadE NAD synthetase;   76.4     5.4 0.00014   19.1   5.3   46  174-219   263-309 (325)
292 pfam08220 HTH_DeoR DeoR-like h  76.3       5 0.00013   19.4   4.4   38  177-214     1-40  (57)
293 PRK11569 transcriptional repre  75.9     5.6 0.00014   19.0   5.7   26  116-141   221-247 (274)
294 pfam05043 Mga Mga helix-turn-h  75.5     5.2 0.00013   19.2   4.3   32  186-217    28-59  (87)
295 cd04761 HTH_MerR-SF Helix-Turn  75.5     2.8 7.1E-05   21.2   2.9   23  189-211     1-23  (49)
296 smart00422 HTH_MERR helix_turn  75.4     2.9 7.3E-05   21.1   2.9   15  185-199    54-68  (70)
297 pfam00325 Crp Bacterial regula  75.3     3.5   9E-05   20.4   3.4   27  189-215     3-29  (32)
298 cd01107 HTH_BmrR Helix-Turn-He  75.2     2.9 7.4E-05   21.0   2.9   17  183-199    53-69  (108)
299 TIGR02393 RpoD_Cterm RNA polym  75.1     5.8 0.00015   18.9   8.8   85  130-224   144-234 (240)
300 cd04787 HTH_HMRTR_unk Helix-Tu  74.9       3 7.7E-05   20.9   2.9   14  205-218    84-97  (133)
301 cd04776 HTH_GnyR Helix-Turn-He  74.9       3 7.6E-05   21.0   2.9   15  186-200    53-67  (118)
302 cd04774 HTH_YfmP Helix-Turn-He  74.8       3 7.6E-05   20.9   2.9   43  174-216    38-85  (96)
303 cd04781 HTH_MerR-like_sg6 Heli  74.7       3 7.6E-05   21.0   2.8   31  186-216    54-90  (120)
304 COG0789 SoxR Predicted transcr  74.7     3.1 7.8E-05   20.9   2.9   15  186-200    55-69  (124)
305 cd04764 HTH_MlrA-like_sg1 Heli  74.3     3.1 7.9E-05   20.8   2.9   26  174-199    38-67  (67)
306 TIGR02835 spore_sigmaE RNA pol  74.0     4.6 0.00012   19.6   3.7   46  172-217   177-227 (234)
307 PRK09430 djlA Dna-J like membr  73.9     6.2 0.00016   18.7   4.9   17  171-187   142-158 (269)
308 cd04789 HTH_Cfa Helix-Turn-Hel  73.8     3.2 8.3E-05   20.7   2.9   33  183-215    52-86  (102)
309 cd04770 HTH_HMRTR Helix-Turn-H  73.8     3.3 8.5E-05   20.6   2.9   37  181-217    50-96  (123)
310 COG2512 Predicted membrane-ass  73.7     6.3 0.00016   18.6   5.7   44  171-214   190-236 (258)
311 cd01106 HTH_TipAL-Mta Helix-Tu  73.6     3.4 8.7E-05   20.6   2.9   41  174-214    39-83  (103)
312 COG3682 Predicted transcriptio  73.4     6.4 0.00016   18.6   5.2   14  173-186   103-116 (123)
313 PRK04140 hypothetical protein;  73.2     3.7 9.4E-05   20.3   3.0   25  186-210   136-160 (319)
314 pfam01381 HTH_3 Helix-turn-hel  73.2     6.5 0.00017   18.6   5.0   43  186-232     7-49  (55)
315 PRK10094 DNA-binding transcrip  72.9     6.6 0.00017   18.5   6.1   18   14-31     30-47  (308)
316 cd04782 HTH_BltR Helix-Turn-He  72.8     3.7 9.3E-05   20.3   2.9   27  174-200    39-69  (97)
317 PRK10820 DNA-binding transcrip  72.5     6.7 0.00017   18.4   4.9   40  178-221   469-509 (513)
318 smart00529 HTH_DTXR Helix-turn  72.5       4  0.0001   20.0   3.1   19  193-211     4-22  (96)
319 cd04783 HTH_MerR1 Helix-Turn-H  72.4     3.7 9.5E-05   20.3   2.9   19  182-200    51-69  (126)
320 COG2973 TrpR Trp operon repres  72.4     6.2 0.00016   18.7   4.0   36  174-209    38-81  (103)
321 pfam08784 RPA_C Replication pr  72.2     6.8 0.00017   18.4   5.9   40  173-212    44-90  (103)
322 cd04766 HTH_HspR Helix-Turn-He  72.1     3.7 9.5E-05   20.3   2.8   43  174-216    39-88  (91)
323 cd04773 HTH_TioE_rpt2 Second H  72.0     3.9   1E-04   20.1   2.9   20  181-200    50-69  (108)
324 smart00530 HTH_XRE Helix-turn-  71.8     4.6 0.00012   19.6   3.2   28  185-212     7-34  (56)
325 PRK10668 DNA-binding transcrip  71.7     2.5 6.4E-05   21.5   1.9   17   19-35     15-31  (216)
326 cd01111 HTH_MerD Helix-Turn-He  71.5     4.4 0.00011   19.7   3.1   15  186-200    55-69  (107)
327 TIGR02947 SigH_actino RNA poly  71.4     7.1 0.00018   18.3   5.4   49  181-233   140-188 (193)
328 TIGR03384 betaine_BetI transcr  71.4       3 7.5E-05   21.0   2.2   14   21-34     14-27  (189)
329 cd01109 HTH_YyaN Helix-Turn-He  71.2     4.1 0.00011   19.9   2.9   27  174-200    39-69  (113)
330 COG1414 IclR Transcriptional r  71.1     7.2 0.00018   18.2   5.8   28  115-142   194-222 (246)
331 cd01108 HTH_CueR Helix-Turn-He  71.0     4.2 0.00011   19.9   2.9   18  183-200    52-69  (127)
332 PHA01976 helix-turn-helix prot  70.8     5.1 0.00013   19.3   3.3   27  183-209    10-36  (67)
333 pfam02787 CPSase_L_D3 Carbamoy  70.7     7.3 0.00019   18.2   4.9   42  173-220    58-99  (122)
334 cd04785 HTH_CadR-PbrR-like Hel  70.2     4.5 0.00011   19.7   2.9   20  181-200    50-69  (126)
335 PRK13752 putative transcriptio  70.2     4.1 0.00011   20.0   2.7   10  189-198    65-74  (144)
336 cd04775 HTH_Cfa-like Helix-Tur  70.1     4.5 0.00011   19.7   2.9   36  181-216    50-87  (102)
337 cd04763 HTH_MlrA-like Helix-Tu  69.9     4.1  0.0001   20.0   2.7   25  174-198    39-67  (68)
338 cd04780 HTH_MerR-like_sg5 Heli  69.8     5.5 0.00014   19.1   3.3   45  174-218    39-90  (95)
339 pfam08535 KorB KorB domain. Th  69.7     5.3 0.00014   19.2   3.2   24  187-210     2-25  (93)
340 COG4496 Uncharacterized protei  69.6     6.7 0.00017   18.5   3.7   40  178-221    46-85  (100)
341 cd04777 HTH_MerR-like_sg1 Heli  69.5     4.7 0.00012   19.6   2.9   21  180-200    47-67  (107)
342 PRK11161 fumarate/nitrate redu  68.8       7 0.00018   18.3   3.6   27  189-215   185-211 (235)
343 cd00592 HTH_MerR-like Helix-Tu  68.7       5 0.00013   19.3   2.9   29  174-202    38-70  (100)
344 COG1405 SUA7 Transcription ini  68.6     4.9 0.00013   19.4   2.8   34  187-220   250-283 (285)
345 pfam11662 DUF3263 Protein of u  68.6     8.1 0.00021   17.9   4.5   41  173-213     2-47  (77)
346 cd04786 HTH_MerR-like_sg7 Heli  68.3     5.2 0.00013   19.2   2.9   17  184-200    53-69  (131)
347 PHA00542 putative Cro-like pro  68.3       7 0.00018   18.3   3.6   37  173-210    17-53  (82)
348 PRK09975 DNA-binding transcrip  68.2     3.2 8.3E-05   20.7   1.8   16   20-35     16-31  (213)
349 PRK06266 transcription initiat  68.0     7.1 0.00018   18.3   3.5   13  193-205    41-53  (178)
350 cd01392 HTH_LacI Helix-turn-he  67.7     2.6 6.5E-05   21.4   1.2   41  192-233     1-41  (52)
351 PRK13824 replication initiatio  67.7       8  0.0002   17.9   3.8   33  191-227   324-356 (404)
352 cd04779 HTH_MerR-like_sg4 Heli  67.6     5.4 0.00014   19.2   2.9   11  188-198    56-66  (134)
353 cd04788 HTH_NolA-AlbR Helix-Tu  67.4     5.5 0.00014   19.1   2.9   30  174-203    39-72  (96)
354 PRK00767 transcriptional regul  67.2     4.4 0.00011   19.8   2.3   42  177-218   151-196 (197)
355 cd01282 HTH_MerR-like_sg3 Heli  66.8     5.9 0.00015   18.9   2.9   19  181-199    49-67  (112)
356 pfam04552 Sigma54_DBD Sigma-54  66.7     6.7 0.00017   18.5   3.2   28  190-221   123-155 (160)
357 cd04784 HTH_CadR-PbrR Helix-Tu  66.4       6 0.00015   18.8   2.9   34  184-217    53-96  (127)
358 PRK09514 zntR zinc-responsive   66.3       6 0.00015   18.8   2.9   11  188-198    58-68  (140)
359 TIGR03418 chol_sulf_TF putativ  66.3       9 0.00023   17.6   6.2   17   15-31     30-46  (291)
360 cd01104 HTH_MlrA-CarA Helix-Tu  66.0       6 0.00015   18.8   2.9   24  174-197    39-66  (68)
361 COG0640 ArsR Predicted transcr  65.1     9.4 0.00024   17.4   4.9   38  177-214    26-65  (110)
362 pfam00046 Homeobox Homeobox do  64.9     9.5 0.00024   17.4   5.1   44  173-216     6-55  (57)
363 cd01105 HTH_GlnR-like Helix-Tu  64.7     7.1 0.00018   18.3   3.0   27  174-200    40-70  (88)
364 KOG0489 consensus               64.6     5.8 0.00015   18.9   2.6   30  192-221   190-219 (261)
365 cd00093 HTH_XRE Helix-turn-hel  64.4     9.7 0.00025   17.3   3.9   44  185-232     9-52  (58)
366 pfam05263 DUF722 Protein of un  64.2     9.8 0.00025   17.3   5.6   44  173-216    81-127 (130)
367 COG3677 Transposase and inacti  64.0     9.8 0.00025   17.3   3.8   45  173-217    74-118 (129)
368 PRK10072 putative transcriptio  64.0     7.5 0.00019   18.1   3.0   32  178-210    37-68  (96)
369 TIGR02939 RpoE_Sigma70 RNA pol  63.4     3.8 9.7E-05   20.2   1.4   34  174-214   149-182 (192)
370 TIGR01369 CPSaseII_lrg carbamo  63.1      10 0.00026   17.2   3.8   43  176-218   489-534 (1089)
371 PRK11477 carbohydrate diacid t  63.0      10 0.00026   17.1   5.0   42  180-221   326-367 (385)
372 PRK09508 leuO leucine transcri  62.3      11 0.00027   17.1   5.4   12   19-30     55-66  (314)
373 PRK11753 cAMP-regulatory prote  62.2      11 0.00027   17.0   3.7   27  189-215   169-195 (211)
374 PRK09480 slmA nucleoid occlusi  62.1     5.3 0.00014   19.2   2.0   14   20-33     15-28  (194)
375 PRK09392 ftrB transcriptional   61.9      11 0.00027   17.0   3.6   30  189-219   174-203 (236)
376 PRK13756 tetracycline represso  61.6     4.6 0.00012   19.6   1.6   14  205-218   190-203 (205)
377 smart00351 PAX Paired Box doma  61.4      11 0.00028   16.9   4.6   38  179-216    24-61  (125)
378 COG3177 Fic family protein [Fu  61.3      11 0.00028   16.9   3.6   28  187-214   303-330 (348)
379 TIGR02612 mob_myst_A mobile my  61.1     6.2 0.00016   18.7   2.2   16  188-203    38-53  (150)
380 PRK00135 scpB segregation and   60.9      11 0.00028   16.9   4.3   28   13-40     26-55  (182)
381 TIGR02607 antidote_HigA addict  60.8     7.9  0.0002   17.9   2.7   26  185-210    17-42  (81)
382 KOG0723 consensus               60.6     5.7 0.00015   18.9   1.9   33  189-221    53-85  (112)
383 cd00086 homeodomain Homeodomai  60.2      11 0.00029   16.8   3.4   29  190-218    29-57  (59)
384 PRK09706 transcriptional repre  60.1      10 0.00025   17.2   3.1   35  173-208    84-118 (135)
385 COG2469 Uncharacterized conser  60.0     7.8  0.0002   18.0   2.5   52  164-215   204-255 (284)
386 TIGR02850 spore_sigG RNA polym  59.8      12  0.0003   16.8   3.9   45  173-217   206-251 (254)
387 pfam08069 Ribosomal_S13_N Ribo  59.6     9.3 0.00024   17.4   2.9   27  173-199    27-55  (60)
388 smart00345 HTH_GNTR helix_turn  59.6      12  0.0003   16.7   3.5   25  190-214    22-46  (60)
389 cd04765 HTH_MlrA-like_sg2 Heli  59.1     9.7 0.00025   17.3   2.9   28  173-200    38-70  (99)
390 cd04767 HTH_HspR-like_MBC Heli  58.1     9.8 0.00025   17.3   2.8   20  181-200    49-69  (120)
391 TIGR03613 RutR pyrimidine util  58.0     7.2 0.00018   18.2   2.1   16  174-189   184-199 (202)
392 COG3093 VapI Plasmid maintenan  57.7     9.9 0.00025   17.2   2.7   24  188-211    23-46  (104)
393 PRK03887 methylated-DNA--prote  57.6      13 0.00032   16.5   4.7   41  170-210    86-132 (172)
394 pfam04539 Sigma70_r3 Sigma-70   57.5      12  0.0003   16.7   3.1   34  179-212    11-44  (78)
395 COG1476 Predicted transcriptio  57.4      10 0.00025   17.2   2.7   25  185-209    11-35  (68)
396 pfam00392 GntR Bacterial regul  56.3      13 0.00034   16.4   3.3   24  190-213    26-49  (64)
397 pfam08280 HTH_Mga M protein tr  55.9      13 0.00034   16.3   3.6   41  176-216     5-47  (59)
398 pfam10078 DUF2316 Uncharacteri  55.8      13 0.00034   16.3   3.4   24  184-207    19-42  (89)
399 cd01279 HTH_HspR-like Helix-Tu  55.8      12  0.0003   16.7   2.9   31  174-204    39-74  (98)
400 smart00389 HOX Homeodomain. DN  55.7      13 0.00033   16.4   3.1   43  174-216     7-55  (56)
401 pfam06970 RepA_N Replication i  55.7      11 0.00029   16.8   2.8   22  189-210    53-74  (76)
402 PRK11388 DNA-binding transcrip  55.6      14 0.00034   16.3   5.4   35  177-211   593-627 (639)
403 KOG2581 consensus               55.4      14 0.00035   16.3   3.2   25  190-214   379-404 (493)
404 KOG0848 consensus               54.7     9.8 0.00025   17.3   2.3   27  191-217   229-255 (317)
405 pfam02954 HTH_8 Bacterial regu  53.8      14 0.00037   16.1   5.2   31  181-211    11-41  (42)
406 pfam05344 DUF746 Domain of Unk  53.6      14 0.00037   16.1   4.7   48  177-224     2-52  (65)
407 PRK09940 transcriptional regul  53.6      14 0.00037   16.1   3.1   26  186-211   148-173 (253)
408 KOG0709 consensus               53.4      15 0.00037   16.0   4.5   53  165-220   233-285 (472)
409 COG2378 Predicted transcriptio  53.1      15 0.00038   16.0   4.9   10   12-21     23-32  (311)
410 pfam05331 DUF742 Protein of un  52.8      15 0.00038   16.0   3.2   44  171-214    38-81  (114)
411 pfam06322 Phage_NinH Phage Nin  52.8       9 0.00023   17.5   1.9   26  190-215    18-43  (64)
412 PRK11062 nhaR transcriptional   52.7      15 0.00038   16.0   6.1   17   15-31     33-49  (296)
413 COG1395 Predicted transcriptio  52.7      13 0.00034   16.4   2.7   28  184-211   134-161 (313)
414 COG4197 Uncharacterized protei  52.5      13 0.00033   16.4   2.6   38  191-230    15-52  (96)
415 PRK10402 DNA-binding transcrip  52.2      15 0.00039   15.9   3.6   26  189-214   157-182 (213)
416 COG1974 LexA SOS-response tran  51.1      16  0.0004   15.8   4.4   14   12-25     38-51  (201)
417 cd07377 WHTH_GntR Winged helix  50.9      16  0.0004   15.8   3.6   24  190-213    27-50  (66)
418 pfam04233 Phage_Mu_F Phage Mu   50.0      16 0.00041   15.7   2.8   11  116-126    83-93  (110)
419 PRK09391 fixK transcriptional   49.1      17 0.00043   15.6   3.7   27  189-215   174-200 (224)
420 pfam04492 Phage_rep_O Bacterio  49.1      17 0.00043   15.6   4.8   41  173-213    29-79  (100)
421 PRK05932 RNA polymerase factor  48.3      14 0.00036   16.1   2.3   26  188-213   349-374 (461)
422 pfam01498 Transposase_5 Transp  48.3      15 0.00039   15.9   2.5   23  189-211    14-41  (72)
423 PRK11202 DNA-binding transcrip  47.8     9.2 0.00023   17.5   1.3   18   21-38     17-35  (203)
424 COG1725 Predicted transcriptio  47.3      18 0.00046   15.4   3.4   15  181-195    99-113 (125)
425 smart00342 HTH_ARAC helix_turn  46.9      18 0.00046   15.4   3.5   28  176-203    37-65  (84)
426 pfam07022 Phage_CI_repr Bacter  46.7      18 0.00047   15.3   2.9   22  189-210    13-34  (65)
427 pfam07037 DUF1323 Putative tra  45.7      19 0.00048   15.2   3.1   16  173-188    92-109 (122)
428 KOG2252 consensus               44.6      20  0.0005   15.1   3.2   43  173-215   426-474 (558)
429 TIGR01817 nifA Nif-specific re  44.5      20  0.0005   15.1   4.9   37  173-209   528-564 (574)
430 PRK13918 CRP/FNR family transc  43.8      20 0.00052   15.0   3.6   26  189-214   146-171 (201)
431 TIGR02943 Sig70_famx1 RNA poly  43.6      20 0.00052   15.0   3.2   37  174-217   146-182 (194)
432 pfam11740 KfrA_N Plasmid repli  43.1      21 0.00053   15.0   4.7   37  183-219    12-51  (120)
433 pfam12116 SpoIIID Stage III sp  43.0      21 0.00053   14.9   5.3   42  176-217     6-48  (82)
434 KOG0843 consensus               43.0      18 0.00047   15.3   2.2   45  172-216   107-157 (197)
435 PRK13832 plasmid partitioning   42.8      21 0.00053   14.9   4.6   30  179-208   109-138 (518)
436 PTZ00100 DnaJ chaperone protei  42.2      18 0.00045   15.5   2.0   31  188-218    59-89  (114)
437 TIGR00738 rrf2_super rrf2 fami  41.8      22 0.00055   14.8   3.1   41   85-128    24-64  (133)
438 pfam07453 NUMOD1 NUMOD1 domain  41.7      13 0.00032   16.5   1.2   21  189-209    17-37  (37)
439 PRK05782 precorrin-8X methylmu  41.6      19 0.00049   15.2   2.1   59  172-230   161-219 (332)
440 KOG0487 consensus               41.4     9.5 0.00024   17.4   0.5   50  174-224   247-298 (308)
441 PRK12469 RNA polymerase factor  41.0      17 0.00044   15.5   1.8   40  174-213   346-388 (475)
442 PRK08561 rps15p 30S ribosomal   40.9      20  0.0005   15.1   2.1   16  143-158    85-100 (151)
443 pfam02082 Rrf2 Transcriptional  40.7      22 0.00057   14.7   4.7   25  189-213    25-49  (82)
444 KOG1597 consensus               40.5      23 0.00058   14.7   3.3   35  182-216   254-288 (308)
445 TIGR03070 couple_hipB transcri  40.4      23 0.00058   14.7   3.1   25  184-208    11-35  (58)
446 pfam06971 Put_DNA-bind_N Putat  40.1      22 0.00057   14.7   2.3   19  190-208    29-47  (49)
447 PRK10870 transcriptional repre  39.5      23  0.0006   14.6   6.6   12  174-185   143-154 (176)
448 pfam08765 Mor Mor transcriptio  39.5      23  0.0006   14.6   5.2   43  173-216    57-99  (107)
449 pfam04936 DUF658 Protein of un  39.5      23 0.00058   14.7   2.2   44  184-229    84-127 (134)
450 KOG0484 consensus               39.4      23  0.0006   14.6   3.0   40  186-225    42-81  (125)
451 PRK10856 hypothetical protein;  39.4      23  0.0006   14.6   5.8   52   13-80     29-83  (332)
452 TIGR01610 phage_O_Nterm phage   39.1      24  0.0006   14.5   4.4   45  171-215    20-81  (104)
453 TIGR02154 PhoB phosphate regul  38.4     2.9 7.3E-05   21.1  -2.5   52  173-224   154-214 (226)
454 PTZ00072 40S ribosomal protein  38.1      19 0.00049   15.2   1.7   19  142-160    81-99  (148)
455 pfam10252 PP28 Casein kinase s  37.8      25 0.00063   14.4   3.6   28  170-197    21-58  (82)
456 PRK11608 pspF phage shock prot  37.6      25 0.00064   14.4   5.3   36  176-211   285-322 (325)
457 PRK04158 transcriptional repre  36.2      26 0.00067   14.2   4.7  101  116-220   111-229 (256)
458 COG3284 AcoR Transcriptional a  35.2      27 0.00069   14.1   5.2   36  176-211   566-601 (606)
459 PRK13626 transcriptional regul  35.2      27 0.00069   14.1   3.4   15   13-27    197-211 (551)
460 COG4533 ABC-type uncharacteriz  35.2      27 0.00069   14.1   4.7   14   14-27    200-213 (564)
461 pfam02042 RWP-RK RWP-RK domain  35.1      27 0.00069   14.1   3.7   29  188-220    15-43  (52)
462 pfam09012 FeoC FeoC like trans  35.1      27 0.00069   14.1   3.5   30  188-217    14-43  (68)
463 TIGR02948 SigW_bacill RNA poly  34.9      15 0.00037   16.1   0.6   36  177-213   142-177 (187)
464 cd06571 Bac_DnaA_C C-terminal   34.9      27  0.0007   14.1   6.3   54  174-229    29-86  (90)
465 COG1961 PinR Site-specific rec  34.9      21 0.00054   14.9   1.5   44  174-217   162-206 (222)
466 PRK05629 hypothetical protein;  34.7      28  0.0007   14.1   4.5   40  174-213   245-286 (331)
467 PRK11552 putative DNA-binding   34.6      24 0.00062   14.4   1.8   18   17-34     15-32  (224)
468 PTZ00037 DnaJ_C chaperone prot  34.4      18 0.00045   15.4   1.0   17  173-189   349-365 (422)
469 PRK10130 transcriptional regul  34.3      28 0.00071   14.0   3.4   31  181-211   249-279 (350)
470 cd00131 PAX Paired Box domain   34.2      28 0.00072   14.0   4.6   32  180-211    25-56  (128)
471 COG3655 Predicted transcriptio  34.0      28 0.00072   14.0   2.4   27  183-209    10-36  (73)
472 TIGR02392 rpoH_proteo alternat  34.0      28 0.00072   14.0   4.6   44  173-216   226-273 (279)
473 COG2944 Predicted transcriptio  33.9      28 0.00072   14.0   5.1   39  168-207    38-76  (104)
474 pfam06627 DUF1153 Protein of u  33.7      21 0.00054   14.9   1.3   17  218-234    34-50  (90)
475 pfam00382 TFIIB Transcription   33.7      21 0.00054   14.9   1.3   25  181-205    47-71  (71)
476 pfam07508 Recombinase Recombin  33.2      29 0.00074   13.9   2.8   33  179-211     8-51  (101)
477 COG3088 CcmH Uncharacterized p  33.1      29 0.00075   13.9   2.3   16  179-194    68-83  (153)
478 pfam11994 DUF3489 Protein of u  33.0      29 0.00075   13.9   3.8   29  187-215    23-51  (72)
479 COG5407 SEC63 Preprotein trans  33.0      21 0.00052   15.0   1.2   39  181-219    74-125 (610)
480 COG4941 Predicted RNA polymera  32.7      30 0.00076   13.9   4.1   32  185-216   133-164 (415)
481 COG3710 CadC DNA-binding winge  32.3      10 0.00027   17.1  -0.4   59  174-233    32-100 (148)
482 pfam04182 B-block_TFIIIC B-blo  31.9      30 0.00078   13.8   4.1   41  175-215     1-45  (73)
483 COG2344 AT-rich DNA-binding pr  31.8      31 0.00078   13.8   2.5   18  190-207    34-51  (211)
484 pfam04703 FaeA FaeA-like prote  31.7      31 0.00078   13.7   4.1   33  180-212     4-39  (61)
485 TIGR01321 TrpR trp operon repr  31.7      31 0.00078   13.7   3.0   32  174-205    42-73  (95)
486 pfam00292 PAX 'Paired box' dom  31.7      31 0.00078   13.7   4.6   36  179-214    24-59  (125)
487 TIGR03192 benz_CoA_bzdQ benzoy  31.6      31 0.00079   13.7   3.6   40  178-220   202-241 (293)
488 TIGR02748 GerC3_HepT heptapren  30.8      31  0.0008   13.7   1.8   22  205-233   161-182 (325)
489 PRK11014 transcriptional repre  30.7      32 0.00081   13.6   3.5   26  190-215    27-52  (141)
490 smart00531 TFIIE Transcription  30.6      32 0.00081   13.6   3.8   25  190-214    17-41  (147)
491 TIGR02698 CopY_TcrY copper tra  30.4      32 0.00082   13.6   3.4   41  175-215     3-49  (130)
492 PRK05022 anaerobic nitric oxid  30.2      32 0.00083   13.6   5.8   41  176-220   470-510 (510)
493 COG2508 Regulator of polyketid  30.1      33 0.00083   13.6   5.8   45  175-219   353-397 (421)
494 COG1378 Predicted transcriptio  30.0      33 0.00083   13.5   5.0   43  173-215    13-57  (247)
495 TIGR02395 rpoN_sigma RNA polym  29.9      21 0.00054   14.9   0.8   17  189-205   366-382 (477)
496 COG3311 AlpA Predicted transcr  29.5      33 0.00085   13.5   2.6   19  192-210    17-35  (70)
497 pfam03918 CcmH Cytochrome C bi  29.3      34 0.00086   13.5   2.4   16  179-194    61-76  (145)
498 PHA00675 hypothetical protein   29.2      34 0.00086   13.5   4.7   40  166-205    15-56  (78)
499 TIGR02047 CadR-PbrR Cd(II)/Pb(  28.5      26 0.00066   14.3   1.1   16  193-208     5-20  (127)
500 PRK12815 carB carbamoyl phosph  28.0      35  0.0009   13.3   4.5   31  181-211   484-514 (1068)

No 1  
>PRK13870 transcriptional regulator TraR; Provisional
Probab=100.00  E-value=3.1e-36  Score=277.51  Aligned_cols=215  Identities=20%  Similarity=0.156  Sum_probs=169.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCEEECC
Q ss_conf             25999999999999985837858998417778731025044227877899962487444120879999961799837310
Q gi|254780693|r   12 SSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQS   91 (235)
Q Consensus        12 ~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~~~~~   91 (235)
                      ..-..+...|..+.+.+++++|+|..+        ..+.+...+|||.+|.++|....|..+||++.++..+..|+.|+.
T Consensus        16 ~de~~~~~~l~~~a~~~gf~~~ayl~~--------~~~~~~~isnYP~eW~~~Y~~~~Y~~iDPVv~~a~~~~~Pf~Ws~   87 (234)
T PRK13870         16 GDECILKTGLADIAEHFGFTGYAYLHI--------QHRHITAVTNYHREWQSTYFDKKFDALDPVVKRARSRKHIFTWSG   87 (234)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEEE--------CCCCEEEEECCCHHHHHHHHHCCCEEECHHHHHHHCCCCCEEECC
T ss_conf             539999999999999839985798750--------799757872799999999998889030879998834898976087


Q ss_pred             HHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHH---HHHHHHHHHCCCCC
Q ss_conf             133146672136789965425855358997216887523454105887899899999999999---99999985124678
Q gi|254780693|r   92 IQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACY---QVITDFLELFKKRS  168 (235)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~  168 (235)
                      ..+.........-+......+|+++|+++|++++.+..+++++++..+..+.+...+......   .++.....+.....
T Consensus        88 ~~~~~~~~~~~r~f~~eA~~~Gl~~G~tiPi~~~~G~~~~lSlas~~~~~~~~~~~~~~~~~~~~~~~h~~~~~l~~~~~  167 (234)
T PRK13870         88 EQERPSLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARISFLRTTPT  167 (234)
T ss_pred             CCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             65544348689999999998599966999888799998999981399842167889999999999999999986204888


Q ss_pred             -CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             -874449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  169 -SAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       169 -~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                       .+...||+||+|||+|+|+|||++|||.+||||++||++|++|+++||||.||+|||++|+++|||
T Consensus       168 ~~~~~~LT~RE~E~L~W~A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a~nr~qAVa~Ai~~gLI  234 (234)
T PRK13870        168 AEDAAWLDPKEATYLRWIAVGMTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI  234 (234)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             8776679979999999997899899999997988999999999999995899899999999985899


No 2  
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=100.00  E-value=1.1e-35  Score=273.47  Aligned_cols=219  Identities=18%  Similarity=0.115  Sum_probs=175.7

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCE
Q ss_conf             98622599999999999998583785899841777873102504422787789996248744412087999996179983
Q gi|254780693|r    8 GKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPI   87 (235)
Q Consensus         8 ~~~~~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~   87 (235)
                      -+++.+.++++..+....+.+++++|+|.   ...+.|..++.+...+|||..|.++|...+|...||++.++..+..|+
T Consensus        17 ~~~a~~~~~~~~~l~~~~~~lGFey~~~~---~~~p~p~~~p~~~l~snYP~~W~~~Y~~~~y~~iDPvv~~~~~s~~P~   93 (240)
T PRK10188         17 FQEMAAAEEVYHELQLQTQQLEYDYYSLC---VRHPVPFTRPKVAFYTTYPEAWVSHYQAENYLAIDPVLKPENFSQGHL   93 (240)
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCEEEEE---EECCCCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCE
T ss_conf             98479999999999999997598258988---742688888766887289999999999877914495102444689873


Q ss_pred             EECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCH---HH-HHHHHHHHHHHHHHHHHH
Q ss_conf             73101331466721367899654258553589972168875234541058878998---99-999999999999999851
Q gi|254780693|r   88 IWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLAN---EV-IIEAHGACYQVITDFLEL  163 (235)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~~~~~~~~~~~~~  163 (235)
                      .|++....     ....+++....+|++.|+++|++.+.+..+++++++.......   .+ ...+...+...+....+.
T Consensus        94 ~W~~~l~~-----~~~~~~~eA~~~Gl~~G~t~p~~~~~g~~g~lSla~~~~~~~~~~~~~~~l~l~~l~~~~~~~~~~~  168 (240)
T PRK10188         94 MWNDDLFS-----EAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRSSLREIPILSDELELRLQLLVRESLMALMRL  168 (240)
T ss_pred             ECCCCHHH-----HHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             07840124-----2099999999829867617888727998389998547887775435599999999999999999864


Q ss_pred             CCC-CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             246-78874449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  164 FKK-RSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       164 ~~~-~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ... ..++...||+||+|||+|+|+|||++|||.+|+||++||++|++|+++||||.||+|||++|+++|||
T Consensus       169 ~~~~~~~~~~~LT~RE~E~L~W~A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~Nr~qAva~A~~~GLI  240 (240)
T PRK10188        169 EDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI  240 (240)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             044457987889989999999997799999999883999999999999999995899899999999985899


No 3  
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=100.00  E-value=1.2e-34  Score=266.10  Aligned_cols=222  Identities=23%  Similarity=0.222  Sum_probs=174.7

Q ss_pred             CHHHHCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             19862259999999999999858378589984177787310250442278778999624874441208799999617998
Q gi|254780693|r    7 TGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLP   86 (235)
Q Consensus         7 ~~~~~~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p   86 (235)
                      .-++++|++++...+..+.+.+++++|.|+.......... .......+.|.. +...|....|...||++.++.....|
T Consensus        10 ~l~~a~t~~~l~~~l~~~~~~~Gfd~~~y~~~~~~~~~~~-~~~~~~~~~w~~-~~~~y~~~~Y~~~DPvv~~~~~~~~P   87 (232)
T TIGR03541        10 QIEQASTLEAIQDAVREFAQNLGYDRFVLFSAHSAKDELI-ERIFWVEGDWFD-DGNAVDAQTYLRHCPVTRHILEADEP   87 (232)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC-CCEECCCCCHHH-HHHHHHHCCCCCCCCHHHHHHHCCCC
T ss_conf             9984899999999999999984998899963477766556-400037874577-89999883991069899999857999


Q ss_pred             EEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             37310133146672136789965425855358997216887523454105887899899999999999999999851246
Q gi|254780693|r   87 IIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKK  166 (235)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (235)
                      +.|+......   .+...+.+.....|. .|+++|++.+.+..+++++++...+..+.....+...+..++....++...
T Consensus        88 f~Ws~~~~~~---~~~~~~~~~a~~~G~-~G~tvPi~~~~G~~g~~s~a~~~~d~~~~~~~~l~l~~~~a~~~~~~l~~~  163 (232)
T TIGR03541        88 FFWSKTPNEN---GERYRVVRNPSGRGV-HGLQVPVFGRTGLEGAVSLGGKLIDLSARFRLALQLLCVTAFFAARRLLEA  163 (232)
T ss_pred             EECCCCCCCC---HHHHHHHHHHHHCCC-CEEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             6238887668---778999999986399-589998888999868998416877789999999999999999999997358


Q ss_pred             CCC-CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             788-74449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  167 RSS-AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       167 ~~~-~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ..+ +...||+||+|||+|+|+|||++|||.+|+||++||++|++|+++||||.||+|||++|+++|+|
T Consensus       164 ~~~~~~~~LT~RE~E~L~w~A~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga~nr~qAVa~Ai~~GlI  232 (232)
T TIGR03541       164 PLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKGDI  232 (232)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             998889998989999999998799999999996989999999999999984899999999999987999


No 4  
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=99.85  E-value=2.6e-19  Score=156.78  Aligned_cols=214  Identities=19%  Similarity=0.027  Sum_probs=120.2

Q ss_pred             HHHCCHHHHHHHHH-HHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHH-----HHHH
Q ss_conf             86225999999999-99998583785899841777873102504422787789996248744412087999-----9961
Q gi|254780693|r    9 KKSSSLQELSPRLH-LIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLF-----HFNS   82 (235)
Q Consensus         9 ~~~~sl~dl~~~l~-~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~-----~~~~   82 (235)
                      -+..+--+++..++ .++..++.+-+.- .+.........-..+............    ......++++.     +...
T Consensus        17 l~v~~~~~ff~WlQg~~Q~lLPHeill~-~~g~~~~g~i~~d~~S~~~~~~~~~~~----~~~~~~~~l~~~~~~~W~~~   91 (247)
T TIGR03020        17 LRIRRRHQFFSWLQGEVQSLLPHEILLC-GWADFEGGNVLHERFSPLRYVRDAQYS----RAIHPPDGLLHRLTNAWGAG   91 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHEEE-EEECCCCCCEEEEEEECCCCCCHHHHH----HCCCCCCCHHHHHHHHHHHC
T ss_conf             8677889999999986653066021145-565056771799987358887617676----21267520459999999974


Q ss_pred             CCCCEEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCC-EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             79983731013314667213678996542585535899721688752-34541058878998999999999999999998
Q gi|254780693|r   83 GLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKN-GYVIFTSEFLMLANEVIIEAHGACYQVITDFL  161 (235)
Q Consensus        83 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (235)
                      ...|+.-............  +.... ...-.+...+..+.+..+.. -+.+|.+.....++.....+.....++...+.
T Consensus        92 ~r~P~~l~~~~~~~~~~~~--~~~~~-~~~~l~~~~~hGi~D~~g~~~cl~~f~~~~~~~~~~~~~~LelL~P~Lh~AL~  168 (247)
T TIGR03020        92 KRQPRLVCALTLDDDGWLR--FSVNL-LLLNLKNIAFHGLSDVDGRHDCLYSFSRSSVPLDARHAYFLELLLPYLDSALR  168 (247)
T ss_pred             CCCCEEECCCCCCCCCHHH--HHHHH-HHHHHHHHHHEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9986785377777663034--30067-89887667520012678985559999715889987799999976889999999


Q ss_pred             HHCCCC----CCC------CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             512467----887------444998999999999879997899999499988999999999998079978999999997
Q gi|254780693|r  162 ELFKKR----SSA------ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR  230 (235)
Q Consensus       162 ~~~~~~----~~~------~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~  230 (235)
                      +.....    ..+      ...||+||.|||+|+++|+||+|||.+|+||++||++|+++|++||||+||+|||++|+.
T Consensus       169 rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~va~G~sn~eIA~~L~iS~~TVk~H~~~i~~KL~v~nR~qAV~kAla  247 (247)
T TIGR03020       169 RVLFLPNQHRTRPLGERHSAGLITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAIA  247 (247)
T ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHC
T ss_conf             8631643354555556776789998999999999879999999999497999999999999998099989999999859


No 5  
>PRK04841 transcriptional regulator MalT; Provisional
Probab=99.78  E-value=7.7e-19  Score=153.47  Aligned_cols=60  Identities=30%  Similarity=0.406  Sum_probs=57.8

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             449989999999998799978999994999889999999999980799789999999976
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF  231 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~  231 (235)
                      ..||+||.|||+++++|+||||||..|+||++|||+|++|||+||||+||+|||++|..+
T Consensus       837 ~~LT~RE~eVL~lLa~GlSNkeIA~~L~IS~~TVK~HlrnIy~KLgV~sR~~AV~~AreL  896 (903)
T PRK04841        837 SPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLAQQL  896 (903)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             897999999999997689999999881998769999999998565999899999999999


No 6  
>PRK09483 response regulator; Provisional
Probab=99.75  E-value=5.8e-18  Score=147.22  Aligned_cols=66  Identities=32%  Similarity=0.413  Sum_probs=63.1

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             874449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  169 SAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       169 ~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      .+...||+||.|||+|+++|+||+|||..|+||++||++|+++|++|||++||+|++.+|++.|||
T Consensus       144 ~~~~~LT~RE~eVl~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~gli  209 (216)
T PRK09483        144 NPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL  209 (216)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             654568999999999998799999999996989999999999999980999999999999995991


No 7  
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=99.73  E-value=1.8e-17  Score=143.79  Aligned_cols=63  Identities=29%  Similarity=0.318  Sum_probs=61.5

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ..||+||.|||+++++|+||+|||..|+||++||++|+++|++||||+||+|+|.+|.+.|||
T Consensus       148 ~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~~A~~~~Li  210 (210)
T PRK09935        148 MPLSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL  210 (210)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             899989999999998699999999894988999999999999981999999999999985999


No 8  
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=99.73  E-value=2.9e-17  Score=142.25  Aligned_cols=62  Identities=32%  Similarity=0.242  Sum_probs=58.4

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             74449989999999998799978999994999889999999999980799789999999976
Q gi|254780693|r  170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF  231 (235)
Q Consensus       170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~  231 (235)
                      +...||+||+|||+++++|+||+|||..|+||++||++|+.+|++|||++||+|||.+|...
T Consensus       152 ~~~~LT~RE~eIL~lla~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~v~~R~qav~~A~~n  213 (216)
T PRK10100        152 ESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN  213 (216)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             77899989999999998799999999894988989999999999980999999999999986


No 9  
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=99.72  E-value=4.6e-17  Score=140.79  Aligned_cols=64  Identities=28%  Similarity=0.377  Sum_probs=62.0

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             4449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ...||+||.|||+++++|+||+|||..|+||++||++|+++|++|||++||+|+|.+|.+.||+
T Consensus       148 ~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~~~gl~  211 (216)
T PRK10840        148 DKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLS  211 (216)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
T ss_conf             7899989999999998699999999896989999999999999982999899999999986999


No 10 
>PRK10651 transcriptional regulator NarL; Provisional
Probab=99.72  E-value=5.7e-17  Score=140.12  Aligned_cols=63  Identities=24%  Similarity=0.298  Sum_probs=60.5

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             444998999999999879997899999499988999999999998079978999999997699
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ...||+||.|||+++++|+||+|||.+|+||++||++|+++|++|||++||+||+.+|++.+|
T Consensus       153 ~~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~nr~ea~~~a~~~~l  215 (216)
T PRK10651        153 VNQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI  215 (216)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             234898999999999859999999999697899999999999998489999999999998369


No 11 
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=99.71  E-value=3.4e-17  Score=141.74  Aligned_cols=63  Identities=27%  Similarity=0.363  Sum_probs=61.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ..||+||+|||+++++|+||+|||..|+||++||++|++||++|||+.||+|+|.+|++.|+|
T Consensus       140 ~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~~A~~~Gll  202 (202)
T PRK09390        140 ASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAGAL  202 (202)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             669989999999998389689999997987889999999999996889889999999985999


No 12 
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.71  E-value=3.7e-17  Score=141.44  Aligned_cols=63  Identities=40%  Similarity=0.538  Sum_probs=61.4

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ..||+||.+||+++++|+||+|||..|+||++||++|+.||++|||++||+||+.+|.+.|++
T Consensus       147 ~~LT~RE~eVl~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea~~~a~~~g~~  209 (211)
T COG2197         147 ELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLGLI  209 (211)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
T ss_conf             789989999999998799889999997878989999999999983999899999999982675


No 13 
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=99.71  E-value=1.1e-16  Score=138.02  Aligned_cols=63  Identities=27%  Similarity=0.297  Sum_probs=60.8

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             444998999999999879997899999499988999999999998079978999999997699
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ...||+||+|||+++++|+||+|||.+|+||++||++|+++|++||||+||+|++.+|.+.||
T Consensus       141 ~~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~~l  203 (204)
T PRK09958        141 LDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI  203 (204)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             256899999999999869999999989788999999999999998489999999999998289


No 14 
>PRK10403 transcriptional regulator NarP; Provisional
Probab=99.69  E-value=1.1e-16  Score=138.21  Aligned_cols=62  Identities=27%  Similarity=0.315  Sum_probs=58.3

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             74449989999999998799978999994999889999999999980799789999999976
Q gi|254780693|r  170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF  231 (235)
Q Consensus       170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~  231 (235)
                      +...||+||.|||+++++|+||+|||..|+||++||++|++||++|||++||+|||.+|++.
T Consensus       150 ~~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~nR~ea~~~~~~~  211 (215)
T PRK10403        150 PFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ  211 (215)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             44568999999999998699999999997982999999999999986899899999999998


No 15 
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=99.68  E-value=2.1e-16  Score=136.06  Aligned_cols=62  Identities=29%  Similarity=0.395  Sum_probs=59.0

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             444998999999999879997899999499988999999999998079978999999997699
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ...||+||+|||+++++|+||+|||..|+||++||++|+++|++|||++||+|++-+|.. ||
T Consensus       135 ~~~LT~RE~eVL~lia~G~snkeIA~~L~IS~~TVk~h~~~i~~KL~v~~r~el~r~a~~-~~  196 (196)
T PRK10360        135 QDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFD-GW  196 (196)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHC-CC
T ss_conf             689997999999999879999999999699999999999999998199999999999970-69


No 16 
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=99.68  E-value=6.4e-17  Score=139.78  Aligned_cols=62  Identities=35%  Similarity=0.505  Sum_probs=60.6

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             49989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      +||.||.|||.++++|.||+|||.+|.||.+|||+|+.|||.||||+||+|||.+|-.+|++
T Consensus       831 ~Ls~RE~eVL~Lia~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqAV~rAk~L~lL  892 (894)
T COG2909         831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLL  892 (894)
T ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             76388999999998257778999998898988999999999884821589999999998754


No 17 
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=99.59  E-value=4.2e-15  Score=126.84  Aligned_cols=57  Identities=33%  Similarity=0.446  Sum_probs=55.4

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             449989999999998799978999994999889999999999980799789999999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA  228 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A  228 (235)
                      +.|||||.+||.|+++|+|++|||..|+||++||++|+++|++||||+||+|+|.+|
T Consensus         2 ~~LT~RE~~il~~l~~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~nr~elv~~A   58 (58)
T pfam00196         2 DSLSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA   58 (58)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHC
T ss_conf             977999999999998079999999997888999999999999980999999999559


No 18 
>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=99.56  E-value=1.1e-14  Score=123.73  Aligned_cols=57  Identities=44%  Similarity=0.539  Sum_probs=55.9

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             998999999999879997899999499988999999999998079978999999997
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR  230 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~  230 (235)
                      |||||.+||.|+++|+|++|||..|+||++||++|++++++|||+.||+|+|.+|++
T Consensus         1 LT~rE~~il~~~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~~r~elv~~A~r   57 (57)
T cd06170           1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR   57 (57)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             988999999999807999999999897899999999999998689999999998729


No 19 
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=99.52  E-value=3.2e-14  Score=120.57  Aligned_cols=57  Identities=42%  Similarity=0.546  Sum_probs=55.2

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             449989999999998799978999994999889999999999980799789999999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA  228 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A  228 (235)
                      ..||+||.+||.|+++|+|++|||..|+||++||++|+++|++|||+.||+|+|++|
T Consensus         2 ~~LT~rE~~il~~l~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~elv~~A   58 (58)
T smart00421        2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA   58 (58)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf             761899999999998179999999898978989999999999984899999999549


No 20 
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=99.50  E-value=2.7e-13  Score=113.95  Aligned_cols=62  Identities=24%  Similarity=0.286  Sum_probs=57.4

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             74449989999999998799978999994999889999999999980799789999999976
Q gi|254780693|r  170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF  231 (235)
Q Consensus       170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~  231 (235)
                      ....|||||+|||+++++|+|++|||..|+||.+||++|.+|+++|||++|.+++|-.|--+
T Consensus       131 ~~~~Lt~rE~eVl~l~a~G~s~~eIA~~L~~S~kTv~thr~~~m~KLgv~s~a~Li~~a~~~  192 (205)
T PRK11475        131 QSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAADIL  192 (205)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             67889858999999997699999999997888889999999999982999879999999999


No 21 
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=99.38  E-value=2.4e-12  Score=107.14  Aligned_cols=63  Identities=29%  Similarity=0.351  Sum_probs=60.0

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             444998999999999879997899999499988999999999998079978999999997699
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ...|||||+|||..+.+|+.||+||..||||++||+.|..|+++|+++.|-.+.|-.|...|.
T Consensus       140 l~tLT~RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~~~~~  202 (202)
T COG4566         140 LATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMALSLGL  202 (202)
T ss_pred             HHHCCHHHHHHHHHHHCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC
T ss_conf             986698899999999837630899998398664599999999999733319999999985459


No 22 
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=99.38  E-value=2.4e-12  Score=107.24  Aligned_cols=63  Identities=40%  Similarity=0.553  Sum_probs=60.7

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ..||+||.+|++|++.|++++|||..|+||++||++|+.++++|||+.||+++++++.+.|.+
T Consensus         3 ~~Lt~rE~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~~~~~~   65 (65)
T COG2771           3 ADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI   65 (65)
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC
T ss_conf             113888999999998699899999998779999999999999997758699999999985449


No 23 
>pfam03472 Autoind_bind Autoinducer binding domain. This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules.
Probab=99.31  E-value=2.6e-10  Score=92.66  Aligned_cols=129  Identities=16%  Similarity=0.052  Sum_probs=103.6

Q ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCEEECCH
Q ss_conf             59999999999999858378589984177787310250442278778999624874441208799999617998373101
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSI   92 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~~~~~~   92 (235)
                      +.+++...+..+.+.+++++|+|.....   ...........+||+.+|.+.|....+...||++.++..+..|+.|+..
T Consensus         1 ~~~~l~~~l~~~~~~lGf~~~~y~~~~~---~~~~~~~~~~~~~yP~~W~~~Y~~~~y~~~DPv~~~~~~~~~p~~W~~~   77 (146)
T pfam03472         1 SEEELWDLLERLAAALGFDYFAYGLLPP---SPGSRPDVLLLSNYPAEWVERYVEEGYYRIDPVVRHALRSSTPFSWSDL   77 (146)
T ss_pred             CHHHHHHHHHHHHHHCCCCEEEEEEECC---CCCCCCCEEEEECCCHHHHHHHHHCCCEECCHHHHHHHCCCCCEECCCC
T ss_conf             9799999999999976998799974358---9899876799708999999999977955508799998628999887768


Q ss_pred             HHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             3314667213678996542585535899721688752345410588789989999
Q gi|254780693|r   93 QEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVII  147 (235)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~  147 (235)
                      ..   .......++.....+|++.|+++|++.+.+..+++++++......+.+..
T Consensus        78 ~~---~~~~~~~~~~~a~~~Gl~~G~~~pv~~~~g~~g~~s~a~~~~~~~~~~~~  129 (146)
T pfam03472        78 DL---ASPRARRVFDEARDFGLRAGYTVPVHGPNGRLGALSLAGDGRDLDAVELI  129 (146)
T ss_pred             CC---CCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCCCCCCHHHHH
T ss_conf             66---79779999999998599625899988799988999985699998989999


No 24 
>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=98.46  E-value=3.7e-07  Score=70.16  Aligned_cols=46  Identities=35%  Similarity=0.406  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999-987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      +.|.++-++|-.+ --+|+|++|||..||||++||++|++.++++|-
T Consensus       118 ~~LPe~~R~iF~lsr~eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR  164 (167)
T TIGR02985       118 EKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR  164 (167)
T ss_pred             HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             75689899999998861798678998848988899999999999998


No 25 
>PRK06930 positive control sigma-like factor; Validated
Probab=98.20  E-value=3.2e-06  Score=63.50  Aligned_cols=46  Identities=35%  Similarity=0.405  Sum_probs=42.4

Q ss_pred             CCCHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             499899999-9999879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSC-LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~ev-L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .||+||++| +-.-.+|+|..|||..||||..||+.|+.++.+|+.-
T Consensus       114 ~Lt~rErevfll~~~~glsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~  160 (170)
T PRK06930        114 VLTEREKEVYLMHRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIAK  160 (170)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             56988889998897618889999999798899999999999999999


No 26 
>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=98.16  E-value=5.4e-06  Score=61.91  Aligned_cols=45  Identities=33%  Similarity=0.443  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.|++++|+.|-- +|+|++|||..||||++||+.++..++++|.
T Consensus       135 ~Lpp~~r~v~~L~~~eglS~~EIAe~Lgis~~TVk~rl~~Ar~~Lr  180 (185)
T pfam07638       135 SLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAWLH  180 (185)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4899888898889975999999999979699899999999999999


No 27 
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=98.16  E-value=5.6e-06  Score=61.81  Aligned_cols=45  Identities=31%  Similarity=0.459  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4499899999999-98799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++++++|+.| --+|+|.+|||.+||||++||+.|+.++++++
T Consensus       118 ~~Lp~~~R~v~~L~~~eGls~~EIA~~LgiS~~tVk~~l~rAl~~~  163 (172)
T PRK12523        118 GKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC  163 (172)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             6499999999999999399999999998939999999999999999


No 28 
>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=98.10  E-value=8.4e-06  Score=60.54  Aligned_cols=45  Identities=44%  Similarity=0.507  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+++|++|+.+- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       114 ~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ra~~~L~  159 (162)
T TIGR02937       114 KLPEREREVLVLRYLEGLSYKEIAEILGISEGTVKSRLKRARKKLR  159 (162)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4799899999999971899889999868999999999999999998


No 29 
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=98.08  E-value=4.6e-05  Score=55.28  Aligned_cols=45  Identities=33%  Similarity=0.420  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+++|++|+.+--+|+|.+|||.+||||+.||+.-+.++++||-
T Consensus       155 ~l~~~e~~V~~~~~eg~s~~EIA~~l~is~~tV~~~l~RarkkLr  199 (209)
T PRK08295        155 LLSDLEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLE  199 (209)
T ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             691899999999986999999999989299999999999999999


No 30 
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=98.07  E-value=1e-05  Score=59.89  Aligned_cols=46  Identities=24%  Similarity=0.265  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4998999999999-879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|+|++++|+.+- -+|+|.+|||..||||++||+.|+.+++++|-.
T Consensus       105 ~Lp~~~R~v~~L~~~egls~~EIA~~lgis~~tVk~~l~rA~k~Lr~  151 (159)
T PRK12527        105 ELPPICRESFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV  151 (159)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             69999989998898739799999999891999999999999999999


No 31 
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=98.07  E-value=1e-05  Score=59.94  Aligned_cols=45  Identities=24%  Similarity=0.296  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|.+++++|+.+. -+|+|.+|||.+||||++||+.|+.+++++|
T Consensus       122 ~~LP~~~R~v~~L~~~eg~s~~EIAe~LgiS~~tVk~~l~rAl~~L  167 (183)
T PRK07037        122 DELPARTRAAFEMVRLRGETLQDIARELNVSQTLVNFMIRDALRHC  167 (183)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             8199999999898987398999999998929999999999999999


No 32 
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=98.05  E-value=1.2e-05  Score=59.47  Aligned_cols=44  Identities=25%  Similarity=0.405  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999-8799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|+|+.++|+.+- -+|+|.+|||.+||||++||+.|+.++++..
T Consensus       118 ~LP~~~R~vflL~~~eGlsy~EIAe~LgIS~~tV~~~l~rAl~~c  162 (168)
T PRK12525        118 GLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCC  162 (168)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             399999999999999299999999998979999999999999999


No 33 
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=98.04  E-value=1.1e-05  Score=59.80  Aligned_cols=45  Identities=29%  Similarity=0.428  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++++++|+.+. -+|+|.+|||.+||||+.||+.|+.++++||
T Consensus       141 ~~Lp~~~R~vi~L~~~~g~s~~EIA~~Lgis~~TVk~rl~rA~~~L  186 (194)
T PRK09646        141 DALTDTQREAITLAYYGGLTYREVAERLAVPLGTVKTRMRDGLRRL  186 (194)
T ss_pred             HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             8678157899999999399999999998919999999999999999


No 34 
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=98.01  E-value=1.6e-05  Score=58.46  Aligned_cols=46  Identities=37%  Similarity=0.527  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       105 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~L~is~~tVksrl~RAr~~Lr  151 (181)
T PRK09637        105 DALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLK  151 (181)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             76999998997999885999999999989499999999999999999


No 35 
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=98.01  E-value=1.6e-05  Score=58.51  Aligned_cols=44  Identities=30%  Similarity=0.302  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999-8799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.++++||
T Consensus       149 ~Lp~~~R~v~~L~~~eglS~~EIA~~Lgis~~TVKsrL~RArk~L  193 (231)
T PRK11922        149 ALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL  193 (231)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             099999999999999399999999998939999999999999999


No 36 
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=97.99  E-value=2e-05  Score=57.86  Aligned_cols=45  Identities=31%  Similarity=0.449  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+|++++|+.+ --+|+|.+|||.+||||++||+.|+.++++||.
T Consensus       136 ~L~~~~r~vi~L~~~~g~s~~EIA~~L~is~~TVk~~l~rA~k~Lr  181 (187)
T PRK13919        136 ALSPEERRVIEVLYYQGYTHREAARLLGLPLGTLKTWARRALSKLK  181 (187)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4999999999999985999999999989399999999999999999


No 37 
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=97.98  E-value=1.9e-05  Score=57.99  Aligned_cols=46  Identities=26%  Similarity=0.343  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+. -+|+|.+|||.+||||++||+.|+.++++||-
T Consensus       115 ~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~ra~~~Lr  161 (171)
T PRK09645        115 AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAVRALR  161 (171)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             75999988798999986999999999989299999999999999999


No 38 
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=97.98  E-value=1.8e-05  Score=58.10  Aligned_cols=45  Identities=24%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.|- -+|+|.+|||.+||||+.||+.|+.++++||-
T Consensus       106 ~Lp~~qR~vl~L~~~egls~~EIA~~l~is~~tVk~~l~RAr~~Lr  151 (161)
T PRK09047        106 KLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHTLA  151 (161)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1999999998999998779999999989699999999999999999


No 39 
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=97.96  E-value=2e-05  Score=57.89  Aligned_cols=46  Identities=33%  Similarity=0.474  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999-987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++||-
T Consensus       140 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVk~rl~rA~~~Lr  186 (194)
T PRK12519        140 AQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLR  186 (194)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             81998875688999981999999999989499999999999999999


No 40 
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=97.96  E-value=2.2e-05  Score=57.48  Aligned_cols=45  Identities=33%  Similarity=0.482  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4499899999999-98799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++++++|+.+ --+|+|.+|||.+||||++||+.|+.++.+.+
T Consensus       118 ~~Lp~~~R~v~~L~~~egls~~EIA~~lgiS~~tVk~~l~rAlk~c  163 (172)
T PRK09651        118 DGLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHC  163 (172)
T ss_pred             HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             7099999999999988399999999998939999999999999999


No 41 
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=97.96  E-value=2.1e-05  Score=57.63  Aligned_cols=45  Identities=31%  Similarity=0.373  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+. -+|+|.+|||.+||||+.||+.|+.++++||.
T Consensus       137 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~Lr  182 (192)
T PRK09652        137 SLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR  182 (192)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             3999999888899972999999999989399999999999999999


No 42 
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=97.94  E-value=2.5e-05  Score=57.15  Aligned_cols=46  Identities=30%  Similarity=0.315  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++||-
T Consensus       126 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr  172 (177)
T PRK09638        126 MKLPPELRAPFILKHYYGYTYEEIAKMLGIPEGTVKSRVHHGLKKIR  172 (177)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             75999898999999991999999999989399999999999999999


No 43 
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=97.94  E-value=2.3e-05  Score=57.39  Aligned_cols=45  Identities=36%  Similarity=0.519  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+--+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       112 ~Lp~~~r~v~~l~~~g~s~~EIA~~l~is~~tVk~~l~RA~~~Lr  156 (166)
T PRK09639        112 KMTERDRTVLLLRFSGYSYKEIAQALGIDESSVGTTLHRAKKKFR  156 (166)
T ss_pred             HCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             399999999999993899999999989199999999999999999


No 44 
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=97.94  E-value=3.8e-05  Score=55.87  Aligned_cols=57  Identities=23%  Similarity=0.236  Sum_probs=50.0

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             499899999999-9879997899999499988999999999998079978999999997699
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      .|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++||    |.++-+..+..||
T Consensus       131 ~L~~~~R~vi~l~~~e~~s~~EIA~~lgis~~tV~~~l~RAr~~L----r~~L~~~g~~~g~  188 (189)
T PRK12515        131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL----AELLKAAGVERGW  188 (189)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHCCCCCC
T ss_conf             599999999999998499999999998929999999999999999----9999972833589


No 45 
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=97.93  E-value=2.8e-05  Score=56.79  Aligned_cols=45  Identities=24%  Similarity=0.330  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+.+++|+.+.- +|+|.+|||.+||||++||+.|+.++++||.
T Consensus       153 ~LP~~~R~vi~L~~~egls~~EIA~~l~is~~TVksrl~rAlk~LR  198 (206)
T PRK12526        153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLK  198 (206)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6899988898999985999999999989399999999999999999


No 46 
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=97.93  E-value=2.6e-05  Score=56.99  Aligned_cols=46  Identities=30%  Similarity=0.403  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999-987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++||-
T Consensus       127 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~l~is~~tVk~~l~RAr~~Lr  173 (186)
T PRK05602        127 AALPERQREAIVLQYYQGLSNIEAARVMGLSVDALESLLARARRALR  173 (186)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             75998788999999863899999999989399999999999999999


No 47 
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=97.93  E-value=2.7e-05  Score=56.95  Aligned_cols=46  Identities=26%  Similarity=0.376  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.|- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       135 ~~Lp~~~R~vi~L~~~eg~s~~EIA~~lgis~~tVk~~l~Rark~Lr  181 (196)
T PRK12524        135 AALPERQRQAVVLRHIEGLSNPEIAEVMQIGVEAVESLTARGKRALA  181 (196)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             85999999998999980899999999989299999999999999999


No 48 
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=97.93  E-value=2.6e-05  Score=56.99  Aligned_cols=45  Identities=31%  Similarity=0.499  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+|.+++|+.+. -+|+|.+|||.+||||++||+.|+.++++||-
T Consensus       135 ~L~~~~r~~i~l~~~eg~s~~EIA~~l~is~~TVk~rl~rA~~~LR  180 (184)
T PRK12537        135 QLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR  180 (184)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             0999899999998843999999999989299999999999999999


No 49 
>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=97.92  E-value=2.3e-05  Score=57.43  Aligned_cols=45  Identities=38%  Similarity=0.455  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++++++++.+- -+|+|.+|||.+||+|++||+.++.++++||
T Consensus         9 ~~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~l~RA~~~L   54 (54)
T pfam08281         9 EELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL   54 (54)
T ss_pred             HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             8599999989687998785999999998949999999999999719


No 50 
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=97.91  E-value=3e-05  Score=56.61  Aligned_cols=45  Identities=27%  Similarity=0.451  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+ --+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       119 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~~TVksrl~RAr~~Lr  164 (190)
T PRK12516        119 QLPDDQREAIILIGASGFAYEEAAEICGCAVGTIKSRVSRARARLQ  164 (190)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1999998999989982999999999989499999999999999999


No 51 
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=97.91  E-value=3.1e-05  Score=56.45  Aligned_cols=44  Identities=30%  Similarity=0.453  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             44998999999999-879997899999499988999999999998
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ..|+||.++|..+- .+|+|.+|||..||||++||+.|+.+++..
T Consensus       126 ~~Lp~r~R~vF~L~r~eGls~~EIAe~LgiS~~tV~~~l~rAl~~  170 (178)
T PRK12529        126 DTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVT  170 (178)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             569978889987998829999999999895999999999999999


No 52 
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=97.91  E-value=3.2e-05  Score=56.36  Aligned_cols=46  Identities=30%  Similarity=0.325  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             499899999999-9879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|++++++|+.+ --+|+|.+|||.+||||+.||+.++.++++||..
T Consensus       131 ~Lp~~~R~vi~L~~~~g~s~~EIA~~lgis~~tVk~~l~RA~~~Lr~  177 (184)
T PRK12512        131 TLPPRQRDVVQSIAVEGASIKETAAKLSMSEGAVRVALHRGLAALAA  177 (184)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             89999999999998559799999999891999999999999999999


No 53 
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=97.90  E-value=3.3e-05  Score=56.27  Aligned_cols=45  Identities=29%  Similarity=0.313  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       112 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr  157 (161)
T PRK12541        112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK  157 (161)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1999999999989974999999999989399999999999999998


No 54 
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=97.90  E-value=3.6e-05  Score=56.05  Aligned_cols=44  Identities=27%  Similarity=0.359  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999-8799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++||
T Consensus       129 ~Lp~~~R~vi~L~~~~g~s~~EIA~~l~is~~tVk~rl~rA~k~L  173 (190)
T PRK12543        129 KLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL  173 (190)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             499999999999998599999999998939999999999999999


No 55 
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=97.89  E-value=3.3e-05  Score=56.29  Aligned_cols=45  Identities=22%  Similarity=0.419  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+. -+|+|.+|||.+||||++||+.++.++++||-
T Consensus       129 ~Lp~~~r~~~~l~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr  174 (179)
T PRK12514        129 ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLR  174 (179)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             7559999999999606998999999889099999999999999999


No 56 
>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=97.88  E-value=3.7e-05  Score=55.94  Aligned_cols=46  Identities=43%  Similarity=0.481  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             449989999999998-7999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.|-- +|+|.+|||.+||||+.||+.++.++++||-
T Consensus         9 ~~L~~~~r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~rA~~~Lr   55 (55)
T cd06171           9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             83999998989999980999999999989599999999999998758


No 57 
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=97.86  E-value=3.9e-05  Score=55.76  Aligned_cols=45  Identities=24%  Similarity=0.304  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.|- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       136 ~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~~l~RAr~~Lr  181 (187)
T PRK09641        136 QLPDKYRTVIVLKYIEELSLKEISEILDLPVGTVKTRIHRGREALR  181 (187)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             2898888999999982998999999989399999999999999999


No 58 
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=97.86  E-value=4.4e-05  Score=55.38  Aligned_cols=45  Identities=22%  Similarity=0.332  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.| .-+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       131 ~Lp~~~R~vl~L~~~eg~s~~EIA~~lgis~~tVKsrl~RAr~~Lr  176 (197)
T PRK09643        131 RLPVEQRAALVAVDMQGYSVADTARMLGVAEGTVKSRCARGRARLA  176 (197)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999887999999981999999999989399999999999999999


No 59 
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=97.86  E-value=4.5e-05  Score=55.33  Aligned_cols=45  Identities=27%  Similarity=0.384  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+. -+|+|.+|||.+||||++||+.++.++++||-
T Consensus       112 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVksrl~rAr~~Lr  157 (164)
T PRK12547        112 LLPADQREAIILIGASGFSYEEAAEICGCAVGTIKSRVSRARNRLQ  157 (164)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5899999999989984999999999989399999999999999999


No 60 
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=97.85  E-value=4.7e-05  Score=55.23  Aligned_cols=45  Identities=33%  Similarity=0.448  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4499899999999-98799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|.++.++|+.+ --+|+|.+|||.+||||+.||+.|+.+++..-
T Consensus       118 ~~LP~~~R~vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~rA~~~c  163 (167)
T PRK12528        118 DGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC  163 (167)
T ss_pred             HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             7099999999999998298999999997979999999999999999


No 61 
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=97.85  E-value=4.8e-05  Score=55.15  Aligned_cols=45  Identities=24%  Similarity=0.361  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+|.+++|+.+. -+|+|.+|||.+||||++||+.++.++++||-
T Consensus       137 ~L~~~~r~vi~l~~~eg~s~~EIA~~l~i~~gTVksrl~ra~~~Lr  182 (187)
T PRK12534        137 ELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK  182 (187)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6899899999999984999999999989199999999999999999


No 62 
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=97.85  E-value=4.8e-05  Score=55.12  Aligned_cols=45  Identities=24%  Similarity=0.338  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+++++|+.|.- +|+|.+|||.+||||+.||+.++.++++||-
T Consensus       171 ~Lp~~~R~vl~L~~~egls~~EIA~~Lgis~~TVKsrL~RAr~~LR  216 (233)
T PRK12538        171 RLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLR  216 (233)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5999999999999984999999999989299999999999999999


No 63 
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=97.82  E-value=5.7e-05  Score=54.59  Aligned_cols=45  Identities=36%  Similarity=0.335  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|- -+|+|.+|||.+||||+.||+.++.++++||.
T Consensus       128 ~Lp~~~R~vi~L~~~eg~s~~EIA~~Lgis~~tVksrl~RAr~~Lr  173 (188)
T PRK12517        128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLK  173 (188)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999999999999983999999999989399999999999999999


No 64 
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=97.82  E-value=5.7e-05  Score=54.60  Aligned_cols=45  Identities=29%  Similarity=0.361  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+ .-+|+|.+|||.+||+|++||+.++.++++||-
T Consensus       139 ~Lp~~~r~il~L~~~~g~s~~EIA~~l~is~~tVk~~l~rA~~~Lr  184 (194)
T PRK12513        139 TLPDEQREVFLLREHGDLSLEEIAQLTGVPLETVKSRLRYALQKLR  184 (194)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             2998999999999984999999999989499999999999999999


No 65 
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=97.81  E-value=5.4e-05  Score=54.75  Aligned_cols=44  Identities=18%  Similarity=0.272  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             49989999999998-799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|++++++|+.+-- +|+|.+|||.+||||+.||+.++.++++||
T Consensus       122 ~Lp~~~R~v~~L~~~~gls~~EIA~~L~is~~tVk~rl~RArk~L  166 (185)
T PRK12542        122 ELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV  166 (185)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             299988899767998399999999998929999999999999999


No 66 
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=97.81  E-value=5.5e-05  Score=54.73  Aligned_cols=45  Identities=33%  Similarity=0.495  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+|++++|+.+. .+|++.+|||.+||||++||+.|+.++++||-
T Consensus       125 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr  170 (180)
T PRK11924        125 ALPEKQREVFLLRYVEGLSYQEIADQLGVPLGTVKSRLRRARQKLR  170 (180)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5999999999999996859999999989499999999999999999


No 67 
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=97.81  E-value=6e-05  Score=54.43  Aligned_cols=46  Identities=28%  Similarity=0.287  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.+- -+|+|.+|||.+||+|+.||+.++.++++||.
T Consensus       136 ~~Lp~~~R~vl~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RA~~~Lr  182 (187)
T PRK09648        136 EILPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALSRLR  182 (187)
T ss_pred             HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             83999999999999984999999999989399999999999999999


No 68 
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=97.81  E-value=6e-05  Score=54.45  Aligned_cols=45  Identities=31%  Similarity=0.330  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.++++||.
T Consensus       138 ~Lp~~~R~v~~L~~~egls~~EIA~~l~is~~tVk~rl~RAr~~Lr  183 (193)
T PRK11923        138 QLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAID  183 (193)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1789899999999994999999999989299999999999999999


No 69 
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=97.80  E-value=6.1e-05  Score=54.40  Aligned_cols=46  Identities=26%  Similarity=0.340  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++++++|+.|. -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       156 ~~Lp~~qR~vl~Lr~~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR  202 (222)
T PRK09647        156 DSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQALR  202 (222)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             82999998899879963999999999989399999999999999999


No 70 
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=97.79  E-value=6.6e-05  Score=54.17  Aligned_cols=46  Identities=24%  Similarity=0.302  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             449989999999-9987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++.+++|+. ..-+|+|.+|||.+|+||++||+.|+.++++||-
T Consensus       140 ~~Lp~~~R~vi~L~~~e~~s~~EIAe~l~is~~TVKsrl~rA~k~LR  186 (194)
T PRK12531        140 DRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR  186 (194)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             86999999999999886999999999989299999999999999999


No 71 
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=97.78  E-value=7.2e-05  Score=53.89  Aligned_cols=45  Identities=29%  Similarity=0.338  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++.+++|+.+- -+|+|.+|||.+||||+.||+.++.++++||
T Consensus       127 ~~L~~~~r~v~~l~~~~~~s~~EIA~~l~is~~tVk~rl~Rar~~L  172 (185)
T PRK06811        127 NDLKKLDREIFIKRYLLGESIEEIAKKLGLTRSAIDNRLSRGRKKL  172 (185)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             4899999999999999499999999998929999999999999999


No 72 
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=97.76  E-value=7.9e-05  Score=53.57  Aligned_cols=46  Identities=24%  Similarity=0.268  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999-987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|.+++++|+.+ -.+|+|.+|||.+||||+.||+.++.++++||.
T Consensus       130 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~Rark~Lr  176 (184)
T PRK12539        130 ARLPEKMRLAIQAVKLDGLSVAEAATRSGMSESAVKVSVHRGLKALA  176 (184)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             84999999999999994999999999989199999999999999999


No 73 
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=97.76  E-value=8e-05  Score=53.56  Aligned_cols=45  Identities=27%  Similarity=0.222  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|- -+|+|.+|||.+|||++.|||.++.++++||-
T Consensus       137 ~Lp~~~R~vl~Lr~~eglS~~EIAeiLgip~gTVKSRL~RAR~~Lr  182 (217)
T PRK12533        137 KLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLA  182 (217)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             0999886899999980999999999989499999999999999999


No 74 
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=97.76  E-value=8.5e-05  Score=53.37  Aligned_cols=45  Identities=27%  Similarity=0.337  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|.- +|+|.+|||.+||||++||+.++.++++||-
T Consensus       119 ~L~~~~R~vi~L~~~~~~s~~EIA~~l~is~~tVksrl~rAr~~Lr  164 (173)
T PRK12522        119 LLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR  164 (173)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1999999999999983999999999989399999999999999999


No 75 
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=97.75  E-value=7.3e-05  Score=53.83  Aligned_cols=45  Identities=27%  Similarity=0.210  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       108 ~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~rl~RAr~~Lr  153 (165)
T PRK09644        108 TLPVIEAQAILLCDVHELTYEEAASVLDLKENTYKSHLFRGRKRLK  153 (165)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             2999999999999998889999999989399999999999999999


No 76 
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=97.74  E-value=7.8e-05  Score=53.61  Aligned_cols=45  Identities=20%  Similarity=0.273  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+-- +|+|.+|||..||+|+.||+.++.+++++|-
T Consensus       131 ~Lp~~~R~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr  176 (191)
T PRK12520        131 RLPARTGRVFMMREWLELETEEICKELQITATNLWVMLYRARLRLR  176 (191)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             7749999999999993899999999989499999999999999999


No 77 
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=97.73  E-value=9.4e-05  Score=53.06  Aligned_cols=45  Identities=24%  Similarity=0.256  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++++.+. -+|+|.+|||.+||||+.||+.++.+++++|-
T Consensus       126 ~Lp~~~R~~~~l~~~eg~s~~EIA~~lgis~~tVk~rl~Ra~k~Lr  171 (178)
T PRK12536        126 QLPDRQRLPIVHVKLEGLSVEETAQLTGLSESAVKVGIHRGLKALA  171 (178)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999899999999885999999999989299999999999999999


No 78 
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=97.73  E-value=9.1e-05  Score=53.15  Aligned_cols=45  Identities=31%  Similarity=0.470  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+.+++|+.|. -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       113 ~LP~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsRL~RAR~~Lr  158 (188)
T PRK12546        113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLA  158 (188)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999998895879982989999999989399999999999999999


No 79 
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=97.73  E-value=3.6e-05  Score=56.04  Aligned_cols=45  Identities=29%  Similarity=0.482  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|. -+|+|.+|||.+||||+.||+.++.+++++|-
T Consensus       111 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsrl~RAr~~LR  156 (182)
T PRK12511        111 DLPEEQRAALHLVAIEGLSYQEAANVLGIPIGTLMSRIGRARAALR  156 (182)
T ss_pred             CCCHHHHHHEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999895011241007999999999989399999999999999999


No 80 
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=97.72  E-value=9.8e-05  Score=52.92  Aligned_cols=45  Identities=31%  Similarity=0.301  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+ .-+|+|.+|||.+||||++||+.++.++++||-
T Consensus       120 ~Lp~~~r~vi~l~~~~~~s~~EIA~~l~is~~tVk~~l~Ra~k~Lr  165 (175)
T PRK12518        120 TLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLR  165 (175)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999999999999992999999999989599999999999999999


No 81 
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=97.70  E-value=0.00012  Score=52.41  Aligned_cols=45  Identities=18%  Similarity=0.152  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|+|.+++|+.+ .-+|+|.+|||.+||+|+.||+.++.++++||-
T Consensus       134 ~L~~~~R~vl~L~~~~~ls~~EIA~~l~is~~tVksrl~RAr~~Lr  179 (188)
T PRK09640        134 HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLR  179 (188)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4899999999999992999999999989299999999999999999


No 82 
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=97.69  E-value=0.00011  Score=52.43  Aligned_cols=45  Identities=27%  Similarity=0.417  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.|. -+|+|.+|||.+||||+.||+..+.++++||-
T Consensus       111 ~Lp~~~R~vl~L~~~egls~~EIA~iL~is~gTVKsRL~RAr~kLr  156 (181)
T PRK12540        111 KLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLS  156 (181)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             1999998998879980999999999989499999999999999999


No 83 
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=97.69  E-value=0.00012  Score=52.26  Aligned_cols=45  Identities=22%  Similarity=0.228  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++||.
T Consensus       127 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~rl~Rark~Lr  172 (177)
T PRK09415        127 SLPIKYREVIYLFYYEELSIKEIATVTGVNENTIKTRLKKAKELLK  172 (177)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999999999999980998999999889299999999999999999


No 84 
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=97.68  E-value=0.00013  Score=52.03  Aligned_cols=45  Identities=24%  Similarity=0.099  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.++.+. -.|+|-+|||.+||||..||+...+++.+||-
T Consensus       106 ~L~~re~~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~Al~KLR  151 (154)
T PRK06759        106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMR  151 (154)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4999999999999996998999999989899999999999999987


No 85 
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=97.66  E-value=0.00014  Score=51.79  Aligned_cols=45  Identities=22%  Similarity=0.141  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.+++++|-
T Consensus       106 ~Lp~~~R~v~~L~~~e~~s~~EIA~~l~is~~tVk~~l~RArk~Lk  151 (160)
T PRK09642        106 ELPENYRDVVLAHYLEEKSYQEIALQENIEVKTVEMKLYRARKWIK  151 (160)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             7999999997999982999999999989199999999999999999


No 86 
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=97.64  E-value=0.00014  Score=51.74  Aligned_cols=45  Identities=29%  Similarity=0.302  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+.+++|+.|. -+|+|.+|||.+||||+.||+..+.++++||-
T Consensus       132 ~Lp~~~R~~l~L~~~~g~s~~EIA~ilgi~~gTVKsRl~RAr~~Lr  177 (195)
T PRK12535        132 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLV  177 (195)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4999887999999982998999999989399999999999999999


No 87 
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=97.61  E-value=0.00018  Score=51.02  Aligned_cols=45  Identities=27%  Similarity=0.377  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+++++|+.+- -+|+|.+|||.+||||+.||+.++.++++||-
T Consensus       136 ~Lp~~~R~vl~L~~~egls~~EIA~~lgis~~tVks~l~RAR~~Lr  181 (195)
T PRK12532        136 NLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLR  181 (195)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5999998999999981999999999989599999999999999999


No 88 
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=97.61  E-value=0.00019  Score=50.92  Aligned_cols=46  Identities=26%  Similarity=0.237  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4998999999999-879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|++.+++|+.|. -+|+|.+|||.+||||+.|||.++.++++||-+
T Consensus       130 ~Lp~~~R~vl~L~~~egls~~EIA~~lg~~~gTVKsRl~RAR~~L~a  176 (185)
T PRK09649        130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA  176 (185)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             49999999999899729999999999893999999999999999997


No 89 
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=97.61  E-value=0.00018  Score=51.04  Aligned_cols=45  Identities=18%  Similarity=0.214  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++.+++|+.+- -+|+|.+|||.+||||+.||+..+.++++||-
T Consensus       149 ~Lp~~~R~vl~Lr~~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr  194 (207)
T PRK12544        149 ALPAKYARVFMMREFIELETPEICHNEDLTVSNLNVMLYRSRLRLR  194 (207)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             3999999999999981999999999979799999999999999999


No 90 
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=97.55  E-value=0.00025  Score=49.98  Aligned_cols=45  Identities=16%  Similarity=0.247  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+- -+|+|.+|||.+||||+.||+.++.+++++|.
T Consensus       136 ~LP~~~R~v~~Lr~~~~ls~~EIA~~l~is~~tVksrL~RAR~~Lr  181 (191)
T PRK12530        136 KLPAQQARVFMMREFLELSSEQICQECHITTSNLHVLLYRARLQLQ  181 (191)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6999999999999992999999999989699999999999999999


No 91 
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=97.55  E-value=0.0009  Score=46.05  Aligned_cols=45  Identities=33%  Similarity=0.448  Sum_probs=40.6

Q ss_pred             CCCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             449989999999998--------799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..||+||+++|+..-        +.-+-+++|.+||||..|+..|++++-+||
T Consensus       154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl  206 (215)
T COG3413         154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL  206 (215)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             46999999999999985898887658999999995998889999999999999


No 92 
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=97.51  E-value=0.00028  Score=49.68  Aligned_cols=45  Identities=42%  Similarity=0.504  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++++++|+.+.- +|+|.+|||..||||..||+.++.++++||.
T Consensus       127 ~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~  172 (182)
T COG1595         127 RLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKLR  172 (182)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             3999999999999985999999998959999999999999999999


No 93 
>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=97.45  E-value=0.0003  Score=49.44  Aligned_cols=46  Identities=41%  Similarity=0.515  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|+++|++|+.+. -+|+|-.|||..||||+.||+..+.++.+||-
T Consensus         3 ~~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR   49 (50)
T pfam04545         3 ASLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALRKLR   49 (50)
T ss_pred             HHCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf             66899999999987068824999999989799999999999999862


No 94 
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=97.35  E-value=0.00064  Score=47.12  Aligned_cols=43  Identities=37%  Similarity=0.465  Sum_probs=39.7

Q ss_pred             CCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             9989999999998--------799978999994999889999999999980
Q gi|254780693|r  174 LTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       174 LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ||+||++||...-        ++-+-+|||.+||||..|+..|++++-+|+
T Consensus         1 LT~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lgis~sT~~~hLr~ae~ki   51 (53)
T pfam04967         1 LTDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLRRAESKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             988999999999986897788768899999996989999999999999987


No 95 
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=97.24  E-value=0.0057  Score=40.36  Aligned_cols=45  Identities=18%  Similarity=0.250  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+.+++|+.+- -+|++.+|||.+||||+.||+..+.+++++|-
T Consensus       139 ~LP~~~R~v~~Lr~~egls~~EIA~~L~is~~tVksrL~RAR~~LR  184 (201)
T PRK12545        139 HLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLR  184 (201)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5999998898999992898999999989699999999999999999


No 96 
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=97.19  E-value=0.0042  Score=41.27  Aligned_cols=49  Identities=24%  Similarity=0.227  Sum_probs=43.7

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             44998999999999-87999789999949998899999999999807997
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      +.|+|+|+.|+-|- ..|++..|||.+||+|+.||+..+.++++||....
T Consensus       110 ~~L~p~qRav~vLrdv~g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~~  159 (289)
T PRK09636        110 ERLSPLERAAFLLHDVFGVPFDEIASTLGRSEAACRQLASRARKHVRAAR  159 (289)
T ss_pred             HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             73999896254049860999999999981799999999999999873448


No 97 
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.14  E-value=0.00088  Score=46.14  Aligned_cols=44  Identities=30%  Similarity=0.345  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             49989999999998--------799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .||+||+++|+..=        +.-|-+|||..|+||+.|.+.|++.+-+||
T Consensus       616 ~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL  667 (674)
T PRK13558        616 DLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKL  667 (674)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             6049899999999864757788778789999870988388999999999999


No 98 
>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=97.14  E-value=0.00046  Score=48.16  Aligned_cols=45  Identities=33%  Similarity=0.476  Sum_probs=36.8

Q ss_pred             CCCHHHHHH--HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             499899999--9999879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSC--LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~ev--L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|.+||+.|  |+. -+++|.+|||.+||||..|||.|+.+..++|.-
T Consensus       113 ~LP~rQR~vvVLRY-~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~  159 (165)
T TIGR02983       113 RLPARQRAVVVLRY-YEDLSEAEVAEVLGISVGTVKSRLSRALARLRE  159 (165)
T ss_pred             HCCHHCCEEEEEEC-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             35641236723204-578986899988199932289989999999887


No 99 
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=97.10  E-value=0.0015  Score=44.45  Aligned_cols=46  Identities=30%  Similarity=0.373  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++||++|+.+. -+|+|-+|||..||||...|+...+++.+||-
T Consensus       204 ~~L~erEr~Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~Al~kLR  250 (257)
T PRK08583        204 PVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLR  250 (257)
T ss_pred             HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             54999999999999579999999999989699999999999999987


No 100
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=97.04  E-value=0.0019  Score=43.67  Aligned_cols=46  Identities=30%  Similarity=0.380  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++||+.|+.+- -.++|-+|||..||||...|....+++.+||-
T Consensus       202 ~~L~eREr~Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~~AL~kLR  248 (256)
T PRK07408        202 AQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLQQLK  248 (256)
T ss_pred             HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             56999999999999637998999998979899999999999999999


No 101
>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=97.02  E-value=0.0015  Score=44.40  Aligned_cols=46  Identities=37%  Similarity=0.362  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4998999999999-879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ...||..+|+.|= =-|+|++|||..|+||++||+.+.+-++..|..
T Consensus       145 ~~~Pr~a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~Rdw~~ARaWL~~  191 (194)
T TIGR02999       145 QVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLLD  191 (194)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             00678899885311048898999998688887899879999999987


No 102
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.97  E-value=0.0084  Score=39.16  Aligned_cols=45  Identities=29%  Similarity=0.356  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.|+.+. -+++|-+|||.+||||...|+...+++.+||-
T Consensus       197 ~L~~rEr~Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~AL~kLr  242 (250)
T PRK07670        197 ELNEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLK  242 (250)
T ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5899999999997489868999999989799999999999999999


No 103
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=96.96  E-value=0.0025  Score=42.92  Aligned_cols=45  Identities=33%  Similarity=0.464  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||++|+.+- -+|+|-+|||.+||||...|+.-.+++.+||-
T Consensus       214 ~L~eREr~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~AL~KLR  259 (263)
T PRK07122        214 ALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKSLARLR  259 (263)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             5999999999999569998999999989799999999999999999


No 104
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=96.94  E-value=0.0022  Score=43.23  Aligned_cols=47  Identities=26%  Similarity=0.285  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4499899999999-9879997899999499988999999999998079
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ..|++||+.|+.+ --+|+|-+|||.+||||+..|..-.+++.+||-.
T Consensus       180 ~~L~erEr~Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~kal~kLR~  227 (229)
T PRK12427        180 SQLDEREQMILHLYYQQELSMKEIAQVLDLTEARICQLNKKLVQKIKS  227 (229)
T ss_pred             HHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             719999999999980589989999999798899999999999999884


No 105
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163   Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=96.84  E-value=0.003  Score=42.32  Aligned_cols=47  Identities=28%  Similarity=0.336  Sum_probs=41.7

Q ss_pred             CCCCCCCHHHHHHHHHHHC--C-CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             8744499899999999987--9-997899999499988999999999998
Q gi|254780693|r  169 SAARNLTERETSCLQLAGD--G-YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       169 ~~~~~LT~RE~evL~l~a~--G-~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ++..++|.+|.+||..+..  | ++.+.||..||+|+.|+..|++...+|
T Consensus       162 ~~~~~~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~  211 (231)
T TIGR01884       162 PLLAGLSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKK  211 (231)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             44678889999999998507880528779988578887999999988744


No 106
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=96.81  E-value=0.0037  Score=41.68  Aligned_cols=45  Identities=29%  Similarity=0.378  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||++|+.+- -+|+|-.|||.+||||...|+.--+++..||-
T Consensus       209 ~L~~REr~Ii~~ry~~~~Tl~eIa~~lGvSreRVrQie~~AL~kLR  254 (257)
T PRK08215        209 RLNDREKMILNLRFFQGKTQMEVADEIGISQAQVSRLEKAALKHMR  254 (257)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4999999999999479998999999989699999999999999998


No 107
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298   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, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=96.80  E-value=0.0066  Score=39.87  Aligned_cols=45  Identities=27%  Similarity=0.281  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|||.|.+|+.| -++|++++|||++||+.++.|+.-.-++.++|.
T Consensus       123 ~L~p~qq~viaLrF~~~L~~~EvA~ilGk~~gavk~Lq~rAv~~L~  168 (171)
T TIGR02952       123 KLTPKQQEVIALRFAQNLPIAEVARILGKTEGAVKALQFRAVKKLA  168 (171)
T ss_pred             HCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             1083231203332116883878998726897468999999999987


No 108
>PRK05572 sporulation sigma factor SigF; Validated
Probab=96.80  E-value=0.0038  Score=41.56  Aligned_cols=45  Identities=27%  Similarity=0.299  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.|+.+- -.++|-+|||.+||||...|+...+++.+||-
T Consensus       201 ~L~~rEr~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~Al~kLR  246 (251)
T PRK05572        201 ELDERERLIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMK  246 (251)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             2899999999998178988999999979799999999999999999


No 109
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=96.76  E-value=0.018  Score=36.81  Aligned_cols=45  Identities=36%  Similarity=0.398  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHH---HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999---987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL---AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l---~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.|+.+   --+|+|-+|||..||||..-|+.--+++.+||-
T Consensus       227 ~L~eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR  274 (289)
T PRK07500        227 TLNERELFIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLR  274 (289)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             499999999999766899858999999979799999999999999999


No 110
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=96.74  E-value=0.0041  Score=41.36  Aligned_cols=45  Identities=29%  Similarity=0.393  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||++|+.+ --+|+|-+|||.+||||...|+.--+++.+||-
T Consensus       208 ~L~erEr~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~AL~kLR  253 (261)
T PRK06288        208 TLPEREKKVITLYYYEDLTLKEIGEVLGVTESRISQIHTKAVLQLR  253 (261)
T ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             0899999999998079988999999979789999999999999999


No 111
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=96.74  E-value=0.0041  Score=41.38  Aligned_cols=45  Identities=27%  Similarity=0.458  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-----8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..|++||++|+.+-     -..+|-+|||..||||...|+.--+++.+||
T Consensus       182 ~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~AL~KL  231 (239)
T PRK08301        182 KKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKRIIKRL  231 (239)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             64899999999999578899840699999998978999999999999999


No 112
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=96.68  E-value=0.0048  Score=40.87  Aligned_cols=46  Identities=33%  Similarity=0.339  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-----87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++||++|+.+-     -+.+|-+|||..||||...|+..-+++++||.
T Consensus       173 ~~L~~REr~II~~RfGL~~~~~~Tl~eIg~~lgiSrERVRQIe~~Al~KLr  223 (228)
T PRK05803        173 DILDPREKEVIEMRYGLGDGKEKTQREIAKALGISRSYVSRIEKKALKKLF  223 (228)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             518988999999986478999715999999989799999999999999999


No 113
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=96.67  E-value=0.027  Score=35.55  Aligned_cols=45  Identities=27%  Similarity=0.319  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998---7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||++|+.+-=   +++|-+|||..||||...|+.--+++++||-
T Consensus       230 ~L~~REr~Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR  277 (284)
T PRK06596        230 TLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERIRQIEKNAMKKLK  277 (284)
T ss_pred             HCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             099999999999767999948999999979799999999999999999


No 114
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=96.66  E-value=0.024  Score=35.85  Aligned_cols=48  Identities=21%  Similarity=0.207  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             499899999999-987999789999949998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .|||.|+.|+-| =..|++..|||.+||+|+.+|+..+.++++||....
T Consensus       118 ~L~P~eRaa~vLrdvfg~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~~~  166 (290)
T PRK09635        118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             2998685455269860898899999968998999999999999873238


No 115
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=96.66  E-value=0.0058  Score=40.31  Aligned_cols=45  Identities=31%  Similarity=0.338  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.|+.+-- +++|-+|||..||||...|+.-.+++.+||-
T Consensus       183 ~L~~rEr~Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR  228 (234)
T PRK06986        183 KLPEREQLVLSLYYDEELNLKEIGAVLGVSESRVSQIHSQAIKRLR  228 (234)
T ss_pred             HCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             0999999999987389989999999979789999999999999999


No 116
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=96.57  E-value=0.0048  Score=40.85  Aligned_cols=48  Identities=23%  Similarity=0.199  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             44998999999999879----99789999949-----99889999999999980799
Q gi|254780693|r  172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      -.||++|.++|.++++.    .|.++|...+.     ++.+||+.|+.++++||+..
T Consensus       148 i~LT~~E~~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLRkKl~~~  204 (219)
T PRK10336        148 LTLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGSD  204 (219)
T ss_pred             EEECHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             983789999999999689963979999999628898888581999999999767988


No 117
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=96.56  E-value=0.0034  Score=41.90  Aligned_cols=56  Identities=29%  Similarity=0.332  Sum_probs=47.2

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             49989999999998799978999994999889999999999980799789999999
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA  228 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A  228 (235)
                      -||+||.+||++=.+|+|-.|||..||.|...|-.--++++++..=.-.|=+...+
T Consensus         4 ~Lt~~q~~vL~lR~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIekAreTl~~~~~   59 (139)
T PRK03975          4 FLTERQIEVLRLRKRGLTQQEIADILGTSRANISIIEKRARENIEKARNTLAFWNT   59 (139)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             56899999999998289799999997732889999999999999999999999996


No 118
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=96.56  E-value=0.017  Score=36.96  Aligned_cols=46  Identities=35%  Similarity=0.454  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             4998999999999-879997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|+|+|+.|+-|- ..|++.+|||.+||+|+.+||..+.++++.|..
T Consensus       156 ~Lpp~QRavlvLRdV~g~s~~EiAe~Lg~S~aAVks~L~RARa~L~~  202 (341)
T PRK08241        156 HLPPRQRAVLLLRDVLGWSAAEVAEALGTSTAAVNSALQRARATLAE  202 (341)
T ss_pred             HCCHHHHEEEEHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             39997902001297529988999999789999999999999999986


No 119
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=96.43  E-value=0.008  Score=39.29  Aligned_cols=46  Identities=28%  Similarity=0.320  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999-987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|++||+.|+.+ --+++|-+|||.+||||...|+.-.+++.+||-
T Consensus       204 ~~L~erEr~Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~AL~kLR  250 (257)
T PRK05911        204 LALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR  250 (257)
T ss_pred             HCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             65899999999987489878999998979889999999999999999


No 120
>PRK12423 LexA repressor; Provisional
Probab=96.34  E-value=0.0064  Score=40.00  Aligned_cols=43  Identities=21%  Similarity=0.311  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHC-----CC--CHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf             499899999999987-----99--97899999499-988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAGD-----GY--TSEEIAEKLGL-SVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a~-----G~--t~~eIA~~L~i-S~~TV~~hl~~i~~K  215 (235)
                      .||+||.+||.++.+     |+  |-+||+..+|+ |..||..|++.+-+|
T Consensus         3 ~LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~k   53 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA   53 (202)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             208999999999999999629898899999982999867899999999988


No 121
>PRK00215 LexA repressor; Validated
Probab=96.34  E-value=0.0084  Score=39.15  Aligned_cols=42  Identities=38%  Similarity=0.484  Sum_probs=28.8

Q ss_pred             CCHHHHHHHHHHHC-----C--CCHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf             99899999999987-----9--997899999499-988999999999998
Q gi|254780693|r  174 LTERETSCLQLAGD-----G--YTSEEIAEKLGL-SVHTVNAYLGSATVK  215 (235)
Q Consensus       174 LT~RE~evL~l~a~-----G--~t~~eIA~~L~i-S~~TV~~hl~~i~~K  215 (235)
                      ||+||.+||.++.+     |  =|-+|||..+|+ |..||..|++.+-+|
T Consensus         2 LT~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~k   51 (204)
T PRK00215          2 LTARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERK   51 (204)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             89899999999999999748899899999980999818999999999879


No 122
>PRK05949 RNA polymerase sigma factor; Validated
Probab=96.34  E-value=0.054  Score=33.36  Aligned_cols=47  Identities=21%  Similarity=0.227  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             49989999999998-----799978999994999889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .|++||++|+.+-=     +-+|-+|||.+||||.--|+.--+++++||--+
T Consensus       266 ~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~~  317 (327)
T PRK05949        266 ELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRRR  317 (327)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             6999999999997189996985799999998959999999999999998625


No 123
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=96.31  E-value=0.048  Score=33.77  Aligned_cols=48  Identities=21%  Similarity=0.298  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             4998999999999-----87999789999949998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .|++||++|+.+=     -+.+|-+|||..||||.--|+.--+++.+||--.-
T Consensus       265 ~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l  317 (328)
T PRK05657        265 ELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREIL  317 (328)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             69999999999980889989605999998969799999999999999987999


No 124
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=96.30  E-value=0.0098  Score=38.65  Aligned_cols=44  Identities=36%  Similarity=0.530  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHHHHHHC-----CC--CHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf             4499899999999987-----99--97899999499-988999999999998
Q gi|254780693|r  172 RNLTERETSCLQLAGD-----GY--TSEEIAEKLGL-SVHTVNAYLGSATVK  215 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~-----G~--t~~eIA~~L~i-S~~TV~~hl~~i~~K  215 (235)
                      ..||+||.+||.++..     |+  |-+||+..+|+ |..||..|++.+-+|
T Consensus         2 ~~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~k   53 (65)
T pfam01726         2 KPLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERK   53 (65)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf             6337999999999999999828898799999993899809999999999998


No 125
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=96.29  E-value=0.012  Score=38.10  Aligned_cols=45  Identities=36%  Similarity=0.382  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..||.-|.|.++|+ -+|++-.|.|..||||..|+..-+.++++|+
T Consensus        35 v~L~~dE~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~ARkKv   80 (100)
T pfam02001        35 VIITLDEFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSARKKI   80 (100)
T ss_pred             EEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             8734999999998736079899999884976999999999999999


No 126
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=96.23  E-value=0.091  Score=31.78  Aligned_cols=51  Identities=27%  Similarity=0.290  Sum_probs=44.5

Q ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             49989999999998-----7999789999949998899999999999807997899
Q gi|254780693|r  173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQ  223 (235)
Q Consensus       173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~q  223 (235)
                      .|++||++|+.+-=     +-+|-+|||.+||||.--|+.--+++++||--..|.+
T Consensus       258 ~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~~  313 (320)
T PRK07921        258 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERAD  313 (320)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             59999999999974899989747999998979699999999999999970728888


No 127
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=96.09  E-value=0.017  Score=36.94  Aligned_cols=41  Identities=29%  Similarity=0.306  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99899999999987999789999949998899999999999
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      +...+..+..|+..|+|..+||..+|||..||..|++.+..
T Consensus       158 ~~~~~~~i~~~~~~g~s~~~iak~~gvsrsTvyR~lK~~~e  198 (200)
T PRK13413        158 LHGKEEVITKELKKGTTKSEIAKKLKVSRTTLARFLKTMYE  198 (200)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf             47999999999988899999999989299999999974410


No 128
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=96.07  E-value=0.024  Score=35.91  Aligned_cols=52  Identities=25%  Similarity=0.371  Sum_probs=46.7

Q ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             4998999999999-----879997899999499988999999999998079978999
Q gi|254780693|r  173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      .|++||+.|+.+-     -+-+|-+|||..||||.--|+.--+++++||--.+|.+-
T Consensus       335 ~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~kAL~KLR~~~~~~~  391 (398)
T PRK05901        335 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTMRKLRHPSRSQV  391 (398)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             899999999999758999896039999989796999999999999999678378879


No 129
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=96.04  E-value=0.11  Score=31.10  Aligned_cols=52  Identities=27%  Similarity=0.315  Sum_probs=45.4

Q ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             49989999999998-----79997899999499988999999999998079978999
Q gi|254780693|r  173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      .|++||+.|+++-=     +-+|-+|||..+|||.--|+.--+++++||-=.+|..-
T Consensus       306 ~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~~  362 (368)
T PRK09210        306 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ  362 (368)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             799999999999759996896149999989697989999999999999767368789


No 130
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=96.02  E-value=0.031  Score=35.06  Aligned_cols=53  Identities=32%  Similarity=0.412  Sum_probs=46.0

Q ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             4998999999999-----8799978999994999889999999999980799789999
Q gi|254780693|r  173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI  225 (235)
Q Consensus       173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav  225 (235)
                      .|++||++|+.+-     -+-+|-+|||..||||.--|+.--+++++||--..|.+..
T Consensus       345 ~L~~REr~IL~lRfGL~dg~~~TL~EIG~~lgISRERVRQIE~kAL~KLR~p~r~~~L  402 (410)
T PRK07598        345 DLTSRERDVIRMRFGLADGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRI  402 (410)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             6999999999996489997966899999897969999999999999996773778999


No 131
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=95.93  E-value=0.034  Score=34.83  Aligned_cols=54  Identities=30%  Similarity=0.345  Sum_probs=47.0

Q ss_pred             CCCCHHHHHHHHHHH---CC--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             449989999999998---79--9978999994999889999999999980799789999
Q gi|254780693|r  172 RNLTERETSCLQLAG---DG--YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI  225 (235)
Q Consensus       172 ~~LT~RE~evL~l~a---~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav  225 (235)
                      ..|++||++|+.+==   .|  +|-+|||.+||||.--|+.--+++++||--.+|.+..
T Consensus       322 ~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~~L  380 (385)
T PRK07406        322 ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL  380 (385)
T ss_pred             HCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             64999999999997589999964699999897959999999999999996771778999


No 132
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.92  E-value=0.023  Score=36.08  Aligned_cols=45  Identities=40%  Similarity=0.400  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             49989999999998-7999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||+.|+.+.= +++|-+|||..||||+-+|-.-.+.+..||-
T Consensus       196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~kLr  241 (247)
T COG1191         196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIKKLR  241 (247)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             6689999999999970157999999949149899999999999999


No 133
>PRK04217 hypothetical protein; Provisional
Probab=95.81  E-value=0.027  Score=35.54  Aligned_cols=45  Identities=36%  Similarity=0.360  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             44998999999999-8799978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..||.-|.|.++|+ -+|++-.|.|..|+||..|+..-+.++++|+
T Consensus        41 V~LtvdE~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~AR~Kv   86 (110)
T PRK04217         41 IIMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKV   86 (110)
T ss_pred             EEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             5611999999998736079899999884976999999999999999


No 134
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=95.81  E-value=0.028  Score=35.47  Aligned_cols=47  Identities=26%  Similarity=0.264  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             449989999999998-----79997899999499988999999999998079
Q gi|254780693|r  172 RNLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       172 ~~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ..|++||++|+.+-=     +-+|-+|||.+||||..-|+.--+++++||-=
T Consensus       256 ~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~  307 (318)
T PRK07405        256 ADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK  307 (318)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             6299989999999807789897479999989795999999999999999987


No 135
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=95.74  E-value=0.091  Score=31.77  Aligned_cols=64  Identities=22%  Similarity=0.190  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC--------CHHHHHHHHHHCCCC
Q ss_conf             44499899999999-98799978999994999889999999999980799--------789999999976999
Q gi|254780693|r  171 ARNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV--------NRIQAIAKAIRFGYI  234 (235)
Q Consensus       171 ~~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~--------nR~qava~A~~~Gli  234 (235)
                      -..||+-+.+.++. +....+-++++..||||..||+..+.++.+|||-.        .+..-|..++..|-|
T Consensus        31 f~~L~~E~l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy~~~~~~~~~~~~~eIL~~Le~GEI  103 (113)
T pfam09862        31 FCRLTPEQLEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEILDKLEKGEI  103 (113)
T ss_pred             HHCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf             5238999999999999916889999999788818899999999998089877777776229999999984997


No 136
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326   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 (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=95.68  E-value=0.12  Score=30.89  Aligned_cols=45  Identities=24%  Similarity=0.269  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+-.+||+.+ -.+|+|++|||..|+.|+.+|.--.-+..+||-
T Consensus       141 ~L~e~~REvi~LR~~EGLS~~EvA~~Md~~~~av~~l~~Ral~~Lr  186 (190)
T TIGR02984       141 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRALARLR  186 (190)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             4792258999998760355589998707975898758999999998


No 137
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=95.65  E-value=0.028  Score=35.39  Aligned_cols=48  Identities=19%  Similarity=0.297  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             44998999999999879----99789999949-----99889999999999980799
Q gi|254780693|r  172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      ..||++|.++|.+++..    .|.++|...+.     ++.+||+.|+.++++||...
T Consensus       159 i~LT~~E~~lL~~L~~~~g~vvSre~L~~~vw~~~~~~~~rsid~~I~rLRkKl~~~  215 (240)
T PRK10710        159 LDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESL  215 (240)
T ss_pred             EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             855899999999999779973989999999628888888465999999999960106


No 138
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=95.54  E-value=0.12  Score=30.83  Aligned_cols=44  Identities=41%  Similarity=0.475  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHHH-----HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             499899999999-----98799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQL-----AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l-----~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|||||++||.|     =-+.+|=.|||..||||..=|+.==+.+++||
T Consensus       287 ~L~p~e~~VL~LRfGL~~~~~~TL~eiG~~l~lSRERVRQiE~~AL~kL  335 (336)
T TIGR02997       287 ELTPRERQVLRLRFGLDDGEPLTLAEIGERLNLSRERVRQIEAKALRKL  335 (336)
T ss_pred             HCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             3798899999985789989753278999883883688889999997534


No 139
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=95.49  E-value=0.035  Score=34.76  Aligned_cols=41  Identities=29%  Similarity=0.344  Sum_probs=32.5

Q ss_pred             HHHHHHHHHH--CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9999999998--79-997899999499988999999999998079
Q gi|254780693|r  177 RETSCLQLAG--DG-YTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       177 RE~evL~l~a--~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      |..++|.++.  ++ .|.+++|..|+||.+||..+++.+. ..|+
T Consensus         1 R~~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~-~~G~   44 (55)
T pfam08279         1 RLLQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALE-ALGV   44 (55)
T ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCC
T ss_conf             9899999999769991899999996988999999999999-8899


No 140
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=95.17  E-value=0.033  Score=34.86  Aligned_cols=41  Identities=29%  Similarity=0.284  Sum_probs=32.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999987999789999949998899999999999807997
Q gi|254780693|r  180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      ....|-..|+|..|||.+|++|..|+.+.+.+..++..+..
T Consensus        10 kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~   50 (203)
T COG0856          10 KARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA   50 (203)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999877985777676641048778888754431147888


No 141
>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=95.17  E-value=0.059  Score=33.12  Aligned_cols=41  Identities=37%  Similarity=0.420  Sum_probs=36.2

Q ss_pred             CC-HHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99-8999999999879-99789999949998899999999999
Q gi|254780693|r  174 LT-ERETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       174 LT-~RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      |+ +.-.+++..+.+| ++..|||..++||..||..|++.+.+
T Consensus         4 l~~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~   46 (78)
T cd00090           4 LSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEE   46 (78)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             2799999999999848906999987778487899999999998


No 142
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300   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, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=95.12  E-value=0.015  Score=37.45  Aligned_cols=37  Identities=35%  Similarity=0.372  Sum_probs=32.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             99999879997899999499988999999999998079
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ||+.--+ ++-+|||..|.++++||++|++++..+|+.
T Consensus       132 IL~Yy~D-L~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~  168 (173)
T TIGR02954       132 ILRYYHD-LKIKEIAEVMNKPEGTVKTYLRRAKKKLKK  168 (173)
T ss_pred             HHHHCCC-CCHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             4332179-984259985168985178999999999888


No 143
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.10  E-value=0.056  Score=33.24  Aligned_cols=46  Identities=37%  Similarity=0.375  Sum_probs=42.2

Q ss_pred             CCCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             444998999999999-8799978999994999889999999999980
Q gi|254780693|r  171 ARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       171 ~~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ...||.-|.|.++|+ -.|++-+|.|.+||||..|+-.-++++++|.
T Consensus        31 ~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv   77 (99)
T COG1342          31 PVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKV   77 (99)
T ss_pred             CEEECHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             43522999889998868610578999984642999999999999999


No 144
>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=94.96  E-value=0.065  Score=32.79  Aligned_cols=47  Identities=38%  Similarity=0.394  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             44998999999999-879997899999499988999999999998079
Q gi|254780693|r  172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ..||+||+-|+.|- -+|+|-||||..|||||.=|-.--+.+..||..
T Consensus       177 ~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~  224 (227)
T TIGR02479       177 EKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIHSQALKKLRA  224 (227)
T ss_pred             HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             406855788888864127668899988378705799999999999987


No 145
>PRK00118 putative DNA-binding protein; Validated
Probab=94.86  E-value=0.099  Score=31.50  Aligned_cols=45  Identities=29%  Similarity=0.379  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      -||+++++++.+- -+-+|-.|||..++||...|..+++++.++|.
T Consensus        17 LLT~kQ~~~~~lyy~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~   62 (105)
T PRK00118         17 LLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE   62 (105)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             7559999999999885499999989969859999999999999999


No 146
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=94.73  E-value=0.04  Score=34.34  Aligned_cols=60  Identities=13%  Similarity=0.093  Sum_probs=54.7

Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       175 T~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      |.=|.+|.-+-+-|.+-+.||..|+|+..|=+.++.++++++|.+||-++.-....-|+|
T Consensus       147 ~~~~~~vf~~Ys~G~SH~~ia~~L~It~~sSkn~~s~i~k~~gissrde~l~~l~~s~~~  206 (220)
T PRK13719        147 TSIQYDVFILYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSRDELLIILHTSEMI  206 (220)
T ss_pred             EEEEEEEEEEEECCCCHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             200466898875242468899884741354077999999972988599999999997689


No 147
>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=94.73  E-value=0.11  Score=31.21  Aligned_cols=44  Identities=25%  Similarity=0.311  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999-8799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      -||+++++++.+- -+-.|-.|||..+|||...|..+++++.++|
T Consensus        17 LLT~KQ~~~~~lyy~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L   61 (101)
T pfam04297        17 LLTDKQKNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKML   61 (101)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             765999999999987639899999881985999999999999999


No 148
>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=94.63  E-value=0.022  Score=36.14  Aligned_cols=45  Identities=40%  Similarity=0.442  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|.+||++||.|- -++||-+|||.+||||.==|-.-++++.+||-
T Consensus       180 ~LpeRER~il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR  225 (229)
T TIGR02980       180 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKRLR  225 (229)
T ss_pred             HCCHHHCEEEEEEEECCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             0790270761000106977899997818436788999999999999


No 149
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=94.55  E-value=0.099  Score=31.50  Aligned_cols=50  Identities=36%  Similarity=0.444  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCCHHH
Q ss_conf             998999999999-----87999789999949998899999999999807-997899
Q gi|254780693|r  174 LTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD-AVNRIQ  223 (235)
Q Consensus       174 LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg-~~nR~q  223 (235)
                      ||+||+.|+++-     -.++|-.|||.+++||.--|+.--+++++||- ..++..
T Consensus       280 Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~~  335 (342)
T COG0568         280 LTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSA  335 (342)
T ss_pred             CCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999955679995519999989598699999999999999987063222


No 150
>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=94.53  E-value=0.063  Score=32.90  Aligned_cols=38  Identities=34%  Similarity=0.483  Sum_probs=32.4

Q ss_pred             CCCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             4499899-9999999879997899999499988999999
Q gi|254780693|r  172 RNLTERE-TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       172 ~~LT~RE-~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      ..||+-+ .++.++++.|.|-.+||..+|||..|+..|+
T Consensus         4 ~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             869999999999999978989999999797999998659


No 151
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331   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 of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.43  E-value=0.1  Score=31.38  Aligned_cols=45  Identities=38%  Similarity=0.493  Sum_probs=43.4

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      +|.++++++|.+ --+|.+..+||..+|.|+++|..-+.+|+.+|.
T Consensus       115 ~L~~~~R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~L~R~R~~L~  160 (163)
T TIGR02989       115 KLPERQRELLQLRYQRGVSLEALAEQLGRTVNAVYKALSRLRVRLR  160 (163)
T ss_pred             HCCHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             3597889999998227978789998847138999999999999975


No 152
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=94.41  E-value=0.093  Score=31.71  Aligned_cols=49  Identities=22%  Similarity=0.258  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             44998999999999879----99789999949-----998899999999999807997
Q gi|254780693|r  172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      -.||++|.++|.++..-    .|-.+|...+.     .+.++|+.|+.++++||+-..
T Consensus        22 i~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~   79 (95)
T cd00383          22 VELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDP   79 (95)
T ss_pred             EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             8779999999999987799745699999985397645574549999999999975268


No 153
>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=94.35  E-value=0.087  Score=31.92  Aligned_cols=47  Identities=36%  Similarity=0.416  Sum_probs=43.5

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             4998999999999-8799978999994999889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .|+|||+-||-|- +-|....|+|..||.|.-.||.-+++++..|+..
T Consensus       143 ~LpPrQRAvL~LRdvlGw~A~E~A~~L~~s~ASVnSaLQRARAtL~~~  190 (329)
T TIGR02960       143 LLPPRQRAVLLLRDVLGWKAAEVAELLGTSVASVNSALQRARATLAES  190 (329)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             488145789998988355556899874383267865888878866531


No 154
>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=94.27  E-value=0.079  Score=32.22  Aligned_cols=44  Identities=32%  Similarity=0.480  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999-8799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|.+-.++.+.|+ -+|.|-+|||..||+|-.++|.=+++.+.||
T Consensus       100 ~LP~~~r~a~~L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR~~L  144 (170)
T TIGR02959       100 ELPDEYREAIRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRKKL  144 (170)
T ss_pred             HCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             569867889888750799827998761753351567889999999


No 155
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.21  E-value=0.11  Score=31.30  Aligned_cols=41  Identities=24%  Similarity=0.374  Sum_probs=35.3

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99899999999987999789999949998899999999999
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .-.|++-+-..+.+|+|.+|||.++|+|..||...+++-.+
T Consensus         7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e   47 (138)
T COG3415           7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE   47 (138)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             89999999999976854999999969229999999987333


No 156
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=94.17  E-value=0.14  Score=30.44  Aligned_cols=46  Identities=20%  Similarity=0.194  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCC
Q ss_conf             4998999999999879----9978999994-----99988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .||++|.++|.+++..    .|-++|-..+     ..+.+||+.|+.++++||+-
T Consensus       162 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~sid~~I~rLRkKl~~  216 (224)
T PRK10766        162 KLTKAEYELLVAFVTNPGQVLSRERLLRMLSHRVEDPNDRTIDVLIRRLRHKLNP  216 (224)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             6789999999999967997396999999964888788847299999999976798


No 157
>pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal.
Probab=94.15  E-value=0.12  Score=31.04  Aligned_cols=48  Identities=25%  Similarity=0.321  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             44998999999999879----9978999994-----999889999999999980799
Q gi|254780693|r  172 RNLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      -.||++|.++|..+.+-    .|..+|...+     .++.++|+.|+.++++||+..
T Consensus         4 i~Lt~~E~~lL~~L~~~~~~~vsr~~l~~~iw~~~~~~~~~sl~~~I~rLR~kl~~~   60 (77)
T pfam00486         4 VELTPKEFDLLELLARNPGRVVSREELLEEVWGEDFDVDDNTVDVHISRLRKKLEDD   60 (77)
T ss_pred             EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             233899999999999679971979999999638766655330999999999987544


No 158
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.14  E-value=0.16  Score=29.93  Aligned_cols=43  Identities=26%  Similarity=0.166  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             49989999999998---79997899999499988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +||+.+.+|+.-+.   .++|..+||.+|++|..||+.-++|...+
T Consensus        24 GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~   69 (126)
T COG3355          24 GLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA   69 (126)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             8968899999999864699579999999783199999999999985


No 159
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=94.13  E-value=0.11  Score=31.15  Aligned_cols=47  Identities=9%  Similarity=0.088  Sum_probs=39.6

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             4998999999999879----9978999994-----999889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|.+++..    .|-++|-..+     ..+.+||+.|+.++++||+..
T Consensus       161 ~LT~~E~~LL~~L~~~~g~vvsre~Ll~~vwg~~~~~~~rtidv~I~rLRkKl~~~  216 (239)
T PRK09468        161 PLTTGEFAVLKALVRHPREPLSRDKLMNLARGREYSAMERSIDVQISRLRRLIEPD  216 (239)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             76789999999999779966769999999629887888483999999999975207


No 160
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=94.09  E-value=0.09  Score=31.81  Aligned_cols=42  Identities=24%  Similarity=0.317  Sum_probs=33.1

Q ss_pred             CCHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9989999-99999879997899999499988999999999998
Q gi|254780693|r  174 LTERETS-CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       174 LT~RE~e-vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      -+.+-+. |=.++-.|++.+||+..|||--+||.+|+++..+|
T Consensus        94 yd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k~~  136 (139)
T COG1710          94 YDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLKKK  136 (139)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             3454899999999849987788886098622069999987665


No 161
>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218   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 RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=93.98  E-value=0.16  Score=30.01  Aligned_cols=90  Identities=22%  Similarity=0.207  Sum_probs=60.0

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             89972168875234541058878998999999999999999998512467887444998999999999879997899999
Q gi|254780693|r  118 IAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEK  197 (235)
Q Consensus       118 ~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~  197 (235)
                      +.-|+.+.......+-..+.....+++++.-..-....+-..          -..-||.-|.+||..-.+|++..|||..
T Consensus       105 l~kPiy~~~sdrtl~d~~~~~~~~dP~~l~i~~e~~~~~~~~----------~~~~ls~le~~vl~~yl~G~~yqei~~~  174 (198)
T TIGR02859       105 LNKPIYDEESDRTLLDVVSEAKVADPEELIISKEEYEKIESK----------LEELLSDLELKVLVLYLDGKSYQEIAED  174 (198)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             256525452014799988544322527776316889999999----------9999999999999998457407889988


Q ss_pred             HCCCHHHHHHHHHHHHHHCC
Q ss_conf             49998899999999999807
Q gi|254780693|r  198 LGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       198 L~iS~~TV~~hl~~i~~KLg  217 (235)
                      |+-..+.+.+-++++.+||.
T Consensus       175 l~r~~ksidnalqrvkrkle  194 (198)
T TIGR02859       175 LNRHVKSIDNALQRVKRKLE  194 (198)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             64566789999999999997


No 162
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=93.93  E-value=0.035  Score=34.73  Aligned_cols=37  Identities=35%  Similarity=0.325  Sum_probs=29.9

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             9999987999789999949998899999999999807
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ++-.--.|+|..+||..||+++.||++|++.--++.+
T Consensus        54 a~arekag~Ti~EIAeelG~TeqTir~hlkgetkAG~   90 (182)
T COG1318          54 ALAREKAGMTISEIAEELGRTEQTVRNHLKGETKAGQ   90 (182)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHHH
T ss_conf             9999870374999999968779999999751403316


No 163
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=93.78  E-value=0.12  Score=30.81  Aligned_cols=39  Identities=31%  Similarity=0.469  Sum_probs=33.4

Q ss_pred             CCCCH-HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             44998-9999999998799978999994999889999999
Q gi|254780693|r  172 RNLTE-RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       172 ~~LT~-RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      ..|++ .-.++.+|+..|.+-++||.+.+||..||..++.
T Consensus         4 ~kl~~~~~~~v~~L~~~G~~i~~IA~~~~vsrsTvYRyl~   43 (45)
T pfam02796         4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLA   43 (45)
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHCC
T ss_conf             1038999999999998799499999998600888876445


No 164
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=93.72  E-value=0.15  Score=30.18  Aligned_cols=48  Identities=23%  Similarity=0.257  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHHHHHCC----CCHHHHHHHH------CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             44998999999999879----9978999994------999889999999999980799
Q gi|254780693|r  172 RNLTERETSCLQLAGDG----YTSEEIAEKL------GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L------~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      ..||++|.++|.++++-    .|-++|...+      ..+.++++.|+.++++||+-.
T Consensus         4 v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~I~~LR~kl~~~   61 (78)
T smart00862        4 IKLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLEDD   61 (78)
T ss_pred             EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             3248999999999984799629699999876288878888602789999999997645


No 165
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=93.69  E-value=0.15  Score=30.29  Aligned_cols=48  Identities=17%  Similarity=0.123  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             4998999999999879----99789999949-----998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .||++|.++|.+++.-    .|-++|...+.     .+.+||+.|+.++++||+...
T Consensus       150 ~LT~~E~~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLR~Kl~~~~  206 (226)
T PRK09836        150 TLTSKEFTLLEFFLRHQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKIDNDF  206 (226)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             568899999999986899648799999996288878885889999999999857889


No 166
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=93.69  E-value=0.15  Score=30.18  Aligned_cols=47  Identities=23%  Similarity=0.226  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             4998999999999879----99789999949-----99889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|..++.-    .|-.+|...+.     .+.+||+.|+.++++||+-.
T Consensus       147 ~LT~~E~~LL~~L~~~~g~vvsre~l~~~vwg~~~~~~~~~idv~I~rLRkKl~~~  202 (223)
T PRK11517        147 TLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDP  202 (223)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             29999999999998689985989999999629887888587999999999985788


No 167
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=93.67  E-value=0.13  Score=30.56  Aligned_cols=47  Identities=13%  Similarity=0.046  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             49989999999998799----978999994-----999889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|..++.-.    |-++|-..+     ..+.+||+.|+.++++||+-.
T Consensus       161 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtvdv~I~rLRkKl~~~  216 (240)
T PRK10701        161 SLSTADFELLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLDN  216 (240)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             76789999999999779987389999998539887888678999999999987528


No 168
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=93.65  E-value=0.15  Score=30.21  Aligned_cols=58  Identities=24%  Similarity=0.305  Sum_probs=47.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC-----------HHHHHHHHHH
Q ss_conf             4998999999999-87999789999949998899999999999807997-----------8999999997
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN-----------RIQAIAKAIR  230 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n-----------R~qava~A~~  230 (235)
                      .|||++.-|+.+- .-+++..|||.++++||.+|+.-+.+.+.+|.-.|           -.++++.|++
T Consensus       116 ~L~p~Q~vIfLLkDVF~ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee~~~~~~~~~D~e~~V~air  185 (228)
T PRK06704        116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIR  185 (228)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHH
T ss_conf             2588889999999998755999999955663499999999999987338531245666776279999998


No 169
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=93.60  E-value=0.13  Score=30.73  Aligned_cols=45  Identities=31%  Similarity=0.303  Sum_probs=35.5

Q ss_pred             CCCHHHHHHHHHHHC-----C--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             499899999999987-----9--997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLAGD-----G--YTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~a~-----G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .||++++++|+-+.+     |  -.+++||..+++|+.||++-+... +.||-
T Consensus         1 ~LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L-~~LGL   52 (79)
T pfam03444         1 ELTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSL-KALGL   52 (79)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCC
T ss_conf             97789999999999999972998667999999878908899999999-98588


No 170
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=93.59  E-value=0.17  Score=29.79  Aligned_cols=47  Identities=17%  Similarity=0.047  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCC
Q ss_conf             449989999999998799----978999994-----99988999999999998079
Q gi|254780693|r  172 RNLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~  218 (235)
                      ..||++|.++|.++..-.    |-++|...+     ..+.+||+.|+.++++||+=
T Consensus       148 i~LT~~E~~lL~~L~~~~g~vvsre~L~~~v~~~~~~~~~~~ld~~I~rLRkKl~~  203 (222)
T PRK10643        148 LILTPKEYALLSRLMLKAGSPVHREILYNDIYNWDNEPSTNTLEVHIHNLRDKVGK  203 (222)
T ss_pred             EEECHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             87087999999999967999868999999960878888867699999999976699


No 171
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=93.48  E-value=0.15  Score=30.22  Aligned_cols=47  Identities=17%  Similarity=0.180  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             4998999999999879----9978999994-----999889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|.++++-    .|-++|...+     ..+.+||+.|+.++++||+-.
T Consensus       156 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtidv~I~rLRkKL~~~  211 (232)
T PRK10955        156 ELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDR  211 (232)
T ss_pred             ECCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             66899999999999789950979999999718898888582999999999954116


No 172
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.38  E-value=0.22  Score=29.05  Aligned_cols=48  Identities=23%  Similarity=0.251  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             8999999999879--997899999499988999999999998079978999
Q gi|254780693|r  176 ERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       176 ~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      +-.+++|+.+.+.  .|..+||+.+|+|+.||...++++. +-|+=.++.+
T Consensus         3 ~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~-~~GiI~~~~~   52 (108)
T smart00344        3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE-EEGVIKGYTA   52 (108)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCCCCEEEE
T ss_conf             8999999999982899999999998939999999999996-0897320289


No 173
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.33  E-value=0.11  Score=31.11  Aligned_cols=37  Identities=24%  Similarity=0.258  Sum_probs=26.1

Q ss_pred             HCCCHHHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCC
Q ss_conf             4999889999999999980------799789999999976999
Q gi|254780693|r  198 LGLSVHTVNAYLGSATVKL------DAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       198 L~iS~~TV~~hl~~i~~KL------g~~nR~qava~A~~~Gli  234 (235)
                      ..+..+|+---+..+.++=      |=.++++|+.-|++-|+|
T Consensus       261 ~~ln~r~igl~L~~l~~ip~vI~vAgG~~K~~AI~aaL~gg~~  303 (321)
T COG2390         261 TPLNDRVIGLSLDDLRQIPKVIAVAGGESKAEAILAALRGGYI  303 (321)
T ss_pred             CCCCCCEECCCHHHHHCCCCEEEEECCCCCHHHHHHHHHCCCC
T ss_conf             5565716437788973278389995786028999999847998


No 174
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=93.31  E-value=0.2  Score=29.26  Aligned_cols=48  Identities=21%  Similarity=0.192  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             4998999999999879----99789999949-----998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .||++|.++|.+++.-    .|-++|-..+.     .+.+||+.|+.++++||...+
T Consensus       155 ~LT~~E~~LL~~L~~~~g~vvsr~~L~~~vw~~~~~~~~rtidv~I~rLR~KL~~~~  211 (229)
T PRK11083        155 SLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAIN  211 (229)
T ss_pred             CCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             599999999999986799409699999985599888884669999999999875268


No 175
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=93.12  E-value=0.094  Score=31.65  Aligned_cols=43  Identities=28%  Similarity=0.320  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             49989999999998---79997899999499988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +|-+-|..|-.|+.   .|+...||+.+|+||++||+.|+.+.++|
T Consensus        18 glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rr   63 (113)
T COG5625          18 GLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRR   63 (113)
T ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7783300155689884677417899999829999999999999985


No 176
>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=93.11  E-value=0.12  Score=30.90  Aligned_cols=45  Identities=29%  Similarity=0.371  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4998999999999-87999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      -||+||++|+.++ -+|++-||.+..||||.==|-.--+.+.+||.
T Consensus       206 iLserE~~ii~c~f~enlsQKeTGErlGiSQMHVSRl~R~ai~KL~  251 (256)
T TIGR02941       206 ILSEREKEIIECTFIENLSQKETGERLGISQMHVSRLQRRAIKKLK  251 (256)
T ss_pred             HCCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             0054456766655314787300232224035567788899999999


No 177
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=93.05  E-value=0.099  Score=31.51  Aligned_cols=30  Identities=33%  Similarity=0.489  Sum_probs=11.8

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999987999789999949998899999999
Q gi|254780693|r  182 LQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       182 L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      ..|-..|++..|||.+|++|..||.+.+.+
T Consensus        12 ~eL~~~Gls~geIAdELnvS~eT~~WLl~~   41 (201)
T PRK02277         12 LELRSEGLSTGEIADELNVSRETATWLLTR   41 (201)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999986997666355540269999999834


No 178
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=92.99  E-value=0.23  Score=28.96  Aligned_cols=47  Identities=13%  Similarity=0.100  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             49989999999998799----9789999949-----99889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|.+++...    |-++|-..+.     ++.+||+.|+.++++||.-.
T Consensus       154 ~LT~~E~~LL~~L~~~~g~vvsr~~L~~~vwg~~~~~~~rtldv~I~rLRkKl~~~  209 (229)
T PRK10161        154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPG  209 (229)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             70689999999999779987979999998639998988473999999999974567


No 179
>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=92.92  E-value=0.2  Score=29.35  Aligned_cols=56  Identities=21%  Similarity=0.310  Sum_probs=50.7

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             4499899999999-9879997899999499988999999999998079978999999
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK  227 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~  227 (235)
                      ..||+||+..|+| .-+|+|..+||.-=+.|..||-.+++.++.++=-.+|.++..+
T Consensus       165 ~~L~~rER~LLRLHfv~~Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La~R  221 (249)
T TIGR03001       165 AALSERERTLLRLHFVEGLSMDRLGAMYQVHRSTVSRWVAQARERLLERTRRRLAER  221 (249)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             328986876555688203329999877457750789999999999999999999997


No 180
>PRK09191 two-component response regulator; Provisional
Probab=92.81  E-value=0.3  Score=28.08  Aligned_cols=46  Identities=28%  Similarity=0.432  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             49989999999998-79997899999499988999999999998079
Q gi|254780693|r  173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .|||+.++.+.|.+ +|.+..|+|.+|++++..|..-+..+++-+..
T Consensus        88 ~ltp~~RqAlLL~alEgFs~~eaA~Il~v~~~e~~~l~~~A~~ei~~  134 (261)
T PRK09191         88 AITPLPRQAFLLTALEGFSEEEAAEILGVDPAEVAALLDDASREIAR  134 (261)
T ss_pred             HCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             48930349999898828988999999789999999999999999973


No 181
>CHL00148 orf27 Ycf27; Reviewed
Probab=92.80  E-value=0.25  Score=28.67  Aligned_cols=47  Identities=21%  Similarity=0.202  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHHC-------CCHHHHHHHHHHHHHHCCCC
Q ss_conf             49989999999998799----9789999949-------99889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKLG-------LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-------iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|..++.-.    |-++|-..+.       .+.+||+.|+.++++||+..
T Consensus       161 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vWg~~~~~~~~~r~vdv~I~rLRkKl~~~  218 (240)
T CHL00148        161 RLTGMEFSLLELLISESGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLEDD  218 (240)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             6589999999999967997496999999972888766787557999999999974107


No 182
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=92.80  E-value=0.33  Score=27.76  Aligned_cols=19  Identities=5%  Similarity=0.235  Sum_probs=11.9

Q ss_pred             HHHHHHHHHCCCCEEEEEE
Q ss_conf             9999999858378589984
Q gi|254780693|r   20 RLHLIQNRIKARNFALYTI   38 (235)
Q Consensus        20 ~l~~l~~~~~~~~f~~~~~   38 (235)
                      .+..+++.+++.||.-|..
T Consensus        50 TVvRf~kkLGf~Gf~efK~   68 (282)
T PRK11557         50 SVVKFAQKLGYKGFPALKL   68 (282)
T ss_pred             HHHHHHHHHCCCCHHHHHH
T ss_conf             9999999938998999999


No 183
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=92.75  E-value=0.21  Score=29.20  Aligned_cols=48  Identities=23%  Similarity=0.253  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             49989999999998799----9789999949-----998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .||++|.++|..+++-.    |-.+|-..+.     ...+||+.|++++++||+...
T Consensus       153 ~Lt~~Ef~lL~~L~~~~g~v~sR~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~  209 (229)
T COG0745         153 TLTPKEFELLELLARHPGRVLSREQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDP  209 (229)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCEEHHHHHHHHHHHCCCC
T ss_conf             178899999999996699526899999986086668764330599889999733567


No 184
>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=92.74  E-value=0.17  Score=29.90  Aligned_cols=45  Identities=33%  Similarity=0.346  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHH-----HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-----987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-----AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-----~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|++||++|+..     -..-+|-+|||..||||..=|-.==+++..||-
T Consensus       175 ~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~  224 (228)
T TIGR02846       175 VLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVSRIEKKALKKLY  224 (228)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             74088899998743668889541789987708650045488899999998


No 185
>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=92.64  E-value=0.23  Score=28.85  Aligned_cols=46  Identities=28%  Similarity=0.318  Sum_probs=40.9

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             4499899999999987999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .-||++|..||.|=..|.+-++||..|+-|...|-.-=++++.+..
T Consensus         5 tFLTe~Q~kVL~lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIe   50 (142)
T TIGR00721         5 TFLTERQIKVLELREKGLKQKEIAKILKTTRANVSIIEKRALENIE   50 (142)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             4340656899998633888788987726720137898887443237


No 186
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=92.51  E-value=0.46  Score=26.74  Aligned_cols=44  Identities=30%  Similarity=0.227  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             449989999999998--79997899999499988999999999998
Q gi|254780693|r  172 RNLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       172 ~~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      -+||+.|.+|-..+.  -..|..|||..++|+..+|...+++..+|
T Consensus         4 ~Gls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~k   49 (68)
T pfam01978         4 LGLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKK   49 (68)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             3989999999999998199889999999598898999999999988


No 187
>PRK11886 biotin--protein ligase; Provisional
Probab=92.48  E-value=0.34  Score=27.71  Aligned_cols=37  Identities=5%  Similarity=0.190  Sum_probs=21.0

Q ss_pred             HHCCHHHHCCHHHHHH-HHHHHHHHHCCCCEEEEEECC
Q ss_conf             0211986225999999-999999985837858998417
Q gi|254780693|r    4 NTLTGKKSSSLQELSP-RLHLIQNRIKARNFALYTINS   40 (235)
Q Consensus         4 ~~~~~~~~~sl~dl~~-~l~~l~~~~~~~~f~~~~~~~   40 (235)
                      +.+||++.+..-.+.+ .++..-+.+...||.+.+...
T Consensus        17 ~~~SGe~la~~LgvSR~aVwK~i~~L~~~G~~I~s~~~   54 (319)
T PRK11886         17 DFHSGEQLAEELGISRAAIWKHIQTLEEWGLDIFSVKG   54 (319)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             92969999998798899999999999977973999789


No 188
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=92.42  E-value=0.22  Score=29.10  Aligned_cols=38  Identities=29%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             CCCHHHHH-------HHH-HHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             49989999-------999-998799978999994999889999999
Q gi|254780693|r  173 NLTERETS-------CLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       173 ~LT~RE~e-------vL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      -+||.|.+       |++ ++..|+|-.+|+..+|+|..||-.=-+
T Consensus        26 l~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr   71 (88)
T pfam01371        26 LLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATITRGSN   71 (88)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             3999999999999999999997899899999985985231478899


No 189
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=92.40  E-value=0.082  Score=32.09  Aligned_cols=52  Identities=27%  Similarity=0.261  Sum_probs=41.8

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             4449989999999998799978999994999889999999999980799789
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRI  222 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~  222 (235)
                      ..-||+++.+||.+=.+|.|-+|||.+|+-+...|..-=++++.+..-.-+|
T Consensus         6 dtflte~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT   57 (143)
T COG1356           6 DTFLTEQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRALENIEKARNT   57 (143)
T ss_pred             HCEEEHHHEEEEEHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             1110023023565264056489999997545101799999999989999889


No 190
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.36  E-value=0.27  Score=28.38  Aligned_cols=35  Identities=29%  Similarity=0.165  Sum_probs=28.5

Q ss_pred             HHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             9999999879--9978999994999889999999999
Q gi|254780693|r  179 TSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       179 ~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      +.+...+-++  .|+.+||..+++|..||.+|++++-
T Consensus       177 k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~  213 (240)
T COG3398         177 KAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLE  213 (240)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             8999998628741599998870865999999999898


No 191
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=92.31  E-value=0.2  Score=29.40  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             4998999999999879----99789999949-----99889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|.++...    .|-++|-..+.     .+.+||+.|+.++++||...
T Consensus       149 ~LT~~E~~LL~~L~~~~~~vvsre~l~~~vw~~~~~~~~~sld~~I~rLRkKl~~~  204 (223)
T PRK10816        149 KLTAFEYTIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQ  204 (223)
T ss_pred             EECHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             70689999999999879923839999998549987888677999999999974335


No 192
>pfam03811 Ins_element1 Insertion element protein.
Probab=92.21  E-value=0.19  Score=29.51  Aligned_cols=36  Identities=19%  Similarity=0.242  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             999999999879997899999499988999999999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      -..+|+.+...|.--++||+.|+||.+||=.+|++.
T Consensus        52 vkeqiv~m~~nG~GiRdtaRvl~Is~nTVlrtLK~s   87 (88)
T pfam03811        52 TKEQIVDMAMNGAGCRYTARTLKIGINTVIRTLKNS   87 (88)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             789999997679854044787375689999987535


No 193
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=92.00  E-value=0.47  Score=26.69  Aligned_cols=18  Identities=6%  Similarity=0.026  Sum_probs=11.1

Q ss_pred             HHHHHHHHHCCCCEEEEE
Q ss_conf             999999985837858998
Q gi|254780693|r   20 RLHLIQNRIKARNFALYT   37 (235)
Q Consensus        20 ~l~~l~~~~~~~~f~~~~   37 (235)
                      .+..+++.+++.||.-|.
T Consensus        63 TVvRf~kkLGf~Gf~efK   80 (293)
T PRK11337         63 MIVKVAKLLGFSGFRNLR   80 (293)
T ss_pred             HHHHHHHHHCCCCHHHHH
T ss_conf             999999995789789999


No 194
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=91.97  E-value=0.45  Score=26.83  Aligned_cols=19  Identities=5%  Similarity=0.259  Sum_probs=11.3

Q ss_pred             HHHHHHHHHCCCCEEEEEE
Q ss_conf             9999999858378589984
Q gi|254780693|r   20 RLHLIQNRIKARNFALYTI   38 (235)
Q Consensus        20 ~l~~l~~~~~~~~f~~~~~   38 (235)
                      .+..+++.++++||.-|..
T Consensus        52 Tv~Rf~~kLGf~Gf~efk~   70 (281)
T COG1737          52 TVVRFARKLGFEGFSEFKL   70 (281)
T ss_pred             HHHHHHHHCCCCCHHHHHH
T ss_conf             9999999859998899999


No 195
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=91.91  E-value=0.34  Score=27.72  Aligned_cols=47  Identities=21%  Similarity=0.241  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC
Q ss_conf             49989999999998799----9789999949-----99889999999999980799
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .||++|.++|.+++.-.    |-++|-..+.     .+.+||+.|++++++||+..
T Consensus       151 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~~idv~I~rLRkKl~~~  206 (225)
T PRK10529        151 HLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQD  206 (225)
T ss_pred             CCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             13668999999999779961969999999649998988687999999999972007


No 196
>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=91.91  E-value=0.55  Score=26.19  Aligned_cols=38  Identities=34%  Similarity=0.327  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999999999879-99789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      --.+|+.++++| ++..||+..+++|+.||..|++..+.
T Consensus         3 ~Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~   41 (47)
T pfam01022         3 TRLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLRE   41 (47)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             899999999808996999999989588699999999989


No 197
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=91.56  E-value=0.55  Score=26.19  Aligned_cols=45  Identities=27%  Similarity=0.284  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             4449989999999998--79997899999499988999999999998
Q gi|254780693|r  171 ARNLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      .-+||+.|..||..+.  .|.|..+||..++++..||...++++-+|
T Consensus         5 ~~glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~   51 (101)
T smart00347        5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK   51 (101)
T ss_pred             HCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC
T ss_conf             13949999999999997699799999999896887999999999458


No 198
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=91.32  E-value=0.68  Score=25.52  Aligned_cols=43  Identities=26%  Similarity=0.322  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHHHHHCCC--CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             449989999999998799--9789999949998899999999999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGY--TSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~--t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      ..|++-+.++|..+..+.  +..+||..+|+|+.||...++++-+
T Consensus         4 ~~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~   48 (154)
T COG1522           4 MKLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEE   48 (154)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             553799999999999727657999999979798999999999998


No 199
>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=91.12  E-value=0.69  Score=25.47  Aligned_cols=42  Identities=33%  Similarity=0.320  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9989999999998--79997899999499988999999999998
Q gi|254780693|r  174 LTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       174 LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ||.-|..||..+.  .|.+..+||..++++..||-.-++++-+|
T Consensus         1 lT~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~   44 (59)
T pfam01047         1 LTLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKK   44 (59)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             98999999999994699299999999885865499999999889


No 200
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.03  E-value=0.56  Score=26.12  Aligned_cols=51  Identities=22%  Similarity=0.168  Sum_probs=41.6

Q ss_pred             CCCCCCCHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             8744499899999999987-99978999994999889999999999980799
Q gi|254780693|r  169 SAARNLTERETSCLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       169 ~~~~~LT~RE~evL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .+-+.||+-|.+.+.+.-+ -..-|||-+.||+|..||+..+..+.+++|-.
T Consensus        37 s~F~~Lt~d~LeFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~vlramgy~   88 (122)
T COG3877          37 SKFEYLTSDQLEFVELFLRCRGNLKEVERELGISYPTVRTKLDEVLRAMGYN   88 (122)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCC
T ss_conf             6332358757689999999725799999997776178998999999980899


No 201
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303   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 and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=90.63  E-value=1.3  Score=23.48  Aligned_cols=48  Identities=27%  Similarity=0.248  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCC
Q ss_conf             499899999999-98799978999994999889999999999980-7997
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL-DAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL-g~~n  220 (235)
                      .|||-|+-|.-| =+-++.-+|||.++|.|+..++.-..++++|| ...-
T Consensus       109 rL~P~ERAVF~LREVF~y~Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~r  158 (287)
T TIGR02957       109 RLSPLERAVFLLREVFDYDYEEIASIVGKSEANCRQLVSRARRHLRAARR  158 (287)
T ss_pred             HCCHHHHHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             07978999999998745882678976068957999999999999975288


No 202
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=90.56  E-value=0.99  Score=24.38  Aligned_cols=40  Identities=15%  Similarity=0.243  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             998999999999879--9978999994999889999999999
Q gi|254780693|r  174 LTERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       174 LT~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      |.+--+.+|+.+.+-  .|+.|||..+|+|+.||...++++.
T Consensus         7 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe   48 (153)
T PRK11179          7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK   48 (153)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             789999999999984899999999998929999999999999


No 203
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=90.45  E-value=0.53  Score=26.31  Aligned_cols=42  Identities=29%  Similarity=0.435  Sum_probs=38.4

Q ss_pred             CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             499899999999987--999789999949998899999999999
Q gi|254780693|r  173 NLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       173 ~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .++.|+..|+.|+.+  =.|+++++.+|++|..|+..++.+..+
T Consensus       399 ~~~~~~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~  442 (467)
T COG2865         399 SLSERQEKILELIKENGKVTARELREILGISSETIRRRIANLVK  442 (467)
T ss_pred             CHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf             76677899999975266558899998857564569999999844


No 204
>PRK11173 two-component response regulator; Provisional
Probab=90.40  E-value=0.59  Score=25.98  Aligned_cols=48  Identities=13%  Similarity=0.143  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             49989999999998799----978999994-----9998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .||++|.++|.+++.-.    |-++|-..+     ..+.+||+.|+.++++||+...
T Consensus       160 ~Lt~~E~~lL~~L~~~~~~vvsR~~L~~~vwg~~~~~~~r~ld~~I~rLRkKl~~~~  216 (237)
T PRK11173        160 KLPRSEFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTP  216 (237)
T ss_pred             ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             769999999999986799876899999996198878885869999999999765279


No 205
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=90.36  E-value=0.53  Score=26.30  Aligned_cols=56  Identities=23%  Similarity=0.325  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             4499899999999-9879997899999499988999999999998079978999999
Q gi|254780693|r  172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK  227 (235)
Q Consensus       172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~  227 (235)
                      ..|++||+++|++ .-+|.|-+.||..=+.+..||-.++..+...|--.+|-....+
T Consensus        23 a~L~~~eR~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~~Tr~~LaeR   79 (106)
T TIGR02233        23 AALSERERTLLRLHHVEGLSLDRLGTLYGVHRSTVARWVAGARELLLERTRQELAER   79 (106)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             528963335666776236558999988478861699999999999999989987674


No 206
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=90.29  E-value=0.54  Score=26.27  Aligned_cols=35  Identities=31%  Similarity=0.469  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999999987999789999949998899999999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      |-.-...|+-+|+|-.+||..||||+..|..|++.
T Consensus        11 Ra~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~   45 (119)
T COG2522          11 RALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG   45 (119)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             99999999995886999999968889999999736


No 207
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=90.16  E-value=0.78  Score=25.11  Aligned_cols=13  Identities=15%  Similarity=0.164  Sum_probs=7.1

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             4998999999999
Q gi|254780693|r  173 NLTERETSCLQLA  185 (235)
Q Consensus       173 ~LT~RE~evL~l~  185 (235)
                      .||+-|.+-|+-+
T Consensus       100 ~ls~~el~~L~~~  112 (115)
T pfam03965       100 KLSPDDIEELREL  112 (115)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             9999999999998


No 208
>pfam08461 HTH_12 Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
Probab=90.02  E-value=0.56  Score=26.17  Aligned_cols=34  Identities=21%  Similarity=0.244  Sum_probs=27.0

Q ss_pred             HHHHHHHCC---CCHHHHHHHH-----CCCHHHHHHHHHHHH
Q ss_conf             999999879---9978999994-----999889999999999
Q gi|254780693|r  180 SCLQLAGDG---YTSEEIAEKL-----GLSVHTVNAYLGSAT  213 (235)
Q Consensus       180 evL~l~a~G---~t~~eIA~~L-----~iS~~TV~~hl~~i~  213 (235)
                      |||+.++.-   .++++||..|     .|+++||++|++.+=
T Consensus         2 eILriL~~~~~Pigak~ia~~L~~rG~~i~eRaVRYhL~~Ld   43 (66)
T pfam08461         2 EILRILAESDKPIGAKIIAEELNLRGYDIGERAVRYHLRILD   43 (66)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             789999985998649999999998285840899999999998


No 209
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=89.95  E-value=0.97  Score=24.43  Aligned_cols=43  Identities=21%  Similarity=0.218  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9999999998799978999994999889999999999980799
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      +..+++..+++=.+-...|..|+||+.||-.+++++-..||+.
T Consensus         2 ~~l~~f~~v~~~gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~   44 (60)
T pfam00126         2 RQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVP   44 (60)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
T ss_conf             7799999999809999999997989889999999999995997


No 210
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=89.72  E-value=1.6  Score=22.97  Aligned_cols=52  Identities=23%  Similarity=0.309  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             4998999999999-----879997899999499988999999999998079978999
Q gi|254780693|r  173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      .|||||.+||++=     ..-+|=+|++...+|+.-=|+.-=+++.+||--.+|...
T Consensus       557 ~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~r~~~  613 (620)
T PRK05658        557 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRK  613 (620)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             799999999999579999996789999988297689899999999998568725788


No 211
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=89.58  E-value=1.1  Score=24.08  Aligned_cols=19  Identities=16%  Similarity=0.319  Sum_probs=9.2

Q ss_pred             CHHHHHHHHHHHHHHHCCC
Q ss_conf             5999999999999985837
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~   31 (235)
                      |-..+...+..+.+.++..
T Consensus        28 sQ~avS~~i~~LE~~lg~~   46 (292)
T PRK11242         28 SQPTLSQQIRQLEESLGVQ   46 (292)
T ss_pred             CHHHHHHHHHHHHHHHCCE
T ss_conf             9899999999999996987


No 212
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=89.53  E-value=1.4  Score=23.35  Aligned_cols=14  Identities=7%  Similarity=0.188  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999999998583
Q gi|254780693|r   17 LSPRLHLIQNRIKA   30 (235)
Q Consensus        17 l~~~l~~l~~~~~~   30 (235)
                      +...+..+.+.++.
T Consensus        33 VS~~I~~LE~~LG~   46 (300)
T PRK11074         33 VSYTVRQLEEWLAV   46 (300)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             99999999999599


No 213
>PRK13856 two-component response regulator VirG; Provisional
Probab=89.49  E-value=0.31  Score=27.95  Aligned_cols=48  Identities=15%  Similarity=0.047  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC
Q ss_conf             449989999999998799----978999994-----999889999999999980799
Q gi|254780693|r  172 RNLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      ..||++|.++|.+++...    |-.+|-..+     .++.+||+.|+.++++||.-.
T Consensus       154 v~LT~~E~~lL~~L~~~~~~vvsRe~L~~~~~~~~~~~~~r~id~~I~rLRkKL~~~  210 (241)
T PRK13856        154 VKLTAGEFNLLVAFLEKPRDVLSREQLLIASRVREEEVYDRSIDVLILRLRRKLEQD  210 (241)
T ss_pred             EECCHHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             867889999999998769943819999998445677888686999999999973138


No 214
>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=89.16  E-value=1.1  Score=24.03  Aligned_cols=49  Identities=20%  Similarity=0.126  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             44998999999999879------997899999499988999999999998079978999
Q gi|254780693|r  172 RNLTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      +.||+.|+.|+.++..-      +|..++|...|+|+.||-    +..+|||..+=.+.
T Consensus        12 ~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~----Rf~kklG~~Gf~ef   66 (106)
T pfam01418        12 SKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVV----RFCRKLGFSGFSDL   66 (106)
T ss_pred             HHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHH----HHHHHHCCCCHHHH
T ss_conf             76499999999999929999988339999989699899999----99999589989999


No 215
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=89.00  E-value=0.86  Score=24.81  Aligned_cols=39  Identities=26%  Similarity=0.239  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             98999999999879--99789999949998899999999999
Q gi|254780693|r  175 TERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       175 T~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      +.+...++.+ +.|  .|-.+||..||||+.+|..|++.++.
T Consensus         5 ~~~~~~ll~~-~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~   45 (79)
T COG1654           5 SQMLLLLLLL-LTGNFVSGEKLAEELGISRTAVWKHIQQLRE   45 (79)
T ss_pred             HHHHHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             8999999997-3799666899999978659999999999998


No 216
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=88.72  E-value=1.6  Score=22.88  Aligned_cols=26  Identities=19%  Similarity=0.192  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             49989999999998799978999994
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKL  198 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L  198 (235)
                      .||+.-...+.++..-.+-.+|+..|
T Consensus       279 ~Ls~~a~~Fie~l~~~l~~~~~~~~~  304 (308)
T PRK12683        279 YLRGYAYRFIEMFAPHLSEAEIAGAL  304 (308)
T ss_pred             CCCHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf             57999999999988862989999987


No 217
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=88.65  E-value=0.88  Score=24.73  Aligned_cols=34  Identities=35%  Similarity=0.335  Sum_probs=26.8

Q ss_pred             HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9999987-999789999949998899999999999
Q gi|254780693|r  181 CLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       181 vL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      ++.++.+ .++..||+..+++|+.||..|++.+.+
T Consensus         2 Il~~L~~~~~~~~ela~~l~is~~tvs~HL~~L~~   36 (66)
T smart00418        2 ILKLLAEGELCVCELAEILGLSQSTVSHHLKKLRE   36 (66)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             58897739966999999988298888799999998


No 218
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=88.61  E-value=1.2  Score=23.76  Aligned_cols=42  Identities=31%  Similarity=0.272  Sum_probs=36.4

Q ss_pred             CCHHHHHHHHHHHCCCCH--HHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             998999999999879997--899999499988999999999998
Q gi|254780693|r  174 LTERETSCLQLAGDGYTS--EEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~--~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ||+.|..+|..+......  .+||..|+++..||..+++++-+|
T Consensus        20 l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~   63 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK   63 (126)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             99899999999998489999999999787888899999999988


No 219
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=88.58  E-value=0.79  Score=25.08  Aligned_cols=19  Identities=16%  Similarity=0.001  Sum_probs=13.6

Q ss_pred             CCCCHHHHHHHHHHHCCCC
Q ss_conf             4499899999999987999
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYT  190 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t  190 (235)
                      .-+|.||..+..++..|--
T Consensus       152 ~~~s~~E~~i~k~~~~~e~  170 (279)
T COG5484         152 TWYSAREAFIDKLTTKQEM  170 (279)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             1246788888876521356


No 220
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=88.29  E-value=1.5  Score=23.01  Aligned_cols=38  Identities=26%  Similarity=0.364  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99999999987---999789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      |=.+||.+++.   +.+.+|||..+|++..||..++....+
T Consensus         4 r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~   44 (52)
T pfam09339         4 RALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVE   44 (52)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999999862899989999999989199999999999998


No 221
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=88.21  E-value=2  Score=22.27  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=18.7

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             9989999999998799978999994
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKL  198 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L  198 (235)
                      |++-=.+.+.+.+...|.++|.+.+
T Consensus       280 l~~~~~~Fi~~~~~~l~~~~~~~~~  304 (316)
T PRK12679        280 QRNYVWRFLELCNAGLSVEDIKRQV  304 (316)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             5699999999752028999999998


No 222
>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=88.17  E-value=0.67  Score=25.59  Aligned_cols=28  Identities=25%  Similarity=0.325  Sum_probs=18.7

Q ss_pred             HHCC-CCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9879-997899999499988999999999
Q gi|254780693|r  185 AGDG-YTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       185 ~a~G-~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      +.+| .|+-+||..|+||+-.|+.|+|..
T Consensus        11 L~~Gq~sA~~lA~~L~iSpQAvRrHLKDL   39 (215)
T TIGR02702        11 LKEGQASALALAEELAISPQAVRRHLKDL   39 (215)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             86004889999997278867887654332


No 223
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=87.92  E-value=1.4  Score=23.35  Aligned_cols=39  Identities=31%  Similarity=0.390  Sum_probs=18.1

Q ss_pred             CCHHHHHHHHHHH-----CC-CCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9989999999998-----79-997899999499988999999999
Q gi|254780693|r  174 LTERETSCLQLAG-----DG-YTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       174 LT~RE~evL~l~a-----~G-~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      +|+++-+.|.-+-     .| -..++||..|+||+.||...+++.
T Consensus         4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL   48 (154)
T COG1321           4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRL   48 (154)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             421689999999999843687519999998589927899999999


No 224
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=87.90  E-value=1.9  Score=22.38  Aligned_cols=19  Identities=11%  Similarity=0.235  Sum_probs=9.1

Q ss_pred             CHHHHHHHHHHHHHHHCCC
Q ss_conf             5999999999999985837
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~   31 (235)
                      |-..+...+..+.+.++..
T Consensus        32 sQpavS~~I~~LE~~lg~~   50 (307)
T CHL00180         32 SQPAVSLQIQNLEKQLNIP   50 (307)
T ss_pred             CHHHHHHHHHHHHHHHCCE
T ss_conf             8789999999999986999


No 225
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=87.68  E-value=2.1  Score=22.05  Aligned_cols=44  Identities=16%  Similarity=0.160  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             4499899999999987---9997899999499988999999999998
Q gi|254780693|r  172 RNLTERETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      -+||+-+..||..+.+   |.|.+|+|..++|...||-..++++-+|
T Consensus        27 ~gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~   73 (144)
T PRK03573         27 LELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEK   73 (144)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             69982599999999973989899999999798783699999999988


No 226
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=87.55  E-value=1.7  Score=22.65  Aligned_cols=21  Identities=10%  Similarity=0.420  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHCCCCEEEEEEC
Q ss_conf             999999998583785899841
Q gi|254780693|r   19 PRLHLIQNRIKARNFALYTIN   39 (235)
Q Consensus        19 ~~l~~l~~~~~~~~f~~~~~~   39 (235)
                      +.+..+++.+++.||.-|...
T Consensus        49 aTV~Rf~kkLGf~Gf~efK~~   69 (284)
T PRK11302         49 PTVNRFCRSLDTKGFPDFKLH   69 (284)
T ss_pred             HHHHHHHHHHCCCCHHHHHHH
T ss_conf             899999999578978999999


No 227
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=87.53  E-value=1.8  Score=22.46  Aligned_cols=17  Identities=12%  Similarity=0.145  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+...+..+.+.++..
T Consensus        36 pavS~~I~~LE~eLG~~   52 (312)
T PRK10341         36 PAVSKIINDIEDYFGVE   52 (312)
T ss_pred             HHHHHHHHHHHHHHCCE
T ss_conf             89999999999984985


No 228
>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=87.16  E-value=0.94  Score=24.52  Aligned_cols=31  Identities=35%  Similarity=0.511  Sum_probs=25.6

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999987999789999949998899999999
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .-.|--+|.+.+|||..||++++||.+-.++
T Consensus         6 Ar~LY~qg~~~~eIA~~Lg~~~~tVysWk~r   36 (58)
T pfam06056         6 ARTLYWQGYRPAEIAQELGLKARTVYSWKDR   36 (58)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             9999996898999999978993145658652


No 229
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=87.15  E-value=2.2  Score=21.84  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=13.3

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             9989999999998799978999994
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKL  198 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L  198 (235)
                      ||+.-+..+.++.+-++-+-+-..|
T Consensus       280 ls~~~r~FIe~l~e~l~r~~~~~~~  304 (313)
T PRK12684        280 LRGYVYTFIELFSPTLNRKLVEQAL  304 (313)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             6899999999987465989999998


No 230
>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=87.05  E-value=0.61  Score=25.88  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=20.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99789999949998899999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      +|.+|.|..||||+.|++...++
T Consensus         1 lt~~e~A~~lgVs~~TlrrW~~~   23 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             98899999979899999999987


No 231
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=86.53  E-value=2.4  Score=21.61  Aligned_cols=12  Identities=8%  Similarity=0.279  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHHC
Q ss_conf             999999999858
Q gi|254780693|r   18 SPRLHLIQNRIK   29 (235)
Q Consensus        18 ~~~l~~l~~~~~   29 (235)
                      ..++..+.+.++
T Consensus        38 S~~I~~LE~~lG   49 (295)
T PRK11139         38 SHQIKALEDFLG   49 (295)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999859


No 232
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=86.45  E-value=1.1  Score=24.13  Aligned_cols=38  Identities=24%  Similarity=0.251  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99999999987999789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      +=.++|+-...+.|..|||..+|||.-|++.|+.-.-.
T Consensus       166 ~v~~~l~~~~~~~ta~eva~~~giSrvTaRRYLe~L~~  203 (225)
T PRK10046        166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCAS  203 (225)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999971799868999999858519999999999986


No 233
>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=86.15  E-value=1.9  Score=22.35  Aligned_cols=42  Identities=26%  Similarity=0.385  Sum_probs=33.9

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             74449989999999998799978999994999889999999999
Q gi|254780693|r  170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      ....|||||.|  ..|..|.|..|||...|+++.-|+.|-.-+.
T Consensus        52 ~~~~lspreIQ--arIRaGas~eevA~~~g~~~~rVerfa~PVl   93 (169)
T pfam11268        52 VDPTLSPREIQ--ARIRAGASAEEVAEAAGVPEERVERFEGPVL   93 (169)
T ss_pred             CCCCCCHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHCCCHHH
T ss_conf             47888989999--9988799999999995999999874223388


No 234
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=86.09  E-value=2.5  Score=21.46  Aligned_cols=17  Identities=18%  Similarity=0.141  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+...+..+.+.++..
T Consensus        33 pavS~~I~~LE~~LG~~   49 (309)
T PRK11013         33 PTVSRELARFEQVIGLT   49 (309)
T ss_pred             HHHHHHHHHHHHHHCCE
T ss_conf             89999999999997999


No 235
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family; InterPro: IPR014296   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 family of RNA polymerase sigma factors is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors, as two proteins from this family are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these do not apparently represent the same two sigma factors in each species). One of these proteins is designated as SigM in B. subtilis (SP: SIGM_BACSU) and is activated by various stressors , .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=86.00  E-value=0.72  Score=25.34  Aligned_cols=45  Identities=33%  Similarity=0.320  Sum_probs=36.8

Q ss_pred             CCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             998999999999-879997899999499988999999999998079
Q gi|254780693|r  174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       174 LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      |-.-.++||-|. -.|.|-+|||..||+|..-||.-+=++++.|..
T Consensus       114 Lpe~yr~vl~Lr~~~efSYkEia~~~n~sl~~vK~~LfRaR~eLk~  159 (162)
T TIGR02950       114 LPENYRTVLLLREFKEFSYKEIAELLNLSLAKVKSELFRARKELKK  159 (162)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             7087656567543126688899998456022100444487799987


No 236
>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=86.00  E-value=0.83  Score=24.92  Aligned_cols=19  Identities=11%  Similarity=0.111  Sum_probs=8.2

Q ss_pred             EEEECCCCCCEEEEECCCCCC
Q ss_conf             972168875234541058878
Q gi|254780693|r  120 FPVRLGFHKNGYVIFTSEFLM  140 (235)
Q Consensus       120 ~pv~~~~~~~~~~~~~~~~~~  140 (235)
                      .|+.++..  --+.|++....
T Consensus       120 WPiGdP~~--~dF~FCG~~~~  138 (162)
T pfam07750       120 WPIGDPLS--EDFAFCGNKSS  138 (162)
T ss_pred             CCCCCCCC--CCCCCCCCCCC
T ss_conf             88889898--88654288898


No 237
>PRK09801 transcriptional activator TtdR; Provisional
Probab=85.95  E-value=2.6  Score=21.41  Aligned_cols=13  Identities=8%  Similarity=0.317  Sum_probs=6.3

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             9989999999998
Q gi|254780693|r  174 LTERETSCLQLAG  186 (235)
Q Consensus       174 LT~RE~evL~l~a  186 (235)
                      +++|=+-++.|+.
T Consensus       281 ~~~rvr~fidfl~  293 (310)
T PRK09801        281 RSMKLRVCVEFLA  293 (310)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             7879999999999


No 238
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=85.90  E-value=1.4  Score=23.25  Aligned_cols=30  Identities=30%  Similarity=0.427  Sum_probs=19.3

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999999879997899999499988999999
Q gi|254780693|r  180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      +|..++..|++.+|||...|+|++.|.-|.
T Consensus       189 rV~~l~~kg~~~~ei~~~tG~s~~lv~eY~  218 (220)
T pfam07900       189 RVEKLTEKGMSEEEIRYITGISERLVEEYV  218 (220)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999867879999999776589999997


No 239
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=85.79  E-value=1.6  Score=22.82  Aligned_cols=15  Identities=7%  Similarity=0.060  Sum_probs=5.7

Q ss_pred             HCCCHHHHHHHHHHH
Q ss_conf             499988999999999
Q gi|254780693|r  198 LGLSVHTVNAYLGSA  212 (235)
Q Consensus       198 L~iS~~TV~~hl~~i  212 (235)
                      +-++.+-.+.+++++
T Consensus       231 vv~t~~ml~~~~~~l  245 (260)
T COG1497         231 VVITRRMLRYLLRKL  245 (260)
T ss_pred             EEEEHHHHHHHHHHH
T ss_conf             997077799999888


No 240
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=85.68  E-value=2.7  Score=21.32  Aligned_cols=17  Identities=12%  Similarity=0.282  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+...+..+.+.++..
T Consensus        30 pavS~~I~~LE~~LG~~   46 (305)
T PRK11151         30 PTLSGQIRKLEDELGVM   46 (305)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             89999999999997986


No 241
>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=85.58  E-value=1.7  Score=22.67  Aligned_cols=38  Identities=18%  Similarity=0.145  Sum_probs=29.9

Q ss_pred             HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             99999-987999789999949998899999999999807
Q gi|254780693|r  180 SCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       180 evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      +++.+ +..|+|..+||..+|||+.|+..-++....-+.
T Consensus        14 ~~V~~~~~~g~sv~~var~~gi~~~~l~~W~k~~~~g~~   52 (75)
T pfam01527        14 RAVKESLEPGASVSELAREHGVSPATLYKWRKKYRGGLL   52 (75)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCC
T ss_conf             999999809984999999989599999999999846898


No 242
>PRK01381 Trp operon repressor; Provisional
Probab=85.30  E-value=0.99  Score=24.38  Aligned_cols=35  Identities=26%  Similarity=0.377  Sum_probs=27.8

Q ss_pred             CCCHHHHH-------HHHHHHCC-CCHHHHHHHHCCCHHHHHH
Q ss_conf             49989999-------99999879-9978999994999889999
Q gi|254780693|r  173 NLTERETS-------CLQLAGDG-YTSEEIAEKLGLSVHTVNA  207 (235)
Q Consensus       173 ~LT~RE~e-------vL~l~a~G-~t~~eIA~~L~iS~~TV~~  207 (235)
                      -|||.|++       |.+.+..| +|-+|||..||+|.-||-.
T Consensus        32 lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITR   74 (99)
T PRK01381         32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR   74 (99)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCC
T ss_conf             7899999999999999999994876499999984974020000


No 243
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=85.25  E-value=2.8  Score=21.18  Aligned_cols=18  Identities=17%  Similarity=0.289  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999985837
Q gi|254780693|r   14 LQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        14 l~dl~~~l~~l~~~~~~~   31 (235)
                      -..+...+..+.+.++..
T Consensus        33 QpavS~~I~~LE~~lg~~   50 (302)
T PRK09791         33 QPALSKSIQELEEGLAAQ   50 (302)
T ss_pred             HHHHHHHHHHHHHHHCCE
T ss_conf             799999999999995996


No 244
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=84.90  E-value=2.9  Score=21.08  Aligned_cols=57  Identities=30%  Similarity=0.374  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHCC
Q ss_conf             899999999987---9997899999499988999999999998-----07997899999999769
Q gi|254780693|r  176 ERETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATVK-----LDAVNRIQAIAKAIRFG  232 (235)
Q Consensus       176 ~RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~K-----Lg~~nR~qava~A~~~G  232 (235)
                      .|=.+||..+++   +.|..|||..+|++..||..+++.....     -....++....+..++|
T Consensus         5 ~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~~~~~~~Y~lG~~~~~lg   69 (91)
T smart00346        5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELG   69 (91)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEECHHHHHHH
T ss_conf             99999999997289998999999998909999999999999889968849999775309999999


No 245
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.87  E-value=2.5  Score=21.53  Aligned_cols=44  Identities=25%  Similarity=0.307  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             499899999999-98799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      -||.++...+.+ ..+-+|-.|||...+||...|..++++--..|
T Consensus        17 LLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L   61 (105)
T COG2739          17 LLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKIL   61 (105)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             986889999999998116699999995750999999999999999


No 246
>pfam07374 DUF1492 Protein of unknown function (DUF1492). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281.
Probab=84.78  E-value=1.5  Score=23.05  Aligned_cols=42  Identities=24%  Similarity=0.200  Sum_probs=35.9

Q ss_pred             HHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             8999999999-87999789999949998899999999999807
Q gi|254780693|r  176 ERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       176 ~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      |-++-||++. -++++.++|+.+|++|..|+...++.+.+-||
T Consensus        58 p~~RtvL~m~Yid~~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L~  100 (100)
T pfam07374        58 PDSRTILRMVYIDKMTVWQVCDKLNCSRTTYYRKLRVAIKELN  100 (100)
T ss_pred             HHHHHHHEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             0221311143443474999999976666789999999998529


No 247
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=84.40  E-value=3  Score=20.93  Aligned_cols=19  Identities=16%  Similarity=0.235  Sum_probs=8.4

Q ss_pred             CHHHHHHHHHHHHHHHCCC
Q ss_conf             5999999999999985837
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~   31 (235)
                      |-.-+...+..+.+.++..
T Consensus        29 SQPaVSkqIk~LE~eLGv~   47 (327)
T PRK12680         29 TQPGLSKQLKQLEDELGFL   47 (327)
T ss_pred             CHHHHHHHHHHHHHHHCCE
T ss_conf             7679999999999985996


No 248
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=84.23  E-value=2  Score=22.24  Aligned_cols=41  Identities=29%  Similarity=0.329  Sum_probs=32.4

Q ss_pred             CCCH-HHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             4998-9999999998---799978999994999889999999999
Q gi|254780693|r  173 NLTE-RETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       173 ~LT~-RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      +|++ -...|..|+.   +++|..|.|..+|||.-|++.|+.=.-
T Consensus       154 Gi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~  198 (224)
T COG4565         154 GLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLV  198 (224)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             767999999999986757764799999883721999999999998


No 249
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.21  E-value=1.5  Score=23.03  Aligned_cols=39  Identities=18%  Similarity=0.254  Sum_probs=17.9

Q ss_pred             CCHHHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             99899999999987-9-997899999499988999999999
Q gi|254780693|r  174 LTERETSCLQLAGD-G-YTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       174 LT~RE~evL~l~a~-G-~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      |-+--+.+|..+-+ | .|+.|||..+|+|+.||...++++
T Consensus        12 LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrL   52 (164)
T PRK11169         12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRL   52 (164)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             51999999999998489999999999892999999999999


No 250
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242).
Probab=84.20  E-value=3.1  Score=20.87  Aligned_cols=19  Identities=16%  Similarity=0.366  Sum_probs=8.7

Q ss_pred             CHHHHHHHHHHHHHHHCCC
Q ss_conf             5999999999999985837
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~   31 (235)
                      |-..+..++..+.+.++..
T Consensus        28 sqsaVS~~I~~LE~~LG~~   46 (292)
T TIGR03298        28 TPSAVSQRIKALEERLGQP   46 (292)
T ss_pred             CHHHHHHHHHHHHHHHCCH
T ss_conf             8789999999999982962


No 251
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.96  E-value=1.5  Score=23.16  Aligned_cols=26  Identities=42%  Similarity=0.437  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99789999949998899999999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      +|.+|||..+|+|+.||...++...+
T Consensus         9 lt~~~iA~~lG~tretvsR~l~~l~~   34 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEK   34 (48)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             79999999979979999999999998


No 252
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.80  E-value=1.2  Score=23.77  Aligned_cols=38  Identities=29%  Similarity=0.398  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHCCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             89999999998799-----978999994999889999999999
Q gi|254780693|r  176 ERETSCLQLAGDGY-----TSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       176 ~RE~evL~l~a~G~-----t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      .+-.-|..|-..|.     ....+|..|+||++||..|++.+.
T Consensus       174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k  216 (220)
T COG2964         174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFK  216 (220)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             7899999998667641144899999996887589999999865


No 253
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=83.45  E-value=2.9  Score=21.02  Aligned_cols=38  Identities=13%  Similarity=0.116  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99999999987-9-99789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGD-G-YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      -=..|+.++.+ | ++.-||+..|++|..||-.|++-+..
T Consensus        15 tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~   54 (106)
T PRK10141         15 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE   54 (106)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             9999999998749956999998869988899999999998


No 254
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=83.28  E-value=2.8  Score=21.10  Aligned_cols=42  Identities=31%  Similarity=0.302  Sum_probs=31.7

Q ss_pred             HHHHHHHHH---CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             999999998---79-9978999994999889999999999980799
Q gi|254780693|r  178 ETSCLQLAG---DG-YTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       178 E~evL~l~a---~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      |.-||..+.   .+ -|..+||..|||+.+.||.++-++.++=.|.
T Consensus         8 eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~LY~L~k~g~v~   53 (68)
T smart00550        8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC   53 (68)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf             9999999997488640399999994998999999999999748831


No 255
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=83.27  E-value=1.8  Score=22.53  Aligned_cols=42  Identities=21%  Similarity=0.262  Sum_probs=30.1

Q ss_pred             CCCHHHH-HHHHHH---HCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             4998999-999999---879-99789999949998899999999999
Q gi|254780693|r  173 NLTERET-SCLQLA---GDG-YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       173 ~LT~RE~-evL~l~---a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      +|++--. .|...+   ..| .|..|||..+|||.-|++.|+.-.-.
T Consensus       158 Gl~~~TL~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999999999999827999846999998858529889999999986


No 256
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=82.91  E-value=3.4  Score=20.51  Aligned_cols=20  Identities=10%  Similarity=0.218  Sum_probs=11.2

Q ss_pred             CHHHHHHHHHHHHHHHCCCC
Q ss_conf             59999999999999858378
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKARN   32 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~~   32 (235)
                      |-..+..++..+.+.++..-
T Consensus        29 sqsavS~~I~~LE~~LG~~L   48 (294)
T PRK13348         29 TRSAVSQRIKALEESLGQPL   48 (294)
T ss_pred             CHHHHHHHHHHHHHHHCCEE
T ss_conf             87899999999999839843


No 257
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=82.22  E-value=3.6  Score=20.34  Aligned_cols=12  Identities=0%  Similarity=0.271  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998583
Q gi|254780693|r   19 PRLHLIQNRIKA   30 (235)
Q Consensus        19 ~~l~~l~~~~~~   30 (235)
                      ..+..+.+.++.
T Consensus        34 ~~I~~LE~~LG~   45 (305)
T PRK11233         34 QQVATLEGELNQ   45 (305)
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999999699


No 258
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=82.10  E-value=3.7  Score=20.31  Aligned_cols=19  Identities=16%  Similarity=0.384  Sum_probs=9.2

Q ss_pred             CHHHHHHHHHHHHHHHCCC
Q ss_conf             5999999999999985837
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~   31 (235)
                      |-..+..++..+.+.++..
T Consensus        29 tqsaVS~~I~~LE~~LG~~   47 (295)
T PRK03635         29 TQSAVSQRIKALEERVGQP   47 (295)
T ss_pred             CHHHHHHHHHHHHHHHCCC
T ss_conf             8669999999999994972


No 259
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=82.07  E-value=3.7  Score=20.30  Aligned_cols=14  Identities=36%  Similarity=0.629  Sum_probs=5.2

Q ss_pred             CCCCHHHHHHHHCC
Q ss_conf             79997899999499
Q gi|254780693|r  187 DGYTSEEIAEKLGL  200 (235)
Q Consensus       187 ~G~t~~eIA~~L~i  200 (235)
                      .|+-..|+=.-+||
T Consensus       449 ~G~~~pevl~~~g~  462 (501)
T PRK04172        449 AGIFRPEVTEPLGI  462 (501)
T ss_pred             CCCCCHHHHHHCCC
T ss_conf             75788899975599


No 260
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=82.05  E-value=3.7  Score=20.30  Aligned_cols=29  Identities=28%  Similarity=0.218  Sum_probs=15.7

Q ss_pred             CEEEEEEECCCCCCEEEEECCCCCCCCHH
Q ss_conf             35899721688752345410588789989
Q gi|254780693|r  116 AGIAFPVRLGFHKNGYVIFTSEFLMLANE  144 (235)
Q Consensus       116 ~~~~~pv~~~~~~~~~~~~~~~~~~~~~~  144 (235)
                      .++..|++.+..-.+.++..+.......+
T Consensus       206 ~~vAvPi~~~g~vvaalsvs~p~~r~~~~  234 (264)
T PRK09834        206 ASIAVPVRSGQRVLACLNLVYIASAMSIE  234 (264)
T ss_pred             EEEEEEECCCCEEEEEEEEEEECCCCCHH
T ss_conf             99999971799299999996531229999


No 261
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=82.02  E-value=0.93  Score=24.56  Aligned_cols=44  Identities=27%  Similarity=0.388  Sum_probs=29.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             978999994999889999999999980799789999999976999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      |-++||...|+|..||-..+.+- .+....+|..--..|-.+||.
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln~~-~~Vs~~tr~rV~~~a~~lgY~   45 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNGN-GRVSEETREKVLAAMEELGYI   45 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHCCC
T ss_conf             89999999895999999997799-989999999999999997899


No 262
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=81.90  E-value=3.7  Score=20.26  Aligned_cols=18  Identities=17%  Similarity=0.235  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999985837
Q gi|254780693|r   14 LQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        14 l~dl~~~l~~l~~~~~~~   31 (235)
                      -..+...+..+.+.++..
T Consensus        29 QpalS~~I~~LE~~lG~~   46 (296)
T PRK09906         29 QPSLSQQIKDLENCVGVP   46 (296)
T ss_pred             HHHHHHHHHHHHHHHCCE
T ss_conf             789999999999985988


No 263
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=81.86  E-value=3.8  Score=20.25  Aligned_cols=11  Identities=27%  Similarity=0.362  Sum_probs=7.9

Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999999879
Q gi|254780693|r  178 ETSCLQLAGDG  188 (235)
Q Consensus       178 E~evL~l~a~G  188 (235)
                      -..++.++..|
T Consensus       222 ~~~~~~~v~~g  232 (297)
T COG0583         222 AEALLQAVAAG  232 (297)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999999969


No 264
>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=81.69  E-value=3.3  Score=20.67  Aligned_cols=24  Identities=21%  Similarity=0.243  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999789999949998899999999
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      ..+-.|+|..+|||+.||...+++
T Consensus        71 D~tl~E~A~~~gVs~~tI~~aLkr   94 (120)
T pfam01710        71 DAYLKERAKKFGVTPSSIHYALKK   94 (120)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             720999999839879999999999


No 265
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=81.67  E-value=3.8  Score=20.20  Aligned_cols=27  Identities=11%  Similarity=-0.052  Sum_probs=13.0

Q ss_pred             CEEEEEEECCCCCC-EEEEECCCCCCCC
Q ss_conf             35899721688752-3454105887899
Q gi|254780693|r  116 AGIAFPVRLGFHKN-GYVIFTSEFLMLA  142 (235)
Q Consensus       116 ~~~~~pv~~~~~~~-~~~~~~~~~~~~~  142 (235)
                      .++..||++..+.. +.++..+......
T Consensus       216 ~~iaaPV~d~~G~~vaAisv~gp~~r~~  243 (271)
T PRK10163        216 NCIASAIYDDVGSVVAAISISGPSSRLT  243 (271)
T ss_pred             EEEEEEEECCCCCEEEEEEEEEEHHHCC
T ss_conf             8999989889999999999976856579


No 266
>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=81.58  E-value=1  Score=24.20  Aligned_cols=21  Identities=24%  Similarity=0.390  Sum_probs=18.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999789999949998899999
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAY  208 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~h  208 (235)
                      .+++++||.+|++|+.||+.-
T Consensus        22 ~~~l~~IA~~L~vs~~~IrkW   42 (60)
T pfam10668        22 TMKLKDIANKLNVSESQIRKW   42 (60)
T ss_pred             CEEHHHHHHHHCCCHHHHHHC
T ss_conf             644999999968798887603


No 267
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=81.53  E-value=3.8  Score=20.17  Aligned_cols=39  Identities=31%  Similarity=0.312  Sum_probs=34.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             999998799978999994999889999999999980799
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      +.++.-.+.|-++||..-+||+-|++.-.+.+.+.|+..
T Consensus       269 a~~~~~~~~t~~~Ia~v~~vsevTIr~~ykel~~~l~~~  307 (310)
T PRK00423        269 ASLLEGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIK  307 (310)
T ss_pred             HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf             999948898999999896988999999999999984872


No 268
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=81.47  E-value=3.9  Score=20.16  Aligned_cols=17  Identities=12%  Similarity=0.386  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+..++..+.+.++..
T Consensus        43 saVS~~I~~LE~~LG~~   59 (311)
T PRK10086         43 SAVSHRINQLEEELGIK   59 (311)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             99999999999985984


No 269
>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=81.40  E-value=3.3  Score=20.64  Aligned_cols=43  Identities=21%  Similarity=0.298  Sum_probs=36.2

Q ss_pred             CCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             499899-9999999879997899999499988999999999998
Q gi|254780693|r  173 NLTERE-TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE-~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      .||-.| .+|++-+-+|.+..++|...||.+.||+.-++|--+-
T Consensus         6 ~LTl~eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knkeki   49 (53)
T pfam04218         6 SLTLREKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNKEKL   49 (53)
T ss_pred             EECHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             41699999999999858968899999698797999999809999


No 270
>pfam00376 MerR MerR family regulatory protein.
Probab=81.14  E-value=1.7  Score=22.72  Aligned_cols=22  Identities=36%  Similarity=0.395  Sum_probs=19.6

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9789999949998899999999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      |..|+|..+|||++|++++-+.
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~   22 (38)
T pfam00376         1 TIGEVAKLLGVSPRTLRYYEKI   22 (38)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHC
T ss_conf             9899999988799999999986


No 271
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.96  E-value=3  Score=20.94  Aligned_cols=39  Identities=31%  Similarity=0.381  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             999999999879--997899999499988999999999998
Q gi|254780693|r  177 RETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       177 RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      |..+++.++.+-  .+..+++..++||+.||+.-+..+-.+
T Consensus         1 R~~~Il~~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L~~~   41 (53)
T smart00420        1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQ   41 (53)
T ss_pred             CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             98999999998697979999999897999999969999988


No 272
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=80.88  E-value=4  Score=20.02  Aligned_cols=43  Identities=16%  Similarity=0.179  Sum_probs=29.9

Q ss_pred             CCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             49989999999998--79997899999499988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +||+.|..||..+.  .|.|..|+|..+++...||-..+.++-+|
T Consensus        37 gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~   81 (144)
T PRK11512         37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK   81 (144)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999999999999998699799999999788887899999999978


No 273
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=80.82  E-value=1.2  Score=23.84  Aligned_cols=44  Identities=25%  Similarity=0.358  Sum_probs=31.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             978999994999889999999999980799789999999976999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      |-++||...|+|..||-..+.+- .+..-.+|..--..|-.+||.
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln~~-~~vs~~tr~rI~~~a~~lgY~   44 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLNNP-ERVSEETREKVEAAMEELGYV   44 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHCCC
T ss_conf             99999999897999999998797-989999999999999997899


No 274
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=80.30  E-value=4.2  Score=19.89  Aligned_cols=18  Identities=17%  Similarity=0.320  Sum_probs=8.4

Q ss_pred             HHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999985837
Q gi|254780693|r   14 LQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        14 l~dl~~~l~~l~~~~~~~   31 (235)
                      -..+..++..+.+.++..
T Consensus        29 QsavS~~Ik~LE~~LG~~   46 (275)
T PRK03601         29 QSAVSFRIRQLENQLGVN   46 (275)
T ss_pred             HHHHHHHHHHHHHHHCCE
T ss_conf             789999999999996983


No 275
>PRK10082 putative DNA-binding transcriptional regulator; Provisional
Probab=79.91  E-value=4.3  Score=19.80  Aligned_cols=16  Identities=19%  Similarity=0.380  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             9999999999985837
Q gi|254780693|r   16 ELSPRLHLIQNRIKAR   31 (235)
Q Consensus        16 dl~~~l~~l~~~~~~~   31 (235)
                      .+..++..+.+.++..
T Consensus        41 avS~~I~~LE~~LGv~   56 (303)
T PRK10082         41 AFSRRIRALEQAIGVE   56 (303)
T ss_pred             HHHHHHHHHHHHHCCE
T ss_conf             9999999999996995


No 276
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=79.88  E-value=2.2  Score=21.91  Aligned_cols=29  Identities=14%  Similarity=0.272  Sum_probs=22.7

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             99999998799978999994999889999
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNA  207 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~  207 (235)
                      .+|...+|+|.-+......|--..-||+.
T Consensus       221 ~dI~~aia~g~~~~kV~~~M~k~vitI~e  249 (294)
T COG2524         221 SDIAKAIANGNLDAKVSDYMRKNVITINE  249 (294)
T ss_pred             HHHHHHHHCCCCCCCHHHHHCCCCCEECC
T ss_conf             99999997689654388875057704757


No 277
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=79.83  E-value=4.4  Score=19.78  Aligned_cols=12  Identities=8%  Similarity=0.050  Sum_probs=4.1

Q ss_pred             CHHHHHHHHHHH
Q ss_conf             599999999999
Q gi|254780693|r   13 SLQELSPRLHLI   24 (235)
Q Consensus        13 sl~dl~~~l~~l   24 (235)
                      |.+.+..-|..+
T Consensus        32 S~~TIRRDL~~L   43 (251)
T PRK13509         32 SPATARRDINKL   43 (251)
T ss_pred             CHHHHHHHHHHH
T ss_conf             998999839999


No 278
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=79.76  E-value=2.8  Score=21.19  Aligned_cols=28  Identities=29%  Similarity=0.304  Sum_probs=17.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             9978999994999889999999999980
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .+..+.|..|++|..||..+++++..++
T Consensus       101 ~~l~~La~~l~vs~~ti~~dl~~v~~~l  128 (491)
T COG3711         101 LSLHELADELFVSKSTIINDLKDVRLKL  128 (491)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             5799999998466999999999899999


No 279
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=79.33  E-value=4.5  Score=19.68  Aligned_cols=14  Identities=14%  Similarity=0.169  Sum_probs=8.0

Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             99899999999987
Q gi|254780693|r  174 LTERETSCLQLAGD  187 (235)
Q Consensus       174 LT~RE~evL~l~a~  187 (235)
                      +++|=+-++.++.+
T Consensus       277 ~~~rvr~fidfl~e  290 (309)
T PRK10632        277 LPLKVQVVINYLTD  290 (309)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             48999999999999


No 280
>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=79.33  E-value=2  Score=22.21  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99789999949998899999999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      -++.+||..|++|+.||...++++-.
T Consensus        21 v~~~~iA~~L~Vs~~SVt~mlkkL~~   46 (58)
T pfam01325        21 VKTKDLAERLNVSPSTVSEMLKKLEK   46 (58)
T ss_pred             EEHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             12999999959992529999999998


No 281
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=79.16  E-value=4.6  Score=19.64  Aligned_cols=27  Identities=11%  Similarity=0.122  Sum_probs=16.7

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             998999999999879997899999499
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~i  200 (235)
                      |++--.+..++.+..+|-+.|-.-+..
T Consensus       280 l~~~~~~Fi~~~~p~l~~~~~~~~~~~  306 (324)
T PRK12681        280 LRSYMYDFIERFAPHLTRDVVEKAVAL  306 (324)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             579999999986120489999999834


No 282
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=78.88  E-value=4.6  Score=19.59  Aligned_cols=13  Identities=23%  Similarity=0.284  Sum_probs=4.6

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             5999999999999
Q gi|254780693|r   13 SLQELSPRLHLIQ   25 (235)
Q Consensus        13 sl~dl~~~l~~l~   25 (235)
                      |.+.+..-|..+.
T Consensus        31 S~~TIRRDL~~Le   43 (240)
T PRK10411         31 SKETIRRDLNELQ   43 (240)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9989998299897


No 283
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=78.59  E-value=4.7  Score=19.53  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=9.4

Q ss_pred             CHHHHHHHHHHHHHHHCCCC
Q ss_conf             59999999999999858378
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKARN   32 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~~~   32 (235)
                      |-..+..++..+.+.++..-
T Consensus        30 sQpavS~~I~~LE~~Lg~~L   49 (291)
T PRK10837         30 SQSAVSAALTDLEGQLGVQL   49 (291)
T ss_pred             CHHHHHHHHHHHHHHHCCCC
T ss_conf             87899999999999969922


No 284
>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=78.29  E-value=1.9  Score=22.31  Aligned_cols=23  Identities=43%  Similarity=0.445  Sum_probs=20.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99789999949998899999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      +|.+|+|.-||||..||..-+.+
T Consensus         2 lTv~EaA~yLgv~~~t~~~l~~~   24 (49)
T TIGR01764         2 LTVEEAAEYLGVSKSTVYRLIEE   24 (49)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHC
T ss_conf             87788997719990578999971


No 285
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=77.87  E-value=5  Score=19.38  Aligned_cols=18  Identities=11%  Similarity=0.110  Sum_probs=9.9

Q ss_pred             CCHHHHHHHHHHHCCCCH
Q ss_conf             998999999999879997
Q gi|254780693|r  174 LTERETSCLQLAGDGYTS  191 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~  191 (235)
                      ||+.-+..+.++++-.+-
T Consensus       280 l~~~~~~FId~l~e~l~~  297 (309)
T PRK12682        280 LRNYVYDFIELLAPHLSR  297 (309)
T ss_pred             CCHHHHHHHHHHHHHCCH
T ss_conf             189999999999987298


No 286
>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=77.63  E-value=3.5  Score=20.49  Aligned_cols=28  Identities=36%  Similarity=0.331  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             7999789999949998899999999999
Q gi|254780693|r  187 DGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      --+|-+|||..+|+|..||...++...+
T Consensus        24 l~ltr~eiA~~lG~t~eTVsR~l~~l~~   51 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEE   51 (67)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             1779999999978909999999999998


No 287
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=77.44  E-value=4.6  Score=19.60  Aligned_cols=11  Identities=27%  Similarity=0.389  Sum_probs=4.3

Q ss_pred             HCCHHHHHHHH
Q ss_conf             22599999999
Q gi|254780693|r   11 SSSLQELSPRL   21 (235)
Q Consensus        11 ~~sl~dl~~~l   21 (235)
                      .-+++||...+
T Consensus        19 ~v~v~eLa~~~   29 (253)
T COG1349          19 KVSVEELAELF   29 (253)
T ss_pred             CEEHHHHHHHH
T ss_conf             69799999885


No 288
>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=77.11  E-value=2.4  Score=21.61  Aligned_cols=29  Identities=31%  Similarity=0.370  Sum_probs=17.4

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999879997899999499988999999
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      |..+-..|.+-+||...|.-+...+...+
T Consensus        50 I~~lr~~G~~L~eIk~~l~~~~~~~~~~l   78 (96)
T cd04768          50 ILFLRELGFSLAEIKELLDTEMEELTAML   78 (96)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf             99999979999999999939969999999


No 289
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=77.05  E-value=1.6  Score=22.86  Aligned_cols=27  Identities=30%  Similarity=0.252  Sum_probs=23.5

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             879997899999499988999999999
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      -+|.|..+||...|||..|+.+|.++-
T Consensus        14 ~~~~s~~~Ia~~agvs~~~iy~~F~~K   40 (47)
T pfam00440        14 YDATTVREIAKEAGVSKGALYRHFPSK   40 (47)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHCCCH
T ss_conf             150779999999796988999887699


No 290
>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=76.56  E-value=2.6  Score=21.43  Aligned_cols=12  Identities=25%  Similarity=0.390  Sum_probs=4.2

Q ss_pred             CCCCHHHHHHHH
Q ss_conf             799978999994
Q gi|254780693|r  187 DGYTSEEIAEKL  198 (235)
Q Consensus       187 ~G~t~~eIA~~L  198 (235)
                      -|.|-+||...|
T Consensus        55 ~GfsL~eI~~ll   66 (116)
T cd04769          55 LGFTLAELKAIF   66 (116)
T ss_pred             CCCCHHHHHHHH
T ss_conf             799999999999


No 291
>PRK00876 nadE NAD synthetase; Reviewed
Probab=76.43  E-value=5.4  Score=19.11  Aligned_cols=46  Identities=24%  Similarity=0.303  Sum_probs=36.4

Q ss_pred             CCHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9989999-999998799978999994999889999999999980799
Q gi|254780693|r  174 LTERETS-CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       174 LT~RE~e-vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      ++=.+.+ ||...-.|.+.++||..|||+..+|+.-.+.|-+|=...
T Consensus       263 ~~Y~~lD~~L~~~~~~~~~~~~~~~~g~~~e~v~~v~~~i~~kr~~t  309 (325)
T PRK00876        263 LPYDIMDLCLYAQNHGVPAEVVAAALGLTPEQVERVWRDIEAKRRTT  309 (325)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             98899999999876499999999883989999999999999875302


No 292
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=76.35  E-value=5  Score=19.37  Aligned_cols=38  Identities=32%  Similarity=0.336  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999999999879--99789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      |..+++.++.+-  .+.+|++..+++|+-||+.-+..+-.
T Consensus         1 R~~~Il~~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~   40 (57)
T pfam08220         1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEE   40 (57)
T ss_pred             CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             9899999999869797999999989599999996999998


No 293
>PRK11569 transcriptional repressor IclR; Provisional
Probab=75.86  E-value=5.6  Score=19.01  Aligned_cols=26  Identities=4%  Similarity=-0.060  Sum_probs=12.5

Q ss_pred             CEEEEEEECCCCCC-EEEEECCCCCCC
Q ss_conf             35899721688752-345410588789
Q gi|254780693|r  116 AGIAFPVRLGFHKN-GYVIFTSEFLML  141 (235)
Q Consensus       116 ~~~~~pv~~~~~~~-~~~~~~~~~~~~  141 (235)
                      .++..|+++..+.. +.+++++.....
T Consensus       221 ~~iAaPV~d~~g~~vaAlsv~gp~~r~  247 (274)
T PRK11569        221 RCLAACIFDEHREPFAAISISGPISRI  247 (274)
T ss_pred             EEEEEEEECCCCCEEEEEEEEEEHHHC
T ss_conf             899998988999899999998885868


No 294
>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=75.50  E-value=5.2  Score=19.21  Aligned_cols=32  Identities=19%  Similarity=0.175  Sum_probs=27.6

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             87999789999949998899999999999807
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ....|..+.|..+.||+.|+..+++.+..-|.
T Consensus        28 ~~~~s~~~~a~~l~iS~sTl~R~ik~l~~~L~   59 (87)
T pfam05043        28 HEFFSLTSLAQKLFISESTLYRLIKKLNKLLK   59 (87)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             89998999999978899999999999999999


No 295
>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=75.48  E-value=2.8  Score=21.18  Aligned_cols=23  Identities=35%  Similarity=0.400  Sum_probs=19.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99789999949998899999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      +|-.|+|..+|||++|++++-+.
T Consensus         1 ytI~eva~~~gvs~~tlR~ye~~   23 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERI   23 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             95889999989399999999997


No 296
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=75.42  E-value=2.9  Score=21.09  Aligned_cols=15  Identities=40%  Similarity=0.477  Sum_probs=7.2

Q ss_pred             HHCCCCHHHHHHHHC
Q ss_conf             987999789999949
Q gi|254780693|r  185 AGDGYTSEEIAEKLG  199 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~  199 (235)
                      -..|.+-++|...|.
T Consensus        54 r~~G~~l~~Ik~~l~   68 (70)
T smart00422       54 KELGFSLEEIKELLE   68 (70)
T ss_pred             HHCCCCHHHHHHHHH
T ss_conf             997899999999996


No 297
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=75.35  E-value=3.5  Score=20.43  Aligned_cols=27  Identities=37%  Similarity=0.454  Sum_probs=23.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             997899999499988999999999998
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +|..+||.-||.+..||..-+++..+|
T Consensus         3 msrqdIadylGlt~ETVsR~l~~L~~~   29 (32)
T pfam00325         3 MSRQEIADYLGLTRETVSRLLKRLREK   29 (32)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf             658899998472599999999999985


No 298
>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=75.24  E-value=2.9  Score=21.03  Aligned_cols=17  Identities=41%  Similarity=0.470  Sum_probs=9.7

Q ss_pred             HHHHCCCCHHHHHHHHC
Q ss_conf             99987999789999949
Q gi|254780693|r  183 QLAGDGYTSEEIAEKLG  199 (235)
Q Consensus       183 ~l~a~G~t~~eIA~~L~  199 (235)
                      .+-..|.|-+||...|.
T Consensus        53 ~lr~~G~sL~eI~~~l~   69 (108)
T cd01107          53 YLRDLGFPLEEIKEILD   69 (108)
T ss_pred             HHHHCCCCHHHHHHHHH
T ss_conf             99997999999999981


No 299
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760   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 C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=75.13  E-value=5.8  Score=18.88  Aligned_cols=85  Identities=24%  Similarity=0.225  Sum_probs=58.5

Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH---HHCC---CCHHHHHHHHCCCHH
Q ss_conf             3454105887899899999999999999999851246788744499899999999---9879---997899999499988
Q gi|254780693|r  130 GYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQL---AGDG---YTSEEIAEKLGLSVH  203 (235)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~evL~l---~a~G---~t~~eIA~~L~iS~~  203 (235)
                      .+.-|..+.....+.+...-......+ ...+.         ..||+||..||++   +.+|   +|=+|++..++|+.-
T Consensus       144 ~l~DFi~D~~~~~P~~~~~~~~l~~~l-~~vL~---------~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRE  213 (240)
T TIGR02393       144 SLGDFIEDESIESPEDAAAKELLREQL-EEVLE---------NTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRE  213 (240)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHH---------CCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCH
T ss_conf             442652574446858999999999999-99986---------01788899999874389988765337888765178711


Q ss_pred             HHHHHHHHHHHHCCCCCHHHH
Q ss_conf             999999999998079978999
Q gi|254780693|r  204 TVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       204 TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      =|+.-=.+|.|||--.+|..-
T Consensus       214 RIRQIE~KALRKLrhp~r~~~  234 (240)
T TIGR02393       214 RIRQIESKALRKLRHPSRSKK  234 (240)
T ss_pred             HHHHHHHHHHHHCCCHHHHHH
T ss_conf             456888999885028436677


No 300
>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=74.92  E-value=3  Score=20.94  Aligned_cols=14  Identities=7%  Similarity=0.268  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             99999999998079
Q gi|254780693|r  205 VNAYLGSATVKLDA  218 (235)
Q Consensus       205 V~~hl~~i~~KLg~  218 (235)
                      ++.|+..+-+|+.-
T Consensus        84 l~~~l~~i~~kI~e   97 (133)
T cd04787          84 IEQRLAETERRIKE   97 (133)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999999


No 301
>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=74.90  E-value=3  Score=20.95  Aligned_cols=15  Identities=47%  Similarity=0.585  Sum_probs=8.0

Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             879997899999499
Q gi|254780693|r  186 GDGYTSEEIAEKLGL  200 (235)
Q Consensus       186 a~G~t~~eIA~~L~i  200 (235)
                      .-|.|-+||...|.+
T Consensus        53 ~~G~sL~eI~~~L~l   67 (118)
T cd04776          53 RLGFSLEEIRELLDL   67 (118)
T ss_pred             HCCCCHHHHHHHHHH
T ss_conf             829989999999964


No 302
>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=74.83  E-value=3  Score=20.95  Aligned_cols=43  Identities=19%  Similarity=0.248  Sum_probs=29.3

Q ss_pred             CCHHHH----HHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             998999----9999998-799978999994999889999999999980
Q gi|254780693|r  174 LTERET----SCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       174 LT~RE~----evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      -|+...    .|..+-. .|.|-+||...|..-...++...+.+..||
T Consensus        38 Y~~~dl~rL~~I~~l~~~lGfsL~eIk~lL~~~~~p~~~~~~~~~e~L   85 (96)
T cd04774          38 YSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYSAESL   85 (96)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             599999999999999995799899999998198883045999999999


No 303
>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=74.71  E-value=3  Score=20.97  Aligned_cols=31  Identities=16%  Similarity=0.269  Sum_probs=12.8

Q ss_pred             HCCCCHHHHHHHHCCC------HHHHHHHHHHHHHHC
Q ss_conf             8799978999994999------889999999999980
Q gi|254780693|r  186 GDGYTSEEIAEKLGLS------VHTVNAYLGSATVKL  216 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS------~~TV~~hl~~i~~KL  216 (235)
                      ..|.|-+||...|...      ...++.|+..+-.|.
T Consensus        54 ~lGfsL~EI~~ll~~~~~~~~~~~~l~~~~~~i~~~I   90 (120)
T cd04781          54 AAGFSLDEIQAMLSHDGKPPIDRQLLKAKAAELDQQI   90 (120)
T ss_pred             HCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9599999999988426898379999999999999999


No 304
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=74.71  E-value=3.1  Score=20.88  Aligned_cols=15  Identities=40%  Similarity=0.514  Sum_probs=7.2

Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             879997899999499
Q gi|254780693|r  186 GDGYTSEEIAEKLGL  200 (235)
Q Consensus       186 a~G~t~~eIA~~L~i  200 (235)
                      ..|.+-++|...|..
T Consensus        55 ~~G~sL~eI~~~l~~   69 (124)
T COG0789          55 ELGFSLAEIKELLDL   69 (124)
T ss_pred             HCCCCHHHHHHHHHH
T ss_conf             869989999999985


No 305
>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=74.28  E-value=3.1  Score=20.83  Aligned_cols=26  Identities=31%  Similarity=0.450  Sum_probs=12.6

Q ss_pred             CCHHHHHHHH----HHHCCCCHHHHHHHHC
Q ss_conf             9989999999----9987999789999949
Q gi|254780693|r  174 LTERETSCLQ----LAGDGYTSEEIAEKLG  199 (235)
Q Consensus       174 LT~RE~evL~----l~a~G~t~~eIA~~L~  199 (235)
                      -|+...+-|+    |...|+|-++|...|+
T Consensus        38 Ys~~di~~l~~I~~l~~~G~sl~~Ik~~LN   67 (67)
T cd04764          38 YTDEDIELLKKIKTLLEKGLSIKEIKEILN   67 (67)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf             399999999999999996998999999859


No 306
>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=73.96  E-value=4.6  Score=19.62  Aligned_cols=46  Identities=26%  Similarity=0.421  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             44998999999999-----87999789999949998899999999999807
Q gi|254780693|r  172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ..|+.||++++.+-     ..-+|.+++|..||||..-+...=++|.++|.
T Consensus       177 ~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lGisqsyisrlek~i~krl~  227 (234)
T TIGR02835       177 KKLNDREKKIMELRFGLAGGTEKTQKEVADLLGISQSYISRLEKRILKRLK  227 (234)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             987676787667630436772146788898862468999999999999999


No 307
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=73.90  E-value=6.2  Score=18.67  Aligned_cols=17  Identities=18%  Similarity=0.260  Sum_probs=12.2

Q ss_pred             CCCCCHHHHHHHHHHHC
Q ss_conf             44499899999999987
Q gi|254780693|r  171 ARNLTERETSCLQLAGD  187 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~  187 (235)
                      ...+++.|.++|+-++.
T Consensus       142 DG~l~~~E~~~L~~Ia~  158 (269)
T PRK09430        142 DGSLHPNERQVLYVIAE  158 (269)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             58999999999999999


No 308
>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=73.77  E-value=3.2  Score=20.70  Aligned_cols=33  Identities=21%  Similarity=0.123  Sum_probs=14.2

Q ss_pred             HHHHCCCCHHHHHHHHCC--CHHHHHHHHHHHHHH
Q ss_conf             999879997899999499--988999999999998
Q gi|254780693|r  183 QLAGDGYTSEEIAEKLGL--SVHTVNAYLGSATVK  215 (235)
Q Consensus       183 ~l~a~G~t~~eIA~~L~i--S~~TV~~hl~~i~~K  215 (235)
                      .+-..|.|-+||...|.-  +......++..+-++
T Consensus        52 ~lr~~G~sL~eI~~~l~~~~~~~~l~~~~~~l~~~   86 (102)
T cd04789          52 QLQAGGLSLKECLACLQGKLTRSLLLERLSSLAEQ   86 (102)
T ss_pred             HHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             99997998999999985985569999999999999


No 309
>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=73.76  E-value=3.3  Score=20.62  Aligned_cols=37  Identities=22%  Similarity=0.247  Sum_probs=19.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCH----------HHHHHHHHHHHHHCC
Q ss_conf             9999987999789999949998----------899999999999807
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSV----------HTVNAYLGSATVKLD  217 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~----------~TV~~hl~~i~~KLg  217 (235)
                      |..+-..|.|-+||...|....          ..++.|+..+-+|..
T Consensus        50 I~~lr~~G~sL~eI~~ll~~~~~~~~~~~~~~~~l~~~~~~i~~~i~   96 (123)
T cd04770          50 IRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIA   96 (123)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999869999999999852506999889999999999999999999


No 310
>COG2512 Predicted membrane-associated trancriptional regulator    [Transcription]
Probab=73.73  E-value=6.3  Score=18.64  Aligned_cols=44  Identities=34%  Similarity=0.420  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHHHHHHHC-C--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             44499899999999987-9--99789999949998899999999999
Q gi|254780693|r  171 ARNLTERETSCLQLAGD-G--YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~-G--~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      ...|++-|++|+..+.. |  -+-+|+.+.||+|+.||-.++++.=+
T Consensus       190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk  236 (258)
T COG2512         190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK  236 (258)
T ss_pred             CCCCCHHHHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             57899789999999998589786999888609976779999999986


No 311
>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=73.56  E-value=3.4  Score=20.56  Aligned_cols=41  Identities=24%  Similarity=0.203  Sum_probs=22.5

Q ss_pred             CCHHHHH----HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9989999----9999987999789999949998899999999999
Q gi|254780693|r  174 LTERETS----CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .|+.+.+    |..+-..|.+-++|...|.-+.......+..-.+
T Consensus        39 Y~~~~i~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~L~~~~~   83 (103)
T cd01106          39 YTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKE   83 (103)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             689999999999999997999999999980897119999999999


No 312
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=73.38  E-value=6.4  Score=18.59  Aligned_cols=14  Identities=29%  Similarity=0.235  Sum_probs=7.5

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             49989999999998
Q gi|254780693|r  173 NLTERETSCLQLAG  186 (235)
Q Consensus       173 ~LT~RE~evL~l~a  186 (235)
                      .||+-|.+-|+-+.
T Consensus       103 ~l~~~eie~L~~il  116 (123)
T COG3682         103 KLTADEIEALKAIL  116 (123)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             79999999999999


No 313
>PRK04140 hypothetical protein; Provisional
Probab=73.22  E-value=3.7  Score=20.31  Aligned_cols=25  Identities=32%  Similarity=0.468  Sum_probs=20.2

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             8799978999994999889999999
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      -.|+|-.+.|..||+|.+||..|=+
T Consensus       136 ~~g~SlG~LA~~LGVSRrtv~~YE~  160 (319)
T PRK04140        136 KLGLSLGELASELGVSRRTISKYEN  160 (319)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8198888999984986999999970


No 314
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=73.17  E-value=6.5  Score=18.55  Aligned_cols=43  Identities=28%  Similarity=0.251  Sum_probs=29.7

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf             87999789999949998899999999999807997899999999769
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG  232 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~G  232 (235)
                      ..|+|-++.|..+|||+.||..+-+.    -...+-..+...|-.+|
T Consensus         7 ~~g~tq~~lA~~~gis~~~is~~E~g----~~~p~~~~l~~ia~~l~   49 (55)
T pfam01381         7 ELGLSQEELAEKLGVSRSTISKIENG----KREPSLETLKKLAEALG   49 (55)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHC
T ss_conf             82998999999989699999999879----99999999999999978


No 315
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=72.86  E-value=6.6  Score=18.50  Aligned_cols=18  Identities=17%  Similarity=0.296  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999985837
Q gi|254780693|r   14 LQELSPRLHLIQNRIKAR   31 (235)
Q Consensus        14 l~dl~~~l~~l~~~~~~~   31 (235)
                      -..+...+..+.+.++..
T Consensus        30 qsavS~~I~~LE~~LGv~   47 (308)
T PRK10094         30 TATISYRIKLLEENTGVA   47 (308)
T ss_pred             HHHHHHHHHHHHHHHCCE
T ss_conf             789999999999996996


No 316
>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=72.79  E-value=3.7  Score=20.33  Aligned_cols=27  Identities=26%  Similarity=0.175  Sum_probs=14.0

Q ss_pred             CCHHHHHH----HHHHHCCCCHHHHHHHHCC
Q ss_conf             99899999----9999879997899999499
Q gi|254780693|r  174 LTERETSC----LQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       174 LT~RE~ev----L~l~a~G~t~~eIA~~L~i  200 (235)
                      -|.....-    ..+-..|.+-+||...+.-
T Consensus        39 Y~~~~~~~l~~I~~~r~lG~sL~eI~~~~~~   69 (97)
T cd04782          39 YTLEQFEQLDIILLLKELGISLKEIKDYLDN   69 (97)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             7999999999999999969999999999827


No 317
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=72.50  E-value=6.7  Score=18.45  Aligned_cols=40  Identities=23%  Similarity=0.310  Sum_probs=29.4

Q ss_pred             HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             999999-99879997899999499988999999999998079978
Q gi|254780693|r  178 ETSCLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       178 E~evL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      |+++++ +.....+.++.|..||||..|+..-+    +|+|...+
T Consensus       469 Er~~l~~l~~~~~~~~kaAk~LGISrttL~~Kl----kkyGI~~k  509 (513)
T PRK10820        469 ERSVLTQLYRNYPSTRKLAKRLGVSHTAIANKL----REYGLSQK  509 (513)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH----HHCCCCCC
T ss_conf             999999999878899999999799899999999----98089987


No 318
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=72.50  E-value=4  Score=20.04  Aligned_cols=19  Identities=47%  Similarity=0.541  Sum_probs=7.0

Q ss_pred             HHHHHHCCCHHHHHHHHHH
Q ss_conf             9999949998899999999
Q gi|254780693|r  193 EIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       193 eIA~~L~iS~~TV~~hl~~  211 (235)
                      +||..|++|+.||...+++
T Consensus         4 diA~~L~vs~~sVs~~l~~   22 (96)
T smart00529        4 EIAERLNVSPPTVTQMLKK   22 (96)
T ss_pred             HHHHHHCCCCHHHHHHHHH
T ss_conf             8998849991679999999


No 319
>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=72.37  E-value=3.7  Score=20.29  Aligned_cols=19  Identities=42%  Similarity=0.469  Sum_probs=9.2

Q ss_pred             HHHHHCCCCHHHHHHHHCC
Q ss_conf             9999879997899999499
Q gi|254780693|r  182 LQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       182 L~l~a~G~t~~eIA~~L~i  200 (235)
                      ..+-..|.|-+||...|..
T Consensus        51 ~~~r~~G~sL~eI~~ll~~   69 (126)
T cd04783          51 KRAQELGFTLDEIAELLEL   69 (126)
T ss_pred             HHHHHCCCCHHHHHHHHCC
T ss_conf             9999879989999999742


No 320
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=72.36  E-value=6.2  Score=18.68  Aligned_cols=36  Identities=33%  Similarity=0.396  Sum_probs=28.0

Q ss_pred             CCHHHHH--------HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9989999--------99999879997899999499988999999
Q gi|254780693|r  174 LTERETS--------CLQLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       174 LT~RE~e--------vL~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      |||-|++        |-.++---+|-+||+..||+|..|+..--
T Consensus        38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGS   81 (103)
T COG2973          38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGS   81 (103)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCH
T ss_conf             68768999999999999999563539999998586256550444


No 321
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=72.17  E-value=6.8  Score=18.40  Aligned_cols=40  Identities=28%  Similarity=0.429  Sum_probs=34.5

Q ss_pred             CCCHHHHHHHHHHH------CCCCHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf             49989999999998------799978999994-99988999999999
Q gi|254780693|r  173 NLTERETSCLQLAG------DGYTSEEIAEKL-GLSVHTVNAYLGSA  212 (235)
Q Consensus       173 ~LT~RE~evL~l~a------~G~t~~eIA~~L-~iS~~TV~~hl~~i  212 (235)
                      .||+-.++|+.++.      +|....||+.+| ++++..|+.-+..+
T Consensus        44 ~ls~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~a~d~L   90 (103)
T pfam08784        44 GLTPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQAVDFL   90 (103)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             87899999999999548898872799999998299999999999999


No 322
>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=72.09  E-value=3.7  Score=20.28  Aligned_cols=43  Identities=21%  Similarity=0.227  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHH--HHHHHHHHHHHHC
Q ss_conf             998999999999-----879997899999499988--9999999999980
Q gi|254780693|r  174 LTERETSCLQLA-----GDGYTSEEIAEKLGLSVH--TVNAYLGSATVKL  216 (235)
Q Consensus       174 LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~--TV~~hl~~i~~KL  216 (235)
                      .|+.+.+-|+.+     ..|.|-++|...|..-+.  ....+++.+..|+
T Consensus        39 Ys~~di~~l~~I~~L~~~~G~sl~~I~~~L~l~~~~~~l~a~~~~l~~r~   88 (91)
T cd04766          39 YSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRARL   88 (91)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             47999999999999999869989999999980844999999999999998


No 323
>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=71.98  E-value=3.9  Score=20.12  Aligned_cols=20  Identities=30%  Similarity=0.305  Sum_probs=12.8

Q ss_pred             HHHHHHCCCCHHHHHHHHCC
Q ss_conf             99999879997899999499
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~i  200 (235)
                      |..+-..|.|-++|...|..
T Consensus        50 I~~lr~~G~sl~eI~~~l~~   69 (108)
T cd04773          50 IHLLRRGGYLLEQIATVVEQ   69 (108)
T ss_pred             HHHHHHCCCCHHHHHHHHHH
T ss_conf             99999969999999999987


No 324
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=71.81  E-value=4.6  Score=19.63  Aligned_cols=28  Identities=39%  Similarity=0.502  Sum_probs=23.7

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9879997899999499988999999999
Q gi|254780693|r  185 AGDGYTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      ...|+|-++.|..+|||+.||..+.+.-
T Consensus         7 ~~~glsq~~lA~~~gis~~~is~~E~g~   34 (56)
T smart00530        7 EEKGLTQEELAEKLGVSRSTLSRIENGK   34 (56)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf             7729999999999895999999999799


No 325
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=71.71  E-value=2.5  Score=21.50  Aligned_cols=17  Identities=6%  Similarity=0.026  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHCCCCEEE
Q ss_conf             99999999858378589
Q gi|254780693|r   19 PRLHLIQNRIKARNFAL   35 (235)
Q Consensus        19 ~~l~~l~~~~~~~~f~~   35 (235)
                      ..+++..+.+.-.||.-
T Consensus        15 ~Il~AA~~lFaekGy~~   31 (216)
T PRK10668         15 HILDVALRLFSQQGVSA   31 (216)
T ss_pred             HHHHHHHHHHHHHCCCC
T ss_conf             99999999999849351


No 326
>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=71.48  E-value=4.4  Score=19.72  Aligned_cols=15  Identities=20%  Similarity=0.173  Sum_probs=8.5

Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             879997899999499
Q gi|254780693|r  186 GDGYTSEEIAEKLGL  200 (235)
Q Consensus       186 a~G~t~~eIA~~L~i  200 (235)
                      ..|++-+||...|..
T Consensus        55 ~~G~sl~eI~~lL~~   69 (107)
T cd01111          55 EAGIGLDELARLCRA   69 (107)
T ss_pred             HCCCCHHHHHHHHHH
T ss_conf             879999999999960


No 327
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293   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 (IPR014284 from INTERPRO). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=71.45  E-value=7.1  Score=18.29  Aligned_cols=49  Identities=27%  Similarity=0.300  Sum_probs=41.8

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             99999879997899999499988999999999998079978999999997699
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      |+--=.+|...|||+.+|+.-..||-.-+.+.++.|    |.+++-.|..+|+
T Consensus       140 v~~adveGf~ykei~~im~tP~Gtvmsrl~r~rk~l----~~~l~d~a~~rG~  188 (193)
T TIGR02947       140 VYFADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL----RDLLADVAAERGF  188 (193)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHHHHCCC
T ss_conf             887620353157799885474779999989999999----9999988874054


No 328
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=71.43  E-value=3  Score=20.99  Aligned_cols=14  Identities=14%  Similarity=0.102  Sum_probs=6.1

Q ss_pred             HHHHHHHHCCCCEE
Q ss_conf             99999985837858
Q gi|254780693|r   21 LHLIQNRIKARNFA   34 (235)
Q Consensus        21 l~~l~~~~~~~~f~   34 (235)
                      +++..+.+.-.||.
T Consensus        14 l~Aa~~~i~~~G~~   27 (189)
T TIGR03384        14 IDATIESIGERGSL   27 (189)
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999984935


No 329
>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=71.16  E-value=4.1  Score=19.94  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=13.2

Q ss_pred             CCHHHHHHHHH----HHCCCCHHHHHHHHCC
Q ss_conf             99899999999----9879997899999499
Q gi|254780693|r  174 LTERETSCLQL----AGDGYTSEEIAEKLGL  200 (235)
Q Consensus       174 LT~RE~evL~l----~a~G~t~~eIA~~L~i  200 (235)
                      .|+...+.|..    -..|.|-+||...|..
T Consensus        39 Y~~~~v~rl~~I~~lr~lG~sL~eI~~~l~~   69 (113)
T cd01109          39 FTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL   69 (113)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             3498989999797599879989999999988


No 330
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=71.05  E-value=7.2  Score=18.23  Aligned_cols=28  Identities=14%  Similarity=-0.026  Sum_probs=15.8

Q ss_pred             CCEEEEEEECCCCC-CEEEEECCCCCCCC
Q ss_conf             53589972168875-23454105887899
Q gi|254780693|r  115 FAGIAFPVRLGFHK-NGYVIFTSEFLMLA  142 (235)
Q Consensus       115 ~~~~~~pv~~~~~~-~~~~~~~~~~~~~~  142 (235)
                      ..++..|+++..+. .+.++.........
T Consensus       194 v~~iAaPi~~~~g~v~aaisv~~p~~r~~  222 (246)
T COG1414         194 VRCIAAPIFDAGGEVVAAISVSGPASRLT  222 (246)
T ss_pred             CEEEEEEEECCCCCEEEEEEEECHHHHCC
T ss_conf             56999889869997899999626166509


No 331
>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=70.98  E-value=4.2  Score=19.87  Aligned_cols=18  Identities=39%  Similarity=0.510  Sum_probs=9.9

Q ss_pred             HHHHCCCCHHHHHHHHCC
Q ss_conf             999879997899999499
Q gi|254780693|r  183 QLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       183 ~l~a~G~t~~eIA~~L~i  200 (235)
                      .+-..|.|-+||...|.+
T Consensus        52 ~~r~~G~sL~eI~~ll~~   69 (127)
T cd01108          52 RARDLGFSLEEIRELLAL   69 (127)
T ss_pred             HHHHCCCCHHHHHHHHHH
T ss_conf             999879989999999853


No 332
>PHA01976 helix-turn-helix protein
Probab=70.83  E-value=5.1  Score=19.29  Aligned_cols=27  Identities=7%  Similarity=0.273  Sum_probs=23.2

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999879997899999499988999999
Q gi|254780693|r  183 QLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       183 ~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      .--+.|.|-.|.|..+|||..||..+=
T Consensus        10 lR~~~g~sQ~eLA~~lGVs~~~is~wE   36 (67)
T PHA01976         10 ARNARAWSAPELSRRAGVRHSLIYDFE   36 (67)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999869999999999499899999998


No 333
>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=70.75  E-value=7.3  Score=18.18  Aligned_cols=42  Identities=21%  Similarity=0.306  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             499899999999987999789999949998899999999999807997
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .+++-  ...+.-..|-|+++||..+++|+..|+..    ++++|+.-
T Consensus        58 ~~~~~--~l~~aK~~GFSD~~IA~l~~~~e~~Ir~~----R~~~~i~P   99 (122)
T pfam02787        58 PLSDD--LLLKAKKLGFSDAQIAKLLGVTEEEVRKL----RKELGIRP   99 (122)
T ss_pred             CCCHH--HHHHHHHHCCCHHHHHHHHCCCHHHHHHH----HHHCCCCC
T ss_conf             99999--99999994999899998839869999999----99879912


No 334
>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=70.20  E-value=4.5  Score=19.71  Aligned_cols=20  Identities=30%  Similarity=0.345  Sum_probs=10.5

Q ss_pred             HHHHHHCCCCHHHHHHHHCC
Q ss_conf             99999879997899999499
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~i  200 (235)
                      |..+-..|.|-+||...|.+
T Consensus        50 I~~~r~~GfsL~eI~~ll~l   69 (126)
T cd04785          50 IRRARDLGFSLEEIRALLAL   69 (126)
T ss_pred             HHHHHHCCCCHHHHHHHHCC
T ss_conf             99999879989999999713


No 335
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=70.19  E-value=4.1  Score=19.96  Aligned_cols=10  Identities=50%  Similarity=0.757  Sum_probs=3.1

Q ss_pred             CCHHHHHHHH
Q ss_conf             9978999994
Q gi|254780693|r  189 YTSEEIAEKL  198 (235)
Q Consensus       189 ~t~~eIA~~L  198 (235)
                      .|-+||...|
T Consensus        65 fsL~eI~~LL   74 (144)
T PRK13752         65 FSLDEIAELL   74 (144)
T ss_pred             CCHHHHHHHH
T ss_conf             9899999997


No 336
>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=70.14  E-value=4.5  Score=19.70  Aligned_cols=36  Identities=25%  Similarity=0.232  Sum_probs=19.8

Q ss_pred             HHHHHHCCCCHHHHHHHHCCC--HHHHHHHHHHHHHHC
Q ss_conf             999998799978999994999--889999999999980
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLS--VHTVNAYLGSATVKL  216 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS--~~TV~~hl~~i~~KL  216 (235)
                      |..+-..|.|-+||...|.-.  ....+.+++.+-++.
T Consensus        50 I~~lr~~G~sL~eIk~lL~~~~~~~~l~~~~~~i~~~I   87 (102)
T cd04775          50 IVFLQAGGLPLEEIAGCLAQPHVQAILEERLQSLNREI   87 (102)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999969999999999859957999999999999999


No 337
>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=69.92  E-value=4.1  Score=19.97  Aligned_cols=25  Identities=8%  Similarity=0.242  Sum_probs=14.1

Q ss_pred             CCHHHHH----HHHHHHCCCCHHHHHHHH
Q ss_conf             9989999----999998799978999994
Q gi|254780693|r  174 LTERETS----CLQLAGDGYTSEEIAEKL  198 (235)
Q Consensus       174 LT~RE~e----vL~l~a~G~t~~eIA~~L  198 (235)
                      .|+.+.+    |-.|...|+|-++|+..|
T Consensus        39 Ys~~di~~l~~I~~l~~~G~~i~~i~~lL   67 (68)
T cd04763          39 FNDADIDRILEIKRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             49999999999999999799899999972


No 338
>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=69.76  E-value=5.5  Score=19.09  Aligned_cols=45  Identities=20%  Similarity=0.236  Sum_probs=26.3

Q ss_pred             CCHHHHHHHHHH---H--CCCCHHHHHHHHCC--CHHHHHHHHHHHHHHCCC
Q ss_conf             998999999999---8--79997899999499--988999999999998079
Q gi|254780693|r  174 LTERETSCLQLA---G--DGYTSEEIAEKLGL--SVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       174 LT~RE~evL~l~---a--~G~t~~eIA~~L~i--S~~TV~~hl~~i~~KLg~  218 (235)
                      -++...+-|+++   .  .|.+-+||...|..  -+.+-+.-+..+..+++.
T Consensus        39 Y~~~~v~rL~~Ir~l~~~lG~sL~eIr~lL~~~~d~~~p~~l~~~~~~~~~~   90 (95)
T cd04780          39 YSEAHVERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLALAVQRFGL   90 (95)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC
T ss_conf             4999999999999999936999999999984368899951799999999557


No 339
>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=69.69  E-value=5.3  Score=19.16  Aligned_cols=24  Identities=42%  Similarity=0.469  Sum_probs=13.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             799978999994999889999999
Q gi|254780693|r  187 DGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       187 ~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      .|++-.+||..||-|..=|-.|+.
T Consensus         2 ~G~kk~~IAk~LGks~s~VS~hla   25 (93)
T pfam08535         2 KGVKQAEIAKKLGKSKSFVSQHLA   25 (93)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             987799999997889889999999


No 340
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.60  E-value=6.7  Score=18.46  Aligned_cols=40  Identities=20%  Similarity=0.253  Sum_probs=31.2

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             99999999879997899999499988999999999998079978
Q gi|254780693|r  178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      -.+|.+++.+|+|...|..+-|+|..|+..    +.+-|+-.|-
T Consensus        46 RlqVa~mL~eg~tY~~I~~eTGaStaTIsR----VkRcl~yGnd   85 (100)
T COG4496          46 RLQVAKMLKEGRTYRDIEDETGASTATISR----VKRCLNYGND   85 (100)
T ss_pred             HHHHHHHHHCCCCCCHHHHCCCCCHHHHHH----HHHHHHCCCC
T ss_conf             999999997689722466414840555999----9999980770


No 341
>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=69.48  E-value=4.7  Score=19.55  Aligned_cols=21  Identities=29%  Similarity=0.403  Sum_probs=14.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHCC
Q ss_conf             999999879997899999499
Q gi|254780693|r  180 SCLQLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       180 evL~l~a~G~t~~eIA~~L~i  200 (235)
                      -|+.+=.-|.|-+||...|.+
T Consensus        47 ~I~~~k~lgfsL~eIk~ll~l   67 (107)
T cd04777          47 FILELKGLGFSLIEIQKIFSY   67 (107)
T ss_pred             HHHHHHHCCCCHHHHHHHHHH
T ss_conf             999998889989999999962


No 342
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=68.76  E-value=7  Score=18.32  Aligned_cols=27  Identities=33%  Similarity=0.490  Sum_probs=23.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             997899999499988999999999998
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +|.+|||..+|.|+.||...++...++
T Consensus       185 lt~~dLA~~lG~trEtVsR~L~~L~~~  211 (235)
T PRK11161        185 MTRGDIGNYLGLTVETISRLLGRFQKS  211 (235)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             789999988789899999999999978


No 343
>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=68.71  E-value=5  Score=19.34  Aligned_cols=29  Identities=24%  Similarity=0.225  Sum_probs=17.2

Q ss_pred             CCHHHHH----HHHHHHCCCCHHHHHHHHCCCH
Q ss_conf             9989999----9999987999789999949998
Q gi|254780693|r  174 LTERETS----CLQLAGDGYTSEEIAEKLGLSV  202 (235)
Q Consensus       174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~  202 (235)
                      .|+...+    |..+-..|.|-++|...|....
T Consensus        38 Y~~~~i~~l~~I~~lr~~G~sl~~I~~~l~~~~   70 (100)
T cd00592          38 YSEEDLERLRLIRRLRELGLSLKEIRELLDARD   70 (100)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf             569999999999999997999999999983557


No 344
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=68.60  E-value=4.9  Score=19.42  Aligned_cols=34  Identities=21%  Similarity=0.198  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             7999789999949998899999999999807997
Q gi|254780693|r  187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      .=.|-+|||...++++-|++++.+.+...++..+
T Consensus       250 ~~~tq~eva~v~~vtevTIrnrykel~~~~~i~~  283 (285)
T COG1405         250 ERRTQKEVAKVAGVTEVTIRNRYKELADALDIEV  283 (285)
T ss_pred             CCHHHHHHHHHHCCEEEHHHHHHHHHHHHHCCCC
T ss_conf             7027999998838722079988999877322556


No 345
>pfam11662 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=68.60  E-value=8.1  Score=17.87  Aligned_cols=41  Identities=29%  Similarity=0.375  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHH-----HHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             49989999999-----998799978999994999889999999999
Q gi|254780693|r  173 NLTERETSCLQ-----LAGDGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       173 ~LT~RE~evL~-----l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      .||+||..||.     |-..|-....|-..+|+|+---..-+..+.
T Consensus         2 ~Ls~rd~~IL~fEr~ww~~~GaKe~AIRe~fglS~~rYYQ~LN~Li   47 (77)
T pfam11662         2 ELTERDRAILDFERQWWKHAGAKEQAIRELFGLSSTRYYQLLNALI   47 (77)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8889999999999873368781899999997888899999999986


No 346
>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=68.32  E-value=5.2  Score=19.25  Aligned_cols=17  Identities=24%  Similarity=0.372  Sum_probs=8.9

Q ss_pred             HHHCCCCHHHHHHHHCC
Q ss_conf             99879997899999499
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~i  200 (235)
                      +-.-|.|-+||...|.+
T Consensus        53 ~r~lGfsL~eI~~ll~~   69 (131)
T cd04786          53 AQQAGFSLDEIRQLLPA   69 (131)
T ss_pred             HHHCCCCHHHHHHHHCC
T ss_conf             99969999999998684


No 347
>PHA00542 putative Cro-like protein
Probab=68.30  E-value=7  Score=18.33  Aligned_cols=37  Identities=22%  Similarity=0.271  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             49989999999998799978999994999889999999
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      .-+|-|. |..+++.|+|-.||+..-||+..++..-+.
T Consensus        17 ~k~P~E~-V~aLi~~G~tQ~qI~~~tgv~QpsisRils   53 (82)
T PHA00542         17 TQRPDEL-VCALIRAGWSQEQIADATDVSQPTICRIYS   53 (82)
T ss_pred             HCCHHHH-HHHHHHCCCCHHHHHHHHCCCCHHHHHHHC
T ss_conf             3298999-999998225699999860877036899980


No 348
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=68.23  E-value=3.2  Score=20.70  Aligned_cols=16  Identities=13%  Similarity=0.048  Sum_probs=7.5

Q ss_pred             HHHHHHHHHCCCCEEE
Q ss_conf             9999999858378589
Q gi|254780693|r   20 RLHLIQNRIKARNFAL   35 (235)
Q Consensus        20 ~l~~l~~~~~~~~f~~   35 (235)
                      .+.+..+.+.-.||.-
T Consensus        16 Il~AA~~lFae~G~~~   31 (213)
T PRK09975         16 LIETAIAQFALRGVAN   31 (213)
T ss_pred             HHHHHHHHHHHHCCCC
T ss_conf             9999999999859455


No 349
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.99  E-value=7.1  Score=18.29  Aligned_cols=13  Identities=54%  Similarity=0.825  Sum_probs=4.0

Q ss_pred             HHHHHHCCCHHHH
Q ss_conf             9999949998899
Q gi|254780693|r  193 EIAEKLGLSVHTV  205 (235)
Q Consensus       193 eIA~~L~iS~~TV  205 (235)
                      +||..+||..++|
T Consensus        41 eiAe~~gi~lN~V   53 (178)
T PRK06266         41 EIAEQTGIKLNTV   53 (178)
T ss_pred             HHHHHHCCCHHHH
T ss_conf             9999969978999


No 350
>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=67.71  E-value=2.6  Score=21.43  Aligned_cols=41  Identities=32%  Similarity=0.492  Sum_probs=24.5

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             899999499988999999999998079978999999997699
Q gi|254780693|r  192 EEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       192 ~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ++||..+|+|..||...+.+=- ...-.+|-.--..|..+||
T Consensus         1 ~diA~~~gvS~~TVSr~ln~~~-~Vs~~tr~~I~~~~~elgY   41 (52)
T cd01392           1 KDIARAAGVSVATVSRVLNGKP-RVSEETRERVLAAAEELGY   41 (52)
T ss_pred             CHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHCC
T ss_conf             9288887859999999987989-8999999999999999888


No 351
>PRK13824 replication initiation protein RepC; Provisional
Probab=67.69  E-value=8  Score=17.92  Aligned_cols=33  Identities=21%  Similarity=0.158  Sum_probs=20.7

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             7899999499988999999999998079978999999
Q gi|254780693|r  191 SEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK  227 (235)
Q Consensus       191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~  227 (235)
                      ...+...||||+.+..    .+.+.+|-.+=+-+|+.
T Consensus       324 A~~lr~mlGIS~saw~----eA~~~mG~~~AAvaiA~  356 (404)
T PRK13824        324 AVVVRSMLGVSPSAYQ----EACEVMGPENAAIVIAC  356 (404)
T ss_pred             HHHHHHHHCCCHHHHH----HHHHHHCHHHHHHHHHH
T ss_conf             9999987098999999----99998696889999999


No 352
>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=67.63  E-value=5.4  Score=19.15  Aligned_cols=11  Identities=27%  Similarity=0.419  Sum_probs=3.6

Q ss_pred             CCCHHHHHHHH
Q ss_conf             99978999994
Q gi|254780693|r  188 GYTSEEIAEKL  198 (235)
Q Consensus       188 G~t~~eIA~~L  198 (235)
                      |.|-+||-..|
T Consensus        56 g~sL~eIk~lL   66 (134)
T cd04779          56 RLSLAEIKDQL   66 (134)
T ss_pred             CCCHHHHHHHH
T ss_conf             99899999998


No 353
>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=67.35  E-value=5.5  Score=19.07  Aligned_cols=30  Identities=17%  Similarity=0.205  Sum_probs=19.4

Q ss_pred             CCHHHHH----HHHHHHCCCCHHHHHHHHCCCHH
Q ss_conf             9989999----99999879997899999499988
Q gi|254780693|r  174 LTERETS----CLQLAGDGYTSEEIAEKLGLSVH  203 (235)
Q Consensus       174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~~  203 (235)
                      -|..+.+    |..+-..|.+-+||...|.-+..
T Consensus        39 Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~   72 (96)
T cd04788          39 YDRADIRRLHQIIALRRLGFSLREIGRALDGPDF   72 (96)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCC
T ss_conf             8999999999999999979999999999808981


No 354
>PRK00767 transcriptional regulator BetI; Validated
Probab=67.17  E-value=4.4  Score=19.76  Aligned_cols=42  Identities=10%  Similarity=0.002  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCC----CHHHHHHHHHHHHHHCCC
Q ss_conf             999999999879997899999499----988999999999998079
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGL----SVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~i----S~~TV~~hl~~i~~KLg~  218 (235)
                      +..+.|.-+.+|++-...-.-=..    ....+..|+.+.+.+.|.
T Consensus       151 ~~A~~L~AliDGL~l~~~l~p~~~~~e~~~~~~~~~l~~~l~~~~~  196 (197)
T PRK00767        151 EAAEGLAALIDGLWLRGALSGDPEDTEAARALAKDYIDQQLAQYGS  196 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999899999986689999999999999999999886379


No 355
>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=66.82  E-value=5.9  Score=18.87  Aligned_cols=19  Identities=42%  Similarity=0.378  Sum_probs=11.3

Q ss_pred             HHHHHHCCCCHHHHHHHHC
Q ss_conf             9999987999789999949
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLG  199 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~  199 (235)
                      |..+-..|+|-+||...|.
T Consensus        49 I~~lr~~G~sl~eI~~~l~   67 (112)
T cd01282          49 IRRLLAAGLTLEEIREFLP   67 (112)
T ss_pred             HHHHHHCCCCHHHHHHHHH
T ss_conf             9999996999999999998


No 356
>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=66.67  E-value=6.7  Score=18.47  Aligned_cols=28  Identities=25%  Similarity=0.382  Sum_probs=17.3

Q ss_pred             CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             978999994-----99988999999999998079978
Q gi|254780693|r  190 TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       190 t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      |+.+|+..|     .||.|||..|..    .||..+-
T Consensus       123 SD~~I~~~L~~~Gi~IaRRTVaKYR~----~L~Ip~s  155 (160)
T pfam04552       123 SDDKIVELLKEQGIDIARRTVAKYRE----ALNIPSS  155 (160)
T ss_pred             CHHHHHHHHHHCCCCEEHHHHHHHHH----HCCCCCH
T ss_conf             99999999997799521461999998----8399966


No 357
>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=66.36  E-value=6  Score=18.81  Aligned_cols=34  Identities=15%  Similarity=0.158  Sum_probs=15.9

Q ss_pred             HHHCCCCHHHHHHHHCCCH----------HHHHHHHHHHHHHCC
Q ss_conf             9987999789999949998----------899999999999807
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGLSV----------HTVNAYLGSATVKLD  217 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~iS~----------~TV~~hl~~i~~KLg  217 (235)
                      +-..|.|-+||...|.+..          ..+..|+..+-+|+.
T Consensus        53 lr~~GfsL~eI~~ll~l~~~~~~~~~~~~~ll~~kl~~i~~~I~   96 (127)
T cd04784          53 CRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIA   96 (127)
T ss_pred             HHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             98649879999999977728999899999999999999999999


No 358
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=66.29  E-value=6  Score=18.78  Aligned_cols=11  Identities=64%  Similarity=0.854  Sum_probs=3.6

Q ss_pred             CCCHHHHHHHH
Q ss_conf             99978999994
Q gi|254780693|r  188 GYTSEEIAEKL  198 (235)
Q Consensus       188 G~t~~eIA~~L  198 (235)
                      |.|-+||...|
T Consensus        58 GfsL~eI~~ll   68 (140)
T PRK09514         58 GFTLEEIRELL   68 (140)
T ss_pred             CCCHHHHHHHH
T ss_conf             99999999998


No 359
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=66.26  E-value=9  Score=17.56  Aligned_cols=17  Identities=6%  Similarity=0.247  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+..++..+.+.++..
T Consensus        30 savS~~I~~LE~~lG~~   46 (291)
T TIGR03418        30 PAVSQQVKRLEEELGTP   46 (291)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             89999999999996996


No 360
>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=66.02  E-value=6  Score=18.79  Aligned_cols=24  Identities=21%  Similarity=0.338  Sum_probs=11.5

Q ss_pred             CCHHHHHHHHH----HHCCCCHHHHHHH
Q ss_conf             99899999999----9879997899999
Q gi|254780693|r  174 LTERETSCLQL----AGDGYTSEEIAEK  197 (235)
Q Consensus       174 LT~RE~evL~l----~a~G~t~~eIA~~  197 (235)
                      .|+.+.+.|++    ...|.+-++|+..
T Consensus        39 Ys~~dv~~l~~I~~l~~~G~~l~~I~~l   66 (68)
T cd01104          39 YSEADVARLRLIRRLTSEGVRISQAAAL   66 (68)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             4999999999999999978999999987


No 361
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=65.14  E-value=9.4  Score=17.41  Aligned_cols=38  Identities=34%  Similarity=0.331  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99999999987--999789999949998899999999999
Q gi|254780693|r  177 RETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       177 RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      -=.+++..+.+  ..+..+|+..+++|..||..|+.....
T Consensus        26 ~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~   65 (110)
T COG0640          26 TRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLRE   65 (110)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             8999999998735137999998857678899999999987


No 362
>pfam00046 Homeobox Homeobox domain.
Probab=64.93  E-value=9.5  Score=17.38  Aligned_cols=44  Identities=25%  Similarity=0.329  Sum_probs=33.2

Q ss_pred             CCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999999879------9978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .+|+.|.++|.-.=.-      ..-.+||..||+++..|+.-..|-+.|.
T Consensus         6 ~ft~~Q~~~Le~~F~~~~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~   55 (57)
T pfam00046         6 TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKW   55 (57)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             79999999999999857999989999999983999899789768758633


No 363
>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=64.73  E-value=7.1  Score=18.29  Aligned_cols=27  Identities=26%  Similarity=0.364  Sum_probs=18.6

Q ss_pred             CCHHHHHHH----HHHHCCCCHHHHHHHHCC
Q ss_conf             998999999----999879997899999499
Q gi|254780693|r  174 LTERETSCL----QLAGDGYTSEEIAEKLGL  200 (235)
Q Consensus       174 LT~RE~evL----~l~a~G~t~~eIA~~L~i  200 (235)
                      .|+...+.|    .|...|.+-++|...|.-
T Consensus        40 Ys~~dl~~l~~I~~l~~~G~sl~~i~~~L~~   70 (88)
T cd01105          40 YSLADVDRLLVIKELLDEGFTLAAAVEKLRR   70 (88)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             7999999999999999979989999999998


No 364
>KOG0489 consensus
Probab=64.65  E-value=5.8  Score=18.91  Aligned_cols=30  Identities=23%  Similarity=0.368  Sum_probs=26.2

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             899999499988999999999998079978
Q gi|254780693|r  192 EEIAEKLGLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       192 ~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      -|||..|.++|+-||...+|.+.|-.-.++
T Consensus       190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k  219 (261)
T KOG0489         190 IEIAHALNLTERQIKIWFQNRRMKWKKENK  219 (261)
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998740100688999999888999987631


No 365
>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=64.39  E-value=9.7  Score=17.32  Aligned_cols=44  Identities=30%  Similarity=0.294  Sum_probs=29.4

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf             987999789999949998899999999999807997899999999769
Q gi|254780693|r  185 AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG  232 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~G  232 (235)
                      ...|+|-.++|..+|||+.+|..+.+.-.    ..+-..+...|-.+|
T Consensus         9 ~~~~ls~~~lA~~~gis~~~l~~~e~g~~----~p~~~~l~~la~~~~   52 (58)
T cd00093           9 KEKGLTQEELAEKLGVSRSTISRIENGKR----NPSLETLEKLAKALG   52 (58)
T ss_pred             HHCCCCHHHHHHHCCCCHHHHHHHHCCCC----CCCHHHHHHHHHHHC
T ss_conf             97599999995714999999999987998----999999999999938


No 366
>pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function.
Probab=64.16  E-value=9.8  Score=17.29  Aligned_cols=44  Identities=25%  Similarity=0.237  Sum_probs=37.5

Q ss_pred             CCCHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             49989999999998799---978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLAGDGY---TSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~---t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|++-|++|+++=-.|.   |=-+||..|.||++|++....+....+
T Consensus        81 ~~~~~~k~ii~lrY~~r~~~sW~~Va~~l~i~er~~~~~~~~FK~~i  127 (130)
T pfam05263        81 VLTEEEKRIIELRYKGRNGMTWYQVAQELDISEKKAKRIYYSFKNDI  127 (130)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             85189999999986764675499999996511999999999998876


No 367
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.02  E-value=9.8  Score=17.27  Aligned_cols=45  Identities=24%  Similarity=0.324  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|-+.-..+..++-.|..-..||+.++|+..||...+.+...+..
T Consensus        74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~v~r~~~r~~~~~~  118 (129)
T COG3677          74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVE  118 (129)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCHHC
T ss_conf             327799999999864999666999955469999999996031000


No 368
>PRK10072 putative transcriptional regulator; Provisional
Probab=64.01  E-value=7.5  Score=18.09  Aligned_cols=32  Identities=31%  Similarity=0.478  Sum_probs=24.7

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999999998799978999994999889999999
Q gi|254780693|r  178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      |.+-++ -..|++-.|-|..||+|..||+.-=.
T Consensus        37 dvkaIR-~~tgl~q~eFA~~lGvSv~tvksWEq   68 (96)
T PRK10072         37 EFEQLR-KGTGLKIDDFARVLGVSVAMVKEWES   68 (96)
T ss_pred             CHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             399999-88099999999997777999999996


No 369
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286   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 clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=63.40  E-value=3.8  Score=20.19  Aligned_cols=34  Identities=35%  Similarity=0.389  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99899999999987999789999949998899999999999
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .|=||.       +|+|-+|||.+|.+=..||+.-+=+++.
T Consensus       149 i~LREl-------eGLSYe~IA~~MdCPvGTVRSRIFRARE  182 (192)
T TIGR02939       149 ITLREL-------EGLSYEDIAEIMDCPVGTVRSRIFRARE  182 (192)
T ss_pred             HHHHHC-------CCCCHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf             446512-------6878788873306998862114677589


No 370
>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=63.09  E-value=10  Score=17.15  Aligned_cols=43  Identities=14%  Similarity=0.172  Sum_probs=29.9

Q ss_pred             HHHHHHHH-HHHCCCCHHHHHHHHCCCHHH--HHHHHHHHHHHCCC
Q ss_conf             89999999-998799978999994999889--99999999998079
Q gi|254780693|r  176 ERETSCLQ-LAGDGYTSEEIAEKLGLSVHT--VNAYLGSATVKLDA  218 (235)
Q Consensus       176 ~RE~evL~-l~a~G~t~~eIA~~L~iS~~T--V~~hl~~i~~KLg~  218 (235)
                      +--.|.|+ .=..|.|+++||..++.++.+  -...++++++.+|+
T Consensus       489 ~~~~e~L~~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi  534 (1089)
T TIGR01369       489 ELDKELLRKAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGI  534 (1089)
T ss_pred             CCCHHHHHHHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCC
T ss_conf             4898899998641888789999868974442006899999984697


No 371
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=63.02  E-value=10  Score=17.15  Aligned_cols=42  Identities=7%  Similarity=-0.103  Sum_probs=37.2

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             999999879997899999499988999999999998079978
Q gi|254780693|r  180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      .+-.|...+.+-.+.|..|.|=.+|+.+.+++|.+..|..=|
T Consensus       326 TL~~yfe~n~si~~tA~~L~IHRNTL~YRL~KI~~lTGldpr  367 (385)
T PRK11477        326 TLAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLDLG  367 (385)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999809999999998486450699999999999781977


No 372
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=62.27  E-value=11  Score=17.05  Aligned_cols=12  Identities=0%  Similarity=-0.020  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998583
Q gi|254780693|r   19 PRLHLIQNRIKA   30 (235)
Q Consensus        19 ~~l~~l~~~~~~   30 (235)
                      ..+..+.+.++.
T Consensus        55 ~aL~rLr~~~gd   66 (314)
T PRK09508         55 NAVARLKVMFND   66 (314)
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999998199


No 373
>PRK11753 cAMP-regulatory protein; Provisional
Probab=62.17  E-value=11  Score=17.04  Aligned_cols=27  Identities=26%  Similarity=0.218  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             997899999499988999999999998
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      .|-.|||..+|+|..||+.-++...++
T Consensus       169 lt~~eLA~~lG~sretvsR~L~~L~~~  195 (211)
T PRK11753        169 ITRQEIGRIVGCSREMVGRVLKMLEDQ  195 (211)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             699999988699899999999999988


No 374
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=62.11  E-value=5.3  Score=19.16  Aligned_cols=14  Identities=7%  Similarity=0.031  Sum_probs=6.4

Q ss_pred             HHHHHHHHHCCCCE
Q ss_conf             99999998583785
Q gi|254780693|r   20 RLHLIQNRIKARNF   33 (235)
Q Consensus        20 ~l~~l~~~~~~~~f   33 (235)
                      .++++.+.+...++
T Consensus        15 Il~a~~~ll~~~~~   28 (194)
T PRK09480         15 ILQTLAQMLESPPG   28 (194)
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999862797


No 375
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=61.85  E-value=11  Score=17.00  Aligned_cols=30  Identities=13%  Similarity=0.292  Sum_probs=25.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9978999994999889999999999980799
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .|-.+||..||+|+.||...++...++ |+.
T Consensus       174 ~t~~~lA~~lG~tretvsR~L~~L~~~-GI~  203 (236)
T PRK09392        174 YEKRTLASYLGMTPENLSRAFAALASH-GVH  203 (236)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC-CCE
T ss_conf             789999998789899999999999979-968


No 376
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=61.63  E-value=4.6  Score=19.62  Aligned_cols=14  Identities=7%  Similarity=0.133  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             99999999998079
Q gi|254780693|r  205 VNAYLGSATVKLDA  218 (235)
Q Consensus       205 V~~hl~~i~~KLg~  218 (235)
                      .+.-+.-+..+|.+
T Consensus       190 L~llL~Gle~rL~~  203 (205)
T PRK13756        190 LELIICGLEKQLKC  203 (205)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999751


No 377
>smart00351 PAX Paired Box domain.
Probab=61.40  E-value=11  Score=16.95  Aligned_cols=38  Identities=24%  Similarity=0.244  Sum_probs=32.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             99999998799978999994999889999999999980
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .+++.|...|...-+|+++|.||-..|..-+.+.++.-
T Consensus        24 ~kIveLa~~G~rpcdISr~L~VShGCVSKIL~Ry~etG   61 (125)
T smart00351       24 QRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETG   61 (125)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             99999998599899987564577106999999997138


No 378
>COG3177 Fic family protein [Function unknown]
Probab=61.28  E-value=11  Score=16.94  Aligned_cols=28  Identities=29%  Similarity=0.189  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             7999789999949998899999999999
Q gi|254780693|r  187 DGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .+.|.++++.+.+||..|++.+++...+
T Consensus       303 ~~~t~~~~~~~~~~s~~Ta~r~l~~l~~  330 (348)
T COG3177         303 GYLTAAEIEAILGVSKATATRDLKELLE  330 (348)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             7645999999828988889999999974


No 379
>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=61.12  E-value=6.2  Score=18.70  Aligned_cols=16  Identities=25%  Similarity=0.650  Sum_probs=5.0

Q ss_pred             CCCHHHHHHHHCCCHH
Q ss_conf             9997899999499988
Q gi|254780693|r  188 GYTSEEIAEKLGLSVH  203 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~  203 (235)
                      |+|-.+.|.+|||.+.
T Consensus        38 Gms~~QLA~RlGV~p~   53 (150)
T TIGR02612        38 GMSGAQLAARLGVTPQ   53 (150)
T ss_pred             CCCHHHHHHHCCCCHH
T ss_conf             5157887665289737


No 380
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=60.91  E-value=11  Score=16.89  Aligned_cols=28  Identities=18%  Similarity=0.281  Sum_probs=14.8

Q ss_pred             CHHHHHHHHHHHHHHHCC--CCEEEEEECC
Q ss_conf             599999999999998583--7858998417
Q gi|254780693|r   13 SLQELSPRLHLIQNRIKA--RNFALYTINS   40 (235)
Q Consensus        13 sl~dl~~~l~~l~~~~~~--~~f~~~~~~~   40 (235)
                      +.+++...+..+.+.+..  .+|.+.....
T Consensus        26 ~~~~i~~~l~~L~~~Y~~~~~gi~l~~~~~   55 (182)
T PRK00135         26 EPTEVKQLLEELQEKYEGDDRGLKLIEFAE   55 (182)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCEEEEEECC
T ss_conf             989999999999999624897379999999


No 381
>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=60.75  E-value=7.9  Score=17.95  Aligned_cols=26  Identities=23%  Similarity=0.340  Sum_probs=21.7

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             98799978999994999889999999
Q gi|254780693|r  185 AGDGYTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      ---|.|..+.|+.||||+.|++.=+.
T Consensus        17 ~PLg~s~~~LA~~LgVsr~~~sriv~   42 (81)
T TIGR02607        17 EPLGLSVRALAKALGVSRSTLSRIVN   42 (81)
T ss_pred             HCCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             10470689999870999788888874


No 382
>KOG0723 consensus
Probab=60.64  E-value=5.7  Score=18.95  Aligned_cols=33  Identities=18%  Similarity=0.161  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             997899999499988999999999998079978
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR  221 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR  221 (235)
                      +|.+|-+.+|+||+.+.+.-++.+-+|.=+.|.
T Consensus        53 Msr~EA~lIL~v~~s~~k~KikeaHrriM~~NH   85 (112)
T KOG0723          53 MSRREAALILGVTPSLDKDKIKEAHRRIMLANH   85 (112)
T ss_pred             CCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             156889988278754568899999999998079


No 383
>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=60.15  E-value=11  Score=16.80  Aligned_cols=29  Identities=31%  Similarity=0.519  Sum_probs=24.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             97899999499988999999999998079
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      .-.+||..+|+|+..|+....|-+.+..-
T Consensus        29 ~~~~La~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086          29 EREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999792999999999989988873


No 384
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=60.08  E-value=10  Score=17.23  Aligned_cols=35  Identities=20%  Similarity=0.263  Sum_probs=20.5

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             499899999999987999789999949998899999
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAY  208 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~h  208 (235)
                      .||++|.+.|.+.-+ +...|-=..|..=+-.++.+
T Consensus        84 ~L~~~q~~LLeLf~~-LP~sEq~~~l~el~~r~~~~  118 (135)
T PRK09706         84 ELSEDQKELLELFDA-LPESEQEAQLSEMRARVENF  118 (135)
T ss_pred             CCCHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHH
T ss_conf             589999999999997-88999999999999999999


No 385
>COG2469 Uncharacterized conserved protein [Function unknown]
Probab=59.97  E-value=7.8  Score=17.98  Aligned_cols=52  Identities=19%  Similarity=0.141  Sum_probs=44.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             2467887444998999999999879997899999499988999999999998
Q gi|254780693|r  164 FKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       164 ~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ......+...||+-|.++|-++--|..+-++...||++..-++....++..|
T Consensus       204 ~eKe~k~~~~LsE~E~qiLvalYSg~~~~sl~~~lG~~~~el~~l~drlI~~  255 (284)
T COG2469         204 KEKEIKEKETLSEIEKQILVALYSGGDSASLELFLGVDTDELEILYDRLIDK  255 (284)
T ss_pred             HHHHHCCCCCCCHHHHEEEEEEECCCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             8753332223330312113667528982303567487699999999999873


No 386
>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=59.77  E-value=12  Score=16.76  Aligned_cols=45  Identities=33%  Similarity=0.393  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             499899999999-987999789999949998899999999999807
Q gi|254780693|r  173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|..||+-+|.. .-+|+|.-|+|.+.|||...|...=+.+..++.
T Consensus       206 ~l~~re~~il~~rff~G~tqmeva~eiGisqaqvsrlek~a~~~~~  251 (254)
T TIGR02850       206 RLNEREKLILKLRFFEGKTQMEVAEEIGISQAQVSRLEKAALKHMR  251 (254)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             8766788777755314631334565403016888888899999975


No 387
>pfam08069 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021.
Probab=59.62  E-value=9.3  Score=17.44  Aligned_cols=27  Identities=26%  Similarity=0.299  Sum_probs=21.8

Q ss_pred             CCCH--HHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             4998--99999999987999789999949
Q gi|254780693|r  173 NLTE--RETSCLQLAGDGYTSEEIAEKLG  199 (235)
Q Consensus       173 ~LT~--RE~evL~l~a~G~t~~eIA~~L~  199 (235)
                      ..|+  =|..|+++..+|+|..+|+.+|-
T Consensus        27 ~~~~~eve~~I~klakkG~~pSqIG~iLR   55 (60)
T pfam08069        27 KYSPEEVEELIVKLAKKGLTPSQIGVILR   55 (60)
T ss_pred             CCCHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             68999999999999987998889735653


No 388
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=59.57  E-value=12  Score=16.73  Aligned_cols=25  Identities=32%  Similarity=0.424  Sum_probs=19.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9789999949998899999999999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      |.+++|.++++|..||+.-++.+..
T Consensus        22 s~~~la~~~~vSr~tvr~A~~~L~~   46 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEA   46 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             0999999989499999999999998


No 389
>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=59.09  E-value=9.7  Score=17.30  Aligned_cols=28  Identities=25%  Similarity=0.300  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHHCC
Q ss_conf             49989999999998-----79997899999499
Q gi|254780693|r  173 NLTERETSCLQLAG-----DGYTSEEIAEKLGL  200 (235)
Q Consensus       173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~i  200 (235)
                      .-|+...+.++++.     +|+|-+.|-..|.=
T Consensus        38 ~Ys~~di~~l~~Ik~Ll~~~G~ti~~~k~~L~~   70 (99)
T cd04765          38 YYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE   70 (99)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             068999999999999999879879999999983


No 390
>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=58.10  E-value=9.8  Score=17.27  Aligned_cols=20  Identities=15%  Similarity=0.255  Sum_probs=9.8

Q ss_pred             HHHHH-HCCCCHHHHHHHHCC
Q ss_conf             99999-879997899999499
Q gi|254780693|r  181 CLQLA-GDGYTSEEIAEKLGL  200 (235)
Q Consensus       181 vL~l~-a~G~t~~eIA~~L~i  200 (235)
                      |.+|+ ..|.+-.+|..+|.+
T Consensus        49 IkrL~~e~G~nlagI~~iLsl   69 (120)
T cd04767          49 IKKLINEKGLNIAGVKQILSM   69 (120)
T ss_pred             HHHHHHHCCCCHHHHHHHHHC
T ss_conf             999999759689999999806


No 391
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=57.96  E-value=7.2  Score=18.24  Aligned_cols=16  Identities=13%  Similarity=0.262  Sum_probs=7.9

Q ss_pred             CCHHHHHHHHHHHCCC
Q ss_conf             9989999999998799
Q gi|254780693|r  174 LTERETSCLQLAGDGY  189 (235)
Q Consensus       174 LT~RE~evL~l~a~G~  189 (235)
                      ...+-..|..++..|.
T Consensus       184 ~~~~~~~v~~lvL~Gl  199 (202)
T TIGR03613       184 FNETVANVQRIVLEGI  199 (202)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9999999999998302


No 392
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=57.65  E-value=9.9  Score=17.24  Aligned_cols=24  Identities=33%  Similarity=0.617  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999789999949998899999999
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      |+|..+.|..|||+++||+.-+..
T Consensus        23 glt~~~lA~~lgV~r~~is~ling   46 (104)
T COG3093          23 GLTQTELAEALGVTRNTISELING   46 (104)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             698999999939989999999837


No 393
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=57.60  E-value=13  Score=16.51  Aligned_cols=41  Identities=24%  Similarity=0.233  Sum_probs=32.4

Q ss_pred             CCCCCCHHHHHHHHHHHC----C--CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             744499899999999987----9--9978999994999889999999
Q gi|254780693|r  170 AARNLTERETSCLQLAGD----G--YTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       170 ~~~~LT~RE~evL~l~a~----G--~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      ..+.+||=|+.|-.++.+    |  .|..+||..|+.|+|.|-.-+.
T Consensus        86 ~~~g~T~FqrkVy~~L~k~IP~G~t~TYgeiAk~lgts~RAVG~A~~  132 (172)
T PRK03887         86 SFEGLTKFERKVYEWLVKNVKRGEVITYGELAKALNTSPRAVGGAMK  132 (172)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             42579979999999997108998749499999997887789999975


No 394
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=57.45  E-value=12  Score=16.67  Aligned_cols=34  Identities=41%  Similarity=0.409  Sum_probs=23.5

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9999999879997899999499988999999999
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      .+..+-+-+-=|..|||..|++|+..|+..+...
T Consensus        11 ~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~   44 (78)
T pfam04539        11 RELEQELGREPTPEEIAEELGISEEKVREVLEAA   44 (78)
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             9999998889999999999694999999999875


No 395
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=57.43  E-value=10  Score=17.23  Aligned_cols=25  Identities=40%  Similarity=0.424  Sum_probs=21.1

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9879997899999499988999999
Q gi|254780693|r  185 AGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      .-.|+|-.+.|..+|||..|+..-=
T Consensus        11 ~~~~ltQ~elA~~vgVsRQTi~~iE   35 (68)
T COG1476          11 AELGLTQEELAKLVGVSRQTIIAIE   35 (68)
T ss_pred             HHHCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             9828589999999195799999999


No 396
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=56.29  E-value=13  Score=16.36  Aligned_cols=24  Identities=29%  Similarity=0.389  Sum_probs=18.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             978999994999889999999999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      |-+++|..+++|..||+.-++...
T Consensus        26 s~~~La~~~~vSr~tvr~Al~~L~   49 (64)
T pfam00392        26 SERELAAEFGVSRTTVREALRRLE   49 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             799999997969999999999999


No 397
>pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.
Probab=55.94  E-value=13  Score=16.32  Aligned_cols=41  Identities=29%  Similarity=0.446  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             8999999999879--9978999994999889999999999980
Q gi|254780693|r  176 ERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       176 ~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|+.+.+.++-+-  .+-.|+|..||+|+.|++.++..+..=+
T Consensus         5 ~rk~~Ll~lL~~~~~~~l~el~~~l~ls~~tl~~~i~~L~~~f   47 (59)
T pfam08280         5 KRKLKLLELLTENKSITLDELAKQLGLSELTLKSYIHELNELF   47 (59)
T ss_pred             HHHHHHHHHHHCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHC
T ss_conf             8999999999808836499999880997999999999999873


No 398
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=55.83  E-value=13  Score=16.31  Aligned_cols=24  Identities=29%  Similarity=0.389  Sum_probs=18.1

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             998799978999994999889999
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGLSVHTVNA  207 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~iS~~TV~~  207 (235)
                      .--.|+|-++||..|++|+.-|+.
T Consensus        19 f~~~~ls~~~iA~dL~~s~~~ve~   42 (89)
T pfam10078        19 FELSGLTIEQVAKDLNTTPEKVEA   42 (89)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             988389899999894999999999


No 399
>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=55.78  E-value=12  Score=16.72  Aligned_cols=31  Identities=16%  Similarity=0.334  Sum_probs=21.2

Q ss_pred             CCHHHHHHHH----HH-HCCCCHHHHHHHHCCCHHH
Q ss_conf             9989999999----99-8799978999994999889
Q gi|254780693|r  174 LTERETSCLQ----LA-GDGYTSEEIAEKLGLSVHT  204 (235)
Q Consensus       174 LT~RE~evL~----l~-a~G~t~~eIA~~L~iS~~T  204 (235)
                      -|+...+-|+    |+ ..|.|-..|-.+|.+....
T Consensus        39 Ys~~Dl~~L~~I~~L~~~~G~~l~gik~iL~l~~q~   74 (98)
T cd01279          39 YSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQV   74 (98)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             499999999999999995898899999999989999


No 400
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=55.69  E-value=13  Score=16.43  Aligned_cols=43  Identities=28%  Similarity=0.315  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             998999999999879------9978999994999889999999999980
Q gi|254780693|r  174 LTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       174 LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      +|+.+..+|.-.=.=      ..-.+||..||+|+.+|+.-..|-+.|.
T Consensus         7 ~s~~q~~~L~~~f~~~~~P~~~~~~~La~~l~l~~~~I~~WF~NrR~r~   55 (56)
T smart00389        7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             9999999999999877999989999999996949999999878540256


No 401
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=55.68  E-value=11  Score=16.82  Aligned_cols=22  Identities=32%  Similarity=0.309  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             9978999994999889999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      .|++|++..|++|..||-.-.+
T Consensus        53 ft~~el~~~L~~s~~~v~k~~k   74 (76)
T pfam06970        53 FTNEELMELLNCSKQKVIKIKK   74 (76)
T ss_pred             EEHHHHHHHHCCCHHHHHHHHH
T ss_conf             6499999997878889999996


No 402
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=55.57  E-value=14  Score=16.28  Aligned_cols=35  Identities=17%  Similarity=0.108  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999999987999789999949998899999999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      |+.=+-.|-..|..-.+.|+.||||..|...+++.
T Consensus       593 r~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRKlk~  627 (639)
T PRK11388        593 KQAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQ  627 (639)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999994997999999989899999999999


No 403
>KOG2581 consensus
Probab=55.42  E-value=14  Score=16.27  Aligned_cols=25  Identities=32%  Similarity=0.404  Sum_probs=16.3

Q ss_pred             CHHHHHHHHCC-CHHHHHHHHHHHHH
Q ss_conf             97899999499-98899999999999
Q gi|254780693|r  190 TSEEIAEKLGL-SVHTVNAYLGSATV  214 (235)
Q Consensus       190 t~~eIA~~L~i-S~~TV~~hl~~i~~  214 (235)
                      +-++||.+|+| |+.+|++-++++.+
T Consensus       379 Sl~DIA~kL~l~Seed~EyiVakAIR  404 (493)
T KOG2581         379 SLQDIAKKLGLNSEEDAEYIVAKAIR  404 (493)
T ss_pred             CHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             59999999669982027999999987


No 404
>KOG0848 consensus
Probab=54.69  E-value=9.8  Score=17.27  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=22.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             789999949998899999999999807
Q gi|254780693|r  191 SEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      -.|.|..|++|||-||.-.+|-+.|=-
T Consensus       229 KSELA~~LgLsERQVKIWFQNRRAKER  255 (317)
T KOG0848         229 KSELAATLGLSERQVKIWFQNRRAKER  255 (317)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             678877607117666676541027777


No 405
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=53.82  E-value=14  Score=16.09  Aligned_cols=31  Identities=26%  Similarity=0.222  Sum_probs=24.2

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999987999789999949998899999999
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .-.|-..|..-.+.|..||||..|...-++.
T Consensus        11 ~~aL~~~~gn~~~aA~~LGisr~tL~~kmkk   41 (42)
T pfam02954        11 EAALERTGGNKSKAARLLGISRRTLYRKLKK   41 (42)
T ss_pred             HHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999994997999999979699999999973


No 406
>pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons.
Probab=53.65  E-value=14  Score=16.07  Aligned_cols=48  Identities=15%  Similarity=0.225  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH---CCCCCHHHH
Q ss_conf             999999999879997899999499988999999999998---079978999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK---LDAVNRIQA  224 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K---Lg~~nR~qa  224 (235)
                      |..+..+++++-.+-.|.|.+||.++.+|..-++.-++-   |+-+.+-++
T Consensus         2 r~~~~IrlLs~p~s~~qaa~~lg~~~~~i~~wv~~fr~~ll~LDPSG~~e~   52 (65)
T pfam05344         2 RMRLFIRLLSQPISCAQAADQLGTDEGIIRKWVRMFRRWLLQLDPSGHLER   52 (65)
T ss_pred             CHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             387999982666659999999787888999999999999986198877188


No 407
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=53.60  E-value=14  Score=16.07  Aligned_cols=26  Identities=15%  Similarity=0.188  Sum_probs=15.8

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             87999789999949998899999999
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      +.-=+-++||..|.+||.|++.++++
T Consensus       148 s~~W~L~dIA~~L~mSEStLkRkLk~  173 (253)
T PRK09940        148 AHPWKLKDICDCLYISESLLKKKLKQ  173 (253)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             00460999998874589999999998


No 408
>KOG0709 consensus
Probab=53.43  E-value=15  Score=16.05  Aligned_cols=53  Identities=15%  Similarity=0.157  Sum_probs=41.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             46788744499899999999987999789999949998899999999999807997
Q gi|254780693|r  165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       165 ~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      ....+..-.||++|-++|+-+.+=..||++|.+   |.++=|-|+...-.|.++.+
T Consensus       233 G~slPs~lPLTKaEEriLKrvRRKIrNK~SAQE---SRrkKkeYid~LE~rv~~~t  285 (472)
T KOG0709         233 GYSLPSKLPLTKAEERILKRVRRKIRNKRSAQE---SRRKKKEYIDGLESRVSAFT  285 (472)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHCC
T ss_conf             676722377508899999999999876566677---77767667888764221024


No 409
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=53.12  E-value=15  Score=16.02  Aligned_cols=10  Identities=20%  Similarity=0.318  Sum_probs=3.7

Q ss_pred             CCHHHHHHHH
Q ss_conf             2599999999
Q gi|254780693|r   12 SSLQELSPRL   21 (235)
Q Consensus        12 ~sl~dl~~~l   21 (235)
                      .|..++...+
T Consensus        23 vta~~lA~~~   32 (311)
T COG2378          23 VTAAELADEF   32 (311)
T ss_pred             CHHHHHHHHH
T ss_conf             4599999872


No 410
>pfam05331 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=52.83  E-value=15  Score=15.98  Aligned_cols=44  Identities=25%  Similarity=0.280  Sum_probs=37.2

Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             44499899999999987999789999949998899999999999
Q gi|254780693|r  171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      ...|++=+..|+.+...-.|..|||..|++-...|+.-+..+..
T Consensus        38 ~~~l~pE~~~Il~lC~~p~SVAEiAA~L~LPl~VvrVLl~DL~~   81 (114)
T pfam05331        38 PPTLQPEHRRILRLCRAPLSVAEIAARLDLPVGVVRVLLSDLLD   81 (114)
T ss_pred             CCCCCHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEHHHHHH
T ss_conf             88889799999999558520999997318984023015876875


No 411
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=52.77  E-value=9  Score=17.54  Aligned_cols=26  Identities=31%  Similarity=0.368  Sum_probs=19.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             97899999499988999999999998
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      -..|.|+.|++|..||+.|....-.|
T Consensus        18 N~teVaR~L~c~R~TVrkY~~D~~~k   43 (64)
T pfam06322        18 NQTEVARRLNCSRNTVRKYAEDKEGK   43 (64)
T ss_pred             CHHHHHHHHCCHHHHHHHHHCCCCCC
T ss_conf             79999788511088899872355562


No 412
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=52.73  E-value=15  Score=15.97  Aligned_cols=17  Identities=12%  Similarity=0.522  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999985837
Q gi|254780693|r   15 QELSPRLHLIQNRIKAR   31 (235)
Q Consensus        15 ~dl~~~l~~l~~~~~~~   31 (235)
                      ..+...+..+.+.++..
T Consensus        33 ~~vS~qi~~LE~~lg~~   49 (296)
T PRK11062         33 QTITGQIKALEERLQGK   49 (296)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             79999999999995991


No 413
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=52.69  E-value=13  Score=16.36  Aligned_cols=28  Identities=29%  Similarity=0.325  Sum_probs=21.4

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9987999789999949998899999999
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      --.+|+|-.+.|..||+|.+||..|=+-
T Consensus       134 Ree~glSlG~lA~~lgVSRktV~~YE~G  161 (313)
T COG1395         134 REEMGLSLGDLATMLGVSRKTVYKYEKG  161 (313)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHCCC
T ss_conf             9980867878898838468889876247


No 414
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=52.50  E-value=13  Score=16.42  Aligned_cols=38  Identities=29%  Similarity=0.374  Sum_probs=15.8

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             7899999499988999999999998079978999999997
Q gi|254780693|r  191 SEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR  230 (235)
Q Consensus       191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~  230 (235)
                      .+..|..||||+.+|+...+..++  .+..|.-+|.+|..
T Consensus        15 q~a~a~LLgvsp~~vnQw~~g~r~--~~a~r~~aIerAt~   52 (96)
T COG4197          15 QKALARLLGVSPPSVNQWIKGRRQ--VAAERALAIERATS   52 (96)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHEEE--CCCCCCHHHHHHHC
T ss_conf             899999972681478877652010--47553328999853


No 415
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=52.23  E-value=15  Score=15.92  Aligned_cols=26  Identities=23%  Similarity=0.151  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99789999949998899999999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .+..|||..+|+|.+||...++...+
T Consensus       157 ~~~~elA~~lG~Sretl~R~L~~f~~  182 (213)
T PRK10402        157 EKHTQAAEYLGVSYRHLLYVLAQFCQ  182 (213)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             67999999979889999999999998


No 416
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=51.10  E-value=16  Score=15.80  Aligned_cols=14  Identities=14%  Similarity=0.304  Sum_probs=6.0

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             25999999999999
Q gi|254780693|r   12 SSLQELSPRLHLIQ   25 (235)
Q Consensus        12 ~sl~dl~~~l~~l~   25 (235)
                      .|-+.+..++..+.
T Consensus        38 ~s~~~~~~~l~~L~   51 (201)
T COG1974          38 ASPSAIHSHLKALE   51 (201)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             98489999999973


No 417
>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=50.93  E-value=16  Score=15.78  Aligned_cols=24  Identities=38%  Similarity=0.472  Sum_probs=19.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             978999994999889999999999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      |-.++|..+++|..||+.-++...
T Consensus        27 s~~~La~~~~vSr~tvr~Al~~L~   50 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELE   50 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             799999997988899999999999


No 418
>pfam04233 Phage_Mu_F Phage Mu protein F like protein. Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria. A member of this family is required for viral head morphogenesis in bacteriophage SPP1. This family is possibly a minor head protein. This family may be related to the family TT_ORF1 (pfam02956).
Probab=50.02  E-value=16  Score=15.73  Aligned_cols=11  Identities=36%  Similarity=0.434  Sum_probs=5.4

Q ss_pred             CEEEEEEECCC
Q ss_conf             35899721688
Q gi|254780693|r  116 AGIAFPVRLGF  126 (235)
Q Consensus       116 ~~~~~pv~~~~  126 (235)
                      +|..|++..+.
T Consensus        83 dGkv~~~dd~~   93 (110)
T pfam04233        83 DGKIFKVDDPF   93 (110)
T ss_pred             CCEEEECCCCC
T ss_conf             89699678887


No 419
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=49.13  E-value=17  Score=15.59  Aligned_cols=27  Identities=30%  Similarity=0.471  Sum_probs=23.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             997899999499988999999999998
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      .|-++||..+|+|+.||...++...++
T Consensus       174 lT~~dLA~~lG~trETVsR~L~~L~~e  200 (224)
T PRK09391        174 MSRRDIADYLGLTIETVSRALSQLKDR  200 (224)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             799999988799799999999999988


No 420
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=49.08  E-value=17  Score=15.59  Aligned_cols=41  Identities=32%  Similarity=0.261  Sum_probs=32.1

Q ss_pred             CCCHHHHHHHHHHHC----------CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             499899999999987----------99978999994999889999999999
Q gi|254780693|r  173 NLTERETSCLQLAGD----------GYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       173 ~LT~RE~evL~l~a~----------G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      .||.||..|+..+.+          =-|+.+|+...|+++..|..-++...
T Consensus        29 ~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li   79 (100)
T pfam04492        29 DLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLV   79 (100)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             887889999999999860778503362299999997888545999999999


No 421
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=48.33  E-value=14  Score=16.11  Aligned_cols=26  Identities=23%  Similarity=0.268  Sum_probs=16.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99978999994999889999999999
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      -++-++||..||+++.||-.-+++=|
T Consensus       349 PL~lkdiA~~lglheSTVSRav~~Ky  374 (461)
T PRK05932        349 PLVLKDIAEALGMHESTISRATTNKY  374 (461)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHCCE
T ss_conf             76399999873998125889871661


No 422
>pfam01498 Transposase_5 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements.
Probab=48.32  E-value=15  Score=15.91  Aligned_cols=23  Identities=26%  Similarity=0.327  Sum_probs=15.6

Q ss_pred             CCHHHHHHHH-----CCCHHHHHHHHHH
Q ss_conf             9978999994-----9998899999999
Q gi|254780693|r  189 YTSEEIAEKL-----GLSVHTVNAYLGS  211 (235)
Q Consensus       189 ~t~~eIA~~L-----~iS~~TV~~hl~~  211 (235)
                      .|..+|+.+|     .||+.||+..+.+
T Consensus        14 ~T~~~i~~~l~~~g~~vS~~Tvrr~L~~   41 (72)
T pfam01498        14 ITLRDLANELQEIGKSVSRSTIRRRLHK   41 (72)
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             4699999999985997279999999998


No 423
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=47.76  E-value=9.2  Score=17.47  Aligned_cols=18  Identities=11%  Similarity=0.368  Sum_probs=7.5

Q ss_pred             HHHHHHHHC-CCCEEEEEE
Q ss_conf             999999858-378589984
Q gi|254780693|r   21 LHLIQNRIK-ARNFALYTI   38 (235)
Q Consensus        21 l~~l~~~~~-~~~f~~~~~   38 (235)
                      +.+..+.+. -.+|.-.++
T Consensus        17 ldAAl~~l~~~~gf~~lsl   35 (203)
T PRK11202         17 IDAAFSQLSAERSFSSLSL   35 (203)
T ss_pred             HHHHHHHHHCCCCCCCCCH
T ss_conf             9999999860489330679


No 424
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=47.31  E-value=18  Score=15.40  Aligned_cols=15  Identities=27%  Similarity=0.195  Sum_probs=6.0

Q ss_pred             HHHHHHCCCCHHHHH
Q ss_conf             999998799978999
Q gi|254780693|r  181 CLQLAGDGYTSEEIA  195 (235)
Q Consensus       181 vL~l~a~G~t~~eIA  195 (235)
                      |....+.|.+.+||=
T Consensus        99 I~~~~~~G~s~eei~  113 (125)
T COG1725          99 IEEAKALGLSLEEIL  113 (125)
T ss_pred             HHHHHHCCCCHHHHH
T ss_conf             999998699899999


No 425
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.92  E-value=18  Score=15.36  Aligned_cols=28  Identities=29%  Similarity=0.362  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHCC-CCHHHHHHHHCCCHH
Q ss_conf             8999999999879-997899999499988
Q gi|254780693|r  176 ERETSCLQLAGDG-YTSEEIAEKLGLSVH  203 (235)
Q Consensus       176 ~RE~evL~l~a~G-~t~~eIA~~L~iS~~  203 (235)
                      -|=..+..++..+ .+..+||..+|.+-.
T Consensus        37 ~Rl~~a~~~L~~~~~~i~~ia~~~Gy~~~   65 (84)
T smart00342       37 RRLERARRLLRDTDLSVTEIALRVGFSSQ   65 (84)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCCCH
T ss_conf             99999999998576349999888199999


No 426
>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=46.74  E-value=18  Score=15.34  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=17.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             9978999994999889999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~  210 (235)
                      +|..|-|..||||..||..-.+
T Consensus        13 ~t~~eLA~~LgI~~stis~w~~   34 (65)
T pfam07022        13 KSRSELADHLGVSKSTLSTWYK   34 (65)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8699999996988888999998


No 427
>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=45.68  E-value=19  Score=15.23  Aligned_cols=16  Identities=31%  Similarity=0.472  Sum_probs=8.0

Q ss_pred             CCCHHHHHHH--HHHHCC
Q ss_conf             4998999999--999879
Q gi|254780693|r  173 NLTERETSCL--QLAGDG  188 (235)
Q Consensus       173 ~LT~RE~evL--~l~a~G  188 (235)
                      .||+-|++=|  -++.+|
T Consensus        92 ~mT~~Eqekl~~lLlREG  109 (122)
T pfam07037        92 EMTPSEQKQLTSLLSREG  109 (122)
T ss_pred             HCCHHHHHHHHHHHHHHH
T ss_conf             839999999999999982


No 428
>KOG2252 consensus
Probab=44.59  E-value=20  Score=15.12  Aligned_cols=43  Identities=23%  Similarity=0.260  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             49989999999998799------97899999499988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAGDGY------TSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~------t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      -||+-|++-|+-+=+--      .-..|+..|++...||-+..-|++++
T Consensus       426 VfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR  474 (558)
T KOG2252         426 VFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR  474 (558)
T ss_pred             EECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             6458899999999861789879999999998587688899987766651


No 429
>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=44.52  E-value=20  Score=15.11  Aligned_cols=37  Identities=32%  Similarity=0.416  Sum_probs=17.2

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             4998999999999879997899999499988999999
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      .|++||+=|-.|=--|=--.=-|+.||+|||=|-|-|
T Consensus       528 ~l~eRERli~AlE~aGWVQAKAARlLg~TPRQVgYal  564 (574)
T TIGR01817       528 TLSERERLIAALEKAGWVQAKAARLLGLTPRQVGYAL  564 (574)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf             7231789999997515379999997378655899999


No 430
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=43.81  E-value=20  Score=15.04  Aligned_cols=26  Identities=27%  Similarity=0.344  Sum_probs=23.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99789999949998899999999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      .|.+|||..+|.|.-||...++...+
T Consensus       146 lT~~eLA~~iGttREtVsR~L~~l~~  171 (201)
T PRK13918        146 ATHDELAAAVGSVRETVTKVVGELSR  171 (201)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             79999998859868999999999998


No 431
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289   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 part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..
Probab=43.58  E-value=20  Score=15.01  Aligned_cols=37  Identities=32%  Similarity=0.448  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             99899999999987999789999949998899999999999807
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      ++=||.       -|+...||=..|+||...+..-+-+++.+|-
T Consensus       146 F~MRE~-------L~~~~~eIC~~l~is~~N~~VlLyRAR~~LR  182 (194)
T TIGR02943       146 FMMREV-------LGFESEEICQELEISASNCHVLLYRARLSLR  182 (194)
T ss_pred             HHHHHH-------HCCCHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             555654-------2486688753003137679999999999999


No 432
>pfam11740 KfrA_N Plasmid replication region DNA-binding N-term. The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.
Probab=43.08  E-value=21  Score=14.96  Aligned_cols=37  Identities=30%  Similarity=0.340  Sum_probs=18.8

Q ss_pred             HHHHCCC--CHHHHHHHHC-CCHHHHHHHHHHHHHHCCCC
Q ss_conf             9998799--9789999949-99889999999999980799
Q gi|254780693|r  183 QLAGDGY--TSEEIAEKLG-LSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       183 ~l~a~G~--t~~eIA~~L~-iS~~TV~~hl~~i~~KLg~~  219 (235)
                      .+++.|.  |...|=..|| =|..||..|++.-....+..
T Consensus        12 ~L~~~G~~PTv~~VR~~lG~GS~stI~~~L~~w~~~~~~~   51 (120)
T pfam11740        12 ALLAAGERPTVDAVREELGTGSPTTISKYLKEWREEQRAA   51 (120)
T ss_pred             HHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             9987489995999999977978888999999999986501


No 433
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=42.95  E-value=21  Score=14.95  Aligned_cols=42  Identities=21%  Similarity=0.181  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             899999999987-999789999949998899999999999807
Q gi|254780693|r  176 ERETSCLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       176 ~RE~evL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      .|-.++...+.+ ..|.++.|...|||..||..-+..-..+++
T Consensus         6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~in   48 (82)
T pfam12116         6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKIN   48 (82)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             9999999999962628999999969609889887999998739


No 434
>KOG0843 consensus
Probab=42.95  E-value=18  Score=15.31  Aligned_cols=45  Identities=22%  Similarity=0.271  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4499899999999987------99978999994999889999999999980
Q gi|254780693|r  172 RNLTERETSCLQLAGD------GYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~------G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..+|+-+..-|...=+      |..-++.|..|++|+.-|+.-.+|-+.|.
T Consensus       107 T~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~  157 (197)
T KOG0843         107 TAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKH  157 (197)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEECHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             235899999999998408735236899999972987568123433003788


No 435
>PRK13832 plasmid partitioning protein; Provisional
Probab=42.83  E-value=21  Score=14.93  Aligned_cols=30  Identities=30%  Similarity=0.402  Sum_probs=17.5

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             999999987999789999949998899999
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAY  208 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~h  208 (235)
                      +-|-++++.|.|.++|+.-|.++++-|+..
T Consensus       109 RaierlvalGwTeeaIa~ALal~vrqiRkL  138 (518)
T PRK13832        109 RAIERLVALGWTEEAIAVALALPVRQIRKL  138 (518)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999999984998899999966899999999


No 436
>PTZ00100 DnaJ chaperone protein; Provisional
Probab=42.22  E-value=18  Score=15.46  Aligned_cols=31  Identities=10%  Similarity=0.080  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9997899999499988999999999998079
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDA  218 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~  218 (235)
                      -+|-+|-..+||+++..-+.-++.+++||=.
T Consensus        59 ~Mt~~EA~~ILGl~~~as~~~I~~ahrkLM~   89 (114)
T PTZ00100         59 KMSKSEACKILNIPPTANKERIREVHKQLML   89 (114)
T ss_pred             CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             8599999998199999999999999999999


No 437
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=41.82  E-value=22  Score=14.83  Aligned_cols=41  Identities=22%  Similarity=0.043  Sum_probs=19.1

Q ss_pred             CCEEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             98373101331466721367899654258553589972168875
Q gi|254780693|r   85 LPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHK  128 (235)
Q Consensus        85 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~  128 (235)
                      .|+-..++.+......  .|... --....++|++-+++++.||
T Consensus        24 ~~v~~~~ia~~~~Is~--~yL~K-~l~~L~~~GlV~S~rG~~GG   64 (133)
T TIGR00738        24 GPVSVKEIAERQGISR--SYLEK-VLRTLRKAGLVESVRGPGGG   64 (133)
T ss_pred             CCCCHHHHHHHHCCCH--HHHHH-HHHHHHHCCCEECCCCCCCC
T ss_conf             7607899998848998--79999-99988770764211589856


No 438
>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=41.72  E-value=13  Score=16.48  Aligned_cols=21  Identities=43%  Similarity=0.597  Sum_probs=17.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH
Q ss_conf             997899999499988999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      .|..|.|+.|++|.+|++.|+
T Consensus        17 ~Si~~aa~~L~i~~~tI~~~~   37 (37)
T pfam07453        17 SSIREAARALGISHSTINKYL   37 (37)
T ss_pred             HHHHHHHHHHCCCHHHHHCCC
T ss_conf             679999998476465665029


No 439
>PRK05782 precorrin-8X methylmutase; Validated
Probab=41.60  E-value=19  Score=15.17  Aligned_cols=59  Identities=20%  Similarity=0.219  Sum_probs=50.4

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             44998999999999879997899999499988999999999998079978999999997
Q gi|254780693|r  172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR  230 (235)
Q Consensus       172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~  230 (235)
                      ....++|++|++-+-.---+-|++..|..|+..|+.=++.+.+.-.+-.-++.|.-.+.
T Consensus       161 ~~~~~~e~~Vv~R~IHaTgDfe~a~~l~fs~~Av~aGi~AL~~G~~IvtDv~Mv~aGI~  219 (332)
T PRK05782        161 SNWRDREKEIIARAVYASGNLELAKYVYISNDLLDAGIEALKAGIPIVADVKMVAAGIR  219 (332)
T ss_pred             CCCCHHHHHHHHHHEECCCCCCHHHHEEECHHHHHHHHHHHHCCCCEEECHHHHHHHCC
T ss_conf             47994550037764122667212853678905999999999869999982589985377


No 440
>KOG0487 consensus
Probab=41.43  E-value=9.5  Score=17.38  Aligned_cols=50  Identities=22%  Similarity=0.221  Sum_probs=34.9

Q ss_pred             CCHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             9989999999--99879997899999499988999999999998079978999
Q gi|254780693|r  174 LTERETSCLQ--LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       174 LT~RE~evL~--l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      +-+-|+|.|-  .|-. ..-+||++.|++|+|-|+.-.+|=+-|+.--||-+.
T Consensus       247 tlELEkEFlfN~Yitk-eKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487         247 TLELEKEFLFNMYITK-EKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHCCCCHHHEEEEEEHHHHHHHHHHHHHH
T ss_conf             9999999999877728-899999986275123213211010567665407664


No 441
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=40.99  E-value=17  Score=15.50  Aligned_cols=40  Identities=25%  Similarity=0.340  Sum_probs=24.9

Q ss_pred             CCHHHHHHHHH---HHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99899999999---98799978999994999889999999999
Q gi|254780693|r  174 LTERETSCLQL---AGDGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       174 LT~RE~evL~l---~a~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      +=.++.+.+..   --.-++-++||..||+++.||-.-+++=|
T Consensus       346 Iv~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~~Ky  388 (475)
T PRK12469        346 IVARQRDFFRYGEIALKPLVLRDVAEELGLHESTVSRATGNKY  388 (475)
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCCCE
T ss_conf             9999999984785003673499999981998203768862750


No 442
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=40.87  E-value=20  Score=15.12  Aligned_cols=16  Identities=6%  Similarity=0.017  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999
Q gi|254780693|r  143 NEVIIEAHGACYQVIT  158 (235)
Q Consensus       143 ~~~~~~~~~~~~~~~~  158 (235)
                      +++++.+...+..+..
T Consensus        85 PEDL~~LikkAv~lrk  100 (151)
T PRK08561         85 PEDLMNLIKKAVNLRK  100 (151)
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             6799999999999999


No 443
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=40.73  E-value=22  Score=14.71  Aligned_cols=25  Identities=36%  Similarity=0.345  Sum_probs=17.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             9978999994999889999999999
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      .|.++||..+++++..++.-++...
T Consensus        25 ~s~~~iA~~~~i~~~~l~kil~~L~   49 (82)
T pfam02082        25 VTSEEIAERQNISPVYLRKILAKLR   49 (82)
T ss_pred             ECHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9599999878909999999999810


No 444
>KOG1597 consensus
Probab=40.46  E-value=23  Score=14.69  Aligned_cols=35  Identities=23%  Similarity=0.203  Sum_probs=25.1

Q ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             99998799978999994999889999999999980
Q gi|254780693|r  182 LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       182 L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .++-.+-+|-+||....|+++.|++.-.+-+|..+
T Consensus       254 sqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~  288 (308)
T KOG1597         254 SQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHA  288 (308)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_conf             98504765488898885344888998899873046


No 445
>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=40.41  E-value=23  Score=14.68  Aligned_cols=25  Identities=16%  Similarity=0.294  Sum_probs=21.2

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9987999789999949998899999
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGLSVHTVNAY  208 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~iS~~TV~~h  208 (235)
                      --+.|.|-.+.|...|+|.++|..-
T Consensus        11 Rk~~glTQ~~LA~~aGvs~~~Is~i   35 (58)
T TIGR03070        11 RKALGLTQADLADLAGVGLRFIRDI   35 (58)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9994998999998819989999999


No 446
>pfam06971 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
Probab=40.08  E-value=22  Score=14.74  Aligned_cols=19  Identities=21%  Similarity=0.489  Sum_probs=16.6

Q ss_pred             CHHHHHHHHCCCHHHHHHH
Q ss_conf             9789999949998899999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAY  208 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~h  208 (235)
                      +++|+|..+||++.+|+.-
T Consensus        29 SS~eLa~~~gv~~aqiRKD   47 (49)
T pfam06971        29 SSKELSEAIGIDAAQIRKD   47 (49)
T ss_pred             CHHHHHHHHCCCHHHHHCC
T ss_conf             7999999979399996142


No 447
>PRK10870 transcriptional repressor MprA; Provisional
Probab=39.53  E-value=23  Score=14.59  Aligned_cols=12  Identities=25%  Similarity=0.288  Sum_probs=5.4

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             998999999999
Q gi|254780693|r  174 LTERETSCLQLA  185 (235)
Q Consensus       174 LT~RE~evL~l~  185 (235)
                      ||+-|++.|.-+
T Consensus       143 Ls~eE~~qL~~L  154 (176)
T PRK10870        143 LSTTEKDQLEQI  154 (176)
T ss_pred             CCHHHHHHHHHH
T ss_conf             999999999999


No 448
>pfam08765 Mor Mor transcription activator family. Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N terminal region of Mor is the dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA.
Probab=39.48  E-value=23  Score=14.58  Aligned_cols=43  Identities=19%  Similarity=0.194  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             49989999999998799978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      ..+.|..+|-.=- .|..-.|.|.+=++|+++|..-++++++-.
T Consensus        57 ~~~~Rd~~I~~eF-nG~N~~eLArkY~ls~~~i~~ii~~~rk~~   99 (107)
T pfam08765        57 RLALRDLEIYNEF-NGNNHAELARKYGVSEQWIYKIIKRVRKLE   99 (107)
T ss_pred             HHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             8999999999980-798799999996988999999999999999


No 449
>pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages.
Probab=39.46  E-value=23  Score=14.66  Aligned_cols=44  Identities=16%  Similarity=0.032  Sum_probs=19.8

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             9987999789999949998899999999999807997899999999
Q gi|254780693|r  184 LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAI  229 (235)
Q Consensus       184 l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~  229 (235)
                      |.-.|.|..+|+.++  .++--+.|-+.--++|--.-|+|.+.-+.
T Consensus        84 ~fim~GtareIS~e~--k~k~rrkhetkeerrlrrniraqmaie~~  127 (134)
T pfam04936        84 EFIMGGSAREISDEI--KDKDRRKHETKEERRLRRNIRAQMAIEAA  127 (134)
T ss_pred             CCCCCCCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             413466266665888--88887512038899999988999988852


No 450
>KOG0484 consensus
Probab=39.44  E-value=23  Score=14.58  Aligned_cols=40  Identities=30%  Similarity=0.365  Sum_probs=30.9

Q ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             8799978999994999889999999999980799789999
Q gi|254780693|r  186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI  225 (235)
Q Consensus       186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav  225 (235)
                      -+=+|-+|||..+.+++.-|....+|-+.|+----|...+
T Consensus        42 PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~   81 (125)
T KOG0484          42 PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA   81 (125)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7403189998862056889999998668888888999998


No 451
>PRK10856 hypothetical protein; Provisional
Probab=39.39  E-value=23  Score=14.57  Aligned_cols=52  Identities=13%  Similarity=0.008  Sum_probs=29.1

Q ss_pred             CHHHHHHHHH---HHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             5999999999---9999858378589984177787310250442278778999624874441208799999
Q gi|254780693|r   13 SLQELSPRLH---LIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHF   80 (235)
Q Consensus        13 sl~dl~~~l~---~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~   80 (235)
                      |++|+..+|+   ...+.++.+.|..+                ....|...++..|..+.....++++...
T Consensus        29 Si~dvA~~LkL~~~~ieALE~dd~~~L----------------p~~tF~RGylRsYAr~LglD~~~ll~~~   83 (332)
T PRK10856         29 SQQAVAERLCLKVSTVRDIEEDKAPAD----------------LASTFLRGYIRSYARLVHIPEEELLPGL   83 (332)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCHHCC----------------CCHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             999999870898999999857822108----------------7036479999999999788979965421


No 452
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain; InterPro: IPR006497   This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication.
Probab=39.08  E-value=24  Score=14.54  Aligned_cols=45  Identities=29%  Similarity=0.260  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHHHHHHHC---C-------CCHHHHHHHHC-------CCHHHHHHHHHHHHHH
Q ss_conf             44499899999999987---9-------99789999949-------9988999999999998
Q gi|254780693|r  171 ARNLTERETSCLQLAGD---G-------YTSEEIAEKLG-------LSVHTVNAYLGSATVK  215 (235)
Q Consensus       171 ~~~LT~RE~evL~l~a~---G-------~t~~eIA~~L~-------iS~~TV~~hl~~i~~K  215 (235)
                      ...||.||.+|+.-|..   |       -|+.+||...+       ++...|..-+.++.++
T Consensus        20 ~~~L~~Ref~v~~Ai~R~T~Gyn~~~~rvt~~~ia~lt~Pdeakaal~~~~vs~A~~~L~~~   81 (104)
T TIGR01610        20 GADLSGREFRVLLAILRLTYGYNKEADRVTASEIAELTKPDEAKAALERKRVSEAIKSLVRR   81 (104)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHH
T ss_conf             48784357999999998741566603566688888532831355521344788999998875


No 453
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879    PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=38.43  E-value=2.9  Score=21.10  Aligned_cols=52  Identities=12%  Similarity=0.015  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHC---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             499899999999987---------9997899999499988999999999998079978999
Q gi|254780693|r  173 NLTERETSCLQLAGD---------GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA  224 (235)
Q Consensus       173 ~LT~RE~evL~l~a~---------G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa  224 (235)
                      .|+|-|-.-|...=+         =+=|.-=+....|=+|||..|+++.+|.|+.......
T Consensus       154 ~lGPTEfRLL~FFM~HPeRV~SReQLLD~VWG~dvyVE~RTVDVHIRRLRKaL~~~g~~~~  214 (226)
T TIGR02154       154 ELGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALEPGGLEDL  214 (226)
T ss_pred             CCCCHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCEEEECCCEEEEECCHHHHCCCCCCCCC
T ss_conf             4687047889998623773440423201105894325135000322000542387888871


No 454
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=38.06  E-value=19  Score=15.18  Aligned_cols=19  Identities=11%  Similarity=-0.066  Sum_probs=9.4

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999999999999999
Q gi|254780693|r  142 ANEVIIEAHGACYQVITDF  160 (235)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~  160 (235)
                      -++++..+...+..+..++
T Consensus        81 iPEDL~~LikKAv~irkHL   99 (148)
T PTZ00072         81 IPEDLYFLIKKAVQMRKHL   99 (148)
T ss_pred             CCHHHHHHHHHHHHHHHHH
T ss_conf             9589999999999999999


No 455
>pfam10252 PP28 Casein kinase substrate phosphoprotein PP28. This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II.
Probab=37.80  E-value=25  Score=14.41  Aligned_cols=28  Identities=25%  Similarity=0.392  Sum_probs=22.2

Q ss_pred             CCCCCCHHHHH----------HHHHHHCCCCHHHHHHH
Q ss_conf             74449989999----------99999879997899999
Q gi|254780693|r  170 AARNLTERETS----------CLQLAGDGYTSEEIAEK  197 (235)
Q Consensus       170 ~~~~LT~RE~e----------vL~l~a~G~t~~eIA~~  197 (235)
                      ....||.||+|          ..+|-++|+|...-|..
T Consensus        21 ~~~eLSRREREeiekQ~a~~rY~KLh~~GKT~eAraDL   58 (82)
T pfam10252        21 DPVELSRREREEIEKQKARERYMKLHAEGKTEQARADL   58 (82)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             75321578899999889999999999825808899889


No 456
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=37.55  E-value=25  Score=14.38  Aligned_cols=36  Identities=33%  Similarity=0.473  Sum_probs=27.1

Q ss_pred             HHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             89999999--9987999789999949998899999999
Q gi|254780693|r  176 ERETSCLQ--LAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       176 ~RE~evL~--l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .-|++++.  |-..|..-...|..||||.+|....+++
T Consensus       285 ~~Ek~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~klkk  322 (325)
T PRK11608        285 QQEKELLQRSLQQAKFNQKRAAELLGLTYHQFRALLKK  322 (325)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999999993998999999988899999999997


No 457
>PRK04158 transcriptional repressor CodY; Validated
Probab=36.17  E-value=26  Score=14.23  Aligned_cols=101  Identities=17%  Similarity=0.178  Sum_probs=64.9

Q ss_pred             CEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC---------CC--CCCCCCCHHHHHHHHH
Q ss_conf             358997216887523454105887899899999999999999999851246---------78--8744499899999999
Q gi|254780693|r  116 AGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKK---------RS--SAARNLTERETSCLQL  184 (235)
Q Consensus       116 ~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~--~~~~~LT~RE~evL~l  184 (235)
                      ....+|+..+..+.|.+.+...+.....+++......+.-+....++....         ..  -+...||=-|.|....
T Consensus       111 ~ttIvPI~g~GeRLGTLil~r~~~~F~ddDLILaEy~ATVVGmEiLr~~~e~iEeeaRkka~VqmAi~tLSYSEleAv~h  190 (256)
T PRK04158        111 LTTIVPIVGGGERLGTLILARNDKEFTDDDLILAEYSATVVGMEILREKAEEIEEEARKKAAVQMAINTLSYSELEAVEH  190 (256)
T ss_pred             CEEEEEEECCCCEEEEEEEEECCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             38999552277335899999637998866351112567999999999989988999999999999998637878999999


Q ss_pred             HHCCC-------CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             98799-------9789999949998899999999999807997
Q gi|254780693|r  185 AGDGY-------TSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       185 ~a~G~-------t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      +-+-+       ...-||.+-||+..    -+-|+.|||....
T Consensus       191 If~EL~G~EGlLVASkIADrvGITRS----VIVNALRKlESAG  229 (256)
T PRK04158        191 IFEELDGNEGLLVASKIADRVGITRS----VIVNALRKLESAG  229 (256)
T ss_pred             HHHHCCCCCCEEEEHHHHHHHCCCHH----HHHHHHHHHHHCC
T ss_conf             99962897552754333443087156----7787777653146


No 458
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=35.24  E-value=27  Score=14.13  Aligned_cols=36  Identities=25%  Similarity=0.199  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             899999999987999789999949998899999999
Q gi|254780693|r  176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       176 ~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .++.=+..+-+.+--..+.|+.||||..|+..-+++
T Consensus       566 ~~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~  601 (606)
T COG3284         566 EKAALLAALQATNGNISEAARLLGISRSTLYRKLKR  601 (606)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             799999999980897999999859978889999997


No 459
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=35.21  E-value=27  Score=14.13  Aligned_cols=15  Identities=13%  Similarity=0.251  Sum_probs=8.1

Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             599999999999998
Q gi|254780693|r   13 SLQELSPRLHLIQNR   27 (235)
Q Consensus        13 sl~dl~~~l~~l~~~   27 (235)
                      +.+|+...|..+...
T Consensus       197 ta~dV~~sl~rl~~~  211 (551)
T PRK13626        197 EMDDVIASLTRINTL  211 (551)
T ss_pred             CHHHHHHHHHHHHCC
T ss_conf             799999999987326


No 460
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=35.15  E-value=27  Score=14.12  Aligned_cols=14  Identities=7%  Similarity=0.036  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999998
Q gi|254780693|r   14 LQELSPRLHLIQNR   27 (235)
Q Consensus        14 l~dl~~~l~~l~~~   27 (235)
                      .+|+...|..+.+.
T Consensus       200 a~dV~~sL~r~~~l  213 (564)
T COG4533         200 ASDVIASLLRLLQL  213 (564)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             99999999998527


No 461
>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=35.13  E-value=27  Score=14.12  Aligned_cols=29  Identities=21%  Similarity=0.263  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             999789999949998899999999999807997
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      -++-+|.|..|||+..+    ++++.+++|+..
T Consensus        15 ~lpi~~AA~~Lgv~~T~----LKk~CR~~gI~R   43 (52)
T pfam02042        15 HLPIKEAAKELGVCLTV----LKKICRQLGIPR   43 (52)
T ss_pred             CCCHHHHHHHHCCCHHH----HHHHHHHCCCCC
T ss_conf             87599999996877999----999999879987


No 462
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=35.07  E-value=27  Score=14.11  Aligned_cols=30  Identities=23%  Similarity=0.145  Sum_probs=24.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             999789999949998899999999999807
Q gi|254780693|r  188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      --|-.||+..+.+|+.+|+-.+....+|=-
T Consensus        14 ~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGk   43 (68)
T pfam09012        14 RASLAELARHFKMSPDAVEAMLEVWIRKGK   43 (68)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf             847999998979399999999999998797


No 463
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294   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 sigmaW, which is restricted to certain lineages of the order Bacillales..
Probab=34.95  E-value=15  Score=16.05  Aligned_cols=36  Identities=31%  Similarity=0.373  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             9999999998799978999994999889999999999
Q gi|254780693|r  177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      |-.=||+.+-+ +|=+||+.+|++-..||++-+-+=+
T Consensus       142 R~~ivLKY~ed-LSL~EIS~IL~lPVgTVKTRiHRGR  177 (187)
T TIGR02948       142 RSVIVLKYMED-LSLKEISEILDLPVGTVKTRIHRGR  177 (187)
T ss_pred             CEEHHHHHHHH-HHHHHHHHHHCCCCCCEECCCCCCH
T ss_conf             12224544444-2188899985789431002430245


No 464
>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=34.92  E-value=27  Score=14.10  Aligned_cols=54  Identities=15%  Similarity=0.138  Sum_probs=39.0

Q ss_pred             CCHHHHHHHHHHH---CCCCHHHHHHHHC-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             9989999999998---7999789999949-998899999999999807997899999999
Q gi|254780693|r  174 LTERETSCLQLAG---DGYTSEEIAEKLG-LSVHTVNAYLGSATVKLDAVNRIQAIAKAI  229 (235)
Q Consensus       174 LT~RE~evL~l~a---~G~t~~eIA~~L~-iS~~TV~~hl~~i~~KLg~~nR~qava~A~  229 (235)
                      -.+|+  |+-+++   .|+|..+||..+| -.-.||-+-++++-+++............+
T Consensus        29 ~~aR~--ia~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~a~~kv~~~~~~d~~~~~~v~~i   86 (90)
T cd06571          29 ALARQ--IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEEDPELKEDVEEL   86 (90)
T ss_pred             HHHHH--HHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_conf             89999--99999999978899999999589971499999999999998399999999999


No 465
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=34.90  E-value=21  Score=14.91  Aligned_cols=44  Identities=30%  Similarity=0.319  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf             998999999999879-99789999949998899999999999807
Q gi|254780693|r  174 LTERETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATVKLD  217 (235)
Q Consensus       174 LT~RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg  217 (235)
                      -......|..+...| .+..+||..++||..||.....+...+-+
T Consensus       162 ~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~  206 (222)
T COG1961         162 AEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG  206 (222)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEECCCCCCCCCC
T ss_conf             367799999999834634999999817774144400122222210


No 466
>PRK05629 hypothetical protein; Validated
Probab=34.68  E-value=28  Score=14.07  Aligned_cols=40  Identities=20%  Similarity=0.192  Sum_probs=28.5

Q ss_pred             CCHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             998999999999--8799978999994999889999999999
Q gi|254780693|r  174 LTERETSCLQLA--GDGYTSEEIAEKLGLSVHTVNAYLGSAT  213 (235)
Q Consensus       174 LT~RE~evL~l~--a~G~t~~eIA~~L~iS~~TV~~hl~~i~  213 (235)
                      |+-+=++++++.  ..|.+..+||..|||.+=-|+.+...++
T Consensus       245 L~~~~r~l~~~~~~~~~~~~~~iA~~Lgv~P~~vkk~~~qar  286 (331)
T PRK05629        245 LSMKVGQIARLYSTRGRINGFELAKELGMPPFVVEKTAKVAR  286 (331)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999999999751699989999883999899999999982


No 467
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=34.56  E-value=24  Score=14.44  Aligned_cols=18  Identities=0%  Similarity=-0.090  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHCCCCEE
Q ss_conf             999999999985837858
Q gi|254780693|r   17 LSPRLHLIQNRIKARNFA   34 (235)
Q Consensus        17 l~~~l~~l~~~~~~~~f~   34 (235)
                      -...+.+..+.+.-.||.
T Consensus        15 r~~ll~aA~~~F~~~G~~   32 (224)
T PRK11552         15 KQQLIAAALAQFGEYGLH   32 (224)
T ss_pred             HHHHHHHHHHHHHHHCCC
T ss_conf             999999999999884914


No 468
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=34.43  E-value=18  Score=15.43  Aligned_cols=17  Identities=18%  Similarity=0.045  Sum_probs=11.3

Q ss_pred             CCCHHHHHHHHHHHCCC
Q ss_conf             49989999999998799
Q gi|254780693|r  173 NLTERETSCLQLAGDGY  189 (235)
Q Consensus       173 ~LT~RE~evL~l~a~G~  189 (235)
                      .|++.+.+.|+-+.-..
T Consensus       349 ~~~~~~~~~l~~~lp~~  365 (422)
T PTZ00037        349 KFTNEEKELLKELFPQN  365 (422)
T ss_pred             CCCHHHHHHHHHHCCCC
T ss_conf             88999999999848998


No 469
>PRK10130 transcriptional regulator EutR; Provisional
Probab=34.26  E-value=28  Score=14.03  Aligned_cols=31  Identities=16%  Similarity=0.205  Sum_probs=24.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999987999789999949998899999999
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      ++....+-.|..+|+..++||.+|..+..+.
T Consensus       249 i~~~~~~pltv~~lc~~~~vS~RtLq~~F~~  279 (350)
T PRK10130        249 VLENMSEPVTVLDLCNQLHVSRRTLQNAFHA  279 (350)
T ss_pred             HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9848679999999998859779999999998


No 470
>cd00131 PAX Paired Box domain
Probab=34.18  E-value=28  Score=14.02  Aligned_cols=32  Identities=25%  Similarity=0.328  Sum_probs=19.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999987999789999949998899999999
Q gi|254780693|r  180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .+++|..+|...-+|+++|.||-.-|-.-+.+
T Consensus        25 kIVeLa~~G~RpcdISR~L~VShGCVSKIL~R   56 (128)
T cd00131          25 RIVELAQSGIRPCDISRQLRVSHGCVSKILNR   56 (128)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999985997888887637772168999998


No 471
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=34.00  E-value=28  Score=14.00  Aligned_cols=27  Identities=26%  Similarity=0.352  Sum_probs=21.9

Q ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             999879997899999499988999999
Q gi|254780693|r  183 QLAGDGYTSEEIAEKLGLSVHTVNAYL  209 (235)
Q Consensus       183 ~l~a~G~t~~eIA~~L~iS~~TV~~hl  209 (235)
                      -|+..+.+.++-+...|||+.|+..--
T Consensus        10 ~l~~r~~~~~eLa~~igis~~~ls~l~   36 (73)
T COG3655          10 MLADRKISLKELAEAIGISEANLSKLK   36 (73)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             999975017789999843698999997


No 472
>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=33.99  E-value=28  Score=14.00  Aligned_cols=44  Identities=25%  Similarity=0.336  Sum_probs=0.0

Q ss_pred             CCCHHHHHHH--HHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             4998999999--999879--9978999994999889999999999980
Q gi|254780693|r  173 NLTERETSCL--QLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       173 ~LT~RE~evL--~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      .|-.||+.|+  +|+.+-  .|=.++|.+.|||.-=|+.-=+++++|+
T Consensus       226 ~Ld~RsR~I~~~RwL~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~  273 (279)
T TIGR02392       226 SLDARSRRIIEARWLDDDGKLTLHELAAEYGVSAERIRQIEKNAMKKL  273 (279)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             522887999987302788996478999884874667999999999999


No 473
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=33.86  E-value=28  Score=13.98  Aligned_cols=39  Identities=26%  Similarity=0.322  Sum_probs=0.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             8874449989999999998799978999994999889999
Q gi|254780693|r  168 SSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNA  207 (235)
Q Consensus       168 ~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~  207 (235)
                      ......||+-|...++ -..|+|-.+-|+.||+|..||+.
T Consensus        38 l~~~~~ls~~eIk~iR-e~~~lSq~vFA~~L~vs~~Tv~~   76 (104)
T COG2944          38 LLKVKTLSPTEIKAIR-EKLGLSQPVFARYLGVSVSTVRK   76 (104)
T ss_pred             HCCCCCCCHHHHHHHH-HHHCCCHHHHHHHHCCCHHHHHH
T ss_conf             2367899889999999-98288899999998887999999


No 474
>pfam06627 DUF1153 Protein of unknown function (DUF1153). This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=33.73  E-value=21  Score=14.91  Aligned_cols=17  Identities=29%  Similarity=0.454  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHCCCC
Q ss_conf             99789999999976999
Q gi|254780693|r  218 AVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       218 ~~nR~qava~A~~~Gli  234 (235)
                      |.+|-.+|++|+..|||
T Consensus        34 VasRKA~VV~aV~~GLi   50 (90)
T pfam06627        34 VASRKAAVVAAVRGGLL   50 (90)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             68888899999981777


No 475
>pfam00382 TFIIB Transcription factor TFIIB repeat.
Probab=33.68  E-value=21  Score=14.88  Aligned_cols=25  Identities=24%  Similarity=0.173  Sum_probs=0.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHH
Q ss_conf             9999987999789999949998899
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTV  205 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV  205 (235)
                      +.+..-..+|-+||+...+||+.|+
T Consensus        47 Acr~~~~~rt~~eia~v~~vs~~tI   71 (71)
T pfam00382        47 ACRLEEVKRTLKEISSVAQVSEKTI   71 (71)
T ss_pred             HHHHCCCCCCHHHHHHHHCCCCCCC
T ss_conf             9998089989999999968987869


No 476
>pfam07508 Recombinase Recombinase. This domain is usually found associated with pfam00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=33.16  E-value=29  Score=13.90  Aligned_cols=33  Identities=27%  Similarity=0.254  Sum_probs=0.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHHC-----------CCHHHHHHHHHH
Q ss_conf             999999987999789999949-----------998899999999
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLG-----------LSVHTVNAYLGS  211 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~-----------iS~~TV~~hl~~  211 (235)
                      +++-.+.++|++..+||..|+           -+..||..-++|
T Consensus         8 r~if~~~~~g~s~~~Ia~~Ln~~g~~~~~~~~w~~~~I~~iL~N   51 (101)
T pfam07508         8 RLIFELYLEGKSLREIARYLNERGIPTPRGKKWTKSTVRRILTN   51 (101)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCC
T ss_conf             99999998389999999999874996778982464435566208


No 477
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=33.06  E-value=29  Score=13.89  Aligned_cols=16  Identities=19%  Similarity=0.418  Sum_probs=0.0

Q ss_pred             HHHHHHHHCCCCHHHH
Q ss_conf             9999999879997899
Q gi|254780693|r  179 TSCLQLAGDGYTSEEI  194 (235)
Q Consensus       179 ~evL~l~a~G~t~~eI  194 (235)
                      .+|..++.+|+|+.||
T Consensus        68 ~~V~e~l~eGkS~~qI   83 (153)
T COG3088          68 HQVYELLQEGKSDQQI   83 (153)
T ss_pred             HHHHHHHHCCCCHHHH
T ss_conf             9999999857868999


No 478
>pfam11994 DUF3489 Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=33.05  E-value=29  Score=13.89  Aligned_cols=29  Identities=34%  Similarity=0.386  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             79997899999499988999999999998
Q gi|254780693|r  187 DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +|-|..||...+|=-+|||+--+..+.+|
T Consensus        23 ~Gati~~i~~atGWq~HTvRgalaG~lkK   51 (72)
T pfam11994        23 EGATIAAISEATGWQPHTVRGALAGLLKK   51 (72)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             89879999998687403589999888886


No 479
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=32.96  E-value=21  Score=14.98  Aligned_cols=39  Identities=15%  Similarity=0.070  Sum_probs=0.0

Q ss_pred             HHHHHHCCCCHHHHHH-------------HHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9999987999789999-------------94999889999999999980799
Q gi|254780693|r  181 CLQLAGDGYTSEEIAE-------------KLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~-------------~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      ++-|++-|.-..-|+.             +|||+..|-..-+++.|+||-++
T Consensus        74 ivgWl~i~~L~~~I~~~k~~~~~~fDPyEILGI~~~ts~rdik~~yr~Ls~K  125 (610)
T COG5407          74 IVGWLVISYLISNIRTLKIEYRRGFDPYEILGIDQDTSERDIKKRYRMLSMK  125 (610)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHEEE
T ss_conf             8999999999998777789987088818861246787577899999866240


No 480
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=32.69  E-value=30  Score=13.85  Aligned_cols=32  Identities=16%  Similarity=0.206  Sum_probs=0.0

Q ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
Q ss_conf             98799978999994999889999999999980
Q gi|254780693|r  185 AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL  216 (235)
Q Consensus       185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL  216 (235)
                      +.-|+|.+|||+--=+|+.|...-+.++.+|+
T Consensus       133 ~v~GLs~~eIArAFLv~e~am~QRivRAK~ri  164 (415)
T COG4941         133 LVGGLSTAEIARAFLVPEAAMAQRIVRAKARI  164 (415)
T ss_pred             HHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             98287599999998078078999999999999


No 481
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=32.30  E-value=10  Score=17.07  Aligned_cols=59  Identities=24%  Similarity=0.274  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHH---------CCCHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHCCC
Q ss_conf             9989999999998799978999994---------99988999999999998079978-999999997699
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKL---------GLSVHTVNAYLGSATVKLDAVNR-IQAIAKAIRFGY  233 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L---------~iS~~TV~~hl~~i~~KLg~~nR-~qava~A~~~Gl  233 (235)
                      |++||..||.++.+ .-.+-|++.-         .++++|+..++..+++-|+-.+. .+.|+-=-+.||
T Consensus        32 l~~~~~~lL~~L~e-~~geVvsk~eL~~~VW~~~~v~~~~Ltq~I~~LRr~L~d~~~~~~~I~TvPrrGy  100 (148)
T COG3710          32 LGPRELKLLSLLLE-RAGEVVSKDELLDAVWPGRIVTVNTLTQAISALRRALRDIGDGHRLIATVPRRGY  100 (148)
T ss_pred             ECHHHHHHHHHHHH-CCCCEECHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCE
T ss_conf             66678899999985-4686052999999857996264454999999999986346876638998378546


No 482
>pfam04182 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
Probab=31.93  E-value=30  Score=13.77  Aligned_cols=41  Identities=20%  Similarity=0.161  Sum_probs=0.0

Q ss_pred             CHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             989999999998----79997899999499988999999999998
Q gi|254780693|r  175 TERETSCLQLAG----DGYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       175 T~RE~evL~l~a----~G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      ++-|.++|.++|    .|-+..+.+...|+-+++|-.|+++...+
T Consensus         1 ~~~~~~lL~~Ia~~r~~Gi~q~dL~k~~~~D~rs~~~~~k~L~~~   45 (73)
T pfam04182         1 PALQFELLEEIARSRYNGITQSDLAKLTGQDPRSVFYRLKKLEDK   45 (73)
T ss_pred             CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHC
T ss_conf             924899999999517688018999999689964317989999878


No 483
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=31.82  E-value=31  Score=13.76  Aligned_cols=18  Identities=33%  Similarity=0.593  Sum_probs=0.0

Q ss_pred             CHHHHHHHHCCCHHHHHH
Q ss_conf             978999994999889999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNA  207 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~  207 (235)
                      |++|||+.++|...||+.
T Consensus        34 sS~els~~~~vdsatIRr   51 (211)
T COG2344          34 SSKELSEALGVDSATIRR   51 (211)
T ss_pred             CHHHHHHHHCCCHHHHHH
T ss_conf             689999986899999863


No 484
>pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
Probab=31.75  E-value=31  Score=13.75  Aligned_cols=33  Identities=33%  Similarity=0.428  Sum_probs=0.0

Q ss_pred             HHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             99999987---9997899999499988999999999
Q gi|254780693|r  180 SCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSA  212 (235)
Q Consensus       180 evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i  212 (235)
                      +||..+-.   +-...|||.-+|+|.--+++|+...
T Consensus         4 ~Il~~i~~i~~p~~T~eIAda~gls~YQaR~YL~~L   39 (61)
T pfam04703         4 SILTFINSIGAPCKTREIADALGLSAYQARYYLEQL   39 (61)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHH
T ss_conf             899999874898418899998550799999999999


No 485
>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=31.66  E-value=31  Score=13.74  Aligned_cols=32  Identities=38%  Similarity=0.473  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
Q ss_conf             99899999999987999789999949998899
Q gi|254780693|r  174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTV  205 (235)
Q Consensus       174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV  205 (235)
                      |-.|=+=|=.|+-.-+|-+||+..||+|.-|+
T Consensus        42 l~~R~~I~~~LL~~~~~QREi~~~lG~SiA~I   73 (95)
T TIGR01321        42 LGSRVRIVEELLEGEMSQREIAEKLGVSIATI   73 (95)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH
T ss_conf             98799999999614897478888637616678


No 486
>pfam00292 PAX 'Paired box' domain.
Probab=31.65  E-value=31  Score=13.74  Aligned_cols=36  Identities=25%  Similarity=0.307  Sum_probs=0.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999999987999789999949998899999999999
Q gi|254780693|r  179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      ..+++|...|...-+|+++|.||-.-|-.-+.+.++
T Consensus        24 ~kIVeLa~~G~RpCdISR~L~VShGCVSKIL~Ry~e   59 (125)
T pfam00292        24 QKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQE   59 (125)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             999999984997888877626762168999998872


No 487
>TIGR03192 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=31.57  E-value=31  Score=13.73  Aligned_cols=40  Identities=15%  Similarity=0.229  Sum_probs=0.0

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999987999789999949998899999999999807997
Q gi|254780693|r  178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      |.||..++++|.+..+|+.  ||...-++..+ ++.+|++...
T Consensus       202 ESevis~l~~G~~~edI~a--Gl~~sia~rv~-~l~~r~~~~~  241 (293)
T TIGR03192       202 KSEALGLLKAGYTKNMVIA--AYCQAMAERVV-SLLERIGVEE  241 (293)
T ss_pred             EHHHHHHHHCCCCHHHHHH--HHHHHHHHHHH-HHHHHCCCCC
T ss_conf             1769999986998999999--99999999999-9976338899


No 488
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II; InterPro: IPR014119    The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I (IPR009920 from INTERPRO). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis..
Probab=30.82  E-value=31  Score=13.67  Aligned_cols=22  Identities=23%  Similarity=0.214  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             99999999998079978999999997699
Q gi|254780693|r  205 VNAYLGSATVKLDAVNRIQAIAKAIRFGY  233 (235)
Q Consensus       205 V~~hl~~i~~KLg~~nR~qava~A~~~Gl  233 (235)
                      ++.|+++|.||.       |--+|+.++|
T Consensus       161 lR~YLRRIKRKT-------ALLIA~SCqL  182 (325)
T TIGR02748       161 LRTYLRRIKRKT-------ALLIAASCQL  182 (325)
T ss_pred             HHHHHHHHHHHH-------HHHHHHHHHH
T ss_conf             003665666889-------9999987765


No 489
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=30.69  E-value=32  Score=13.63  Aligned_cols=26  Identities=15%  Similarity=0.235  Sum_probs=0.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             97899999499988999999999998
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +.+|||...+||++.+..-++...++
T Consensus        27 ~~~eIae~~~Ip~~~L~KIl~~L~~a   52 (141)
T PRK11014         27 SISEVTEVYGVSRNHMVKIINQLSRA   52 (141)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             49999998794999999999999887


No 490
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=30.63  E-value=32  Score=13.62  Aligned_cols=25  Identities=28%  Similarity=0.284  Sum_probs=0.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9789999949998899999999999
Q gi|254780693|r  190 TSEEIAEKLGLSVHTVNAYLGSATV  214 (235)
Q Consensus       190 t~~eIA~~L~iS~~TV~~hl~~i~~  214 (235)
                      |..+||..||++.+.|+.-+..++.
T Consensus        17 ~dedLa~~l~~~~n~vRkiL~~L~e   41 (147)
T smart00531       17 TEEDLAELLGIKQKQLRKILYLLYD   41 (147)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             7999999979999999999999997


No 491
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family; InterPro: IPR014071   This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferable copper resistance) of an Enterococcus faecium (Streptococcus faecium) plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this entry are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI..
Probab=30.36  E-value=32  Score=13.59  Aligned_cols=41  Identities=22%  Similarity=0.218  Sum_probs=0.0

Q ss_pred             CHHHHHHHH--HHHCCCCHHHHHHHHCC----CHHHHHHHHHHHHHH
Q ss_conf             989999999--99879997899999499----988999999999998
Q gi|254780693|r  175 TERETSCLQ--LAGDGYTSEEIAEKLGL----SVHTVNAYLGSATVK  215 (235)
Q Consensus       175 T~RE~evL~--l~a~G~t~~eIA~~L~i----S~~TV~~hl~~i~~K  215 (235)
                      |+-|-||++  |.-.--|+++|-.+|.=    +..||++-+.+.-.|
T Consensus         3 sDaEWEVMRvvW~~g~~~S~~~i~~L~~k~DW~~STiKTLl~RLV~K   49 (130)
T TIGR02698         3 SDAEWEVMRVVWTLGETTSKDIISVLAEKKDWKDSTIKTLLGRLVDK   49 (130)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             74232433421048872778999986055776267899999765441


No 492
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=30.21  E-value=32  Score=13.57  Aligned_cols=41  Identities=17%  Similarity=0.116  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999999987999789999949998899999999999807997
Q gi|254780693|r  176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN  220 (235)
Q Consensus       176 ~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n  220 (235)
                      +|+.=.-.+-..|..-.+.|+.||||..|..    +.++|||.+.
T Consensus       470 Er~lI~~AL~~~~GN~s~AAr~LGIsRstLy----Rk~KrLGIk~  510 (510)
T PRK05022        470 QRQLIRQALAQHNGNWAAAARALELDRANLH----RLAKRLGLKD  510 (510)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHH----HHHHHHCCCC
T ss_conf             9999999999919989999999798999999----9999808999


No 493
>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=30.12  E-value=33  Score=13.56  Aligned_cols=45  Identities=13%  Similarity=-0.050  Sum_probs=0.0

Q ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             989999999998799978999994999889999999999980799
Q gi|254780693|r  175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV  219 (235)
Q Consensus       175 T~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~  219 (235)
                      |+=...+...+-.+....+.|+.|+|=++|+++-+++|...+|..
T Consensus       353 teLl~TL~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~d  397 (421)
T COG2508         353 TELLETLRAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGID  397 (421)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf             679999999998489799999983745423999999999994879


No 494
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=29.99  E-value=33  Score=13.55  Aligned_cols=43  Identities=30%  Similarity=0.194  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             499899999999987--9997899999499988999999999998
Q gi|254780693|r  173 NLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATVK  215 (235)
Q Consensus       173 ~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~K  215 (235)
                      +||+.|..|-.-+..  ..|.+||+...||-..-|..-++++-.|
T Consensus        13 Glt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~k   57 (247)
T COG1378          13 GLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKK   57 (247)
T ss_pred             CCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             997889999999998188779999986599932299999999878


No 495
>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=29.94  E-value=21  Score=14.90  Aligned_cols=17  Identities=47%  Similarity=0.640  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHCCCHHHH
Q ss_conf             99789999949998899
Q gi|254780693|r  189 YTSEEIAEKLGLSVHTV  205 (235)
Q Consensus       189 ~t~~eIA~~L~iS~~TV  205 (235)
                      +|-++||..|++++.||
T Consensus       366 L~L~~vA~el~~heSTi  382 (477)
T TIGR02395       366 LTLREVAEELGLHESTI  382 (477)
T ss_pred             CCHHHHHHHHCCCCCCE
T ss_conf             63899998858898724


No 496
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=29.54  E-value=33  Score=13.49  Aligned_cols=19  Identities=32%  Similarity=0.401  Sum_probs=0.0

Q ss_pred             HHHHHHHCCCHHHHHHHHH
Q ss_conf             8999994999889999999
Q gi|254780693|r  192 EEIAEKLGLSVHTVNAYLG  210 (235)
Q Consensus       192 ~eIA~~L~iS~~TV~~hl~  210 (235)
                      +|++..+|+|..|+..+++
T Consensus        17 ~ev~~~~GlSrstiYr~i~   35 (70)
T COG3311          17 PEVAQLTGLSRSTIYRLIK   35 (70)
T ss_pred             HHHHHHHCCCHHHHHHHHC
T ss_conf             9999997766899999980


No 497
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=29.30  E-value=34  Score=13.47  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=0.0

Q ss_pred             HHHHHHHHCCCCHHHH
Q ss_conf             9999999879997899
Q gi|254780693|r  179 TSCLQLAGDGYTSEEI  194 (235)
Q Consensus       179 ~evL~l~a~G~t~~eI  194 (235)
                      .+|-+.+.+|+|++||
T Consensus        61 ~~i~~~i~~G~sd~eI   76 (145)
T pfam03918        61 LEVREMLVEGKSDEEI   76 (145)
T ss_pred             HHHHHHHHCCCCHHHH
T ss_conf             9999999859999999


No 498
>PHA00675 hypothetical protein
Probab=29.21  E-value=34  Score=13.46  Aligned_cols=40  Identities=20%  Similarity=0.253  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHH
Q ss_conf             6788744499899999999987--999789999949998899
Q gi|254780693|r  166 KRSSAARNLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTV  205 (235)
Q Consensus       166 ~~~~~~~~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV  205 (235)
                      +.......||.-+.|..+-+.+  |++--.+|...+++..||
T Consensus        15 G~~Hhna~ltd~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtI   56 (78)
T PHA00675         15 GEDHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAI   56 (78)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
T ss_conf             675755657789999999999872843899999972756899


No 499
>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=28.50  E-value=26  Score=14.25  Aligned_cols=16  Identities=50%  Similarity=0.785  Sum_probs=0.0

Q ss_pred             HHHHHHCCCHHHHHHH
Q ss_conf             9999949998899999
Q gi|254780693|r  193 EIAEKLGLSVHTVNAY  208 (235)
Q Consensus       193 eIA~~L~iS~~TV~~h  208 (235)
                      |-|..-|+|..|++||
T Consensus         5 eLA~~t~v~v~TIRFY   20 (127)
T TIGR02047         5 ELAKKTGVSVETIRFY   20 (127)
T ss_pred             HHHHHHCCCCCHHHHH
T ss_conf             4545533440022464


No 500
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=28.03  E-value=35  Score=13.32  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=0.0

Q ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999987999789999949998899999999
Q gi|254780693|r  181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS  211 (235)
Q Consensus       181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~  211 (235)
                      .+++-..|.|+++||..+++|+..|+.+.++
T Consensus       484 l~~aK~~GFSD~~Ia~l~~~~e~~vr~~R~~  514 (1068)
T PRK12815        484 LRKAKEKGFSDRLIAELTGVTEEDVRELRKK  514 (1068)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999984999999997709999999999997


Done!